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QIAamp Circulating Nucleic Acid Kit

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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

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QIAamp Circulating Nucleic Acid Kit

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Qiagen cfdna

cfdna - by Bioz Stars, 2020-04

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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

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

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

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

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

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

Techniques Used: Polymerase Chain Reaction

Techniques Used: Polymerase Chain Reaction, Amplification

Techniques Used: Polymerase Chain Reaction, Concentration Assay, Amplification

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

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

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

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

DNA Extraction:

Article Title: A pilot study of ultra-deep targeted sequencing of plasma DNA identifies driver mutations in hepatocellular carcinoma
Article Snippet: Paragraph title: DNA extraction, quality control and quantification ... Circulating DNA was isolated from 5 mL and 1 mL of plasma and serum, respectively, using the QIAamp Circulating Nucleic Acid Kit (Qiagen).

Article Title: Prenatal non-invasive foetal RHD genotyping: diagnostic accuracy of a test as a guide for appropriate administration of antenatal anti-D immunoprophylaxis
Article Snippet: .. As a result of a validation process, which overcame the problems that had surfaced with the QIAamp® DNA DSP Blood Mini Kit and QIAamp® DSP DNA Virus Kit (Qiagen), the foetal DNA isolation is now performed with QIAamp® Circulating Nucleic Acid Kit (Qiagen), more specific than the previous ones for extraction of small DNA fragments of human origin . shows details about the efficiency of DNA recovery of the extraction kits. ..

Article Title: Circulating tumor DNA analysis depicts subclonal architecture and genomic evolution of small cell lung cancer
Article Snippet: Paragraph title: Sample processing and DNA extraction ... DNA was isolated from plasma using QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany).

Article Title: SMAD4 and NF1 mutations as potential biomarkers for poor prognosis to cetuximab-based therapy in Chinese metastatic colorectal cancer patients
Article Snippet: Paragraph title: Clinical sample collection and DNA extraction ... Circulating tumor DNA (ctDNA) was extracted from the plasma using QIAamp Circulating Nucleic Acid Kit (QIAGEN).

Centrifugation:

Article Title: Fragment size and level of cell-free DNA provide prognostic information in patients with advanced pancreatic cancer
Article Snippet: Blood samples were separated with density centrifugation using Lymphoprep™ (Axis Shield) density gradient media, according to the manufacturer’s instructions. .. We used 4 mL (1–2 mL for the first 8 patients) of plasma (diluted 1:1 with 0.9% NaCl for the density gradient separation protocol) for isolating total cfDNA with the QIAamp Circulating Nucleic Acid kit (Qiagen), as described by the manufacturer. cfDNA was eluted in 50 µL of Buffer AVE (Qiagen) and stored at − 80 °C until further analysis.

Article Title: Circulating tumor DNA analysis depicts subclonal architecture and genomic evolution of small cell lung cancer
Article Snippet: Peripheral blood lymphocytes (PBLs) from the first centrifugation were used for the extraction of germline genomic DNA. .. DNA was isolated from plasma using QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany).

Filtration:

Blocking Assay:

Article Title: Mutation analysis of cell-free DNA and single circulating tumor cells in metastatic breast cancer patients with high CTC counts
Article Snippet: CfDNA was isolated from 3 ml of plasma using the QIAamp Circulating Nucleic Acid Kit (Qiagen) according to manufacturer’s instructions. .. Two separate regions of tumour were then cored from the block using a 1 mm tissue microarray needle.

TaqMan RNAsep Assay:

Article Title: Plasma total cell-free DNA (cfDNA) is a surrogate biomarker for tumour burden and a prognostic biomarker for survival in metastatic melanoma patients
Article Snippet: DNA was extracted from plasma using QIAamp Circulating Nucleic Acid Kits (Qiagen). .. CfDNA was quantified by means of measurement of a reference gene, RNAseP, by quantitative polymerase chain reaction (PCR) using the TaqMan RNAseP Assay (Life Technologies); in 33 patients, ctDNA was additionally quantified by means of droplet digital PCR Bio-Rad QX200 targeted to a specific mutation in melanoma cells and expressed as variant allele frequency (VAF), the fraction of mutant droplets among the total number of mutant and wild-type droplets, as previously described , .

Real-time Polymerase Chain Reaction:

Microarray:

Quantitation Assay:

Article Title: Mutation analysis of cell-free DNA and single circulating tumor cells in metastatic breast cancer patients with high CTC counts
Article Snippet: Paragraph title: Extraction and quantitation of DNA ... CfDNA was isolated from 3 ml of plasma using the QIAamp Circulating Nucleic Acid Kit (Qiagen) according to manufacturer’s instructions.

Formalin-fixed Paraffin-Embedded:

Article Title: Mutation analysis of cell-free DNA and single circulating tumor cells in metastatic breast cancer patients with high CTC counts
Article Snippet: CfDNA was isolated from 3 ml of plasma using the QIAamp Circulating Nucleic Acid Kit (Qiagen) according to manufacturer’s instructions. .. FFPE tissue blocks with matching H & E were retrieved from the histopathology archive and reviewed by a consultant histopathologist.

Article Title: Circulating tumor DNA analysis depicts subclonal architecture and genomic evolution of small cell lung cancer
Article Snippet: DNA was isolated from plasma using QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany). .. Genomic DNA was extracted from FFPE samples using Maxwell® RSC DNA FFPE Kit (Promega, Madison, WI, USA).

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
Article Snippet: DNA was extracted from FFPE slide prepared at the time of laparotomy for the diagnosis of patient's Ewing sarcoma using QIAamp DNA FFPE Tissue kit (Qiagen GmbH). .. The cfDNA was extracted from the patient's plasma using QIAamp Circulating Nucleic Acid kit (Qiagen GmbH).

Article Title: SMAD4 and NF1 mutations as potential biomarkers for poor prognosis to cetuximab-based therapy in Chinese metastatic colorectal cancer patients
Article Snippet: A minimum of 20% tumor content was required for formalin-fixed paraffin-embedded (FFPE) specimens, from which genomic DNA was extracted using QIAamp DNA FFPE Tissue Kit (QIAGEN) following the manufacturer’s instructions. .. Circulating tumor DNA (ctDNA) was extracted from the plasma using QIAamp Circulating Nucleic Acid Kit (QIAGEN).

Introduce:

Article Title: Prenatal non-invasive foetal RHD genotyping: diagnostic accuracy of a test as a guide for appropriate administration of antenatal anti-D immunoprophylaxis
Article Snippet: As a result of a validation process, which overcame the problems that had surfaced with the QIAamp® DNA DSP Blood Mini Kit and QIAamp® DSP DNA Virus Kit (Qiagen), the foetal DNA isolation is now performed with QIAamp® Circulating Nucleic Acid Kit (Qiagen), more specific than the previous ones for extraction of small DNA fragments of human origin . shows details about the efficiency of DNA recovery of the extraction kits. .. In the first sample, the suspicious of a mistake during one of the manual steps of the typing process prompted us to introduce the check-lists; the second sample was probably mistaken by contamination.

Digital PCR:

Sequencing:

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
Article Snippet: Paragraph title: Personal genomic mutation profiling using targeted massively parallel sequencing ... The cfDNA was extracted from the patient's plasma using QIAamp Circulating Nucleic Acid kit (Qiagen GmbH).

Histopathology:

Article Title: Mutation analysis of cell-free DNA and single circulating tumor cells in metastatic breast cancer patients with high CTC counts
Article Snippet: CfDNA was isolated from 3 ml of plasma using the QIAamp Circulating Nucleic Acid Kit (Qiagen) according to manufacturer’s instructions. .. FFPE tissue blocks with matching H & E were retrieved from the histopathology archive and reviewed by a consultant histopathologist.

Sensitive Assay:

Article Title: Circulating tumor DNA analysis depicts subclonal architecture and genomic evolution of small cell lung cancer
Article Snippet: DNA was isolated from plasma using QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany). .. DNA concentration was measured using a Qubit fluorometer and the Qubit dsDNA HS (High Sensitivity) Assay Kit (Invitrogen, Carlsbad, CA, USA).

Mutagenesis:

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
Article Snippet: Paragraph title: Personal genomic mutation profiling using targeted massively parallel sequencing ... The cfDNA was extracted from the patient's plasma using QIAamp Circulating Nucleic Acid kit (Qiagen GmbH).

Isolation:

Article Title: A pilot study of ultra-deep targeted sequencing of plasma DNA identifies driver mutations in hepatocellular carcinoma
Article Snippet: .. Circulating DNA was isolated from 5 mL and 1 mL of plasma and serum, respectively, using the QIAamp Circulating Nucleic Acid Kit (Qiagen). .. Germline DNA was isolated from PBMC using the QIAamp DNA Mini Kit (Qiagen).

Article Title: Fragment size and level of cell-free DNA provide prognostic information in patients with advanced pancreatic cancer
Article Snippet: Paragraph title: Isolation of cfDNA from plasma ... We used 4 mL (1–2 mL for the first 8 patients) of plasma (diluted 1:1 with 0.9% NaCl for the density gradient separation protocol) for isolating total cfDNA with the QIAamp Circulating Nucleic Acid kit (Qiagen), as described by the manufacturer. cfDNA was eluted in 50 µL of Buffer AVE (Qiagen) and stored at − 80 °C until further analysis.

Article Title: Mutation analysis of cell-free DNA and single circulating tumor cells in metastatic breast cancer patients with high CTC counts
Article Snippet: .. CfDNA was isolated from 3 ml of plasma using the QIAamp Circulating Nucleic Acid Kit (Qiagen) according to manufacturer’s instructions. .. Isolation of DNA from lymphocytes and quantitation of total cfDNA was as described previously ( ). cfDNA levels (ng/ml) were converted to copies/ml plasma assuming 3.3 pg DNA per haploid genome.

Article Title: Centrifugation-free extraction of circulating nucleic acids using immiscible liquid under vacuum pressure
Article Snippet: To extract cfDNA from a plasma sample, reagents in the QIAamp circulating nucleic acid kit (55114; QIAGEN, Germany) were utilized. .. Plasma was isolated at 1,900 g for 10 min in a centrifuge (1248; LABOGEN, Denmark) and was re-centrifuged at 12,000 g for 15 min; 500 μL of proteinase K was added to 5 mL of plasma in a 50-mL conical tube; 4 mL of lysate-buffer (ACL) containing 1.0 μg of carrier RNA was added.

Article Title: Circulating tumor DNA analysis depicts subclonal architecture and genomic evolution of small cell lung cancer
Article Snippet: .. DNA was isolated from plasma using QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany). .. Genomic DNA was extracted from FFPE samples using Maxwell® RSC DNA FFPE Kit (Promega, Madison, WI, USA).

Purification:

Article Title: Plasma Cell-Free DNA as a Predictive Marker after Radiotherapy for Hepatocellular Carcinoma
Article Snippet: .. The cfDNA was purified using a QIAamp Circulating Nucleic Acid Kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions. ..

Polymerase Chain Reaction:

Article Title: Effects of Collection and Processing Procedures on Plasma Circulating Cell-Free DNA from Cancer Patients
Article Snippet: DNA from all samples, except module 5, was extracted from an average 1.4 mL (range, 0.3 to 2.76 mL) plasma using the QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol, except that 6.2 μg of carrier RNA was added per sample. .. A nonhuman spike-in PCR product was added to each sample as an internal quality control to assess extraction efficiency.

Sample Prep:

Article Title: Centrifugation-free extraction of circulating nucleic acids using immiscible liquid under vacuum pressure
Article Snippet: Paragraph title: Blood sample preparation (Ethics statement) ... To extract cfDNA from a plasma sample, reagents in the QIAamp circulating nucleic acid kit (55114; QIAGEN, Germany) were utilized.

Incubation:

Article Title: Magnetic Nanowire Networks for Dual-Isolation and Detection of Tumor-Associated Circulating Biomarkers
Article Snippet: The cfDNA-NW complexes were washed twice with 1× TE buffer, collected by magnetic separation, and incubated in 20 µL of 10 mM Tris-HCl (pH 10) for 30 min to extract cfDNA from MNWs. .. We additionally extracted cfDNA from plasma using the QIAamp circulating nucleic acid kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

Article Title: Plasma Cell-Free DNA as a Predictive Marker after Radiotherapy for Hepatocellular Carcinoma
Article Snippet: The cfDNA was purified using a QIAamp Circulating Nucleic Acid Kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions. .. After incubation at 60℃ for 30 min, 1.8 mL of buffer ACB was added, vortexed, and incubated on ice for 5 min.

Sampling:

Article Title: Prenatal non-invasive foetal RHD genotyping: diagnostic accuracy of a test as a guide for appropriate administration of antenatal anti-D immunoprophylaxis
Article Snippet: The antibody screening performed at the beginning of third trimester of pregnancy was negative in 260/284 pregnant women and positive in 24/284 owing to passive anti-D from previous RhIg, administered after chorionic villous sampling in the first trimester. .. As a result of a validation process, which overcame the problems that had surfaced with the QIAamp® DNA DSP Blood Mini Kit and QIAamp® DSP DNA Virus Kit (Qiagen), the foetal DNA isolation is now performed with QIAamp® Circulating Nucleic Acid Kit (Qiagen), more specific than the previous ones for extraction of small DNA fragments of human origin . shows details about the efficiency of DNA recovery of the extraction kits.

Concentration Assay:

Article Title: Circulating tumor DNA analysis depicts subclonal architecture and genomic evolution of small cell lung cancer
Article Snippet: DNA was isolated from plasma using QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany). .. DNA concentration was measured using a Qubit fluorometer and the Qubit dsDNA HS (High Sensitivity) Assay Kit (Invitrogen, Carlsbad, CA, USA).

DNA Purification:

Article Title: Plasma Cell-Free DNA as a Predictive Marker after Radiotherapy for Hepatocellular Carcinoma
Article Snippet: Paragraph title: Cell-free DNA purification and quantification ... The cfDNA was purified using a QIAamp Circulating Nucleic Acid Kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions.

Lysis:

Article Title: Magnetic Nanowire Networks for Dual-Isolation and Detection of Tumor-Associated Circulating Biomarkers
Article Snippet: After magnetic separation, the cfDNA-NW complexes were incubated in 500 µL of proteinase K-containing lysis buffer consisting of 1.28 M sucrose, 40 mM Tris-HCl, 20 mM MgCl2 , 4% Triton X-100, and 50 mM DTT for 30 min at 60°C. .. We additionally extracted cfDNA from plasma using the QIAamp circulating nucleic acid kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

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DNA Extraction:

Centrifugation:

Filtration:

Blocking Assay:

TaqMan RNAsep Assay:

Real-time Polymerase Chain Reaction:

Microarray:

Quantitation Assay:

Formalin-fixed Paraffin-Embedded:

Introduce:

Digital PCR:

Sequencing:

Histopathology:

Sensitive Assay:

Mutagenesis:

Isolation:

Purification:

Polymerase Chain Reaction:

Sample Prep:

Incubation:

Sampling:

Concentration Assay:

DNA Purification:

Lysis:

Variant Assay:

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