cfdna  (Qiagen)


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    Name:
    QIAamp Circulating Nucleic Acid Kit
    Description:
    For isolation of free circulating DNA and RNA from human plasma or serum Kit contents Qiagen QIAamp Circulating Nucleic Acid Kit 50 preps 1 to 5mL Sample 20 to 150L Elution Volume Serum Plasma Sample Free circulating DNA RNA and miRNA Viral DNA Viral RNA Purification QIAamp Mini Column Format Silica Technology For Isolation of Free circulating DNA and RNA from Human Plasma or Serum Includes QIAamp Mini Columns 20mL Tube Extenders Qiagen Proteinase K Carrier RNA Buffers VacConnectors and 1 5mL and 2mL Collection Tubes Benefits Concentration of nucleic acids with high input and low elution volumes Efficient recovery of fragmented DNA and RNA No organic extraction or ethanol precipitation Removal of contaminants and inhibitors
    Catalog Number:
    55114
    Price:
    1091
    Category:
    QIAamp Circulating Nucleic Acid Kit
    Buy from Supplier


    Structured Review

    Qiagen cfdna
    QIAamp Circulating Nucleic Acid Kit
    For isolation of free circulating DNA and RNA from human plasma or serum Kit contents Qiagen QIAamp Circulating Nucleic Acid Kit 50 preps 1 to 5mL Sample 20 to 150L Elution Volume Serum Plasma Sample Free circulating DNA RNA and miRNA Viral DNA Viral RNA Purification QIAamp Mini Column Format Silica Technology For Isolation of Free circulating DNA and RNA from Human Plasma or Serum Includes QIAamp Mini Columns 20mL Tube Extenders Qiagen Proteinase K Carrier RNA Buffers VacConnectors and 1 5mL and 2mL Collection Tubes Benefits Concentration of nucleic acids with high input and low elution volumes Efficient recovery of fragmented DNA and RNA No organic extraction or ethanol precipitation Removal of contaminants and inhibitors
    https://www.bioz.com/result/cfdna/product/Qiagen
    Average 99 stars, based on 1089 article reviews
    Price from $9.99 to $1999.99
    cfdna - by Bioz Stars, 2020-04
    99/100 stars

    Images

    1) Product Images from "Enrichment of short mutant cell-free DNA fragments enhanced detection of pancreatic cancer"

    Article Title: Enrichment of short mutant cell-free DNA fragments enhanced detection of pancreatic cancer

    Journal: EBioMedicine

    doi: 10.1016/j.ebiom.2019.02.010

    The study design and single-strand library preparation of cfDNA in conception. cfDNA fragments were first denatured into single-strand DNA (ssDNA) fragments. Then, the ssDNA fragments were ligated with a unique molecular identifier. The pre-library was enriched using hybridization and magnetic-beads capture and then subjected to high-throughput sequencing. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
    Figure Legend Snippet: The study design and single-strand library preparation of cfDNA in conception. cfDNA fragments were first denatured into single-strand DNA (ssDNA) fragments. Then, the ssDNA fragments were ligated with a unique molecular identifier. The pre-library was enriched using hybridization and magnetic-beads capture and then subjected to high-throughput sequencing. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

    Techniques Used: Hybridization, Magnetic Beads, Next-Generation Sequencing

    Ultra-short fragments containing the KRAS hotspot alleles in patients with pancreatic cancer. (a) Comprehensive view of fragment lengths bearing KRAS mutated and wild-type alleles derived from cell-free DNA deep-sequencing in patients with pancreatic cancer ( n = 78). (b) The fragment length of cfDNA bearing mutant KRAS alleles tended to be significantly shorter compared with DNA fragments bearing wild-type allele by densitometry in pancreatic cancer (n = 78). The fragments bearing KRAS mutant alleles tended to be enriched in the region below 100 bp in patients (c) PC076 (stage II) and (d) PC092 (IPMN). (e) The distribution of KRAS mutated fragments included a large proportion of overlapping fragment sizes with wild-type KRAS fragments in advanced patients (PC152). (f) There was considerable discrepancy across IPMN ( n = 10), early-stage ( n = 42) and advanced ( n = 26) pancreatic cancer in terms of the length of KRAS mutated fragments by densitometry. (g) Violin plots representing the length of KRAS mutated fragments across different disease stages. (h) The ability of library preparation to enrich shorter fragments has a great impact on the detection of KRAS hotspot mutations in plasma (blue line), and the mutated-to-wild-type fraction of fragments bearing KRAS alleles reached the highest in the interval of 60–100 bp and declined sharply thereafter (red line). (i) Ultra-short fragments (
    Figure Legend Snippet: Ultra-short fragments containing the KRAS hotspot alleles in patients with pancreatic cancer. (a) Comprehensive view of fragment lengths bearing KRAS mutated and wild-type alleles derived from cell-free DNA deep-sequencing in patients with pancreatic cancer ( n = 78). (b) The fragment length of cfDNA bearing mutant KRAS alleles tended to be significantly shorter compared with DNA fragments bearing wild-type allele by densitometry in pancreatic cancer (n = 78). The fragments bearing KRAS mutant alleles tended to be enriched in the region below 100 bp in patients (c) PC076 (stage II) and (d) PC092 (IPMN). (e) The distribution of KRAS mutated fragments included a large proportion of overlapping fragment sizes with wild-type KRAS fragments in advanced patients (PC152). (f) There was considerable discrepancy across IPMN ( n = 10), early-stage ( n = 42) and advanced ( n = 26) pancreatic cancer in terms of the length of KRAS mutated fragments by densitometry. (g) Violin plots representing the length of KRAS mutated fragments across different disease stages. (h) The ability of library preparation to enrich shorter fragments has a great impact on the detection of KRAS hotspot mutations in plasma (blue line), and the mutated-to-wild-type fraction of fragments bearing KRAS alleles reached the highest in the interval of 60–100 bp and declined sharply thereafter (red line). (i) Ultra-short fragments (

    Techniques Used: Derivative Assay, Sequencing, Mutagenesis

    2) Product Images from "T Oligo-Primed Polymerase Chain Reaction (TOP-PCR): A Robust Method for the Amplification of Minute DNA Fragments in Body Fluids"

    Article Title: T Oligo-Primed Polymerase Chain Reaction (TOP-PCR): A Robust Method for the Amplification of Minute DNA Fragments in Body Fluids

    Journal: Scientific Reports

    doi: 10.1038/srep40767

    Comparison of TOP-PCR to Illumina’s PCR method using serial dilutions of plasma cfDNA sample. Serial dilutions (5 ng–0.01 pg) of a plasma cfDNA sample isolated from a healthy female ( BBC ) was prepared and the cfDNA is amplified using either Illumina’s PCR or TOP-PCR. TOP panel: profiles generated by Illumina’s PCR method. Lower panel: profiles generated by TOP-PCR. Notice that the RFU values are no longer accurate because of figure overlay. PCR cycle numbers: 30 for 5–0.5 ng; 40 for 0.05 ng–0.01 pg. Size markers: 1 bp and 6000 bp peaks. Size of two HAs added to each DNA fragment: ~22 bp.
    Figure Legend Snippet: Comparison of TOP-PCR to Illumina’s PCR method using serial dilutions of plasma cfDNA sample. Serial dilutions (5 ng–0.01 pg) of a plasma cfDNA sample isolated from a healthy female ( BBC ) was prepared and the cfDNA is amplified using either Illumina’s PCR or TOP-PCR. TOP panel: profiles generated by Illumina’s PCR method. Lower panel: profiles generated by TOP-PCR. Notice that the RFU values are no longer accurate because of figure overlay. PCR cycle numbers: 30 for 5–0.5 ng; 40 for 0.05 ng–0.01 pg. Size markers: 1 bp and 6000 bp peaks. Size of two HAs added to each DNA fragment: ~22 bp.

    Techniques Used: Polymerase Chain Reaction, Isolation, Amplification, Generated

    Test of TOP-PCR reproducibility and cfDNA consistency. Two blood samples were separately collected from a healthy male ( YFH ) on June 30, 2015 and October 28, 2015. Plasmas were prepared right after the blood collections and stored at −80 °C. Samples of cfDNA were extracted right before TOP-PCR reactions conducted on October 28, 2015. Blue, plasma stock prepared on June 30, 2015; red and black, plasma stock prepared on October 1, 2015. Size markers: 35 bp and 6000 bp peaks. Size of two HAs added to each DNA fragment: ~22 bp.
    Figure Legend Snippet: Test of TOP-PCR reproducibility and cfDNA consistency. Two blood samples were separately collected from a healthy male ( YFH ) on June 30, 2015 and October 28, 2015. Plasmas were prepared right after the blood collections and stored at −80 °C. Samples of cfDNA were extracted right before TOP-PCR reactions conducted on October 28, 2015. Blue, plasma stock prepared on June 30, 2015; red and black, plasma stock prepared on October 1, 2015. Size markers: 35 bp and 6000 bp peaks. Size of two HAs added to each DNA fragment: ~22 bp.

    Techniques Used: Polymerase Chain Reaction

    TOP-PCR amplification of saliva and urine cfDNA. ( a ) Size profile comparison between the original and TOP-PCR amplified normal saliva DNA samples. The saliva cfDNA from a healthy male individual (YFH) was amplified by TOP-PCR and displayed in parallel with the original. (Black, 5 ng of original; blue, 1 ng of TOP-PCR product). ( b ) Comparison between the original and TOP-PCR amplified normal urine cfDNA samples. Urine sample from the same healthy male ( a ) was tested. (Black, original urine DNA; blue, 40-cycle TOP-PCR amplification of 0.1 ng of the original. 5 ng each was displayed by Fragment Analyzer. Size markers: 35 bp and 6000 bp peaks. Size of two HAs added to each DNA fragment: ~22 bp.
    Figure Legend Snippet: TOP-PCR amplification of saliva and urine cfDNA. ( a ) Size profile comparison between the original and TOP-PCR amplified normal saliva DNA samples. The saliva cfDNA from a healthy male individual (YFH) was amplified by TOP-PCR and displayed in parallel with the original. (Black, 5 ng of original; blue, 1 ng of TOP-PCR product). ( b ) Comparison between the original and TOP-PCR amplified normal urine cfDNA samples. Urine sample from the same healthy male ( a ) was tested. (Black, original urine DNA; blue, 40-cycle TOP-PCR amplification of 0.1 ng of the original. 5 ng each was displayed by Fragment Analyzer. Size markers: 35 bp and 6000 bp peaks. Size of two HAs added to each DNA fragment: ~22 bp.

    Techniques Used: Polymerase Chain Reaction, Amplification

    Comparison of TOP-PCR with Illumina’s PCR method using low amount of DNA as the input. ( a ) One micro-liter of original ovarian cancer plasma cfDNA sample with unknown concentration. ( b ) Same DNA sample but after 50 cycles of amplification by TOP-PCR. ( c ) Same DNA sample but after 50 cycles of amplification using Illumina’s protocol. Size markers: 35 bp and 6000 bp peaks. Size of two HAs added to each DNA fragment: ~22 bp.
    Figure Legend Snippet: Comparison of TOP-PCR with Illumina’s PCR method using low amount of DNA as the input. ( a ) One micro-liter of original ovarian cancer plasma cfDNA sample with unknown concentration. ( b ) Same DNA sample but after 50 cycles of amplification by TOP-PCR. ( c ) Same DNA sample but after 50 cycles of amplification using Illumina’s protocol. Size markers: 35 bp and 6000 bp peaks. Size of two HAs added to each DNA fragment: ~22 bp.

    Techniques Used: Polymerase Chain Reaction, Concentration Assay, Amplification

    Comparison of TOP-PCT with Illumina’s PCR method using 20 ng of DNA. ( a ) One nano-gram original plasma cfDNA sample isolated from a healthy female (BBC). ( b ) Same DNA sample but after 20 cycles of amplification using TOP-PCR. ( c ) Same DNA sample but after 20 cycles of amplification using Illumina’s protocol. Size markers: 35 bp and 6000 bp peaks. Size of two HAs added to each DNA fragment: ~22 bp.
    Figure Legend Snippet: Comparison of TOP-PCT with Illumina’s PCR method using 20 ng of DNA. ( a ) One nano-gram original plasma cfDNA sample isolated from a healthy female (BBC). ( b ) Same DNA sample but after 20 cycles of amplification using TOP-PCR. ( c ) Same DNA sample but after 20 cycles of amplification using Illumina’s protocol. Size markers: 35 bp and 6000 bp peaks. Size of two HAs added to each DNA fragment: ~22 bp.

    Techniques Used: Polymerase Chain Reaction, Isolation, Amplification

    3) Product Images from "Innovative methodology for the identification of soluble biomarkers in fresh tissues"

    Article Title: Innovative methodology for the identification of soluble biomarkers in fresh tissues

    Journal: Oncotarget

    doi: 10.18632/oncotarget.24366

    EXPEL extruded fluid contains high quality tumor DNA (tDNA) that is exploitable for genetic profiling (A) Left panel, equivalent yield of tDNA was obtained from FFPE sections and matched EXPEL fluids of CRC primary lesions (n=10) and CRC-liver metastatic lesions (n=10). The quality of the DNA was assessed on the same extracts. The ratios of long 129bp (middle panel) and 305bp (right panel) to short amplified fragments (41bp) indicated that EXPEL tDNA presented with significantly higher amounts of long fragments in comparison with the FFPE tDNA. Dot plots show the mean ± SEM. Statistical significance was calculated using Wilcoxon paired test ( * p
    Figure Legend Snippet: EXPEL extruded fluid contains high quality tumor DNA (tDNA) that is exploitable for genetic profiling (A) Left panel, equivalent yield of tDNA was obtained from FFPE sections and matched EXPEL fluids of CRC primary lesions (n=10) and CRC-liver metastatic lesions (n=10). The quality of the DNA was assessed on the same extracts. The ratios of long 129bp (middle panel) and 305bp (right panel) to short amplified fragments (41bp) indicated that EXPEL tDNA presented with significantly higher amounts of long fragments in comparison with the FFPE tDNA. Dot plots show the mean ± SEM. Statistical significance was calculated using Wilcoxon paired test ( * p

    Techniques Used: Formalin-fixed Paraffin-Embedded, Amplification

    4) Product Images from "Enrichment of short mutant cell-free DNA fragments enhanced detection of pancreatic cancer "

    Article Title: Enrichment of short mutant cell-free DNA fragments enhanced detection of pancreatic cancer

    Journal: EBioMedicine

    doi: 10.1016/j.ebiom.2019.02.010

    The study design and single-strand library preparation of cfDNA in conception. cfDNA fragments were first denatured into single-strand DNA (ssDNA) fragments. Then, the ssDNA fragments were ligated with a unique molecular identifier. The pre-library was enriched using hybridization and magnetic-beads capture and then subjected to high-throughput sequencing. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
    Figure Legend Snippet: The study design and single-strand library preparation of cfDNA in conception. cfDNA fragments were first denatured into single-strand DNA (ssDNA) fragments. Then, the ssDNA fragments were ligated with a unique molecular identifier. The pre-library was enriched using hybridization and magnetic-beads capture and then subjected to high-throughput sequencing. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

    Techniques Used: Hybridization, Magnetic Beads, Next-Generation Sequencing

    Ultra-short fragments containing the KRAS hotspot alleles in patients with pancreatic cancer. (a) Comprehensive view of fragment lengths bearing KRAS mutated and wild-type alleles derived from cell-free DNA deep-sequencing in patients with pancreatic cancer ( n = 78). (b) The fragment length of cfDNA bearing mutant KRAS alleles tended to be significantly shorter compared with DNA fragments bearing wild-type allele by densitometry in pancreatic cancer (n = 78). The fragments bearing KRAS mutant alleles tended to be enriched in the region below 100 bp in patients (c) PC076 (stage II) and (d) PC092 (IPMN). (e) The distribution of KRAS mutated fragments included a large proportion of overlapping fragment sizes with wild-type KRAS fragments in advanced patients (PC152). (f) There was considerable discrepancy across IPMN ( n = 10), early-stage ( n = 42) and advanced ( n = 26) pancreatic cancer in terms of the length of KRAS mutated fragments by densitometry. (g) Violin plots representing the length of KRAS mutated fragments across different disease stages. (h) The ability of library preparation to enrich shorter fragments has a great impact on the detection of KRAS hotspot mutations in plasma (blue line), and the mutated-to-wild-type fraction of fragments bearing KRAS alleles reached the highest in the interval of 60–100 bp and declined sharply thereafter (red line). (i) Ultra-short fragments (
    Figure Legend Snippet: Ultra-short fragments containing the KRAS hotspot alleles in patients with pancreatic cancer. (a) Comprehensive view of fragment lengths bearing KRAS mutated and wild-type alleles derived from cell-free DNA deep-sequencing in patients with pancreatic cancer ( n = 78). (b) The fragment length of cfDNA bearing mutant KRAS alleles tended to be significantly shorter compared with DNA fragments bearing wild-type allele by densitometry in pancreatic cancer (n = 78). The fragments bearing KRAS mutant alleles tended to be enriched in the region below 100 bp in patients (c) PC076 (stage II) and (d) PC092 (IPMN). (e) The distribution of KRAS mutated fragments included a large proportion of overlapping fragment sizes with wild-type KRAS fragments in advanced patients (PC152). (f) There was considerable discrepancy across IPMN ( n = 10), early-stage ( n = 42) and advanced ( n = 26) pancreatic cancer in terms of the length of KRAS mutated fragments by densitometry. (g) Violin plots representing the length of KRAS mutated fragments across different disease stages. (h) The ability of library preparation to enrich shorter fragments has a great impact on the detection of KRAS hotspot mutations in plasma (blue line), and the mutated-to-wild-type fraction of fragments bearing KRAS alleles reached the highest in the interval of 60–100 bp and declined sharply thereafter (red line). (i) Ultra-short fragments (

    Techniques Used: Derivative Assay, Sequencing, Mutagenesis

    5) Product Images from "Innovative methodology for the identification of soluble biomarkers in fresh tissues"

    Article Title: Innovative methodology for the identification of soluble biomarkers in fresh tissues

    Journal: Oncotarget

    doi: 10.18632/oncotarget.24366

    EXPEL extruded fluid contains high quality tumor DNA (tDNA) that is exploitable for genetic profiling (A) Left panel, equivalent yield of tDNA was obtained from FFPE sections and matched EXPEL fluids of CRC primary lesions (n=10) and CRC-liver metastatic lesions (n=10). The quality of the DNA was assessed on the same extracts. The ratios of long 129bp (middle panel) and 305bp (right panel) to short amplified fragments (41bp) indicated that EXPEL tDNA presented with significantly higher amounts of long fragments in comparison with the FFPE tDNA. Dot plots show the mean ± SEM. Statistical significance was calculated using Wilcoxon paired test ( * p
    Figure Legend Snippet: EXPEL extruded fluid contains high quality tumor DNA (tDNA) that is exploitable for genetic profiling (A) Left panel, equivalent yield of tDNA was obtained from FFPE sections and matched EXPEL fluids of CRC primary lesions (n=10) and CRC-liver metastatic lesions (n=10). The quality of the DNA was assessed on the same extracts. The ratios of long 129bp (middle panel) and 305bp (right panel) to short amplified fragments (41bp) indicated that EXPEL tDNA presented with significantly higher amounts of long fragments in comparison with the FFPE tDNA. Dot plots show the mean ± SEM. Statistical significance was calculated using Wilcoxon paired test ( * p

    Techniques Used: Formalin-fixed Paraffin-Embedded, Amplification

    6) Product Images from "T Oligo-Primed Polymerase Chain Reaction (TOP-PCR): A Robust Method for the Amplification of Minute DNA Fragments in Body Fluids"

    Article Title: T Oligo-Primed Polymerase Chain Reaction (TOP-PCR): A Robust Method for the Amplification of Minute DNA Fragments in Body Fluids

    Journal: Scientific Reports

    doi: 10.1038/srep40767

    Comparison of TOP-PCR to Illumina’s PCR method using serial dilutions of plasma cfDNA sample. Serial dilutions (5 ng–0.01 pg) of a plasma cfDNA sample isolated from a healthy female ( BBC ) was prepared and the cfDNA is amplified using either Illumina’s PCR or TOP-PCR. TOP panel: profiles generated by Illumina’s PCR method. Lower panel: profiles generated by TOP-PCR. Notice that the RFU values are no longer accurate because of figure overlay. PCR cycle numbers: 30 for 5–0.5 ng; 40 for 0.05 ng–0.01 pg. Size markers: 1 bp and 6000 bp peaks. Size of two HAs added to each DNA fragment: ~22 bp.
    Figure Legend Snippet: Comparison of TOP-PCR to Illumina’s PCR method using serial dilutions of plasma cfDNA sample. Serial dilutions (5 ng–0.01 pg) of a plasma cfDNA sample isolated from a healthy female ( BBC ) was prepared and the cfDNA is amplified using either Illumina’s PCR or TOP-PCR. TOP panel: profiles generated by Illumina’s PCR method. Lower panel: profiles generated by TOP-PCR. Notice that the RFU values are no longer accurate because of figure overlay. PCR cycle numbers: 30 for 5–0.5 ng; 40 for 0.05 ng–0.01 pg. Size markers: 1 bp and 6000 bp peaks. Size of two HAs added to each DNA fragment: ~22 bp.

    Techniques Used: Polymerase Chain Reaction, Isolation, Amplification, Generated

    Test of TOP-PCR reproducibility and cfDNA consistency. Two blood samples were separately collected from a healthy male ( YFH ) on June 30, 2015 and October 28, 2015. Plasmas were prepared right after the blood collections and stored at −80 °C. Samples of cfDNA were extracted right before TOP-PCR reactions conducted on October 28, 2015. Blue, plasma stock prepared on June 30, 2015; red and black, plasma stock prepared on October 1, 2015. Size markers: 35 bp and 6000 bp peaks. Size of two HAs added to each DNA fragment: ~22 bp.
    Figure Legend Snippet: Test of TOP-PCR reproducibility and cfDNA consistency. Two blood samples were separately collected from a healthy male ( YFH ) on June 30, 2015 and October 28, 2015. Plasmas were prepared right after the blood collections and stored at −80 °C. Samples of cfDNA were extracted right before TOP-PCR reactions conducted on October 28, 2015. Blue, plasma stock prepared on June 30, 2015; red and black, plasma stock prepared on October 1, 2015. Size markers: 35 bp and 6000 bp peaks. Size of two HAs added to each DNA fragment: ~22 bp.

    Techniques Used: Polymerase Chain Reaction

    TOP-PCR amplification of saliva and urine cfDNA. ( a ) Size profile comparison between the original and TOP-PCR amplified normal saliva DNA samples. The saliva cfDNA from a healthy male individual (YFH) was amplified by TOP-PCR and displayed in parallel with the original. (Black, 5 ng of original; blue, 1 ng of TOP-PCR product). ( b ) Comparison between the original and TOP-PCR amplified normal urine cfDNA samples. Urine sample from the same healthy male ( a ) was tested. (Black, original urine DNA; blue, 40-cycle TOP-PCR amplification of 0.1 ng of the original. 5 ng each was displayed by Fragment Analyzer. Size markers: 35 bp and 6000 bp peaks. Size of two HAs added to each DNA fragment: ~22 bp.
    Figure Legend Snippet: TOP-PCR amplification of saliva and urine cfDNA. ( a ) Size profile comparison between the original and TOP-PCR amplified normal saliva DNA samples. The saliva cfDNA from a healthy male individual (YFH) was amplified by TOP-PCR and displayed in parallel with the original. (Black, 5 ng of original; blue, 1 ng of TOP-PCR product). ( b ) Comparison between the original and TOP-PCR amplified normal urine cfDNA samples. Urine sample from the same healthy male ( a ) was tested. (Black, original urine DNA; blue, 40-cycle TOP-PCR amplification of 0.1 ng of the original. 5 ng each was displayed by Fragment Analyzer. Size markers: 35 bp and 6000 bp peaks. Size of two HAs added to each DNA fragment: ~22 bp.

    Techniques Used: Polymerase Chain Reaction, Amplification

    Comparison of TOP-PCR with Illumina’s PCR method using low amount of DNA as the input. ( a ) One micro-liter of original ovarian cancer plasma cfDNA sample with unknown concentration. ( b ) Same DNA sample but after 50 cycles of amplification by TOP-PCR. ( c ) Same DNA sample but after 50 cycles of amplification using Illumina’s protocol. Size markers: 35 bp and 6000 bp peaks. Size of two HAs added to each DNA fragment: ~22 bp.
    Figure Legend Snippet: Comparison of TOP-PCR with Illumina’s PCR method using low amount of DNA as the input. ( a ) One micro-liter of original ovarian cancer plasma cfDNA sample with unknown concentration. ( b ) Same DNA sample but after 50 cycles of amplification by TOP-PCR. ( c ) Same DNA sample but after 50 cycles of amplification using Illumina’s protocol. Size markers: 35 bp and 6000 bp peaks. Size of two HAs added to each DNA fragment: ~22 bp.

    Techniques Used: Polymerase Chain Reaction, Concentration Assay, Amplification

    Comparison of TOP-PCT with Illumina’s PCR method using 20 ng of DNA. ( a ) One nano-gram original plasma cfDNA sample isolated from a healthy female (BBC). ( b ) Same DNA sample but after 20 cycles of amplification using TOP-PCR. ( c ) Same DNA sample but after 20 cycles of amplification using Illumina’s protocol. Size markers: 35 bp and 6000 bp peaks. Size of two HAs added to each DNA fragment: ~22 bp.
    Figure Legend Snippet: Comparison of TOP-PCT with Illumina’s PCR method using 20 ng of DNA. ( a ) One nano-gram original plasma cfDNA sample isolated from a healthy female (BBC). ( b ) Same DNA sample but after 20 cycles of amplification using TOP-PCR. ( c ) Same DNA sample but after 20 cycles of amplification using Illumina’s protocol. Size markers: 35 bp and 6000 bp peaks. Size of two HAs added to each DNA fragment: ~22 bp.

    Techniques Used: Polymerase Chain Reaction, Isolation, Amplification

    7) Product Images from "Enrichment of short mutant cell-free DNA fragments enhanced detection of pancreatic cancer "

    Article Title: Enrichment of short mutant cell-free DNA fragments enhanced detection of pancreatic cancer

    Journal: EBioMedicine

    doi: 10.1016/j.ebiom.2019.02.010

    The study design and single-strand library preparation of cfDNA in conception. cfDNA fragments were first denatured into single-strand DNA (ssDNA) fragments. Then, the ssDNA fragments were ligated with a unique molecular identifier. The pre-library was enriched using hybridization and magnetic-beads capture and then subjected to high-throughput sequencing. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
    Figure Legend Snippet: The study design and single-strand library preparation of cfDNA in conception. cfDNA fragments were first denatured into single-strand DNA (ssDNA) fragments. Then, the ssDNA fragments were ligated with a unique molecular identifier. The pre-library was enriched using hybridization and magnetic-beads capture and then subjected to high-throughput sequencing. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

    Techniques Used: Hybridization, Magnetic Beads, Next-Generation Sequencing

    Ultra-short fragments containing the KRAS hotspot alleles in patients with pancreatic cancer. (a) Comprehensive view of fragment lengths bearing KRAS mutated and wild-type alleles derived from cell-free DNA deep-sequencing in patients with pancreatic cancer ( n = 78). (b) The fragment length of cfDNA bearing mutant KRAS alleles tended to be significantly shorter compared with DNA fragments bearing wild-type allele by densitometry in pancreatic cancer (n = 78). The fragments bearing KRAS mutant alleles tended to be enriched in the region below 100 bp in patients (c) PC076 (stage II) and (d) PC092 (IPMN). (e) The distribution of KRAS mutated fragments included a large proportion of overlapping fragment sizes with wild-type KRAS fragments in advanced patients (PC152). (f) There was considerable discrepancy across IPMN ( n = 10), early-stage ( n = 42) and advanced ( n = 26) pancreatic cancer in terms of the length of KRAS mutated fragments by densitometry. (g) Violin plots representing the length of KRAS mutated fragments across different disease stages. (h) The ability of library preparation to enrich shorter fragments has a great impact on the detection of KRAS hotspot mutations in plasma (blue line), and the mutated-to-wild-type fraction of fragments bearing KRAS alleles reached the highest in the interval of 60–100 bp and declined sharply thereafter (red line). (i) Ultra-short fragments (
    Figure Legend Snippet: Ultra-short fragments containing the KRAS hotspot alleles in patients with pancreatic cancer. (a) Comprehensive view of fragment lengths bearing KRAS mutated and wild-type alleles derived from cell-free DNA deep-sequencing in patients with pancreatic cancer ( n = 78). (b) The fragment length of cfDNA bearing mutant KRAS alleles tended to be significantly shorter compared with DNA fragments bearing wild-type allele by densitometry in pancreatic cancer (n = 78). The fragments bearing KRAS mutant alleles tended to be enriched in the region below 100 bp in patients (c) PC076 (stage II) and (d) PC092 (IPMN). (e) The distribution of KRAS mutated fragments included a large proportion of overlapping fragment sizes with wild-type KRAS fragments in advanced patients (PC152). (f) There was considerable discrepancy across IPMN ( n = 10), early-stage ( n = 42) and advanced ( n = 26) pancreatic cancer in terms of the length of KRAS mutated fragments by densitometry. (g) Violin plots representing the length of KRAS mutated fragments across different disease stages. (h) The ability of library preparation to enrich shorter fragments has a great impact on the detection of KRAS hotspot mutations in plasma (blue line), and the mutated-to-wild-type fraction of fragments bearing KRAS alleles reached the highest in the interval of 60–100 bp and declined sharply thereafter (red line). (i) Ultra-short fragments (

    Techniques Used: Derivative Assay, Sequencing, Mutagenesis

    8) Product Images from "Evaluating Cancer of the Central Nervous System Through Next-Generation Sequencing of Cerebrospinal Fluid"

    Article Title: Evaluating Cancer of the Central Nervous System Through Next-Generation Sequencing of Cerebrospinal Fluid

    Journal: Journal of Clinical Oncology

    doi: 10.1200/JCO.2016.66.6487

    Tumor evolution in patients with primary brain tumors. (A) Spatial and temporal heterogeneity among samples obtained at diagnosis, at recurrence, and from cerebrospinal fluid (CSF) in patient 42 with recurrent glioblastoma. CSF cell-free DNA harbors a PTEN R130* mutation (variant allele frequency, 0.25), whereas resection 2 harbors a PIK3CA H1047R mutation (variant allele frequency, 0.441). (B) CSF molecular profile for patient 45 with anaplastic oligodendroglioma contains the IDH1 R132H mutation and 1p/19q deletion found in tissue resection 2 as well as 454 nonsilent somatic mutations. Four hundred forty-eight SNVs represent C > T/G > A mutations that demonstrate TMZ-induced mutagenesis. Carbo, carboplatin; CCNU, lomustine; rhuMAB VEGF, bevacuzumab; RT, radiotherapy; SNV, single nucleotide variant; TMZ, temozolomide.
    Figure Legend Snippet: Tumor evolution in patients with primary brain tumors. (A) Spatial and temporal heterogeneity among samples obtained at diagnosis, at recurrence, and from cerebrospinal fluid (CSF) in patient 42 with recurrent glioblastoma. CSF cell-free DNA harbors a PTEN R130* mutation (variant allele frequency, 0.25), whereas resection 2 harbors a PIK3CA H1047R mutation (variant allele frequency, 0.441). (B) CSF molecular profile for patient 45 with anaplastic oligodendroglioma contains the IDH1 R132H mutation and 1p/19q deletion found in tissue resection 2 as well as 454 nonsilent somatic mutations. Four hundred forty-eight SNVs represent C > T/G > A mutations that demonstrate TMZ-induced mutagenesis. Carbo, carboplatin; CCNU, lomustine; rhuMAB VEGF, bevacuzumab; RT, radiotherapy; SNV, single nucleotide variant; TMZ, temozolomide.

    Techniques Used: Mutagenesis, Variant Assay

    Comparison of tumor-derived DNA from cerebrospinal fluid (CSF) cell pellet and supernatant. (A) Schematic of separation of CSF pellet and supernatant. Cellular DNA is isolated from the pellet, and cell-free DNA (cfDNA) is isolated from the supernatant. (B) Variant allele frequencies for known mutations in CSF cfDNA and pellet DNA. (C) Log2 ratios of normalized sequence coverage for target exons in CSF cfDNA and pellet DNA for patient 8. Greater than 10-fold amplification of HER2 was observed in CSF cfDNA, whereas HER2 amplification was barely detectable in pellet DNA. (D) Evidence of EML4-ALK gene fusion in CSF cfDNA and pellet DNA for patient 6. Read pairs supporting the fusion (red) were visualized by using the Integrative Genomics Viewer. Pt, patient ID.
    Figure Legend Snippet: Comparison of tumor-derived DNA from cerebrospinal fluid (CSF) cell pellet and supernatant. (A) Schematic of separation of CSF pellet and supernatant. Cellular DNA is isolated from the pellet, and cell-free DNA (cfDNA) is isolated from the supernatant. (B) Variant allele frequencies for known mutations in CSF cfDNA and pellet DNA. (C) Log2 ratios of normalized sequence coverage for target exons in CSF cfDNA and pellet DNA for patient 8. Greater than 10-fold amplification of HER2 was observed in CSF cfDNA, whereas HER2 amplification was barely detectable in pellet DNA. (D) Evidence of EML4-ALK gene fusion in CSF cfDNA and pellet DNA for patient 6. Read pairs supporting the fusion (red) were visualized by using the Integrative Genomics Viewer. Pt, patient ID.

    Techniques Used: Derivative Assay, Isolation, Variant Assay, Sequencing, Amplification

    Drug-resistance mutations in patients whose central nervous system (CNS) disease progresses during kinase inhibitor therapy. (A) Summary of genomic profiling results from cerebrospinal fluid (CSF) and other tumor sites in patients in whom progressive CNS disease developed during treatment with the indicated kinase inhibitors. (B) Disease timeline and brain magnet resonance images (MRIs) from a patient with EGFR -mutant NSCLC (patient 3) who presented with leptomeningeal metastasis (baseline MRI, arrows), responded to erlotinib (follow-up MRI at 26 months), was found to have a secondary EGFR mutation (T790M) in a bone metastasis, and developed progressive CNS disease (brain MRIs at 32 and 35 months) that did not respond to second-generation EGFR TKI or pulse erlotinib. CSF cell-free DNA (cfDNA) identified an EGFR T790M mutation. (C) Disease timeline and brain MRIs from a patient with EGFR -mutant NSCLC (patient 4) who presented with brain metastases (baseline MRI), responded to erlotinib (follow-up brain MRI at 2 months and brain CT scan at 9 months), and later developed progressive brain metastases. Molecular profiling of the recurrent lung tumor showed a secondary EGFR mutation (T790M), whereas CSF cfDNA identified an activating KRAS mutation (and the absence of T790M). Sequenom mass spectrometry genotyping was performed for specific mutations in eight genes: AKT1 , BRAF , EGFR , ERBB2 , KRAS , MEK1 ( MAP2K1 ), NRAS , and PIK3CA . ALK, anaplastic lymphoma kinase; AMP, amplification; BrCa, breast cancer; CT, computed tomography; del, deletion; EGFR, epidermal growth factor receptor; FISH, fluorescent in situ hybridization; HER2, human epidermal growth factor receptor 2; IHC, immunohistochemistry; IMPACT, Integrated Molecular Profiling of Actionable Cancer Targets; ND, not determined; NSCLC, non–small-cell lung cancer; PCR, polymerase chain reaction; pert, pertuzumab; T-DM1, trastuzumab emtansine; TKI, tyrosine kinase inhibitor; trast, trastuzumab; WBRT, whole-brain radiotherapy.
    Figure Legend Snippet: Drug-resistance mutations in patients whose central nervous system (CNS) disease progresses during kinase inhibitor therapy. (A) Summary of genomic profiling results from cerebrospinal fluid (CSF) and other tumor sites in patients in whom progressive CNS disease developed during treatment with the indicated kinase inhibitors. (B) Disease timeline and brain magnet resonance images (MRIs) from a patient with EGFR -mutant NSCLC (patient 3) who presented with leptomeningeal metastasis (baseline MRI, arrows), responded to erlotinib (follow-up MRI at 26 months), was found to have a secondary EGFR mutation (T790M) in a bone metastasis, and developed progressive CNS disease (brain MRIs at 32 and 35 months) that did not respond to second-generation EGFR TKI or pulse erlotinib. CSF cell-free DNA (cfDNA) identified an EGFR T790M mutation. (C) Disease timeline and brain MRIs from a patient with EGFR -mutant NSCLC (patient 4) who presented with brain metastases (baseline MRI), responded to erlotinib (follow-up brain MRI at 2 months and brain CT scan at 9 months), and later developed progressive brain metastases. Molecular profiling of the recurrent lung tumor showed a secondary EGFR mutation (T790M), whereas CSF cfDNA identified an activating KRAS mutation (and the absence of T790M). Sequenom mass spectrometry genotyping was performed for specific mutations in eight genes: AKT1 , BRAF , EGFR , ERBB2 , KRAS , MEK1 ( MAP2K1 ), NRAS , and PIK3CA . ALK, anaplastic lymphoma kinase; AMP, amplification; BrCa, breast cancer; CT, computed tomography; del, deletion; EGFR, epidermal growth factor receptor; FISH, fluorescent in situ hybridization; HER2, human epidermal growth factor receptor 2; IHC, immunohistochemistry; IMPACT, Integrated Molecular Profiling of Actionable Cancer Targets; ND, not determined; NSCLC, non–small-cell lung cancer; PCR, polymerase chain reaction; pert, pertuzumab; T-DM1, trastuzumab emtansine; TKI, tyrosine kinase inhibitor; trast, trastuzumab; WBRT, whole-brain radiotherapy.

    Techniques Used: Mutagenesis, Magnetic Resonance Imaging, Computed Tomography, Mass Spectrometry, Amplification, Fluorescence In Situ Hybridization, In Situ Hybridization, Immunohistochemistry, Polymerase Chain Reaction

    9) Product Images from "Centrifugation-free extraction of circulating nucleic acids using immiscible liquid under vacuum pressure"

    Article Title: Centrifugation-free extraction of circulating nucleic acids using immiscible liquid under vacuum pressure

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-23766-9

    Comparison of extracted cfDNA concentration in qPCR assay. cfDNA concentration in a plasma sample was compared according to extraction methods, QIAamp and PIBEX. cfDNA amount in plasma sample was quantified by qPCR in four reference genes, TERT, RPPH1, GAPDH, and NAGK, in ( a ). The error bar represents standard deviation of triplex qPCR assay in a sample. The relative efficiency of cfDNA extraction in PIBEX was derived based on QIAamp in ( b ). The error bar is standard deviation of samples (n = 7).
    Figure Legend Snippet: Comparison of extracted cfDNA concentration in qPCR assay. cfDNA concentration in a plasma sample was compared according to extraction methods, QIAamp and PIBEX. cfDNA amount in plasma sample was quantified by qPCR in four reference genes, TERT, RPPH1, GAPDH, and NAGK, in ( a ). The error bar represents standard deviation of triplex qPCR assay in a sample. The relative efficiency of cfDNA extraction in PIBEX was derived based on QIAamp in ( b ). The error bar is standard deviation of samples (n = 7).

    Techniques Used: Concentration Assay, Real-time Polymerase Chain Reaction, Standard Deviation, Derivative Assay

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    Centrifugation:

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    Blocking Assay:

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    TaqMan RNAsep Assay:

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    Real-time Polymerase Chain Reaction:

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    Microarray:

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    Quantitation Assay:

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    Formalin-fixed Paraffin-Embedded:

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    Digital PCR:

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    Sensitive Assay:

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    Sample Prep:

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    Incubation:

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    Sampling:

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    Concentration Assay:

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    Variant Assay:

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