qiaamp dna ffpe kit  (Qiagen)

 
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    Name:
    QIAamp DNA FFPE Tissue Kit
    Description:
    For purification of genomic DNA from formalin fixed paraffin embedded tissues Kit contents Qiagen QIAamp DNA FFPE Tissue Kit 50 preps 20 to 100L Elution Volume Up to 8 Sections Sample Formalin Fixed Paraffin Embedded Tissue Sample Silica Technology Genomic DNA Mitochondrial DNA Purification Spin Column Format Ideal for Real time PCR STR Analysis LMD PCR For Purification of Genomic DNA From Formalin fixed Paraffin embedded Tissues Includes 50 QIAamp MinElute Columns Proteinase K Buffers 2mL Collection Tubes Benefits Rapid purification of high quality ready to use DNA Consistent high yields Complete removal of contaminants and inhibitor
    Catalog Number:
    56404
    Price:
    242
    Category:
    QIAamp DNA FFPE Tissue Kit
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    Structured Review

    Qiagen qiaamp dna ffpe kit
    QIAamp DNA FFPE Tissue Kit
    For purification of genomic DNA from formalin fixed paraffin embedded tissues Kit contents Qiagen QIAamp DNA FFPE Tissue Kit 50 preps 20 to 100L Elution Volume Up to 8 Sections Sample Formalin Fixed Paraffin Embedded Tissue Sample Silica Technology Genomic DNA Mitochondrial DNA Purification Spin Column Format Ideal for Real time PCR STR Analysis LMD PCR For Purification of Genomic DNA From Formalin fixed Paraffin embedded Tissues Includes 50 QIAamp MinElute Columns Proteinase K Buffers 2mL Collection Tubes Benefits Rapid purification of high quality ready to use DNA Consistent high yields Complete removal of contaminants and inhibitor
    https://www.bioz.com/result/qiaamp dna ffpe kit/product/Qiagen
    Average 99 stars, based on 10288 article reviews
    Price from $9.99 to $1999.99
    qiaamp dna ffpe kit - by Bioz Stars, 2020-07
    99/100 stars

    Images

    1) Product Images from "Amplicon Sequencing of Colorectal Cancer: Variant Calling in Frozen and Formalin-Fixed Samples"

    Article Title: Amplicon Sequencing of Colorectal Cancer: Variant Calling in Frozen and Formalin-Fixed Samples

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0127146

    Depth of Sequencing correlates with DNA quality. (A) Sample preparation workflow. DNA was isolated from fresh frozen or FFPE CRC liver metastasis resection specimens with Qiagen Blood and Tissue or FFPE kit, respectively. Frozen samples then directly underwent sequencing library preparation, pooling of libraries, quality control and sequencing. FFPE samples were additionally tested for DNA quality by qPCR. Library quality was tested with Bioanalyzer. For samples with low amounts of correctly sized DNA amplicons (fragments at 310bp), new libraries were prepared with higher starting DNA concentrations and re-analyzed with Bioanalyzer. Samples with yet low amounts of DNA with correct size and highly fragmented DNA were excluded. (B) ΔCq-values of quality control PCR indicate poor sample quality. DNA concentration of fragments between 250bp and 450bp after library preparation was calculated with Agilent Bioanalyzer and plotted against ΔCq values of FFPE quality control PCR. (C) higher ΔCq-values correlate with lower mean depth of sequencing. (D) Coverage distribution of amplicons from all paired FFPE and frozen samples, normalized to total sample coverage. Frozen samples had a mean depth of 4,622, FFPE samples 1,852.
    Figure Legend Snippet: Depth of Sequencing correlates with DNA quality. (A) Sample preparation workflow. DNA was isolated from fresh frozen or FFPE CRC liver metastasis resection specimens with Qiagen Blood and Tissue or FFPE kit, respectively. Frozen samples then directly underwent sequencing library preparation, pooling of libraries, quality control and sequencing. FFPE samples were additionally tested for DNA quality by qPCR. Library quality was tested with Bioanalyzer. For samples with low amounts of correctly sized DNA amplicons (fragments at 310bp), new libraries were prepared with higher starting DNA concentrations and re-analyzed with Bioanalyzer. Samples with yet low amounts of DNA with correct size and highly fragmented DNA were excluded. (B) ΔCq-values of quality control PCR indicate poor sample quality. DNA concentration of fragments between 250bp and 450bp after library preparation was calculated with Agilent Bioanalyzer and plotted against ΔCq values of FFPE quality control PCR. (C) higher ΔCq-values correlate with lower mean depth of sequencing. (D) Coverage distribution of amplicons from all paired FFPE and frozen samples, normalized to total sample coverage. Frozen samples had a mean depth of 4,622, FFPE samples 1,852.

    Techniques Used: Sequencing, Sample Prep, Isolation, Formalin-fixed Paraffin-Embedded, Real-time Polymerase Chain Reaction, Polymerase Chain Reaction, Concentration Assay

    2) Product Images from "Characterisation of the changing genomic landscape of metastatic melanoma using cell free DNA"

    Article Title: Characterisation of the changing genomic landscape of metastatic melanoma using cell free DNA

    Journal: NPJ genomic medicine

    doi: 10.1038/s41525-017-0030-7

    Coverage uniformity of WGS libraries. a Represented is the cumulative proportion of sequencing coverage per cumulative proportion of sequence in whole genome sequencing across normal germline DNA (gDNA) from peripheral blood mononuclear cells, two cfDNA time points, and an archival FFPE tissue biopsy from a metastatic melanoma patient. If coverage was perfectly uniform across the genome coverage the relationship would be linear with gradient one. b Mapped depth of coverage distribution for WGS sequencing runs. The range of the coverage distribution is truncated at 150. Each trace is annotated with the mode of the distribution. c Insert size distribution of sequencing reads for the sequencing runs. The distribution is truncated at 300 base pairs. Each trace is annotated with the mode of the distribution
    Figure Legend Snippet: Coverage uniformity of WGS libraries. a Represented is the cumulative proportion of sequencing coverage per cumulative proportion of sequence in whole genome sequencing across normal germline DNA (gDNA) from peripheral blood mononuclear cells, two cfDNA time points, and an archival FFPE tissue biopsy from a metastatic melanoma patient. If coverage was perfectly uniform across the genome coverage the relationship would be linear with gradient one. b Mapped depth of coverage distribution for WGS sequencing runs. The range of the coverage distribution is truncated at 150. Each trace is annotated with the mode of the distribution. c Insert size distribution of sequencing reads for the sequencing runs. The distribution is truncated at 300 base pairs. Each trace is annotated with the mode of the distribution

    Techniques Used: Sequencing, Formalin-fixed Paraffin-Embedded

    3) Product Images from "Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies"

    Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

    Journal: BMC Medical Research Methodology

    doi: 10.1186/s12874-018-0628-1

    Bland-Altman plots for investigation of level of agreements between DNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of DNA yield (ng/μl) of samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. b Comparison of purity (A260/A280) of DNA samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. c Comparison of DNA yield (ng/μl) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit. d Comparison of purity (A260/A280) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit
    Figure Legend Snippet: Bland-Altman plots for investigation of level of agreements between DNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of DNA yield (ng/μl) of samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. b Comparison of purity (A260/A280) of DNA samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. c Comparison of DNA yield (ng/μl) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit. d Comparison of purity (A260/A280) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit

    Techniques Used: DNA Extraction, Formalin-fixed Paraffin-Embedded

    Bland-Altman plots for investigating the level of agreement between RNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of RNA yield (ng/μl) of samples extracted with High Pure FFPE RNA Micro Kit and RNeasy® FFPE kit. b Comparison of purity (A260/A280) of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. c Comparison of RIN-values of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. d Comparison of RNA yield (ng/μl) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. e Comparison of purity (A260/A280) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. f Comparison of RIN-values of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit
    Figure Legend Snippet: Bland-Altman plots for investigating the level of agreement between RNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of RNA yield (ng/μl) of samples extracted with High Pure FFPE RNA Micro Kit and RNeasy® FFPE kit. b Comparison of purity (A260/A280) of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. c Comparison of RIN-values of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. d Comparison of RNA yield (ng/μl) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. e Comparison of purity (A260/A280) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. f Comparison of RIN-values of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit

    Techniques Used: RNA Extraction, Formalin-fixed Paraffin-Embedded

    4) Product Images from "Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies"

    Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

    Journal: BMC Medical Research Methodology

    doi: 10.1186/s12874-018-0628-1

    Bland-Altman plots for investigation of level of agreements between DNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of DNA yield (ng/μl) of samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. b Comparison of purity (A260/A280) of DNA samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. c Comparison of DNA yield (ng/μl) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit. d Comparison of purity (A260/A280) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit
    Figure Legend Snippet: Bland-Altman plots for investigation of level of agreements between DNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of DNA yield (ng/μl) of samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. b Comparison of purity (A260/A280) of DNA samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. c Comparison of DNA yield (ng/μl) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit. d Comparison of purity (A260/A280) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit

    Techniques Used: DNA Extraction, Formalin-fixed Paraffin-Embedded

    Bland-Altman plots for investigating the level of agreement between RNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of RNA yield (ng/μl) of samples extracted with High Pure FFPE RNA Micro Kit and RNeasy® FFPE kit. b Comparison of purity (A260/A280) of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. c Comparison of RIN-values of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. d Comparison of RNA yield (ng/μl) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. e Comparison of purity (A260/A280) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. f Comparison of RIN-values of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit
    Figure Legend Snippet: Bland-Altman plots for investigating the level of agreement between RNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of RNA yield (ng/μl) of samples extracted with High Pure FFPE RNA Micro Kit and RNeasy® FFPE kit. b Comparison of purity (A260/A280) of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. c Comparison of RIN-values of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. d Comparison of RNA yield (ng/μl) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. e Comparison of purity (A260/A280) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. f Comparison of RIN-values of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit

    Techniques Used: RNA Extraction, Formalin-fixed Paraffin-Embedded

    5) Product Images from "Targeted next-generation sequencing of head and neck squamous cell carcinoma identifies novel genetic alterations in HPV+ and HPV- tumors"

    Article Title: Targeted next-generation sequencing of head and neck squamous cell carcinoma identifies novel genetic alterations in HPV+ and HPV- tumors

    Journal: Genome Medicine

    doi: 10.1186/gm453

    Workflow of FFPE sample preparation and selection . Eighty-two FFPE blocks [ 19 ] were stained for p16 of which eight samples were excluded from further analysis, showing mixed p16 staining. Eight samples were excluded after the LCM step, yielding insufficient amounts or quality of DNA and two further samples were excluded due to inconsistent or borderline results in repeat E6 qPCR measurements. In total, 22 confirmed HPV+ (p16+ and E6 qPCR+) and 34 HPV- (p16- and E6 qPCR-) samples were suitable for further analysis. Following age and gender matching, 20 HPV+ HNSCC samples (red) and 20 HPV- HNSCC samples (grey) were then selected for the final analysis (next-generation (NG) sequencing).
    Figure Legend Snippet: Workflow of FFPE sample preparation and selection . Eighty-two FFPE blocks [ 19 ] were stained for p16 of which eight samples were excluded from further analysis, showing mixed p16 staining. Eight samples were excluded after the LCM step, yielding insufficient amounts or quality of DNA and two further samples were excluded due to inconsistent or borderline results in repeat E6 qPCR measurements. In total, 22 confirmed HPV+ (p16+ and E6 qPCR+) and 34 HPV- (p16- and E6 qPCR-) samples were suitable for further analysis. Following age and gender matching, 20 HPV+ HNSCC samples (red) and 20 HPV- HNSCC samples (grey) were then selected for the final analysis (next-generation (NG) sequencing).

    Techniques Used: Formalin-fixed Paraffin-Embedded, Sample Prep, Selection, Staining, Laser Capture Microdissection, Real-time Polymerase Chain Reaction, Sequencing

    6) Product Images from "Critical Issues in Mycobiota Analysis"

    Article Title: Critical Issues in Mycobiota Analysis

    Journal: Frontiers in Microbiology

    doi: 10.3389/fmicb.2017.00180

    DNA isolation from human FFPE skin samples and ITS PCR amplification influenced by beat beating. (A) Significant difference in overall DNA yield from FFPE skin samples ( n = 10) with and without bead beating ( ** p
    Figure Legend Snippet: DNA isolation from human FFPE skin samples and ITS PCR amplification influenced by beat beating. (A) Significant difference in overall DNA yield from FFPE skin samples ( n = 10) with and without bead beating ( ** p

    Techniques Used: DNA Extraction, Formalin-fixed Paraffin-Embedded, Polymerase Chain Reaction, Amplification

    7) Product Images from "Why do results conflict regarding the prognostic value of the methylation status in colon cancers? the role of the preservation method"

    Article Title: Why do results conflict regarding the prognostic value of the methylation status in colon cancers? the role of the preservation method

    Journal: BMC Cancer

    doi: 10.1186/1471-2407-12-12

    Pyrograms of the LINE-1, MLH1 and MGMT methylation markers for different couples of frozen/FFPE DNA . Pyrograms of LINE-1 marker are those obtained for couple n° 10 ( A and B ) and for MLH1 and MGMT markers those for couples n°13 ( C and D ) and n°6 ( E and F ) respectively. Arrows indicate positions of internal controls of conversion, demonstrating no residual cytosines at the non-CpG sites. Gray areas indicate polymorphisms, between T/C, generated by bisulfite treatment. Level of methylation for a given CpG dinucleotide is reported above it (gray square).
    Figure Legend Snippet: Pyrograms of the LINE-1, MLH1 and MGMT methylation markers for different couples of frozen/FFPE DNA . Pyrograms of LINE-1 marker are those obtained for couple n° 10 ( A and B ) and for MLH1 and MGMT markers those for couples n°13 ( C and D ) and n°6 ( E and F ) respectively. Arrows indicate positions of internal controls of conversion, demonstrating no residual cytosines at the non-CpG sites. Gray areas indicate polymorphisms, between T/C, generated by bisulfite treatment. Level of methylation for a given CpG dinucleotide is reported above it (gray square).

    Techniques Used: Methylation, Formalin-fixed Paraffin-Embedded, Marker, Generated

    8) Product Images from "A Comparison of EGFR Mutation Testing Methods in Lung Carcinoma: Direct Sequencing, Real-time PCR and Immunohistochemistry"

    Article Title: A Comparison of EGFR Mutation Testing Methods in Lung Carcinoma: Direct Sequencing, Real-time PCR and Immunohistochemistry

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0043842

    Limit of detection of the Therascreen EGFR Mutation Test Kit in comparison with direct sequencing. Serial dilutions of DNA from EGFR mutant and wild-type FFPE tumours were used to compare the relative sensitivities of both methods. ( A ), the Therascreen EGFR Mutation Test Kit was able to detect an EGFR mutation when the DNA from the mutant tumour represented 1% of the total DNA in half of the analyzed tumours. Sample S08-3853, which harbours an exon 19 deletion, is shown as an example. ( B ), the Therascreen EGFR Mutation Test Kit was able to identify EGFR mutation in a 5% dilution of the total DNA in all the tumours analyzed. Sample S09-397, which harbours an exon 19 deletion, is shown as an example. ( C ), at least 30% mutant DNA was necessary in a background of wild-type DNA to detect EGFR mutations by direct sequencing in most of the analyzed tumours. Sample S08-3853 is shown as an example. Percentages indicate the proportion of DNA from a mutant tumour relative to DNA from a wild-type tumour. The ΔCt cut-off value to detect the presence of an EGFR exon 19 deletion is provided by the manufacturer. It is derived from cell lines and synthetic constructs.
    Figure Legend Snippet: Limit of detection of the Therascreen EGFR Mutation Test Kit in comparison with direct sequencing. Serial dilutions of DNA from EGFR mutant and wild-type FFPE tumours were used to compare the relative sensitivities of both methods. ( A ), the Therascreen EGFR Mutation Test Kit was able to detect an EGFR mutation when the DNA from the mutant tumour represented 1% of the total DNA in half of the analyzed tumours. Sample S08-3853, which harbours an exon 19 deletion, is shown as an example. ( B ), the Therascreen EGFR Mutation Test Kit was able to identify EGFR mutation in a 5% dilution of the total DNA in all the tumours analyzed. Sample S09-397, which harbours an exon 19 deletion, is shown as an example. ( C ), at least 30% mutant DNA was necessary in a background of wild-type DNA to detect EGFR mutations by direct sequencing in most of the analyzed tumours. Sample S08-3853 is shown as an example. Percentages indicate the proportion of DNA from a mutant tumour relative to DNA from a wild-type tumour. The ΔCt cut-off value to detect the presence of an EGFR exon 19 deletion is provided by the manufacturer. It is derived from cell lines and synthetic constructs.

    Techniques Used: Mutagenesis, Sequencing, Formalin-fixed Paraffin-Embedded, Derivative Assay, Construct

    9) Product Images from "Enhancement of Pathologist's Routine Practice: Reuse of DNA Extracted from Immunostained Formalin-fixed Paraffin-embedded (FFPE) Slides in Downstream Molecular Analysis of Cancer"

    Article Title: Enhancement of Pathologist's Routine Practice: Reuse of DNA Extracted from Immunostained Formalin-fixed Paraffin-embedded (FFPE) Slides in Downstream Molecular Analysis of Cancer

    Journal: Cancer Genomics & Proteomics

    doi:

    Gel electrophoresis of CTNNB1 gene (190 bp) from DNA retrieved from already immunostained FFPE IHC slides. L, Gel ladder as a control; lanes 1 to 11, numbers' of assessed samples; IHC, immunohisochemistry, FFPE, formalin-fixed, paraffin-embedded
    Figure Legend Snippet: Gel electrophoresis of CTNNB1 gene (190 bp) from DNA retrieved from already immunostained FFPE IHC slides. L, Gel ladder as a control; lanes 1 to 11, numbers' of assessed samples; IHC, immunohisochemistry, FFPE, formalin-fixed, paraffin-embedded

    Techniques Used: Nucleic Acid Electrophoresis, Formalin-fixed Paraffin-Embedded, Immunohistochemistry

    10) Product Images from "Post-mortem testing; germline BRCA1/2 variant detection using archival FFPE non-tumor tissue. A new paradigm in genetic counseling"

    Article Title: Post-mortem testing; germline BRCA1/2 variant detection using archival FFPE non-tumor tissue. A new paradigm in genetic counseling

    Journal: European Journal of Human Genetics

    doi: 10.1038/ejhg.2015.268

    Flowchart of FFPE DNA sample and QC assays. After DNA extraction, three QC assays were performed to validate the quality of the DNA: (1) QC-PCR was used to estimate the level of fragmentation by comparing two PCR products amplified from FFPE DNA with the amplified PCR products from HapMap DNA (NA12878). According to the results of the QC-PCR, samples were classified as good, medium or poor. (2) DNA concentrations were measured using a PicoGreen assay. (3) All DNA samples were analyzed on a TapeStation to view the fragmentation profile of the DNA. Either the profiled was rated as ‘flat' indicating that DNA was highly degraded or not present, or the profile was rated as ‘peak' indicating that the DNA was degrade but had a peak when looking at the electropherogram. If a sample was rated poor, had a DNA concentration less than 1 ng/ μ l and a ‘flat' fragmentation profile, the DNA sample had failed QC. Only selected DNA samples failing QC were passed on to library preparation and sequencing, if there was a known variant in the family to search for.
    Figure Legend Snippet: Flowchart of FFPE DNA sample and QC assays. After DNA extraction, three QC assays were performed to validate the quality of the DNA: (1) QC-PCR was used to estimate the level of fragmentation by comparing two PCR products amplified from FFPE DNA with the amplified PCR products from HapMap DNA (NA12878). According to the results of the QC-PCR, samples were classified as good, medium or poor. (2) DNA concentrations were measured using a PicoGreen assay. (3) All DNA samples were analyzed on a TapeStation to view the fragmentation profile of the DNA. Either the profiled was rated as ‘flat' indicating that DNA was highly degraded or not present, or the profile was rated as ‘peak' indicating that the DNA was degrade but had a peak when looking at the electropherogram. If a sample was rated poor, had a DNA concentration less than 1 ng/ μ l and a ‘flat' fragmentation profile, the DNA sample had failed QC. Only selected DNA samples failing QC were passed on to library preparation and sequencing, if there was a known variant in the family to search for.

    Techniques Used: Formalin-fixed Paraffin-Embedded, DNA Extraction, Polymerase Chain Reaction, Amplification, Picogreen Assay, Concentration Assay, Sequencing, Variant Assay

    11) Product Images from "Multicenter validation of cancer gene panel-based next-generation sequencing for translational research and molecular diagnostics"

    Article Title: Multicenter validation of cancer gene panel-based next-generation sequencing for translational research and molecular diagnostics

    Journal: Virchows Archiv

    doi: 10.1007/s00428-017-2288-7

    Analysis of 15 FFPE cancer samples with commercial cancer panels. Centrally as well as locally extracted DNA of molecularly pre-characterized cancer samples was sequenced by commercial cancer panels (CHPv2 and TSACP) at five different sequencing sites. Mutations ascertained by conventional Sanger or pyro-sequencing and reproduced by NGS are listed in supplementary Table 2. a Analysis of five Colon cancer samples. b Analysis of five Breast cancer samples. c Analysis of five Lung cancer samples, (#1–#5, respectively). Variant allelic frequencies, detected at different partner sites, are illustrated by bars as indicated. Samples not analyzed are indicated by “X”; variants not detected are indicated by open circles “ ○ .” WT wild type; a, b, and c PGM™ sequencing sites; d and e MiSeq™ sequencing sites
    Figure Legend Snippet: Analysis of 15 FFPE cancer samples with commercial cancer panels. Centrally as well as locally extracted DNA of molecularly pre-characterized cancer samples was sequenced by commercial cancer panels (CHPv2 and TSACP) at five different sequencing sites. Mutations ascertained by conventional Sanger or pyro-sequencing and reproduced by NGS are listed in supplementary Table 2. a Analysis of five Colon cancer samples. b Analysis of five Breast cancer samples. c Analysis of five Lung cancer samples, (#1–#5, respectively). Variant allelic frequencies, detected at different partner sites, are illustrated by bars as indicated. Samples not analyzed are indicated by “X”; variants not detected are indicated by open circles “ ○ .” WT wild type; a, b, and c PGM™ sequencing sites; d and e MiSeq™ sequencing sites

    Techniques Used: Formalin-fixed Paraffin-Embedded, Sequencing, Next-Generation Sequencing, Variant Assay

    Multicenter study design for targeted NGS. a A commercial gene panel (Cancer Hotspot panel 2, CHPv2, Thermo Fisher Scientific) was applied to DNA from the LoVo cell line at four distinct dilutions at three PGM™ sequencing sites (a, b, and c) to demonstrate exemplarily sensitivity. Bioinformatics was performed locally. b Genomic DNA from 15 molecularly pre-characterized tumor samples (five breast, five lung, and five colon cancer cases) was analyzed with commercially available and custom-designed cancer gene panels on PGM™ and MiSeq™ benchtop sequencers at seven sequencing sites (a, b, c, d, e, f, and g). FFPE tissue sections of the very same tumor samples were delivered to the sites a, b, d, and e for local microdissection, DNA Isolation, QC/quantification, and commercial panel sequencing. Partner site c did not receive tissue sections for local DNA extraction and applied only centrally extracted DNA to commercial (c*) and cancer-specific gene panel sequencing (c). Bioinformatics of commercial cancer panel-based data was performed individually whereas cancer-specific panel-based data were collected centrally and compiled
    Figure Legend Snippet: Multicenter study design for targeted NGS. a A commercial gene panel (Cancer Hotspot panel 2, CHPv2, Thermo Fisher Scientific) was applied to DNA from the LoVo cell line at four distinct dilutions at three PGM™ sequencing sites (a, b, and c) to demonstrate exemplarily sensitivity. Bioinformatics was performed locally. b Genomic DNA from 15 molecularly pre-characterized tumor samples (five breast, five lung, and five colon cancer cases) was analyzed with commercially available and custom-designed cancer gene panels on PGM™ and MiSeq™ benchtop sequencers at seven sequencing sites (a, b, c, d, e, f, and g). FFPE tissue sections of the very same tumor samples were delivered to the sites a, b, d, and e for local microdissection, DNA Isolation, QC/quantification, and commercial panel sequencing. Partner site c did not receive tissue sections for local DNA extraction and applied only centrally extracted DNA to commercial (c*) and cancer-specific gene panel sequencing (c). Bioinformatics of commercial cancer panel-based data was performed individually whereas cancer-specific panel-based data were collected centrally and compiled

    Techniques Used: Next-Generation Sequencing, Sequencing, Formalin-fixed Paraffin-Embedded, Laser Capture Microdissection, DNA Extraction

    12) Product Images from "Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies"

    Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

    Journal: BMC Medical Research Methodology

    doi: 10.1186/s12874-018-0628-1

    Bland-Altman plots for investigation of level of agreements between DNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of DNA yield (ng/μl) of samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. b Comparison of purity (A260/A280) of DNA samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. c Comparison of DNA yield (ng/μl) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit. d Comparison of purity (A260/A280) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit
    Figure Legend Snippet: Bland-Altman plots for investigation of level of agreements between DNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of DNA yield (ng/μl) of samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. b Comparison of purity (A260/A280) of DNA samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. c Comparison of DNA yield (ng/μl) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit. d Comparison of purity (A260/A280) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit

    Techniques Used: DNA Extraction, Formalin-fixed Paraffin-Embedded

    Bland-Altman plots for investigating the level of agreement between RNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of RNA yield (ng/μl) of samples extracted with High Pure FFPE RNA Micro Kit and RNeasy® FFPE kit. b Comparison of purity (A260/A280) of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. c Comparison of RIN-values of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. d Comparison of RNA yield (ng/μl) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. e Comparison of purity (A260/A280) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. f Comparison of RIN-values of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit
    Figure Legend Snippet: Bland-Altman plots for investigating the level of agreement between RNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of RNA yield (ng/μl) of samples extracted with High Pure FFPE RNA Micro Kit and RNeasy® FFPE kit. b Comparison of purity (A260/A280) of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. c Comparison of RIN-values of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. d Comparison of RNA yield (ng/μl) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. e Comparison of purity (A260/A280) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. f Comparison of RIN-values of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit

    Techniques Used: RNA Extraction, Formalin-fixed Paraffin-Embedded

    13) Product Images from "The Anatomy to Genomics (ATG) Start Genetics medical school initiative: incorporating exome sequencing data from cadavers used for Anatomy instruction into the first year curriculum"

    Article Title: The Anatomy to Genomics (ATG) Start Genetics medical school initiative: incorporating exome sequencing data from cadavers used for Anatomy instruction into the first year curriculum

    Journal: BMC Medical Genomics

    doi: 10.1186/s12920-016-0223-4

    Agarose gel electrophoresis of DNA isolated from cadaver tissues. MW = GeneRuler 1 kb Plus DNA Ladder (Thermo Fisher Scientific). Lane 1: Heart DNA extracted with DNeasy Blood Tissue Kit. Lane 2: Liver DNA extracted with DNeasy Blood Tissue Kit. Lane 3: Heart DNA extracted with FFPE kit. Lane 4: Liver DNA extracted with FFPE kit
    Figure Legend Snippet: Agarose gel electrophoresis of DNA isolated from cadaver tissues. MW = GeneRuler 1 kb Plus DNA Ladder (Thermo Fisher Scientific). Lane 1: Heart DNA extracted with DNeasy Blood Tissue Kit. Lane 2: Liver DNA extracted with DNeasy Blood Tissue Kit. Lane 3: Heart DNA extracted with FFPE kit. Lane 4: Liver DNA extracted with FFPE kit

    Techniques Used: Agarose Gel Electrophoresis, Isolation, Formalin-fixed Paraffin-Embedded

    14) Product Images from "Analytic validation and real-time clinical application of an amplicon-based targeted gene panel for advanced cancer"

    Article Title: Analytic validation and real-time clinical application of an amplicon-based targeted gene panel for advanced cancer

    Journal: Oncotarget

    doi: 10.18632/oncotarget.20616

    Generation of sample mixes for analytic validation DNA from seven original samples was diluted to generate seven mixes. A. AN3CA and MFE-296 cell lines were mixed 1:1 to create Mix A, which was then mixed 1:1 with HCC827 to create Mix B and once again to create Mix C. B. Two frozen tumor samples and C. two FFPE tumor samples were combined 1:1 and 85:15 to generate mixes D and E (frozen) and F and G (FFPE).
    Figure Legend Snippet: Generation of sample mixes for analytic validation DNA from seven original samples was diluted to generate seven mixes. A. AN3CA and MFE-296 cell lines were mixed 1:1 to create Mix A, which was then mixed 1:1 with HCC827 to create Mix B and once again to create Mix C. B. Two frozen tumor samples and C. two FFPE tumor samples were combined 1:1 and 85:15 to generate mixes D and E (frozen) and F and G (FFPE).

    Techniques Used: Formalin-fixed Paraffin-Embedded

    15) Product Images from "Biomarker-driven trial in metastatic pancreas cancer: feasibility in a multicenter study of saracatinib, an oral Src inhibitor, in previously treated pancreatic cancer"

    Article Title: Biomarker-driven trial in metastatic pancreas cancer: feasibility in a multicenter study of saracatinib, an oral Src inhibitor, in previously treated pancreatic cancer

    Journal: Cancer Medicine

    doi: 10.1002/cam4.27

    (A) Representative figure of patients archival tumor or fresh liver biopsies analyzed for LRRC19 > IGFBP2 and (B) PIK3CA mutation (3′ UTR) of PH1715 (patient enrolled in the biomarker portion of the study).
    Figure Legend Snippet: (A) Representative figure of patients archival tumor or fresh liver biopsies analyzed for LRRC19 > IGFBP2 and (B) PIK3CA mutation (3′ UTR) of PH1715 (patient enrolled in the biomarker portion of the study).

    Techniques Used: Mutagenesis, Biomarker Assay

    Study design: in the unselected portion, 17 patients were enrolled in the study. To move on to enroll 34 patients at least three responses were required. Only two patients made it to the 6-month endpoint. Study was amended for a biomarker-driven study. Results from our preclinical study on 24 patient-derived pancreatic explants identified the KTSP classifier LRRC19 > IGFBP2 and PIK3CA mutant as markers of sensitivity. These markers were used to screen patients for the biomarker-driven study. One patient with a PIK3CA mutation was enrolled in the study.
    Figure Legend Snippet: Study design: in the unselected portion, 17 patients were enrolled in the study. To move on to enroll 34 patients at least three responses were required. Only two patients made it to the 6-month endpoint. Study was amended for a biomarker-driven study. Results from our preclinical study on 24 patient-derived pancreatic explants identified the KTSP classifier LRRC19 > IGFBP2 and PIK3CA mutant as markers of sensitivity. These markers were used to screen patients for the biomarker-driven study. One patient with a PIK3CA mutation was enrolled in the study.

    Techniques Used: Biomarker Assay, Derivative Assay, Mutagenesis

    16) Product Images from "Chronic inflammation initiates multiple forms of K-Ras-independent mouse pancreatic cancer in the absence of TP53"

    Article Title: Chronic inflammation initiates multiple forms of K-Ras-independent mouse pancreatic cancer in the absence of TP53

    Journal: Oncogene

    doi: 10.1038/onc.2016.461

    Ras-independent tumorigenesis was the predominant pathway of carcinogenesis associated with chronic inflammation in the absence of TP53. ( A ) Detection of K-ras mutation. (a) In control mice, only wild-type (WT) DNA (negative control) signal was detected in absence of LNA probe, whereas addition of LNA probe resulted in its complete suppression. (b) In K-Ras G12D expressing mice (LSL G12D /Cre) adding the LNA probe resulted in suppression of WT signal and detection of mutant K-ras as indicated by the difference in the melting temperature for WT DNA and mutant K-ras. (c) The results of gDNA analysis of microdissected tissue from PDAC areas of tumor showing detection of only WT but not mutant K-ras. ( B ) Representative Immunohistochemical images showing for mutant Ras showing positive staining in LSL-K-ras G12V / Cre and LSL-K-ras G12D /Cre tumors, and negative staining in tumors of TP53 −/− /COX-2/Cre mice (scale bar: 200 μm, magnification 20 ×). ( C ) Representative immunohistochemical images showing focal positive staining for phospho-ERK (pERK), in tumors (two representative images of TP53 −/− /COX-2/Cre and TP53 −/− /COX-2/IKK/Cre tumors) (scale bar: 200 μm, magnification 10 ×).
    Figure Legend Snippet: Ras-independent tumorigenesis was the predominant pathway of carcinogenesis associated with chronic inflammation in the absence of TP53. ( A ) Detection of K-ras mutation. (a) In control mice, only wild-type (WT) DNA (negative control) signal was detected in absence of LNA probe, whereas addition of LNA probe resulted in its complete suppression. (b) In K-Ras G12D expressing mice (LSL G12D /Cre) adding the LNA probe resulted in suppression of WT signal and detection of mutant K-ras as indicated by the difference in the melting temperature for WT DNA and mutant K-ras. (c) The results of gDNA analysis of microdissected tissue from PDAC areas of tumor showing detection of only WT but not mutant K-ras. ( B ) Representative Immunohistochemical images showing for mutant Ras showing positive staining in LSL-K-ras G12V / Cre and LSL-K-ras G12D /Cre tumors, and negative staining in tumors of TP53 −/− /COX-2/Cre mice (scale bar: 200 μm, magnification 20 ×). ( C ) Representative immunohistochemical images showing focal positive staining for phospho-ERK (pERK), in tumors (two representative images of TP53 −/− /COX-2/Cre and TP53 −/− /COX-2/IKK/Cre tumors) (scale bar: 200 μm, magnification 10 ×).

    Techniques Used: Mutagenesis, Mouse Assay, Negative Control, Expressing, Immunohistochemistry, Staining, Negative Staining

    17) Product Images from "Impact of storage conditions on the quality of nucleic acids in paraffin embedded tissues"

    Article Title: Impact of storage conditions on the quality of nucleic acids in paraffin embedded tissues

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0203608

    Storage of PET blocks for 9 years at lower temperatures prevents from DNA degradation. Analysis of DNA integrity from FFPE (A) and PFPE (B) tissues of rat liver, kidney, spleen, lung and intestine on Agilent 4200 TapeStation system with genomic DNA Analysis ScreenTape assay. PET blocks were stored prior to DNA extraction for 108 months at 22°C, 4°C, and -20°C. DNA was extracted from 3x 10μm sections in triplicates.
    Figure Legend Snippet: Storage of PET blocks for 9 years at lower temperatures prevents from DNA degradation. Analysis of DNA integrity from FFPE (A) and PFPE (B) tissues of rat liver, kidney, spleen, lung and intestine on Agilent 4200 TapeStation system with genomic DNA Analysis ScreenTape assay. PET blocks were stored prior to DNA extraction for 108 months at 22°C, 4°C, and -20°C. DNA was extracted from 3x 10μm sections in triplicates.

    Techniques Used: Positron Emission Tomography, Formalin-fixed Paraffin-Embedded, DNA Extraction

    Improved qPCR-performance of DNA from PET blocks stored for 9 years at lower temperatures. FFPE and PFPE animal tissues were stored prior to DNA extraction for 108 months at different temperatures (22°C, 4°C, and -20°C). qPCR was performed with four different SYBR-Green qPCR assays of the rat ACTB gene with amplicon length of 271, 523, 650 and 747 base pairs (bp). Triplicate extractions from each PET block were amplified. DNA from cryo-preserved rat tissue was used as reference, shown as dashed line. Mean Ct values with standard deviation from triplicate extractions from each of five different tissues (liver, kidney, spleen, lung and intestine) are shown for each assay.
    Figure Legend Snippet: Improved qPCR-performance of DNA from PET blocks stored for 9 years at lower temperatures. FFPE and PFPE animal tissues were stored prior to DNA extraction for 108 months at different temperatures (22°C, 4°C, and -20°C). qPCR was performed with four different SYBR-Green qPCR assays of the rat ACTB gene with amplicon length of 271, 523, 650 and 747 base pairs (bp). Triplicate extractions from each PET block were amplified. DNA from cryo-preserved rat tissue was used as reference, shown as dashed line. Mean Ct values with standard deviation from triplicate extractions from each of five different tissues (liver, kidney, spleen, lung and intestine) are shown for each assay.

    Techniques Used: Real-time Polymerase Chain Reaction, Positron Emission Tomography, Formalin-fixed Paraffin-Embedded, DNA Extraction, SYBR Green Assay, Amplification, Blocking Assay, Standard Deviation

    18) Product Images from "Personalized genomic analysis based on circulating tumor cells of extra-skeletal Ewing sarcoma of the uterus: A case report of a 16-year-old Korean female"

    Article Title: Personalized genomic analysis based on circulating tumor cells of extra-skeletal Ewing sarcoma of the uterus: A case report of a 16-year-old Korean female

    Journal: Experimental and Therapeutic Medicine

    doi: 10.3892/etm.2018.6323

    Molecular pathology findings of Ewing sarcoma tissue. (A) EWS-FLI1 fusion transcript was detected in the patient's FFPE DNA. (B) Translocation breakpoint of the EWS-FLI1 fusion transcript was observed in the patient's FFPE sample DNA. FFPE, formalin-fixed paraffin-embedded.
    Figure Legend Snippet: Molecular pathology findings of Ewing sarcoma tissue. (A) EWS-FLI1 fusion transcript was detected in the patient's FFPE DNA. (B) Translocation breakpoint of the EWS-FLI1 fusion transcript was observed in the patient's FFPE sample DNA. FFPE, formalin-fixed paraffin-embedded.

    Techniques Used: Formalin-fixed Paraffin-Embedded, Translocation Assay

    19) Product Images from "Multicenter validation of cancer gene panel-based next-generation sequencing for translational research and molecular diagnostics"

    Article Title: Multicenter validation of cancer gene panel-based next-generation sequencing for translational research and molecular diagnostics

    Journal: Virchows Archiv

    doi: 10.1007/s00428-017-2288-7

    Disease-specific gene panel-based analysis of FFPE cancer samples. Centrally extracted DNA of molecularly pre-characterized cancer samples was sequenced using cancer-specific, custom-designed cancer panel at seven sequencing sites. The same cases as depicted in Fig. 3 are used. a Colon/Lung Ca panel-based analysis of five Colon cancer samples. b Custom-designed Breast cancer panel-based analysis of five Breast cancer samples. c Custom-designed Lung Cancer panel-based analysis of five Lung cancer samples (#1–#5, respectively). Mutations ascertained by conventional Sanger or pyro-sequencing and reproduced by NGS are listed in supplementary Table 2. Detected variant allelic frequencies of KRAS (Colon Ca), PIK3CA / PTEN (Breast Ca), and EGFR mutations (Lung Ca) are illustrated by bars in corresponding colors/patterns (a, b, and c represent PGM; d, e, f, and g represent MiSeq sequencing sites). WT wild type
    Figure Legend Snippet: Disease-specific gene panel-based analysis of FFPE cancer samples. Centrally extracted DNA of molecularly pre-characterized cancer samples was sequenced using cancer-specific, custom-designed cancer panel at seven sequencing sites. The same cases as depicted in Fig. 3 are used. a Colon/Lung Ca panel-based analysis of five Colon cancer samples. b Custom-designed Breast cancer panel-based analysis of five Breast cancer samples. c Custom-designed Lung Cancer panel-based analysis of five Lung cancer samples (#1–#5, respectively). Mutations ascertained by conventional Sanger or pyro-sequencing and reproduced by NGS are listed in supplementary Table 2. Detected variant allelic frequencies of KRAS (Colon Ca), PIK3CA / PTEN (Breast Ca), and EGFR mutations (Lung Ca) are illustrated by bars in corresponding colors/patterns (a, b, and c represent PGM; d, e, f, and g represent MiSeq sequencing sites). WT wild type

    Techniques Used: Formalin-fixed Paraffin-Embedded, Sequencing, Next-Generation Sequencing, Variant Assay

    Analysis of 15 FFPE cancer samples with commercial cancer panels. Centrally as well as locally extracted DNA of molecularly pre-characterized cancer samples was sequenced by commercial cancer panels (CHPv2 and TSACP) at five different sequencing sites. Mutations ascertained by conventional Sanger or pyro-sequencing and reproduced by NGS are listed in supplementary Table 2. a Analysis of five Colon cancer samples. b Analysis of five Breast cancer samples. c Analysis of five Lung cancer samples, (#1–#5, respectively). Variant allelic frequencies, detected at different partner sites, are illustrated by bars as indicated. Samples not analyzed are indicated by “X”; variants not detected are indicated by open circles “ ○ .” WT wild type; a, b, and c PGM™ sequencing sites; d and e MiSeq™ sequencing sites
    Figure Legend Snippet: Analysis of 15 FFPE cancer samples with commercial cancer panels. Centrally as well as locally extracted DNA of molecularly pre-characterized cancer samples was sequenced by commercial cancer panels (CHPv2 and TSACP) at five different sequencing sites. Mutations ascertained by conventional Sanger or pyro-sequencing and reproduced by NGS are listed in supplementary Table 2. a Analysis of five Colon cancer samples. b Analysis of five Breast cancer samples. c Analysis of five Lung cancer samples, (#1–#5, respectively). Variant allelic frequencies, detected at different partner sites, are illustrated by bars as indicated. Samples not analyzed are indicated by “X”; variants not detected are indicated by open circles “ ○ .” WT wild type; a, b, and c PGM™ sequencing sites; d and e MiSeq™ sequencing sites

    Techniques Used: Formalin-fixed Paraffin-Embedded, Sequencing, Next-Generation Sequencing, Variant Assay

    Multicenter study design for targeted NGS. a A commercial gene panel (Cancer Hotspot panel 2, CHPv2, Thermo Fisher Scientific) was applied to DNA from the LoVo cell line at four distinct dilutions at three PGM™ sequencing sites (a, b, and c) to demonstrate exemplarily sensitivity. Bioinformatics was performed locally. b Genomic DNA from 15 molecularly pre-characterized tumor samples (five breast, five lung, and five colon cancer cases) was analyzed with commercially available and custom-designed cancer gene panels on PGM™ and MiSeq™ benchtop sequencers at seven sequencing sites (a, b, c, d, e, f, and g). FFPE tissue sections of the very same tumor samples were delivered to the sites a, b, d, and e for local microdissection, DNA Isolation, QC/quantification, and commercial panel sequencing. Partner site c did not receive tissue sections for local DNA extraction and applied only centrally extracted DNA to commercial (c*) and cancer-specific gene panel sequencing (c). Bioinformatics of commercial cancer panel-based data was performed individually whereas cancer-specific panel-based data were collected centrally and compiled
    Figure Legend Snippet: Multicenter study design for targeted NGS. a A commercial gene panel (Cancer Hotspot panel 2, CHPv2, Thermo Fisher Scientific) was applied to DNA from the LoVo cell line at four distinct dilutions at three PGM™ sequencing sites (a, b, and c) to demonstrate exemplarily sensitivity. Bioinformatics was performed locally. b Genomic DNA from 15 molecularly pre-characterized tumor samples (five breast, five lung, and five colon cancer cases) was analyzed with commercially available and custom-designed cancer gene panels on PGM™ and MiSeq™ benchtop sequencers at seven sequencing sites (a, b, c, d, e, f, and g). FFPE tissue sections of the very same tumor samples were delivered to the sites a, b, d, and e for local microdissection, DNA Isolation, QC/quantification, and commercial panel sequencing. Partner site c did not receive tissue sections for local DNA extraction and applied only centrally extracted DNA to commercial (c*) and cancer-specific gene panel sequencing (c). Bioinformatics of commercial cancer panel-based data was performed individually whereas cancer-specific panel-based data were collected centrally and compiled

    Techniques Used: Next-Generation Sequencing, Sequencing, Formalin-fixed Paraffin-Embedded, Laser Capture Microdissection, DNA Extraction

    20) Product Images from "Tumor Content Chart-Assisted HER2/CEP17 Digital PCR Analysis of Gastric Cancer Biopsy Specimens"

    Article Title: Tumor Content Chart-Assisted HER2/CEP17 Digital PCR Analysis of Gastric Cancer Biopsy Specimens

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0154430

    HER2 -DISH in cell blocks and TC chart in the stepwise mixture system. (A–C) Micrographs of HER2 -DISH of LCL, H522, and SK-BR-3 FFPE cell blocks. HER2 signals are shown as black dots or clusters, and CEP17 signals are shown as red dots. HER2 and CEP17 copy numbers measured by HER2 -DISH and digital PCR are shown in Table 2 . (A) The LCL was genomically stable with two pairs of signals corresponding to HER2 and CEP17, mimicking non-cancerous stromal or inflammatory cells. (B) In H522 cells, both HER2 and CEP17 signals appeared as dots and individual signals were discernible. (C) In SK-BR-3 cells, HER2 signals formed clusters and exact measurements were difficult. CEP17 signals varied between 3 and 7, with an average score of 83/20 = 4.15. (D, E) Genomic DNA of H522 and SK-BR-3 cells was mixed with the LCL genome in a stepwise manner and analyzed by digital PCR. The horizontal axis represents the ratio of H522 or SK-BR-3 to LCL, corresponding to TCR [ x ] in clinical cases; the vertical axis represents the ratio of HER2 to CEP17 in digital PCR [ r ]. [ A ] and [ B ] were determined by HER2 -DISH ( Table 1 ). (D) In H522, [ A = 2.05] and [ B = 4.25], yielding [ r = (4.25 x + 2(1 − x ))/(2.05 x + 2(1 − x ))] (solid gray line). Plotted data were approximated by the theoretical line. (E) In SK-BR-3 cells, [ A = 4.15], but HER2 copy number [ B ] was difficult to determine due to cluster formation. HER2 copy number [ B′ ] was predicted [ B′ = 5.69 × 4.15 = 23.61] based on digital PCR data [ r ] and CEP17 copy number [ A ]. The equation [ r = (23.61 x + 2(1 − x ))/(4.15 x + 2(1 − x ))] is represented by the solid gray line. Plotted data were approximated by the theoretical line.
    Figure Legend Snippet: HER2 -DISH in cell blocks and TC chart in the stepwise mixture system. (A–C) Micrographs of HER2 -DISH of LCL, H522, and SK-BR-3 FFPE cell blocks. HER2 signals are shown as black dots or clusters, and CEP17 signals are shown as red dots. HER2 and CEP17 copy numbers measured by HER2 -DISH and digital PCR are shown in Table 2 . (A) The LCL was genomically stable with two pairs of signals corresponding to HER2 and CEP17, mimicking non-cancerous stromal or inflammatory cells. (B) In H522 cells, both HER2 and CEP17 signals appeared as dots and individual signals were discernible. (C) In SK-BR-3 cells, HER2 signals formed clusters and exact measurements were difficult. CEP17 signals varied between 3 and 7, with an average score of 83/20 = 4.15. (D, E) Genomic DNA of H522 and SK-BR-3 cells was mixed with the LCL genome in a stepwise manner and analyzed by digital PCR. The horizontal axis represents the ratio of H522 or SK-BR-3 to LCL, corresponding to TCR [ x ] in clinical cases; the vertical axis represents the ratio of HER2 to CEP17 in digital PCR [ r ]. [ A ] and [ B ] were determined by HER2 -DISH ( Table 1 ). (D) In H522, [ A = 2.05] and [ B = 4.25], yielding [ r = (4.25 x + 2(1 − x ))/(2.05 x + 2(1 − x ))] (solid gray line). Plotted data were approximated by the theoretical line. (E) In SK-BR-3 cells, [ A = 4.15], but HER2 copy number [ B ] was difficult to determine due to cluster formation. HER2 copy number [ B′ ] was predicted [ B′ = 5.69 × 4.15 = 23.61] based on digital PCR data [ r ] and CEP17 copy number [ A ]. The equation [ r = (23.61 x + 2(1 − x ))/(4.15 x + 2(1 − x ))] is represented by the solid gray line. Plotted data were approximated by the theoretical line.

    Techniques Used: Formalin-fixed Paraffin-Embedded, Digital PCR

    21) Product Images from "CRE: a cost effective and rapid approach for PCR-mediated concatenation ofKRAS andEGFR exons"

    Article Title: CRE: a cost effective and rapid approach for PCR-mediated concatenation ofKRAS andEGFR exons

    Journal: F1000Research

    doi: 10.12688/f1000research.6663.2

    Multiplex PCR amplification and concatenation of KRAS and EGFR exons generates CRE product. Panel A . PCR amplification of KRAS and EGFR exons using NCI-H1975 genomic DNA: Lane 1, KRAS exon 2 (151 bp) amplified with OAD176 and OAD177; Lane 2, EGFR exon 18 (209 bp) amplified with OAD 178 and OAD 144; Lane 3, EGFR exon 19 (178 bp) amplified with OAD 145 and OAD 146; Lane 4, EGFR exon 20 (246 bp) amplified with OAD 147 and OAD 150; Lane 5, EGFR exon 21 (251 bp) amplified with OAD 151 and OAD 152; Lane 6, Multiplex PCR of KRAS exon 2 and EGFR exons 18-21 with cocktail of primers used in Lanes 1–5. Concatenated KRAS and EGFR (CRE) product of ~915 bp amplified with OAD 176 and OAD 152 using multiplex PCR product as template derived from NCI-H1975 genomic DNA (shown in Panel B , Lane 2); derived from fresh frozen primary tumor genomic DNA (shown in Panel C , Lane 2); using tumor genomic DNA extracted from FFPE block (shown in Panel D, Lane 2).
    Figure Legend Snippet: Multiplex PCR amplification and concatenation of KRAS and EGFR exons generates CRE product. Panel A . PCR amplification of KRAS and EGFR exons using NCI-H1975 genomic DNA: Lane 1, KRAS exon 2 (151 bp) amplified with OAD176 and OAD177; Lane 2, EGFR exon 18 (209 bp) amplified with OAD 178 and OAD 144; Lane 3, EGFR exon 19 (178 bp) amplified with OAD 145 and OAD 146; Lane 4, EGFR exon 20 (246 bp) amplified with OAD 147 and OAD 150; Lane 5, EGFR exon 21 (251 bp) amplified with OAD 151 and OAD 152; Lane 6, Multiplex PCR of KRAS exon 2 and EGFR exons 18-21 with cocktail of primers used in Lanes 1–5. Concatenated KRAS and EGFR (CRE) product of ~915 bp amplified with OAD 176 and OAD 152 using multiplex PCR product as template derived from NCI-H1975 genomic DNA (shown in Panel B , Lane 2); derived from fresh frozen primary tumor genomic DNA (shown in Panel C , Lane 2); using tumor genomic DNA extracted from FFPE block (shown in Panel D, Lane 2).

    Techniques Used: Multiplex Assay, Polymerase Chain Reaction, Amplification, Derivative Assay, Formalin-fixed Paraffin-Embedded, Blocking Assay

    22) Product Images from "Evaluation of High-Throughput Genomic Assays for the Fc Gamma Receptor Locus"

    Article Title: Evaluation of High-Throughput Genomic Assays for the Fc Gamma Receptor Locus

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0142379

    MLPA probe performance in gDNA from matched PBMC and FFPE-derived material. To evaluate the effects of FFPE treatment on MLPA performance, the variability of FcγR-specific probes was compared in (A) matched DNA from PBMCs and FFPE material. (B) The quality of FFPE material and its effect on FCGR probe MLPA performance was assessed by stratification of FFPE samples according to BIOMED-2 PCR fragment results. (C) The effects of the FFPE treatment process on the MLPA control probes were also assessed. Probes are represented in locus order with exons in brackets. A normalised peak height ratio of 1 represents a diploid copy number. Error bars represent mean +/- SD.
    Figure Legend Snippet: MLPA probe performance in gDNA from matched PBMC and FFPE-derived material. To evaluate the effects of FFPE treatment on MLPA performance, the variability of FcγR-specific probes was compared in (A) matched DNA from PBMCs and FFPE material. (B) The quality of FFPE material and its effect on FCGR probe MLPA performance was assessed by stratification of FFPE samples according to BIOMED-2 PCR fragment results. (C) The effects of the FFPE treatment process on the MLPA control probes were also assessed. Probes are represented in locus order with exons in brackets. A normalised peak height ratio of 1 represents a diploid copy number. Error bars represent mean +/- SD.

    Techniques Used: Multiplex Ligation-dependent Probe Amplification, Formalin-fixed Paraffin-Embedded, Derivative Assay, Polymerase Chain Reaction

    TaqMan allelic discrimination of FcγR SNPs in matched PBMC- and FFPE-derived material. TaqMan allelic discrimination assays were performed and compared in matched DNA from PBMC- (A, C, E) and FFPE- (B, D, F) derived material in n = 9 cases. Assays were performed in triplicate for SNPs (A-B) FCGR2A -131H/R rs1801274, (C-D) FCGR3A -158F/V rs396991 and (E-F) FCGR2B -232I/T rs1050501. All samples were performed in triplicate with non-template controls (NTCs). Axes represent relative fluorescence units (RFU). An outlier sample is defined as one where it was not possible to accurately genotype using Rotor-Gene Q software.
    Figure Legend Snippet: TaqMan allelic discrimination of FcγR SNPs in matched PBMC- and FFPE-derived material. TaqMan allelic discrimination assays were performed and compared in matched DNA from PBMC- (A, C, E) and FFPE- (B, D, F) derived material in n = 9 cases. Assays were performed in triplicate for SNPs (A-B) FCGR2A -131H/R rs1801274, (C-D) FCGR3A -158F/V rs396991 and (E-F) FCGR2B -232I/T rs1050501. All samples were performed in triplicate with non-template controls (NTCs). Axes represent relative fluorescence units (RFU). An outlier sample is defined as one where it was not possible to accurately genotype using Rotor-Gene Q software.

    Techniques Used: Formalin-fixed Paraffin-Embedded, Derivative Assay, Fluorescence, Software

    23) Product Images from "Genomic complexity of urothelial bladder cancer revealed in urinary cfDNA"

    Article Title: Genomic complexity of urothelial bladder cancer revealed in urinary cfDNA

    Journal: European Journal of Human Genetics

    doi: 10.1038/ejhg.2015.281

    Patient 7. DNAs extracted from urine provide improved quality genomic data and clearer characterisation of the tumour profile than DNA from FFPE tumour material, despite repeat slides being cut and extracted. Two TARGET aberrations (CCND1 amplification (may predict sensitivity to CDK4/6 inhibitors) and CCNE1 amplification (may predict sensitivity to CDK2 inhibitors)) were observed in both cfDNA and urinary cellular DNA however none of these aberrations were independently called in two separate DNAs from FFPE tumour material.
    Figure Legend Snippet: Patient 7. DNAs extracted from urine provide improved quality genomic data and clearer characterisation of the tumour profile than DNA from FFPE tumour material, despite repeat slides being cut and extracted. Two TARGET aberrations (CCND1 amplification (may predict sensitivity to CDK4/6 inhibitors) and CCNE1 amplification (may predict sensitivity to CDK2 inhibitors)) were observed in both cfDNA and urinary cellular DNA however none of these aberrations were independently called in two separate DNAs from FFPE tumour material.

    Techniques Used: Formalin-fixed Paraffin-Embedded, Amplification

    24) Product Images from "Differentially Expressed MicroRNAs in Postpartum Breast Cancer in Hispanic Women"

    Article Title: Differentially Expressed MicroRNAs in Postpartum Breast Cancer in Hispanic Women

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0124340

    DNA Methylation of selected miRNAs. Box plots illustrating the DNA methylation of the miRNA genes investigated. The names of the miRNA MassARRAY amplicons analyzed by Sequenom are displayed at the top of each plot. The p-value (Wilcoxon test) for each amplicon analyzed is displayed on the second line at the top of the plot. The x-axis is divided into the two interval groups; early, representing Ella FFPE samples ≤ 5.2 years postpartum, and late, representing Ella FFPE samples ≥ 5.3 years postpartum. The y-axis represents the mean DNA methylation (%) of the amplicon.
    Figure Legend Snippet: DNA Methylation of selected miRNAs. Box plots illustrating the DNA methylation of the miRNA genes investigated. The names of the miRNA MassARRAY amplicons analyzed by Sequenom are displayed at the top of each plot. The p-value (Wilcoxon test) for each amplicon analyzed is displayed on the second line at the top of the plot. The x-axis is divided into the two interval groups; early, representing Ella FFPE samples ≤ 5.2 years postpartum, and late, representing Ella FFPE samples ≥ 5.3 years postpartum. The y-axis represents the mean DNA methylation (%) of the amplicon.

    Techniques Used: DNA Methylation Assay, Amplification, Formalin-fixed Paraffin-Embedded

    25) Product Images from "Performance comparison of three DNA extraction kits on human whole-exome data from formalin-fixed paraffin-embedded normal and tumor samples"

    Article Title: Performance comparison of three DNA extraction kits on human whole-exome data from formalin-fixed paraffin-embedded normal and tumor samples

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0195471

    DNA Integrity Number (DIN) values for FF and FFPE samples. A: FF and FFPE samples. B: FFPE samples grouped by extraction method.
    Figure Legend Snippet: DNA Integrity Number (DIN) values for FF and FFPE samples. A: FF and FFPE samples. B: FFPE samples grouped by extraction method.

    Techniques Used: Formalin-fixed Paraffin-Embedded

    DNA fragment length values for FF and FFPE samples. A: FF and FFPE samples. B: FFPE samples grouped by extraction method.
    Figure Legend Snippet: DNA fragment length values for FF and FFPE samples. A: FF and FFPE samples. B: FFPE samples grouped by extraction method.

    Techniques Used: Formalin-fixed Paraffin-Embedded

    26) Product Images from "A pressure cooking-based DNA extraction from archival formalin fixed, paraffin embedded tissue"

    Article Title: A pressure cooking-based DNA extraction from archival formalin fixed, paraffin embedded tissue

    Journal: Analytical Biochemistry

    doi: 10.1016/j.ab.2012.03.012

    Schematic diagram of DNA extraction procedures from FFPE tissue section or core.
    Figure Legend Snippet: Schematic diagram of DNA extraction procedures from FFPE tissue section or core.

    Techniques Used: DNA Extraction, Formalin-fixed Paraffin-Embedded

    Analysis of the quality of the DNA extracted from archival human colon FFPE tissues by the Nanodrop spectrophotometer. The DNA quality was accessed by distribution of the ratio values (A 260 /A 280 and A 260 /A 230 ).
    Figure Legend Snippet: Analysis of the quality of the DNA extracted from archival human colon FFPE tissues by the Nanodrop spectrophotometer. The DNA quality was accessed by distribution of the ratio values (A 260 /A 280 and A 260 /A 230 ).

    Techniques Used: Formalin-fixed Paraffin-Embedded, Spectrophotometry

    Comparison of DNA extraction yield and quality between a new rapid method and the QIAamp DNA FFPE tissue kit. We performed DNA extraction from archival human liver cores or sections. Representative data were presented as a bar graph ( A ) and a gel image
    Figure Legend Snippet: Comparison of DNA extraction yield and quality between a new rapid method and the QIAamp DNA FFPE tissue kit. We performed DNA extraction from archival human liver cores or sections. Representative data were presented as a bar graph ( A ) and a gel image

    Techniques Used: DNA Extraction, Formalin-fixed Paraffin-Embedded

    MSP analysis of sFRP1 and TFPI2 genes in colon samples using the rapid and classic DNA extraction. Methylation pattern of (A) sFRP1 and (B) TFPI2 gene promoter region in 18 FFPE colon samples using rapid DNA extraction method. Colon FFPE tumor samples
    Figure Legend Snippet: MSP analysis of sFRP1 and TFPI2 genes in colon samples using the rapid and classic DNA extraction. Methylation pattern of (A) sFRP1 and (B) TFPI2 gene promoter region in 18 FFPE colon samples using rapid DNA extraction method. Colon FFPE tumor samples

    Techniques Used: DNA Extraction, Methylation, Formalin-fixed Paraffin-Embedded

    27) Product Images from "A pressure cooking-based DNA extraction from archival formalin fixed, paraffin embedded tissue"

    Article Title: A pressure cooking-based DNA extraction from archival formalin fixed, paraffin embedded tissue

    Journal: Analytical Biochemistry

    doi: 10.1016/j.ab.2012.03.012

    Schematic diagram of DNA extraction procedures from FFPE tissue section or core.
    Figure Legend Snippet: Schematic diagram of DNA extraction procedures from FFPE tissue section or core.

    Techniques Used: DNA Extraction, Formalin-fixed Paraffin-Embedded

    Analysis of the quality of the DNA extracted from archival human colon FFPE tissues by the Nanodrop spectrophotometer. The DNA quality was accessed by distribution of the ratio values (A 260 /A 280 and A 260 /A 230 ).
    Figure Legend Snippet: Analysis of the quality of the DNA extracted from archival human colon FFPE tissues by the Nanodrop spectrophotometer. The DNA quality was accessed by distribution of the ratio values (A 260 /A 280 and A 260 /A 230 ).

    Techniques Used: Formalin-fixed Paraffin-Embedded, Spectrophotometry

    Comparison of DNA extraction yield and quality between a new rapid method and the QIAamp DNA FFPE tissue kit. We performed DNA extraction from archival human liver cores or sections. Representative data were presented as a bar graph ( A ) and a gel image
    Figure Legend Snippet: Comparison of DNA extraction yield and quality between a new rapid method and the QIAamp DNA FFPE tissue kit. We performed DNA extraction from archival human liver cores or sections. Representative data were presented as a bar graph ( A ) and a gel image

    Techniques Used: DNA Extraction, Formalin-fixed Paraffin-Embedded

    MSP analysis of sFRP1 and TFPI2 genes in colon samples using the rapid and classic DNA extraction. Methylation pattern of (A) sFRP1 and (B) TFPI2 gene promoter region in 18 FFPE colon samples using rapid DNA extraction method. Colon FFPE tumor samples
    Figure Legend Snippet: MSP analysis of sFRP1 and TFPI2 genes in colon samples using the rapid and classic DNA extraction. Methylation pattern of (A) sFRP1 and (B) TFPI2 gene promoter region in 18 FFPE colon samples using rapid DNA extraction method. Colon FFPE tumor samples

    Techniques Used: DNA Extraction, Methylation, Formalin-fixed Paraffin-Embedded

    28) Product Images from "Establishment and characterization of an oral tongue squamous cell carcinoma cell line from a never-smoking patient"

    Article Title: Establishment and characterization of an oral tongue squamous cell carcinoma cell line from a never-smoking patient

    Journal: Oral oncology

    doi: 10.1016/j.oraloncology.2017.03.020

    TP53-targeted sequencing of UCSF-OT-1109 (A, forward read; B, reverse read) and the primary tumor (D, forward read; E, reverse read) (C) Western blot analysis with p53 (short and long exposure) and β-Actin antibodies: Lanes 1–5, UCSF-OT-1109 clone; Lanes 6–8, OTSCC lines, Lane 9, cervical cancer cell line HeLa; Lane 10, colon cancer cell line SW480. In D and E, genomic DNA was isolated from microdissected FFPE tissue sections.
    Figure Legend Snippet: TP53-targeted sequencing of UCSF-OT-1109 (A, forward read; B, reverse read) and the primary tumor (D, forward read; E, reverse read) (C) Western blot analysis with p53 (short and long exposure) and β-Actin antibodies: Lanes 1–5, UCSF-OT-1109 clone; Lanes 6–8, OTSCC lines, Lane 9, cervical cancer cell line HeLa; Lane 10, colon cancer cell line SW480. In D and E, genomic DNA was isolated from microdissected FFPE tissue sections.

    Techniques Used: Sequencing, Western Blot, Isolation, Formalin-fixed Paraffin-Embedded

    29) Product Images from "Formalin fixation increases deamination mutation signature but should not lead to false positive mutations in clinical practice"

    Article Title: Formalin fixation increases deamination mutation signature but should not lead to false positive mutations in clinical practice

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0196434

    Read quality in the baseline group does not change by DNA extraction type. Read quality as measured by percent reads mapped. GR UNG = GeneRead uracil-N-glycosylase, QA = QiaAmp FFPE kit.
    Figure Legend Snippet: Read quality in the baseline group does not change by DNA extraction type. Read quality as measured by percent reads mapped. GR UNG = GeneRead uracil-N-glycosylase, QA = QiaAmp FFPE kit.

    Techniques Used: DNA Extraction, Formalin-fixed Paraffin-Embedded

    Deamination events increase with sample age when not treated with UNG. GR UNG = GeneRead uracil-N-glycosylase, QA = QiaAmp FFPE kit.
    Figure Legend Snippet: Deamination events increase with sample age when not treated with UNG. GR UNG = GeneRead uracil-N-glycosylase, QA = QiaAmp FFPE kit.

    Techniques Used: Formalin-fixed Paraffin-Embedded

    Total reads mapped in the baseline group does not change by DNA extraction type. GR UNG = GeneRead uracil-N-glycosylase, QA = QiaAmp FFPE kit.
    Figure Legend Snippet: Total reads mapped in the baseline group does not change by DNA extraction type. GR UNG = GeneRead uracil-N-glycosylase, QA = QiaAmp FFPE kit.

    Techniques Used: DNA Extraction, Formalin-fixed Paraffin-Embedded

    Sequencing read quality decreases over fixation time. Read quality as a measure of percent reads mapped (y-axis) decreases with a longer tissue fixation time (x-axis). Blue dots represent DNA without UNG treatment (extracted using QiaAmp FFPE kit; QA), orange crossed represent matched DNA treated with UNG (extraction using the GeneRead kit; GR UNG). Linear regression line depicted by the central broken line and encompassed by dotted lines representing the 95% confidence interval (CI region colored). Frozen samples used for ground truth are represented by green dots. GR UNG = GeneRead uracil-N-glycosylase, QA = QiaAmp FFPE kit.
    Figure Legend Snippet: Sequencing read quality decreases over fixation time. Read quality as a measure of percent reads mapped (y-axis) decreases with a longer tissue fixation time (x-axis). Blue dots represent DNA without UNG treatment (extracted using QiaAmp FFPE kit; QA), orange crossed represent matched DNA treated with UNG (extraction using the GeneRead kit; GR UNG). Linear regression line depicted by the central broken line and encompassed by dotted lines representing the 95% confidence interval (CI region colored). Frozen samples used for ground truth are represented by green dots. GR UNG = GeneRead uracil-N-glycosylase, QA = QiaAmp FFPE kit.

    Techniques Used: Sequencing, Formalin-fixed Paraffin-Embedded

    Read quality decreases with sample age in the age group. GR UNG = GeneRead uracil-N-glycosylase, QA = QiaAmp FFPE kit.
    Figure Legend Snippet: Read quality decreases with sample age in the age group. GR UNG = GeneRead uracil-N-glycosylase, QA = QiaAmp FFPE kit.

    Techniques Used: Formalin-fixed Paraffin-Embedded

    30) Product Images from "Epigenetic changes around the pX region and spontaneous HTLV-1 transcription are CTCF-independent"

    Article Title: Epigenetic changes around the pX region and spontaneous HTLV-1 transcription are CTCF-independent

    Journal: Wellcome Open Research

    doi: 10.12688/wellcomeopenres.14741.2

    DNA methylation across the body of the HTLV-1 provirus. ( a ) Upper panel: count of CpG dinucleotides in a window of 350 bp in the HTLV-1 reference genome (L36905). Lower panel: schematic diagram of HTLV-1 provirus indicating the two LTRs and the 9 loci examined by MeDIP. ( b ) DNA methylation on the HTLV-1 provirus in the Tax + and Tax – populations from two HTLV-1-infected T cell clones (Clones TBX4B and 11.65). ( c ) DNA methylation on the HTLV-1 provirus in the CADM1 + Tax + and CADM1 + Tax – populations in PBMCs from two unrelated individuals (Patients TDZ and TED). The asterisk (*) indicates that the PCR failed to amplify.
    Figure Legend Snippet: DNA methylation across the body of the HTLV-1 provirus. ( a ) Upper panel: count of CpG dinucleotides in a window of 350 bp in the HTLV-1 reference genome (L36905). Lower panel: schematic diagram of HTLV-1 provirus indicating the two LTRs and the 9 loci examined by MeDIP. ( b ) DNA methylation on the HTLV-1 provirus in the Tax + and Tax – populations from two HTLV-1-infected T cell clones (Clones TBX4B and 11.65). ( c ) DNA methylation on the HTLV-1 provirus in the CADM1 + Tax + and CADM1 + Tax – populations in PBMCs from two unrelated individuals (Patients TDZ and TED). The asterisk (*) indicates that the PCR failed to amplify.

    Techniques Used: DNA Methylation Assay, Methylated DNA Immunoprecipitation, Infection, Clone Assay, Polymerase Chain Reaction

    DNA methylation in the HTLV-1 LTR of patient-derived PBMCs. ( a ) The HTLV-1 LTR sequence (Accession no. L36905) with CpG dinucleotides highlighted in bold. The three TREs are coloured in red; the TATA box is indicated in the rectangle. ( b ) Schematic diagram of HTLV-1 provirus and the regions amplified with indicated sets of primers for bisulfite-sequencing. Sequencing results for each region are shown in the corresponding panels ( c – f ). The three TREs are indicated by red bars. ( c – f ) Schematic representation of DNA methylation for each clone sequenced. Open circles indicate unmethylated cytosine; closed circles methylated cytosine. The numbers indicate the corresponding CpG sites in panel ( a ).
    Figure Legend Snippet: DNA methylation in the HTLV-1 LTR of patient-derived PBMCs. ( a ) The HTLV-1 LTR sequence (Accession no. L36905) with CpG dinucleotides highlighted in bold. The three TREs are coloured in red; the TATA box is indicated in the rectangle. ( b ) Schematic diagram of HTLV-1 provirus and the regions amplified with indicated sets of primers for bisulfite-sequencing. Sequencing results for each region are shown in the corresponding panels ( c – f ). The three TREs are indicated by red bars. ( c – f ) Schematic representation of DNA methylation for each clone sequenced. Open circles indicate unmethylated cytosine; closed circles methylated cytosine. The numbers indicate the corresponding CpG sites in panel ( a ).

    Techniques Used: DNA Methylation Assay, Derivative Assay, Sequencing, Amplification, Methylation Sequencing, Methylation

    Overview of the cell preparations. ( a ) Preparation of Tax + and Tax – populations from PBMCs obtained from HTLV-1-infected patients. PBMCs were stained for CD4, CADM1 and Tax after overnight culture. Tax + and Tax – fractions were collected from the CADM1 + population. ( b ) Preparation of the Tax + and Tax – populations from HTLV-1-infected T cell clones. HTLV-1-infected T cell clones were stained for intracellular Tax and sorted according to Tax expression.
    Figure Legend Snippet: Overview of the cell preparations. ( a ) Preparation of Tax + and Tax – populations from PBMCs obtained from HTLV-1-infected patients. PBMCs were stained for CD4, CADM1 and Tax after overnight culture. Tax + and Tax – fractions were collected from the CADM1 + population. ( b ) Preparation of the Tax + and Tax – populations from HTLV-1-infected T cell clones. HTLV-1-infected T cell clones were stained for intracellular Tax and sorted according to Tax expression.

    Techniques Used: Infection, Staining, Clone Assay, Expressing

    HTLV-1 transcription in two distinct models. a ) Schematic diagram of HTLV-1 provirus inserted in the host genome. The HTLV-1 provirus has two identical LTRs, one at each end of the provirus. As well as genes encoding the canonical retroviral structural components Gag, Pol and Env, the provirus contains a group of regulatory genes in the pX region on the plus-strand. The plus-strand transcripts, represented by tax , are coloured in red, and the minus-strand transcript HBZ in yellow. ( b ) In PBMCs freshly isolated from HTLV-1 carriers, HTLV-1 reactivates and expresses the plus-strand transcripts within a few hours of culture; but these transcripts remain transcriptionally silent for most of the time in vivo . ( c ) In HTLV-1-infected T cell clones cultured in vitro , the promoter activity for plus-strand transcripts shuttles between the on and off state. The plus-strand transcripts are only produced when the promoter activity is on, yielding only a limited fraction of cells that are positive for the plus-strand transcripts at a given time.
    Figure Legend Snippet: HTLV-1 transcription in two distinct models. a ) Schematic diagram of HTLV-1 provirus inserted in the host genome. The HTLV-1 provirus has two identical LTRs, one at each end of the provirus. As well as genes encoding the canonical retroviral structural components Gag, Pol and Env, the provirus contains a group of regulatory genes in the pX region on the plus-strand. The plus-strand transcripts, represented by tax , are coloured in red, and the minus-strand transcript HBZ in yellow. ( b ) In PBMCs freshly isolated from HTLV-1 carriers, HTLV-1 reactivates and expresses the plus-strand transcripts within a few hours of culture; but these transcripts remain transcriptionally silent for most of the time in vivo . ( c ) In HTLV-1-infected T cell clones cultured in vitro , the promoter activity for plus-strand transcripts shuttles between the on and off state. The plus-strand transcripts are only produced when the promoter activity is on, yielding only a limited fraction of cells that are positive for the plus-strand transcripts at a given time.

    Techniques Used: Isolation, In Vivo, Infection, Clone Assay, Cell Culture, In Vitro, Activity Assay, Produced

    Kinetics of the plus- and minus-strand transcription in HTLV-1-infected T cell clones. ( a ) Representative images of HTLV-1 transcripts by single-molecule RNA-FISH (maximum-projection of Z-stacks). Red spots indicate the plus-strand transcripts, and yellow spots the minus-strand transcripts. Blue indicates the DAPI-stained nucleus. Plus- and minus-signs in brackets indicate respectively the presence or absence of the mRNA. Scale bar (white) = 5 µm. ( b ) Spot counts of the plus-strand (upper row) and the minus-strand transcripts (lower row) respectively in the unaltered and ΔCTCF-binding subclones. The insets in the upper row capture low-frequency events on a magnified y-axis. The bar in the first bin in the insets is greyed out because it is out of scale.
    Figure Legend Snippet: Kinetics of the plus- and minus-strand transcription in HTLV-1-infected T cell clones. ( a ) Representative images of HTLV-1 transcripts by single-molecule RNA-FISH (maximum-projection of Z-stacks). Red spots indicate the plus-strand transcripts, and yellow spots the minus-strand transcripts. Blue indicates the DAPI-stained nucleus. Plus- and minus-signs in brackets indicate respectively the presence or absence of the mRNA. Scale bar (white) = 5 µm. ( b ) Spot counts of the plus-strand (upper row) and the minus-strand transcripts (lower row) respectively in the unaltered and ΔCTCF-binding subclones. The insets in the upper row capture low-frequency events on a magnified y-axis. The bar in the first bin in the insets is greyed out because it is out of scale.

    Techniques Used: Infection, Clone Assay, Fluorescence In Situ Hybridization, Staining, Binding Assay

    Histone modifications and CTCF-binding in the HTLV-1 provirus. Chromatin immunoprecipitation (ChIP) was used to identify ( a ) histone modifications and CTCF-binding in the Tax + and Tax – populations from an HTLV-1-infected T cell clone (TBX4B); and ( b ) histone modifications in the CADM1 + Tax + and CADM1 + Tax – populations from PBMCs obtained from HTLV-1-infected patients (Patients TW and TCD). The horizontal axis indicates the nucleotide position in the full-length HTLV-1 provirus (J02029), and the vertical axis the read depth (arbitrary units). The reads that aligned within either one of the LTRs are greyed out. The black bars on the horizontal axis indicates the LTRs.
    Figure Legend Snippet: Histone modifications and CTCF-binding in the HTLV-1 provirus. Chromatin immunoprecipitation (ChIP) was used to identify ( a ) histone modifications and CTCF-binding in the Tax + and Tax – populations from an HTLV-1-infected T cell clone (TBX4B); and ( b ) histone modifications in the CADM1 + Tax + and CADM1 + Tax – populations from PBMCs obtained from HTLV-1-infected patients (Patients TW and TCD). The horizontal axis indicates the nucleotide position in the full-length HTLV-1 provirus (J02029), and the vertical axis the read depth (arbitrary units). The reads that aligned within either one of the LTRs are greyed out. The black bars on the horizontal axis indicates the LTRs.

    Techniques Used: Binding Assay, Chromatin Immunoprecipitation, Infection

    Epigenetic modifications in the HTLV-1 provirus lacking CTCF binding. ( a ) Histone modifications in the Tax + and Tax – populations of the altered HTLV-1-infected T cell clone (Subclone #78 of TBX4B). ( b ) DNA methylation in the body of the provirus in TBX4B-78. Note the similarity to the profiles of epigenetic modifications in the wild-type TBX4B ( Figure 3 ).
    Figure Legend Snippet: Epigenetic modifications in the HTLV-1 provirus lacking CTCF binding. ( a ) Histone modifications in the Tax + and Tax – populations of the altered HTLV-1-infected T cell clone (Subclone #78 of TBX4B). ( b ) DNA methylation in the body of the provirus in TBX4B-78. Note the similarity to the profiles of epigenetic modifications in the wild-type TBX4B ( Figure 3 ).

    Techniques Used: Binding Assay, Infection, DNA Methylation Assay

    CTCF occupancy in the HTLV-1 provirus in patient-derived PBMCs. CTCF occupancy was examined by droplet digital PCR following ChIP for CTCF. The experiment was carried out on PBMCs after overnight incubation in vitro . Replicate 1 is obtained from pooled samples of 4 patients (TCR, TEJ, TED and TW) and Replicate 2 from 3 patients (TED, TCR and TEJ).
    Figure Legend Snippet: CTCF occupancy in the HTLV-1 provirus in patient-derived PBMCs. CTCF occupancy was examined by droplet digital PCR following ChIP for CTCF. The experiment was carried out on PBMCs after overnight incubation in vitro . Replicate 1 is obtained from pooled samples of 4 patients (TCR, TEJ, TED and TW) and Replicate 2 from 3 patients (TED, TCR and TEJ).

    Techniques Used: Derivative Assay, Digital PCR, Chromatin Immunoprecipitation, Incubation, In Vitro

    Alteration of the CTCF-binding site in the provirus in HTLV-1-infected T cell clones. ( a ) The sequence of the CTCF-binding site in the HTLV-1 provirus. The upper panel is from a subclone with the sequence unchanged, and the lower panel from a subclone in which the sequence was altered by CRISPR/Cas9 modification. ( b ) Flow cytometric analysis of the mutated clone after staining for intracellular Tax protein.
    Figure Legend Snippet: Alteration of the CTCF-binding site in the provirus in HTLV-1-infected T cell clones. ( a ) The sequence of the CTCF-binding site in the HTLV-1 provirus. The upper panel is from a subclone with the sequence unchanged, and the lower panel from a subclone in which the sequence was altered by CRISPR/Cas9 modification. ( b ) Flow cytometric analysis of the mutated clone after staining for intracellular Tax protein.

    Techniques Used: Binding Assay, Infection, Clone Assay, Sequencing, CRISPR, Modification, Flow Cytometry, Staining

    31) Product Images from "Profiling Cancer Gene Mutations in Clinical Formalin-Fixed, Paraffin-Embedded Colorectal Tumor Specimens Using Targeted Next-Generation Sequencing"

    Article Title: Profiling Cancer Gene Mutations in Clinical Formalin-Fixed, Paraffin-Embedded Colorectal Tumor Specimens Using Targeted Next-Generation Sequencing

    Journal: The Oncologist

    doi: 10.1634/theoncologist.2013-0180

    Mutation detection using formalin-fixed, paraffin-embedded (FFPE) colorectal cancer tumor specimens. Variants were detected by AmpliSeq (A) and SimpliSeq (B) in 44 FFPE genomic DNA samples. The red shade stands for variants with VF > 5%; blue shade
    Figure Legend Snippet: Mutation detection using formalin-fixed, paraffin-embedded (FFPE) colorectal cancer tumor specimens. Variants were detected by AmpliSeq (A) and SimpliSeq (B) in 44 FFPE genomic DNA samples. The red shade stands for variants with VF > 5%; blue shade

    Techniques Used: Mutagenesis, Formalin-fixed Paraffin-Embedded

    32) Product Images from "The frequency of promoter DNA hypermethylation is decreased in colorectal neoplasms of familial adenomatous polyposis"

    Article Title: The frequency of promoter DNA hypermethylation is decreased in colorectal neoplasms of familial adenomatous polyposis

    Journal: Oncotarget

    doi: 10.18632/oncotarget.25987

    Selection of appropriate probes for analysis of frozen and FFPE samples ( A ) Preparation of frozen and FFPE samples. Three colon tumors (#1–3) were cut into two pieces; one was fixed with formalin and embedded in paraffin ( FFPE ), and the other was frozen with liquid nitrogen and stored at –80° C ( frozen ). Both tissues underwent DNA extraction and Infinium assays. ( B ) Plot of β-values. Probes showing the differences in β-values between frozen and FFPE samples of less than 0.1, i.e., between y = x + 0.1 and y = x−0.1, were extracted ( red ). ( C ) In total, 161,828 overlapped probes among three analyses (tumors #1, #2, and #3) were extracted and used for subsequent DNA methylation analysis.
    Figure Legend Snippet: Selection of appropriate probes for analysis of frozen and FFPE samples ( A ) Preparation of frozen and FFPE samples. Three colon tumors (#1–3) were cut into two pieces; one was fixed with formalin and embedded in paraffin ( FFPE ), and the other was frozen with liquid nitrogen and stored at –80° C ( frozen ). Both tissues underwent DNA extraction and Infinium assays. ( B ) Plot of β-values. Probes showing the differences in β-values between frozen and FFPE samples of less than 0.1, i.e., between y = x + 0.1 and y = x−0.1, were extracted ( red ). ( C ) In total, 161,828 overlapped probes among three analyses (tumors #1, #2, and #3) were extracted and used for subsequent DNA methylation analysis.

    Techniques Used: Selection, Formalin-fixed Paraffin-Embedded, DNA Extraction, DNA Methylation Assay

    33) Product Images from "Multi-Purpose Utility of Circulating Plasma DNA Testing in Patients with Advanced Cancers"

    Article Title: Multi-Purpose Utility of Circulating Plasma DNA Testing in Patients with Advanced Cancers

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0047020

    cpDNA concentrations for mutational detection by Sequenom OncoCarta panel (v1.0). 2A: Nonparametric ROC analyses were used to assess the limit of the Sequenom platform to detect OncoCarta panel mutations in cpDNA. Each dot on the graph corresponds to the sensitivity and specificity at one of the observed concentrations. Mutations were considered ‘available for detection’ if they were detected in the patient's FFPE tissue. Mutations were detected in FFPE samples from 37 patients. The concentration of cpDNA with the optimal ability to detect a mutation is 29.95 ng/ml (Likelihood ratio = 7.3043). The AUC calculated is 0.8075 (95% CI 0.6552–0.9598). Patients whose FFPE was unavailable or tested negative for mutations were excluded from the analysis. The specificity reference lines for quartiles of DNA concentrations are indicated in red dashed lines. 2B: Graph showing the types of mutations and cpDNA concentrations at which they were detected in different tumors. Mutations were detected in six oncogenes. Symbols represent different tumor types.
    Figure Legend Snippet: cpDNA concentrations for mutational detection by Sequenom OncoCarta panel (v1.0). 2A: Nonparametric ROC analyses were used to assess the limit of the Sequenom platform to detect OncoCarta panel mutations in cpDNA. Each dot on the graph corresponds to the sensitivity and specificity at one of the observed concentrations. Mutations were considered ‘available for detection’ if they were detected in the patient's FFPE tissue. Mutations were detected in FFPE samples from 37 patients. The concentration of cpDNA with the optimal ability to detect a mutation is 29.95 ng/ml (Likelihood ratio = 7.3043). The AUC calculated is 0.8075 (95% CI 0.6552–0.9598). Patients whose FFPE was unavailable or tested negative for mutations were excluded from the analysis. The specificity reference lines for quartiles of DNA concentrations are indicated in red dashed lines. 2B: Graph showing the types of mutations and cpDNA concentrations at which they were detected in different tumors. Mutations were detected in six oncogenes. Symbols represent different tumor types.

    Techniques Used: Formalin-fixed Paraffin-Embedded, Concentration Assay, Mutagenesis

    34) Product Images from "Evaluation of pre-analytical conditions and comparison of the performance of several digital PCR assays for the detection of major EGFR mutations in circulating DNA from non-small cell lung cancers: the CIRCAN_0 study"

    Article Title: Evaluation of pre-analytical conditions and comparison of the performance of several digital PCR assays for the detection of major EGFR mutations in circulating DNA from non-small cell lung cancers: the CIRCAN_0 study

    Journal: Oncotarget

    doi: 10.18632/oncotarget.21256

    Optimization of circulating free DNA (cfDNA) extraction and quantification of cfDNA in the samples (A) Reproducibility of cfDNA extraction using the QIAamp Circulating Acid Kit (Qiagen, Cat No 55114, Valencia, CA, USA) on two independent cfDNA samples extracted from 1 mL (Ai) and 3 mL (Aii) of plasma from NSCLC patients. After extraction, cfDNA was quantified by Qubit dsDNA HS Assay Kit (Life Technologies, Q32854, Carlsbad, CA, USA) according to the manufacturer's instructions. (B) Correlation between the initial volume of plasma 1 mL versus 3 mL (Bi) or 3 mL versus 5 mL (Bii) and the quantity of cfDNA extracted (in ng/μL). (Ci) Fragment size visualization of cfDNA (in bp) from a concentrated (left) and a less concentrated (right) sample obtained using the Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) (Cii) , and average size distribution (10 bp increments) of cfDNA fragments in 77 plasma samples. (D) Correlation between cfDNA concentration measured using the Qubit method and the number of amplifiable copies in the corresponding plasma samples determined using the Quantifiler Kit.
    Figure Legend Snippet: Optimization of circulating free DNA (cfDNA) extraction and quantification of cfDNA in the samples (A) Reproducibility of cfDNA extraction using the QIAamp Circulating Acid Kit (Qiagen, Cat No 55114, Valencia, CA, USA) on two independent cfDNA samples extracted from 1 mL (Ai) and 3 mL (Aii) of plasma from NSCLC patients. After extraction, cfDNA was quantified by Qubit dsDNA HS Assay Kit (Life Technologies, Q32854, Carlsbad, CA, USA) according to the manufacturer's instructions. (B) Correlation between the initial volume of plasma 1 mL versus 3 mL (Bi) or 3 mL versus 5 mL (Bii) and the quantity of cfDNA extracted (in ng/μL). (Ci) Fragment size visualization of cfDNA (in bp) from a concentrated (left) and a less concentrated (right) sample obtained using the Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) (Cii) , and average size distribution (10 bp increments) of cfDNA fragments in 77 plasma samples. (D) Correlation between cfDNA concentration measured using the Qubit method and the number of amplifiable copies in the corresponding plasma samples determined using the Quantifiler Kit.

    Techniques Used: Concentration Assay

    35) Product Images from "Performance comparison of three DNA extraction kits on human whole-exome data from formalin-fixed paraffin-embedded normal and tumor samples"

    Article Title: Performance comparison of three DNA extraction kits on human whole-exome data from formalin-fixed paraffin-embedded normal and tumor samples

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0195471

    DNA Integrity Number (DIN) values for FF and FFPE samples. A: FF and FFPE samples. B: FFPE samples grouped by extraction method.
    Figure Legend Snippet: DNA Integrity Number (DIN) values for FF and FFPE samples. A: FF and FFPE samples. B: FFPE samples grouped by extraction method.

    Techniques Used: Formalin-fixed Paraffin-Embedded

    DNA fragment length values for FF and FFPE samples. A: FF and FFPE samples. B: FFPE samples grouped by extraction method.
    Figure Legend Snippet: DNA fragment length values for FF and FFPE samples. A: FF and FFPE samples. B: FFPE samples grouped by extraction method.

    Techniques Used: Formalin-fixed Paraffin-Embedded

    36) Product Images from "Performance comparison of three DNA extraction kits on human whole-exome data from formalin-fixed paraffin-embedded normal and tumor samples"

    Article Title: Performance comparison of three DNA extraction kits on human whole-exome data from formalin-fixed paraffin-embedded normal and tumor samples

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0195471

    DNA Integrity Number (DIN) values for FF and FFPE samples. A: FF and FFPE samples. B: FFPE samples grouped by extraction method.
    Figure Legend Snippet: DNA Integrity Number (DIN) values for FF and FFPE samples. A: FF and FFPE samples. B: FFPE samples grouped by extraction method.

    Techniques Used: Formalin-fixed Paraffin-Embedded

    DNA fragment length values for FF and FFPE samples. A: FF and FFPE samples. B: FFPE samples grouped by extraction method.
    Figure Legend Snippet: DNA fragment length values for FF and FFPE samples. A: FF and FFPE samples. B: FFPE samples grouped by extraction method.

    Techniques Used: Formalin-fixed Paraffin-Embedded

    37) Product Images from "Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples"

    Article Title: Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0197456

    Variants identified in the samples extracted with different DNA extraction methods. (A-D) Venn diagram showing the distribution of variants between DNA extraction methods in four different FFPE samples, SARC1-4. Variants were detected by MuTect and Strelka, using an artificial control as normal. The data was filtered on exonic variants with allele frequency > 5% and coverage > 100x, being present at
    Figure Legend Snippet: Variants identified in the samples extracted with different DNA extraction methods. (A-D) Venn diagram showing the distribution of variants between DNA extraction methods in four different FFPE samples, SARC1-4. Variants were detected by MuTect and Strelka, using an artificial control as normal. The data was filtered on exonic variants with allele frequency > 5% and coverage > 100x, being present at

    Techniques Used: DNA Extraction, Formalin-fixed Paraffin-Embedded

    Yield and amplifiability of extracted DNA and RNA. (A) Average total amount of DNA. (B) Average total amount of RNA. (C) Amplifiable DNA quantified with the FFPE QC kit from Illumina. (D) Amplifiable RNA quantified with the PreSeq QC assay from ArcherDx. The average total amount and average delta Ct values for the different samples and extraction methods are shown. The standard deviation is shown as vertical bars. Methods with significant differences in yield are marked as connected with horizontal bars (p
    Figure Legend Snippet: Yield and amplifiability of extracted DNA and RNA. (A) Average total amount of DNA. (B) Average total amount of RNA. (C) Amplifiable DNA quantified with the FFPE QC kit from Illumina. (D) Amplifiable RNA quantified with the PreSeq QC assay from ArcherDx. The average total amount and average delta Ct values for the different samples and extraction methods are shown. The standard deviation is shown as vertical bars. Methods with significant differences in yield are marked as connected with horizontal bars (p

    Techniques Used: Formalin-fixed Paraffin-Embedded, Standard Deviation

    38) Product Images from "Optimal Fixation Conditions and DNA Extraction Methods for MLPA Analysis on FFPE Tissue-Derived DNA"

    Article Title: Optimal Fixation Conditions and DNA Extraction Methods for MLPA Analysis on FFPE Tissue-Derived DNA

    Journal: American Journal of Clinical Pathology

    doi: 10.1093/ajcp/aqw205

    The influence of five different DNA extraction methods on the multiplex ligation-dependent probe amplification (MLPA) probe’s copy number ratios. MLPA was performed on DNA extracted from eight various formalin-fixed, paraffin-embedded (FFPE) tissues with the P027 probe mix (50 probes). The y-axis represents the percentage of probes showing copy number ratios outside the 0.8 to 1.2 normal copy number range. The x-axis shows five different DNA extraction methods. Each bar represents a separate FFPE tissue-type block. For samples where DNA was extracted with the one-tube FFPE extraction method, results from crude (nonpurified) DNA lysate are presented for all tissues, except the lung. The crude lysate of the lung FFPE tissue was also purified. SEM (as indicated by error bars) was calculated by dividing the standard deviation of the mean of the number of probes with copy number ratios outside the normal range by the square root of the number of samples (triplicate) ( Supplementary Table S6 ). colonSymb, tissue from Symbiant Pathology Expert Centre, Alkmaar; colonUMC, tissue from Department of Pathology, University Medical Centre Utrecht, Utrecht.
    Figure Legend Snippet: The influence of five different DNA extraction methods on the multiplex ligation-dependent probe amplification (MLPA) probe’s copy number ratios. MLPA was performed on DNA extracted from eight various formalin-fixed, paraffin-embedded (FFPE) tissues with the P027 probe mix (50 probes). The y-axis represents the percentage of probes showing copy number ratios outside the 0.8 to 1.2 normal copy number range. The x-axis shows five different DNA extraction methods. Each bar represents a separate FFPE tissue-type block. For samples where DNA was extracted with the one-tube FFPE extraction method, results from crude (nonpurified) DNA lysate are presented for all tissues, except the lung. The crude lysate of the lung FFPE tissue was also purified. SEM (as indicated by error bars) was calculated by dividing the standard deviation of the mean of the number of probes with copy number ratios outside the normal range by the square root of the number of samples (triplicate) ( Supplementary Table S6 ). colonSymb, tissue from Symbiant Pathology Expert Centre, Alkmaar; colonUMC, tissue from Department of Pathology, University Medical Centre Utrecht, Utrecht.

    Techniques Used: DNA Extraction, Multiplex Assay, Ligation, Amplification, Multiplex Ligation-dependent Probe Amplification, Formalin-fixed Paraffin-Embedded, Blocking Assay, Purification, Standard Deviation

    (cont) C , MLPA electropherogram of FFPE lung tissue crude lysate column purified with the DNA Clean Concentrator-5 kit. RFU, residual fluorescence unit.
    Figure Legend Snippet: (cont) C , MLPA electropherogram of FFPE lung tissue crude lysate column purified with the DNA Clean Concentrator-5 kit. RFU, residual fluorescence unit.

    Techniques Used: Multiplex Ligation-dependent Probe Amplification, Formalin-fixed Paraffin-Embedded, Purification, Fluorescence

    39) Product Images from "Sources of erroneous sequences and artifact chimeric reads in next generation sequencing of genomic DNA from formalin-fixed paraffin-embedded samples"

    Article Title: Sources of erroneous sequences and artifact chimeric reads in next generation sequencing of genomic DNA from formalin-fixed paraffin-embedded samples

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gky1142

    SSAR mapping and diagrammatic depiction of the proposed mechanism. The SSAR example shown is a screen shot of an actual IGV image. At the top (I) we depict a ds-DNA region of intact gDNA. In the process of FFPE preparation, storage and extraction (II), gDNA is fragmented and denatured. In the absence of S1 nuclease (III left), ss-DNA fragments from non-contiguous regions of the genome anneal via short complementary repetitive sequences (red asterisks). In contrast, ss-DNA fragments and overhangs are removed upon treatment with S1 nuclease (III right). During the end-repair step of library construction, T4 DNA polymerase removes overhangs (IV) and fills ends (V), resulting in the formation of double-stranded chimeric fragments (‘A’ in V). One class of such chimeric fragments yield SSARs (‘A’ in VI). R1 = read; R2 = read 2. For SSARs, part of Read 2 aligns in the expected paired-end orientation while the distal end of Read 2 does not match the reference at that position and instead aligns to a nearby region of the reference genome in the opposite orientation (denoted as R2′).
    Figure Legend Snippet: SSAR mapping and diagrammatic depiction of the proposed mechanism. The SSAR example shown is a screen shot of an actual IGV image. At the top (I) we depict a ds-DNA region of intact gDNA. In the process of FFPE preparation, storage and extraction (II), gDNA is fragmented and denatured. In the absence of S1 nuclease (III left), ss-DNA fragments from non-contiguous regions of the genome anneal via short complementary repetitive sequences (red asterisks). In contrast, ss-DNA fragments and overhangs are removed upon treatment with S1 nuclease (III right). During the end-repair step of library construction, T4 DNA polymerase removes overhangs (IV) and fills ends (V), resulting in the formation of double-stranded chimeric fragments (‘A’ in V). One class of such chimeric fragments yield SSARs (‘A’ in VI). R1 = read; R2 = read 2. For SSARs, part of Read 2 aligns in the expected paired-end orientation while the distal end of Read 2 does not match the reference at that position and instead aligns to a nearby region of the reference genome in the opposite orientation (denoted as R2′).

    Techniques Used: Formalin-fixed Paraffin-Embedded

    40) Product Images from "Optimised Pre-Analytical Methods Improve KRAS Mutation Detection in Circulating Tumour DNA (ctDNA) from Patients with Non-Small Cell Lung Cancer (NSCLC)"

    Article Title: Optimised Pre-Analytical Methods Improve KRAS Mutation Detection in Circulating Tumour DNA (ctDNA) from Patients with Non-Small Cell Lung Cancer (NSCLC)

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0150197

    Plasma input volume comparison. Three volumes of plasma (1 mL, 2 mL and 3 mL) were processed from each sample in a cohort of 15 NSCLC patients. DNA was extracted using the QIAamp CNA Kit and was measured by qPCR using the ABI TaqMan® RNase P Detection Reagent Kit. Results are displayed for each patient. Statistical analysis was performed using a paired Student’s t-test where; **p
    Figure Legend Snippet: Plasma input volume comparison. Three volumes of plasma (1 mL, 2 mL and 3 mL) were processed from each sample in a cohort of 15 NSCLC patients. DNA was extracted using the QIAamp CNA Kit and was measured by qPCR using the ABI TaqMan® RNase P Detection Reagent Kit. Results are displayed for each patient. Statistical analysis was performed using a paired Student’s t-test where; **p

    Techniques Used: Real-time Polymerase Chain Reaction

    DNA extraction kit comparison. Equal volumes of plasma (2 mL) from 10 NSCLC patients were processed using three different DNA extraction methods: QIAamp Circulating Nucleic Acid Kit (Qiagen CNA Kit); PME free-circulating DNA Extraction Kit (Analytik Jena) and the DSP Virus/Pathogen Midi Kit performed on QIAsymphony (QIAsymphony). DNA was measured by qPCR using the ABI TaqMan® RNase P Detection Reagent Kit. Results are displayed for each patient. Statistical analysis was performed using a paired Student’s t-test where; **p
    Figure Legend Snippet: DNA extraction kit comparison. Equal volumes of plasma (2 mL) from 10 NSCLC patients were processed using three different DNA extraction methods: QIAamp Circulating Nucleic Acid Kit (Qiagen CNA Kit); PME free-circulating DNA Extraction Kit (Analytik Jena) and the DSP Virus/Pathogen Midi Kit performed on QIAsymphony (QIAsymphony). DNA was measured by qPCR using the ABI TaqMan® RNase P Detection Reagent Kit. Results are displayed for each patient. Statistical analysis was performed using a paired Student’s t-test where; **p

    Techniques Used: DNA Extraction, Real-time Polymerase Chain Reaction

    Related Articles

    DNA Extraction:

    Article Title: Critical Issues in Mycobiota Analysis
    Article Snippet: .. To highlight the influence of pre-analytics on ITS based mycobiota investigations we assessed the performance of DNA extraction from human skin FFPE samples (see Supplementary Table for sample information) with a commercially available kit (QIAamp DNA FFPE tissue kit, Qiagen) reported to be efficient for fungal DNA extraction out of FFPE material (Muñoz-Cadavid et al., ). .. We added a mechanical cell disruption step (bead-beating) to the procedure (MagnaLyser, Roche), since this step was shown to be crucial for complete lysis of microbial cells in specimens, significantly influencing correct community representation (de Boer et al., ; Reck et al., ).

    Article Title: Characterisation of the changing genomic landscape of metastatic melanoma using cell free DNA
    Article Snippet: .. TDNA was extracted using the QIAamp FFPE DNA extraction kit (Qiagen) and eluted into 20 µl buffer EB. .. All cfDNA and tDNA samples were quantified on a Qubit fluorometer (Invitrogen) using the high sensitivity dsDNA kit and gDNA was quantified using the broad range dsDNA kit.

    Article Title: A Comparison of EGFR Mutation Testing Methods in Lung Carcinoma: Direct Sequencing, Real-time PCR and Immunohistochemistry
    Article Snippet: .. The DNA extraction was performed with QIAamp™ DNA FFPE Tissue kit and automated on the QIAcube robot (QIAGEN, Valencia, CA, USA), as previously described and according to the manufacturer’s instructions . ..

    Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies
    Article Snippet: .. The macro-dissected tumor area from one tissue section was used for RNA isolation using the RNeasy® FFPE kit (Qiagen, Hilden, Germany) and the tumor area from the second section was used for DNA isolation using the QIAamp® DNA FFPE Tissue kit (Qiagen, Hilden, Germany), following the manufacturers’ instructions. .. Quantity and quality measurements The quantity and purity (A260/A280) of the extracted DNA and RNA was measured using the NanoDrop ND-2000 Spectrophotometer (Thermo Scientific, Waltham, MA, USA).

    Isolation:

    Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies
    Article Snippet: .. Assessment of nucleic acids extraction kits from FFPE biopsies with normal histology The study material, consisting of 30 FFPE prostate biopsies with normal histology, was randomly divided into three different groups; 1) ten biopsies for comparison between the High Pure FFPE RNA Micro Kit (Roche Diagnostics, West Sussex, UK) and the RNeasy® FFPE kit (Qiagen, Hilden, Germany), 2) ten biopsies for comparison between the High Pure DNA FFPET Isolation Kit (Roche Diagnostics, West Sussex, UK) and the QIAamp® DNA FFPE Tissue kit (Qiagen, Hilden, Germany), and 3) ten biopsies for comparison of the best performing DNA and RNA kits from the two previous steps to the AllPrep® DNA/RNA FFPE kit (Qiagen, Hilden, Germany). .. In order to minimize the risk of variation due to different operators, the same operator performed all extractions with one kit (e.g. all extractions using the RNeasy® FFPE kit).

    Article Title: Amplicon Sequencing of Colorectal Cancer: Variant Calling in Frozen and Formalin-Fixed Samples
    Article Snippet: .. DNA was isolated using the Qiagen QIAamp DNA FFPE Kit according to the manufacturer’s instructions. .. DNA was eluted in 40μl Buffer ATE and concentrations were measured with NanoDrop 2000 (NanoDrop, Wilmington, USA) and Qubit BR kit (Life Technologies, Darmstadt, Germany).

    Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies
    Article Snippet: .. The macro-dissected tumor area from one tissue section was used for RNA isolation using the RNeasy® FFPE kit (Qiagen, Hilden, Germany) and the tumor area from the second section was used for DNA isolation using the QIAamp® DNA FFPE Tissue kit (Qiagen, Hilden, Germany), following the manufacturers’ instructions. .. Quantity and quality measurements The quantity and purity (A260/A280) of the extracted DNA and RNA was measured using the NanoDrop ND-2000 Spectrophotometer (Thermo Scientific, Waltham, MA, USA).

    Formalin-fixed Paraffin-Embedded:

    Article Title: Critical Issues in Mycobiota Analysis
    Article Snippet: .. To highlight the influence of pre-analytics on ITS based mycobiota investigations we assessed the performance of DNA extraction from human skin FFPE samples (see Supplementary Table for sample information) with a commercially available kit (QIAamp DNA FFPE tissue kit, Qiagen) reported to be efficient for fungal DNA extraction out of FFPE material (Muñoz-Cadavid et al., ). .. We added a mechanical cell disruption step (bead-beating) to the procedure (MagnaLyser, Roche), since this step was shown to be crucial for complete lysis of microbial cells in specimens, significantly influencing correct community representation (de Boer et al., ; Reck et al., ).

    Article Title: Characterisation of the changing genomic landscape of metastatic melanoma using cell free DNA
    Article Snippet: .. TDNA was extracted using the QIAamp FFPE DNA extraction kit (Qiagen) and eluted into 20 µl buffer EB. .. All cfDNA and tDNA samples were quantified on a Qubit fluorometer (Invitrogen) using the high sensitivity dsDNA kit and gDNA was quantified using the broad range dsDNA kit.

    Article Title: Targeted next-generation sequencing of head and neck squamous cell carcinoma identifies novel genetic alterations in HPV+ and HPV- tumors
    Article Snippet: .. Tissue was collected into extraction tubes and processed using the QIAamp DNA FFPE Tissue Kit (Qiagen, Hilden, Germany). .. Extracted DNA was quantified using a standardized PicoGreen fluorescence assay (LifeTechnologies, Carlsbad, CA, USA).

    Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies
    Article Snippet: .. Assessment of nucleic acids extraction kits from FFPE biopsies with normal histology The study material, consisting of 30 FFPE prostate biopsies with normal histology, was randomly divided into three different groups; 1) ten biopsies for comparison between the High Pure FFPE RNA Micro Kit (Roche Diagnostics, West Sussex, UK) and the RNeasy® FFPE kit (Qiagen, Hilden, Germany), 2) ten biopsies for comparison between the High Pure DNA FFPET Isolation Kit (Roche Diagnostics, West Sussex, UK) and the QIAamp® DNA FFPE Tissue kit (Qiagen, Hilden, Germany), and 3) ten biopsies for comparison of the best performing DNA and RNA kits from the two previous steps to the AllPrep® DNA/RNA FFPE kit (Qiagen, Hilden, Germany). .. In order to minimize the risk of variation due to different operators, the same operator performed all extractions with one kit (e.g. all extractions using the RNeasy® FFPE kit).

    Article Title: Why do results conflict regarding the prognostic value of the methylation status in colon cancers? the role of the preservation method
    Article Snippet: .. Dedicated Method to FFPE tissue: QIAamp® DNA FFPE Tissue kit (QIAGEN® ) For each sample, ten 15-μm-thick tissue sections were transferred into a 1.5 ml tube. ..

    Article Title: A Comparison of EGFR Mutation Testing Methods in Lung Carcinoma: Direct Sequencing, Real-time PCR and Immunohistochemistry
    Article Snippet: .. The DNA extraction was performed with QIAamp™ DNA FFPE Tissue kit and automated on the QIAcube robot (QIAGEN, Valencia, CA, USA), as previously described and according to the manufacturer’s instructions . ..

    Article Title: Amplicon Sequencing of Colorectal Cancer: Variant Calling in Frozen and Formalin-Fixed Samples
    Article Snippet: .. DNA was isolated using the Qiagen QIAamp DNA FFPE Kit according to the manufacturer’s instructions. .. DNA was eluted in 40μl Buffer ATE and concentrations were measured with NanoDrop 2000 (NanoDrop, Wilmington, USA) and Qubit BR kit (Life Technologies, Darmstadt, Germany).

    Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies
    Article Snippet: .. The macro-dissected tumor area from one tissue section was used for RNA isolation using the RNeasy® FFPE kit (Qiagen, Hilden, Germany) and the tumor area from the second section was used for DNA isolation using the QIAamp® DNA FFPE Tissue kit (Qiagen, Hilden, Germany), following the manufacturers’ instructions. .. Quantity and quality measurements The quantity and purity (A260/A280) of the extracted DNA and RNA was measured using the NanoDrop ND-2000 Spectrophotometer (Thermo Scientific, Waltham, MA, USA).

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    Qiagen qiaamp dna ffpe kit
    Depth of Sequencing correlates with <t>DNA</t> quality. (A) Sample preparation workflow. DNA was isolated from fresh frozen or <t>FFPE</t> CRC liver metastasis resection specimens with Qiagen Blood and Tissue or FFPE kit, respectively. Frozen samples then directly underwent sequencing library preparation, pooling of libraries, quality control and sequencing. FFPE samples were additionally tested for DNA quality by qPCR. Library quality was tested with Bioanalyzer. For samples with low amounts of correctly sized DNA amplicons (fragments at 310bp), new libraries were prepared with higher starting DNA concentrations and re-analyzed with Bioanalyzer. Samples with yet low amounts of DNA with correct size and highly fragmented DNA were excluded. (B) ΔCq-values of quality control PCR indicate poor sample quality. DNA concentration of fragments between 250bp and 450bp after library preparation was calculated with Agilent Bioanalyzer and plotted against ΔCq values of FFPE quality control PCR. (C) higher ΔCq-values correlate with lower mean depth of sequencing. (D) Coverage distribution of amplicons from all paired FFPE and frozen samples, normalized to total sample coverage. Frozen samples had a mean depth of 4,622, FFPE samples 1,852.
    Qiaamp Dna Ffpe Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 2184 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Depth of Sequencing correlates with DNA quality. (A) Sample preparation workflow. DNA was isolated from fresh frozen or FFPE CRC liver metastasis resection specimens with Qiagen Blood and Tissue or FFPE kit, respectively. Frozen samples then directly underwent sequencing library preparation, pooling of libraries, quality control and sequencing. FFPE samples were additionally tested for DNA quality by qPCR. Library quality was tested with Bioanalyzer. For samples with low amounts of correctly sized DNA amplicons (fragments at 310bp), new libraries were prepared with higher starting DNA concentrations and re-analyzed with Bioanalyzer. Samples with yet low amounts of DNA with correct size and highly fragmented DNA were excluded. (B) ΔCq-values of quality control PCR indicate poor sample quality. DNA concentration of fragments between 250bp and 450bp after library preparation was calculated with Agilent Bioanalyzer and plotted against ΔCq values of FFPE quality control PCR. (C) higher ΔCq-values correlate with lower mean depth of sequencing. (D) Coverage distribution of amplicons from all paired FFPE and frozen samples, normalized to total sample coverage. Frozen samples had a mean depth of 4,622, FFPE samples 1,852.

    Journal: PLoS ONE

    Article Title: Amplicon Sequencing of Colorectal Cancer: Variant Calling in Frozen and Formalin-Fixed Samples

    doi: 10.1371/journal.pone.0127146

    Figure Lengend Snippet: Depth of Sequencing correlates with DNA quality. (A) Sample preparation workflow. DNA was isolated from fresh frozen or FFPE CRC liver metastasis resection specimens with Qiagen Blood and Tissue or FFPE kit, respectively. Frozen samples then directly underwent sequencing library preparation, pooling of libraries, quality control and sequencing. FFPE samples were additionally tested for DNA quality by qPCR. Library quality was tested with Bioanalyzer. For samples with low amounts of correctly sized DNA amplicons (fragments at 310bp), new libraries were prepared with higher starting DNA concentrations and re-analyzed with Bioanalyzer. Samples with yet low amounts of DNA with correct size and highly fragmented DNA were excluded. (B) ΔCq-values of quality control PCR indicate poor sample quality. DNA concentration of fragments between 250bp and 450bp after library preparation was calculated with Agilent Bioanalyzer and plotted against ΔCq values of FFPE quality control PCR. (C) higher ΔCq-values correlate with lower mean depth of sequencing. (D) Coverage distribution of amplicons from all paired FFPE and frozen samples, normalized to total sample coverage. Frozen samples had a mean depth of 4,622, FFPE samples 1,852.

    Article Snippet: DNA was isolated using the Qiagen QIAamp DNA FFPE Kit according to the manufacturer’s instructions.

    Techniques: Sequencing, Sample Prep, Isolation, Formalin-fixed Paraffin-Embedded, Real-time Polymerase Chain Reaction, Polymerase Chain Reaction, Concentration Assay

    Coverage uniformity of WGS libraries. a Represented is the cumulative proportion of sequencing coverage per cumulative proportion of sequence in whole genome sequencing across normal germline DNA (gDNA) from peripheral blood mononuclear cells, two cfDNA time points, and an archival FFPE tissue biopsy from a metastatic melanoma patient. If coverage was perfectly uniform across the genome coverage the relationship would be linear with gradient one. b Mapped depth of coverage distribution for WGS sequencing runs. The range of the coverage distribution is truncated at 150. Each trace is annotated with the mode of the distribution. c Insert size distribution of sequencing reads for the sequencing runs. The distribution is truncated at 300 base pairs. Each trace is annotated with the mode of the distribution

    Journal: NPJ genomic medicine

    Article Title: Characterisation of the changing genomic landscape of metastatic melanoma using cell free DNA

    doi: 10.1038/s41525-017-0030-7

    Figure Lengend Snippet: Coverage uniformity of WGS libraries. a Represented is the cumulative proportion of sequencing coverage per cumulative proportion of sequence in whole genome sequencing across normal germline DNA (gDNA) from peripheral blood mononuclear cells, two cfDNA time points, and an archival FFPE tissue biopsy from a metastatic melanoma patient. If coverage was perfectly uniform across the genome coverage the relationship would be linear with gradient one. b Mapped depth of coverage distribution for WGS sequencing runs. The range of the coverage distribution is truncated at 150. Each trace is annotated with the mode of the distribution. c Insert size distribution of sequencing reads for the sequencing runs. The distribution is truncated at 300 base pairs. Each trace is annotated with the mode of the distribution

    Article Snippet: TDNA was extracted using the QIAamp FFPE DNA extraction kit (Qiagen) and eluted into 20 µl buffer EB.

    Techniques: Sequencing, Formalin-fixed Paraffin-Embedded

    Bland-Altman plots for investigation of level of agreements between DNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of DNA yield (ng/μl) of samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. b Comparison of purity (A260/A280) of DNA samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. c Comparison of DNA yield (ng/μl) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit. d Comparison of purity (A260/A280) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit

    Journal: BMC Medical Research Methodology

    Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

    doi: 10.1186/s12874-018-0628-1

    Figure Lengend Snippet: Bland-Altman plots for investigation of level of agreements between DNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of DNA yield (ng/μl) of samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. b Comparison of purity (A260/A280) of DNA samples extracted with High Pure FFPET DNA Isolation kit and QIAamp® DNA FFPE Tissue kit. c Comparison of DNA yield (ng/μl) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit. d Comparison of purity (A260/A280) of samples extracted with QIAamp® DNA FFPE Tissue kit and AllPrep® DNA/RNA FFPE kit

    Article Snippet: Assessment of nucleic acids extraction kits from FFPE biopsies with normal histology The study material, consisting of 30 FFPE prostate biopsies with normal histology, was randomly divided into three different groups; 1) ten biopsies for comparison between the High Pure FFPE RNA Micro Kit (Roche Diagnostics, West Sussex, UK) and the RNeasy® FFPE kit (Qiagen, Hilden, Germany), 2) ten biopsies for comparison between the High Pure DNA FFPET Isolation Kit (Roche Diagnostics, West Sussex, UK) and the QIAamp® DNA FFPE Tissue kit (Qiagen, Hilden, Germany), and 3) ten biopsies for comparison of the best performing DNA and RNA kits from the two previous steps to the AllPrep® DNA/RNA FFPE kit (Qiagen, Hilden, Germany).

    Techniques: DNA Extraction, Formalin-fixed Paraffin-Embedded

    Bland-Altman plots for investigating the level of agreement between RNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of RNA yield (ng/μl) of samples extracted with High Pure FFPE RNA Micro Kit and RNeasy® FFPE kit. b Comparison of purity (A260/A280) of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. c Comparison of RIN-values of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. d Comparison of RNA yield (ng/μl) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. e Comparison of purity (A260/A280) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. f Comparison of RIN-values of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit

    Journal: BMC Medical Research Methodology

    Article Title: Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

    doi: 10.1186/s12874-018-0628-1

    Figure Lengend Snippet: Bland-Altman plots for investigating the level of agreement between RNA extraction kits. Each plot shows the differences between the two kits against the averages of the two kits. The lines represent the mean differences and upper and lower limits of agreement (LOA, mean differences ±1.96SD). a Comparison of RNA yield (ng/μl) of samples extracted with High Pure FFPE RNA Micro Kit and RNeasy® FFPE kit. b Comparison of purity (A260/A280) of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. c Comparison of RIN-values of samples extracted with High Pure FFPE RNA Micro kit and RNeasy® FFPE kit. d Comparison of RNA yield (ng/μl) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. e Comparison of purity (A260/A280) of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit. f Comparison of RIN-values of samples extracted with RNeasy® FFPE kit and AllPrep® DNA/RNA FFPE kit

    Article Snippet: Assessment of nucleic acids extraction kits from FFPE biopsies with normal histology The study material, consisting of 30 FFPE prostate biopsies with normal histology, was randomly divided into three different groups; 1) ten biopsies for comparison between the High Pure FFPE RNA Micro Kit (Roche Diagnostics, West Sussex, UK) and the RNeasy® FFPE kit (Qiagen, Hilden, Germany), 2) ten biopsies for comparison between the High Pure DNA FFPET Isolation Kit (Roche Diagnostics, West Sussex, UK) and the QIAamp® DNA FFPE Tissue kit (Qiagen, Hilden, Germany), and 3) ten biopsies for comparison of the best performing DNA and RNA kits from the two previous steps to the AllPrep® DNA/RNA FFPE kit (Qiagen, Hilden, Germany).

    Techniques: RNA Extraction, Formalin-fixed Paraffin-Embedded