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Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA.

Lanman RB, Mortimer SA, Zill OA, Sebisanovic D, Lopez R, Blau S, Collisson EA, Divers SG, Hoon DS, Kopetz ES, Lee J, Nikolinakos PG, Baca AM, Kermani BG, Eltoukhy H, Talasaz A - PLoS ONE (2015)

Bottom Line: Near-perfect analytic specificity (> 99.9999%) enables complete coverage of many genes without the false positives typically seen with traditional sequencing assays at mutant allele frequencies or fractions below 5%.Clinical sensitivity of plasma-derived NGS was 85.0%, comparable to 80.7% sensitivity for tissue.The assay success rate on 1,000 consecutive samples in clinical practice was 99.8%.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Affairs, Guardant Health, Inc., Redwood City, California, United States of America.

ABSTRACT
Next-generation sequencing of cell-free circulating solid tumor DNA addresses two challenges in contemporary cancer care. First this method of massively parallel and deep sequencing enables assessment of a comprehensive panel of genomic targets from a single sample, and second, it obviates the need for repeat invasive tissue biopsies. Digital Sequencing™ is a novel method for high-quality sequencing of circulating tumor DNA simultaneously across a comprehensive panel of over 50 cancer-related genes with a simple blood test. Here we report the analytic and clinical validation of the gene panel. Analytic sensitivity down to 0.1% mutant allele fraction is demonstrated via serial dilution studies of known samples. Near-perfect analytic specificity (> 99.9999%) enables complete coverage of many genes without the false positives typically seen with traditional sequencing assays at mutant allele frequencies or fractions below 5%. We compared digital sequencing of plasma-derived cell-free DNA to tissue-based sequencing on 165 consecutive matched samples from five outside centers in patients with stage III-IV solid tumor cancers. Clinical sensitivity of plasma-derived NGS was 85.0%, comparable to 80.7% sensitivity for tissue. The assay success rate on 1,000 consecutive samples in clinical practice was 99.8%. Digital sequencing of plasma-derived DNA is indicated in advanced cancer patients to prevent repeated invasive biopsies when the initial biopsy is inadequate, unobtainable for genomic testing, or uninformative, or when the patient's cancer has progressed despite treatment. Its clinical utility is derived from reduction in the costs, complications and delays associated with invasive tissue biopsies for genomic testing.

No MeSH data available.


Related in: MedlinePlus

Guardant360 samples stressed by prolonged storage time and high temperature cycling do not impact performance.A) Extent of genomic DNA (gDNA from leukocytes) contamination in the control cell-free DNA (cfDNA) samples compared to prolonged temperature cycled samples sets represented as the ratio of gDNA (> 500 bps) to cfDNA (< 500 bps). Temperature cycled samples were incubated at 37°C for 8 hours followed by 16 hours at room temperature daily for 5 days. Control samples were processed immediately upon receipt at the laboratory. Center lines show the medians; box limits indicate the 25th and 75th percentiles as determined by R software; whiskers extend 1.5 times the interquartile range from the 25th and 75th percentiles, outliers are represented by dots. N = 10 sample points. B) Concordance of control sample set with prolonged temperature cycled sample set shown by a correlation plot of all mutant allele frequencies (MAFs) of the single nucleotide variants (SNVs) from the control sample set versus the corresponding SNV MAFs in the temperature cycled sample set. The total number of different SNVs plotted is 24. The inset shows the correlation of MAFs at less than or equal to 2% between the two data sets, showing excellent correlation even when SNVs are as low as 2.5%.
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pone.0140712.g005: Guardant360 samples stressed by prolonged storage time and high temperature cycling do not impact performance.A) Extent of genomic DNA (gDNA from leukocytes) contamination in the control cell-free DNA (cfDNA) samples compared to prolonged temperature cycled samples sets represented as the ratio of gDNA (> 500 bps) to cfDNA (< 500 bps). Temperature cycled samples were incubated at 37°C for 8 hours followed by 16 hours at room temperature daily for 5 days. Control samples were processed immediately upon receipt at the laboratory. Center lines show the medians; box limits indicate the 25th and 75th percentiles as determined by R software; whiskers extend 1.5 times the interquartile range from the 25th and 75th percentiles, outliers are represented by dots. N = 10 sample points. B) Concordance of control sample set with prolonged temperature cycled sample set shown by a correlation plot of all mutant allele frequencies (MAFs) of the single nucleotide variants (SNVs) from the control sample set versus the corresponding SNV MAFs in the temperature cycled sample set. The total number of different SNVs plotted is 24. The inset shows the correlation of MAFs at less than or equal to 2% between the two data sets, showing excellent correlation even when SNVs are as low as 2.5%.

Mentions: Assay robustness was evaluated by heating 10 plasma samples to 37°C for eight hours per day for a total of five days. The extent of gDNA contamination was determined semi-quantitatively by analysis with the Agilent 2100 bioanalyzer and only 3 of 10 demonstrated contamination with genomic DNA, of which 2 samples demonstrated low levels of gDNA and one sample exhibited a moderate amount of contamination. Next, these samples were compared to 10 split sample controls processed with no time delay upon receipt or temperature cycling (after two days shipping). The MAFs for the 24 SNVs in the paired ten samples were plotted in a correlation plot with R2 = 1.0 (Fig 5). Concordance was 100% between tubes for all SNVs with MAFs above 0.3% and ~90% for MAFs > 0.1% (Fig 5).


Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA.

Lanman RB, Mortimer SA, Zill OA, Sebisanovic D, Lopez R, Blau S, Collisson EA, Divers SG, Hoon DS, Kopetz ES, Lee J, Nikolinakos PG, Baca AM, Kermani BG, Eltoukhy H, Talasaz A - PLoS ONE (2015)

Guardant360 samples stressed by prolonged storage time and high temperature cycling do not impact performance.A) Extent of genomic DNA (gDNA from leukocytes) contamination in the control cell-free DNA (cfDNA) samples compared to prolonged temperature cycled samples sets represented as the ratio of gDNA (> 500 bps) to cfDNA (< 500 bps). Temperature cycled samples were incubated at 37°C for 8 hours followed by 16 hours at room temperature daily for 5 days. Control samples were processed immediately upon receipt at the laboratory. Center lines show the medians; box limits indicate the 25th and 75th percentiles as determined by R software; whiskers extend 1.5 times the interquartile range from the 25th and 75th percentiles, outliers are represented by dots. N = 10 sample points. B) Concordance of control sample set with prolonged temperature cycled sample set shown by a correlation plot of all mutant allele frequencies (MAFs) of the single nucleotide variants (SNVs) from the control sample set versus the corresponding SNV MAFs in the temperature cycled sample set. The total number of different SNVs plotted is 24. The inset shows the correlation of MAFs at less than or equal to 2% between the two data sets, showing excellent correlation even when SNVs are as low as 2.5%.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4608804&req=5

pone.0140712.g005: Guardant360 samples stressed by prolonged storage time and high temperature cycling do not impact performance.A) Extent of genomic DNA (gDNA from leukocytes) contamination in the control cell-free DNA (cfDNA) samples compared to prolonged temperature cycled samples sets represented as the ratio of gDNA (> 500 bps) to cfDNA (< 500 bps). Temperature cycled samples were incubated at 37°C for 8 hours followed by 16 hours at room temperature daily for 5 days. Control samples were processed immediately upon receipt at the laboratory. Center lines show the medians; box limits indicate the 25th and 75th percentiles as determined by R software; whiskers extend 1.5 times the interquartile range from the 25th and 75th percentiles, outliers are represented by dots. N = 10 sample points. B) Concordance of control sample set with prolonged temperature cycled sample set shown by a correlation plot of all mutant allele frequencies (MAFs) of the single nucleotide variants (SNVs) from the control sample set versus the corresponding SNV MAFs in the temperature cycled sample set. The total number of different SNVs plotted is 24. The inset shows the correlation of MAFs at less than or equal to 2% between the two data sets, showing excellent correlation even when SNVs are as low as 2.5%.
Mentions: Assay robustness was evaluated by heating 10 plasma samples to 37°C for eight hours per day for a total of five days. The extent of gDNA contamination was determined semi-quantitatively by analysis with the Agilent 2100 bioanalyzer and only 3 of 10 demonstrated contamination with genomic DNA, of which 2 samples demonstrated low levels of gDNA and one sample exhibited a moderate amount of contamination. Next, these samples were compared to 10 split sample controls processed with no time delay upon receipt or temperature cycling (after two days shipping). The MAFs for the 24 SNVs in the paired ten samples were plotted in a correlation plot with R2 = 1.0 (Fig 5). Concordance was 100% between tubes for all SNVs with MAFs above 0.3% and ~90% for MAFs > 0.1% (Fig 5).

Bottom Line: Near-perfect analytic specificity (> 99.9999%) enables complete coverage of many genes without the false positives typically seen with traditional sequencing assays at mutant allele frequencies or fractions below 5%.Clinical sensitivity of plasma-derived NGS was 85.0%, comparable to 80.7% sensitivity for tissue.The assay success rate on 1,000 consecutive samples in clinical practice was 99.8%.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Affairs, Guardant Health, Inc., Redwood City, California, United States of America.

ABSTRACT
Next-generation sequencing of cell-free circulating solid tumor DNA addresses two challenges in contemporary cancer care. First this method of massively parallel and deep sequencing enables assessment of a comprehensive panel of genomic targets from a single sample, and second, it obviates the need for repeat invasive tissue biopsies. Digital Sequencing™ is a novel method for high-quality sequencing of circulating tumor DNA simultaneously across a comprehensive panel of over 50 cancer-related genes with a simple blood test. Here we report the analytic and clinical validation of the gene panel. Analytic sensitivity down to 0.1% mutant allele fraction is demonstrated via serial dilution studies of known samples. Near-perfect analytic specificity (> 99.9999%) enables complete coverage of many genes without the false positives typically seen with traditional sequencing assays at mutant allele frequencies or fractions below 5%. We compared digital sequencing of plasma-derived cell-free DNA to tissue-based sequencing on 165 consecutive matched samples from five outside centers in patients with stage III-IV solid tumor cancers. Clinical sensitivity of plasma-derived NGS was 85.0%, comparable to 80.7% sensitivity for tissue. The assay success rate on 1,000 consecutive samples in clinical practice was 99.8%. Digital sequencing of plasma-derived DNA is indicated in advanced cancer patients to prevent repeated invasive biopsies when the initial biopsy is inadequate, unobtainable for genomic testing, or uninformative, or when the patient's cancer has progressed despite treatment. Its clinical utility is derived from reduction in the costs, complications and delays associated with invasive tissue biopsies for genomic testing.

No MeSH data available.


Related in: MedlinePlus