research whole exome sequencing deep coverage pipeline Search Results


research whole exome sequencing deep coverage pipeline  (Broad Clinical Labs)
95
Broad Clinical Labs research whole exome sequencing deep coverage pipeline
Fig. 2 Comparison of <t>whole-exome</t> <t>sequencing</t> of cfDNA to whole-exome sequencing of matched tumor biopsies. a Fraction of clonal (≥0.9 cancer cell fraction, CCF) and subclonal (<0.9 CCF) SSNVs detected by MuTect in WES of tumor biopsies and confirmed (i.e., supported by ≥3 variant reads) in WES of cfDNA. Sites with <3 reads that had power <0.9 for mutation calling were not included when computing the fraction of SNVs confirmed (“Methods”). b Fraction of clonal and subclonal SSNVs detected in WES of cfDNA and confirmed in WES of tumor biopsies. For 18 patients with WES of cfDNA at a second time point t2, SSNVs not detected in the matched tumor biopsy but confirmed at t2 are indicated with black. c Analysis of clonal dynamics in an ER+ breast cancer patient diagnosed with metastatic disease 1.5 years (yrs) prior to biopsy and cfDNA collection (t1, Day 0). Clustering analysis of CCF for SSNVs between matched tumor biopsy and cfDNA (t1) is shown in the left panel. The right panel shows the CCF of four mutation clusters, one containing ESR1 L536P (Subclonal Cluster 1, orange) and the other containing ESR1 D538G (Subclonal Cluster 2, light blue), at t1 and t2 (51 days apart) from a patient with ER+ metastatic breast cancer being treated with a SERD. The lymph node biopsy was taken at the same time as cfDNA t1. Mutations were clustered by the CCFs for each pair of samples using Phylogic39 (“Methods”). Error bars represent the 95% credible interval of the joint posterior density of the clusters. Mutations, excluding indels, having ≥90% estimated power based on coverage in both samples are shown; clusters with fewer than three mutations are excluded. The number of mutations in each cluster is indicated in the legend in parentheses
Research Whole Exome Sequencing Deep Coverage Pipeline, supplied by Broad Clinical Labs, used in various techniques. Bioz Stars score: 95/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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exome sequencing  (Sophia Genetics)
97
Sophia Genetics exome sequencing
Fig. 2 Comparison of <t>whole-exome</t> <t>sequencing</t> of cfDNA to whole-exome sequencing of matched tumor biopsies. a Fraction of clonal (≥0.9 cancer cell fraction, CCF) and subclonal (<0.9 CCF) SSNVs detected by MuTect in WES of tumor biopsies and confirmed (i.e., supported by ≥3 variant reads) in WES of cfDNA. Sites with <3 reads that had power <0.9 for mutation calling were not included when computing the fraction of SNVs confirmed (“Methods”). b Fraction of clonal and subclonal SSNVs detected in WES of cfDNA and confirmed in WES of tumor biopsies. For 18 patients with WES of cfDNA at a second time point t2, SSNVs not detected in the matched tumor biopsy but confirmed at t2 are indicated with black. c Analysis of clonal dynamics in an ER+ breast cancer patient diagnosed with metastatic disease 1.5 years (yrs) prior to biopsy and cfDNA collection (t1, Day 0). Clustering analysis of CCF for SSNVs between matched tumor biopsy and cfDNA (t1) is shown in the left panel. The right panel shows the CCF of four mutation clusters, one containing ESR1 L536P (Subclonal Cluster 1, orange) and the other containing ESR1 D538G (Subclonal Cluster 2, light blue), at t1 and t2 (51 days apart) from a patient with ER+ metastatic breast cancer being treated with a SERD. The lymph node biopsy was taken at the same time as cfDNA t1. Mutations were clustered by the CCFs for each pair of samples using Phylogic39 (“Methods”). Error bars represent the 95% credible interval of the joint posterior density of the clusters. Mutations, excluding indels, having ≥90% estimated power based on coverage in both samples are shown; clusters with fewer than three mutations are excluded. The number of mutations in each cluster is indicated in the legend in parentheses
Exome Sequencing, supplied by Sophia Genetics, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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research whole exome sequencing deep coverage pipeline  (Broad Institute Inc)
90
Broad Institute Inc research whole exome sequencing deep coverage pipeline
Fig. 2 Comparison of <t>whole-exome</t> <t>sequencing</t> of cfDNA to whole-exome sequencing of matched tumor biopsies. a Fraction of clonal (≥0.9 cancer cell fraction, CCF) and subclonal (<0.9 CCF) SSNVs detected by MuTect in WES of tumor biopsies and confirmed (i.e., supported by ≥3 variant reads) in WES of cfDNA. Sites with <3 reads that had power <0.9 for mutation calling were not included when computing the fraction of SNVs confirmed (“Methods”). b Fraction of clonal and subclonal SSNVs detected in WES of cfDNA and confirmed in WES of tumor biopsies. For 18 patients with WES of cfDNA at a second time point t2, SSNVs not detected in the matched tumor biopsy but confirmed at t2 are indicated with black. c Analysis of clonal dynamics in an ER+ breast cancer patient diagnosed with metastatic disease 1.5 years (yrs) prior to biopsy and cfDNA collection (t1, Day 0). Clustering analysis of CCF for SSNVs between matched tumor biopsy and cfDNA (t1) is shown in the left panel. The right panel shows the CCF of four mutation clusters, one containing ESR1 L536P (Subclonal Cluster 1, orange) and the other containing ESR1 D538G (Subclonal Cluster 2, light blue), at t1 and t2 (51 days apart) from a patient with ER+ metastatic breast cancer being treated with a SERD. The lymph node biopsy was taken at the same time as cfDNA t1. Mutations were clustered by the CCFs for each pair of samples using Phylogic39 (“Methods”). Error bars represent the 95% credible interval of the joint posterior density of the clusters. Mutations, excluding indels, having ≥90% estimated power based on coverage in both samples are shown; clusters with fewer than three mutations are excluded. The number of mutations in each cluster is indicated in the legend in parentheses
Research Whole Exome Sequencing Deep Coverage Pipeline, supplied by Broad Institute Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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mapping_pipeline  (myDATA GmbH)
90
myDATA GmbH mapping_pipeline
Fig. 2 Comparison of <t>whole-exome</t> <t>sequencing</t> of cfDNA to whole-exome sequencing of matched tumor biopsies. a Fraction of clonal (≥0.9 cancer cell fraction, CCF) and subclonal (<0.9 CCF) SSNVs detected by MuTect in WES of tumor biopsies and confirmed (i.e., supported by ≥3 variant reads) in WES of cfDNA. Sites with <3 reads that had power <0.9 for mutation calling were not included when computing the fraction of SNVs confirmed (“Methods”). b Fraction of clonal and subclonal SSNVs detected in WES of cfDNA and confirmed in WES of tumor biopsies. For 18 patients with WES of cfDNA at a second time point t2, SSNVs not detected in the matched tumor biopsy but confirmed at t2 are indicated with black. c Analysis of clonal dynamics in an ER+ breast cancer patient diagnosed with metastatic disease 1.5 years (yrs) prior to biopsy and cfDNA collection (t1, Day 0). Clustering analysis of CCF for SSNVs between matched tumor biopsy and cfDNA (t1) is shown in the left panel. The right panel shows the CCF of four mutation clusters, one containing ESR1 L536P (Subclonal Cluster 1, orange) and the other containing ESR1 D538G (Subclonal Cluster 2, light blue), at t1 and t2 (51 days apart) from a patient with ER+ metastatic breast cancer being treated with a SERD. The lymph node biopsy was taken at the same time as cfDNA t1. Mutations were clustered by the CCFs for each pair of samples using Phylogic39 (“Methods”). Error bars represent the 95% credible interval of the joint posterior density of the clusters. Mutations, excluding indels, having ≥90% estimated power based on coverage in both samples are shown; clusters with fewer than three mutations are excluded. The number of mutations in each cluster is indicated in the legend in parentheses
Mapping Pipeline, supplied by myDATA GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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pipeline extension  (TransCanada Pipelines)
90
TransCanada Pipelines pipeline extension
Fig. 2 Comparison of <t>whole-exome</t> <t>sequencing</t> of cfDNA to whole-exome sequencing of matched tumor biopsies. a Fraction of clonal (≥0.9 cancer cell fraction, CCF) and subclonal (<0.9 CCF) SSNVs detected by MuTect in WES of tumor biopsies and confirmed (i.e., supported by ≥3 variant reads) in WES of cfDNA. Sites with <3 reads that had power <0.9 for mutation calling were not included when computing the fraction of SNVs confirmed (“Methods”). b Fraction of clonal and subclonal SSNVs detected in WES of cfDNA and confirmed in WES of tumor biopsies. For 18 patients with WES of cfDNA at a second time point t2, SSNVs not detected in the matched tumor biopsy but confirmed at t2 are indicated with black. c Analysis of clonal dynamics in an ER+ breast cancer patient diagnosed with metastatic disease 1.5 years (yrs) prior to biopsy and cfDNA collection (t1, Day 0). Clustering analysis of CCF for SSNVs between matched tumor biopsy and cfDNA (t1) is shown in the left panel. The right panel shows the CCF of four mutation clusters, one containing ESR1 L536P (Subclonal Cluster 1, orange) and the other containing ESR1 D538G (Subclonal Cluster 2, light blue), at t1 and t2 (51 days apart) from a patient with ER+ metastatic breast cancer being treated with a SERD. The lymph node biopsy was taken at the same time as cfDNA t1. Mutations were clustered by the CCFs for each pair of samples using Phylogic39 (“Methods”). Error bars represent the 95% credible interval of the joint posterior density of the clusters. Mutations, excluding indels, having ≥90% estimated power based on coverage in both samples are shown; clusters with fewer than three mutations are excluded. The number of mutations in each cluster is indicated in the legend in parentheses
Pipeline Extension, supplied by TransCanada Pipelines, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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omicsoft rsem pipeline  (OmicSoft Corporation)
90
OmicSoft Corporation omicsoft rsem pipeline
Fig. 2 Comparison of <t>whole-exome</t> <t>sequencing</t> of cfDNA to whole-exome sequencing of matched tumor biopsies. a Fraction of clonal (≥0.9 cancer cell fraction, CCF) and subclonal (<0.9 CCF) SSNVs detected by MuTect in WES of tumor biopsies and confirmed (i.e., supported by ≥3 variant reads) in WES of cfDNA. Sites with <3 reads that had power <0.9 for mutation calling were not included when computing the fraction of SNVs confirmed (“Methods”). b Fraction of clonal and subclonal SSNVs detected in WES of cfDNA and confirmed in WES of tumor biopsies. For 18 patients with WES of cfDNA at a second time point t2, SSNVs not detected in the matched tumor biopsy but confirmed at t2 are indicated with black. c Analysis of clonal dynamics in an ER+ breast cancer patient diagnosed with metastatic disease 1.5 years (yrs) prior to biopsy and cfDNA collection (t1, Day 0). Clustering analysis of CCF for SSNVs between matched tumor biopsy and cfDNA (t1) is shown in the left panel. The right panel shows the CCF of four mutation clusters, one containing ESR1 L536P (Subclonal Cluster 1, orange) and the other containing ESR1 D538G (Subclonal Cluster 2, light blue), at t1 and t2 (51 days apart) from a patient with ER+ metastatic breast cancer being treated with a SERD. The lymph node biopsy was taken at the same time as cfDNA t1. Mutations were clustered by the CCFs for each pair of samples using Phylogic39 (“Methods”). Error bars represent the 95% credible interval of the joint posterior density of the clusters. Mutations, excluding indels, having ≥90% estimated power based on coverage in both samples are shown; clusters with fewer than three mutations are excluded. The number of mutations in each cluster is indicated in the legend in parentheses
Omicsoft Rsem Pipeline, supplied by OmicSoft Corporation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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quantseq pipeline  (Bluebee Inc)
90
Bluebee Inc quantseq pipeline
Fig. 2 Comparison of <t>whole-exome</t> <t>sequencing</t> of cfDNA to whole-exome sequencing of matched tumor biopsies. a Fraction of clonal (≥0.9 cancer cell fraction, CCF) and subclonal (<0.9 CCF) SSNVs detected by MuTect in WES of tumor biopsies and confirmed (i.e., supported by ≥3 variant reads) in WES of cfDNA. Sites with <3 reads that had power <0.9 for mutation calling were not included when computing the fraction of SNVs confirmed (“Methods”). b Fraction of clonal and subclonal SSNVs detected in WES of cfDNA and confirmed in WES of tumor biopsies. For 18 patients with WES of cfDNA at a second time point t2, SSNVs not detected in the matched tumor biopsy but confirmed at t2 are indicated with black. c Analysis of clonal dynamics in an ER+ breast cancer patient diagnosed with metastatic disease 1.5 years (yrs) prior to biopsy and cfDNA collection (t1, Day 0). Clustering analysis of CCF for SSNVs between matched tumor biopsy and cfDNA (t1) is shown in the left panel. The right panel shows the CCF of four mutation clusters, one containing ESR1 L536P (Subclonal Cluster 1, orange) and the other containing ESR1 D538G (Subclonal Cluster 2, light blue), at t1 and t2 (51 days apart) from a patient with ER+ metastatic breast cancer being treated with a SERD. The lymph node biopsy was taken at the same time as cfDNA t1. Mutations were clustered by the CCFs for each pair of samples using Phylogic39 (“Methods”). Error bars represent the 95% credible interval of the joint posterior density of the clusters. Mutations, excluding indels, having ≥90% estimated power based on coverage in both samples are shown; clusters with fewer than three mutations are excluded. The number of mutations in each cluster is indicated in the legend in parentheses
Quantseq Pipeline, supplied by Bluebee Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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lizardtech gpu pipeline  (LizardTech Inc)
90
LizardTech Inc lizardtech gpu pipeline
Fig. 2 Comparison of <t>whole-exome</t> <t>sequencing</t> of cfDNA to whole-exome sequencing of matched tumor biopsies. a Fraction of clonal (≥0.9 cancer cell fraction, CCF) and subclonal (<0.9 CCF) SSNVs detected by MuTect in WES of tumor biopsies and confirmed (i.e., supported by ≥3 variant reads) in WES of cfDNA. Sites with <3 reads that had power <0.9 for mutation calling were not included when computing the fraction of SNVs confirmed (“Methods”). b Fraction of clonal and subclonal SSNVs detected in WES of cfDNA and confirmed in WES of tumor biopsies. For 18 patients with WES of cfDNA at a second time point t2, SSNVs not detected in the matched tumor biopsy but confirmed at t2 are indicated with black. c Analysis of clonal dynamics in an ER+ breast cancer patient diagnosed with metastatic disease 1.5 years (yrs) prior to biopsy and cfDNA collection (t1, Day 0). Clustering analysis of CCF for SSNVs between matched tumor biopsy and cfDNA (t1) is shown in the left panel. The right panel shows the CCF of four mutation clusters, one containing ESR1 L536P (Subclonal Cluster 1, orange) and the other containing ESR1 D538G (Subclonal Cluster 2, light blue), at t1 and t2 (51 days apart) from a patient with ER+ metastatic breast cancer being treated with a SERD. The lymph node biopsy was taken at the same time as cfDNA t1. Mutations were clustered by the CCFs for each pair of samples using Phylogic39 (“Methods”). Error bars represent the 95% credible interval of the joint posterior density of the clusters. Mutations, excluding indels, having ≥90% estimated power based on coverage in both samples are shown; clusters with fewer than three mutations are excluded. The number of mutations in each cluster is indicated in the legend in parentheses
Lizardtech Gpu Pipeline, supplied by LizardTech Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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pipeline  (10X Genomics)
86
10X Genomics pipeline
Fig. 2 Comparison of <t>whole-exome</t> <t>sequencing</t> of cfDNA to whole-exome sequencing of matched tumor biopsies. a Fraction of clonal (≥0.9 cancer cell fraction, CCF) and subclonal (<0.9 CCF) SSNVs detected by MuTect in WES of tumor biopsies and confirmed (i.e., supported by ≥3 variant reads) in WES of cfDNA. Sites with <3 reads that had power <0.9 for mutation calling were not included when computing the fraction of SNVs confirmed (“Methods”). b Fraction of clonal and subclonal SSNVs detected in WES of cfDNA and confirmed in WES of tumor biopsies. For 18 patients with WES of cfDNA at a second time point t2, SSNVs not detected in the matched tumor biopsy but confirmed at t2 are indicated with black. c Analysis of clonal dynamics in an ER+ breast cancer patient diagnosed with metastatic disease 1.5 years (yrs) prior to biopsy and cfDNA collection (t1, Day 0). Clustering analysis of CCF for SSNVs between matched tumor biopsy and cfDNA (t1) is shown in the left panel. The right panel shows the CCF of four mutation clusters, one containing ESR1 L536P (Subclonal Cluster 1, orange) and the other containing ESR1 D538G (Subclonal Cluster 2, light blue), at t1 and t2 (51 days apart) from a patient with ER+ metastatic breast cancer being treated with a SERD. The lymph node biopsy was taken at the same time as cfDNA t1. Mutations were clustered by the CCFs for each pair of samples using Phylogic39 (“Methods”). Error bars represent the 95% credible interval of the joint posterior density of the clusters. Mutations, excluding indels, having ≥90% estimated power based on coverage in both samples are shown; clusters with fewer than three mutations are excluded. The number of mutations in each cluster is indicated in the legend in parentheses
Pipeline, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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pipeline - by Bioz Stars, 2026-08
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in-house pipeline  (Fulgent Genetics)
90
Fulgent Genetics in-house pipeline
Fig. 2 Comparison of <t>whole-exome</t> <t>sequencing</t> of cfDNA to whole-exome sequencing of matched tumor biopsies. a Fraction of clonal (≥0.9 cancer cell fraction, CCF) and subclonal (<0.9 CCF) SSNVs detected by MuTect in WES of tumor biopsies and confirmed (i.e., supported by ≥3 variant reads) in WES of cfDNA. Sites with <3 reads that had power <0.9 for mutation calling were not included when computing the fraction of SNVs confirmed (“Methods”). b Fraction of clonal and subclonal SSNVs detected in WES of cfDNA and confirmed in WES of tumor biopsies. For 18 patients with WES of cfDNA at a second time point t2, SSNVs not detected in the matched tumor biopsy but confirmed at t2 are indicated with black. c Analysis of clonal dynamics in an ER+ breast cancer patient diagnosed with metastatic disease 1.5 years (yrs) prior to biopsy and cfDNA collection (t1, Day 0). Clustering analysis of CCF for SSNVs between matched tumor biopsy and cfDNA (t1) is shown in the left panel. The right panel shows the CCF of four mutation clusters, one containing ESR1 L536P (Subclonal Cluster 1, orange) and the other containing ESR1 D538G (Subclonal Cluster 2, light blue), at t1 and t2 (51 days apart) from a patient with ER+ metastatic breast cancer being treated with a SERD. The lymph node biopsy was taken at the same time as cfDNA t1. Mutations were clustered by the CCFs for each pair of samples using Phylogic39 (“Methods”). Error bars represent the 95% credible interval of the joint posterior density of the clusters. Mutations, excluding indels, having ≥90% estimated power based on coverage in both samples are shown; clusters with fewer than three mutations are excluded. The number of mutations in each cluster is indicated in the legend in parentheses
In House Pipeline, supplied by Fulgent Genetics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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mapping pipeline  (Arima Genomics Inc)
96
Arima Genomics Inc mapping pipeline
Fig. 2 Comparison of <t>whole-exome</t> <t>sequencing</t> of cfDNA to whole-exome sequencing of matched tumor biopsies. a Fraction of clonal (≥0.9 cancer cell fraction, CCF) and subclonal (<0.9 CCF) SSNVs detected by MuTect in WES of tumor biopsies and confirmed (i.e., supported by ≥3 variant reads) in WES of cfDNA. Sites with <3 reads that had power <0.9 for mutation calling were not included when computing the fraction of SNVs confirmed (“Methods”). b Fraction of clonal and subclonal SSNVs detected in WES of cfDNA and confirmed in WES of tumor biopsies. For 18 patients with WES of cfDNA at a second time point t2, SSNVs not detected in the matched tumor biopsy but confirmed at t2 are indicated with black. c Analysis of clonal dynamics in an ER+ breast cancer patient diagnosed with metastatic disease 1.5 years (yrs) prior to biopsy and cfDNA collection (t1, Day 0). Clustering analysis of CCF for SSNVs between matched tumor biopsy and cfDNA (t1) is shown in the left panel. The right panel shows the CCF of four mutation clusters, one containing ESR1 L536P (Subclonal Cluster 1, orange) and the other containing ESR1 D538G (Subclonal Cluster 2, light blue), at t1 and t2 (51 days apart) from a patient with ER+ metastatic breast cancer being treated with a SERD. The lymph node biopsy was taken at the same time as cfDNA t1. Mutations were clustered by the CCFs for each pair of samples using Phylogic39 (“Methods”). Error bars represent the 95% credible interval of the joint posterior density of the clusters. Mutations, excluding indels, having ≥90% estimated power based on coverage in both samples are shown; clusters with fewer than three mutations are excluded. The number of mutations in each cluster is indicated in the legend in parentheses
Mapping Pipeline, supplied by Arima Genomics Inc, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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customized cellprofiler 3.1.8 pipeline  (Broad Institute Inc)
90
Broad Institute Inc customized cellprofiler 3.1.8 pipeline
Fig. 2 Comparison of <t>whole-exome</t> <t>sequencing</t> of cfDNA to whole-exome sequencing of matched tumor biopsies. a Fraction of clonal (≥0.9 cancer cell fraction, CCF) and subclonal (<0.9 CCF) SSNVs detected by MuTect in WES of tumor biopsies and confirmed (i.e., supported by ≥3 variant reads) in WES of cfDNA. Sites with <3 reads that had power <0.9 for mutation calling were not included when computing the fraction of SNVs confirmed (“Methods”). b Fraction of clonal and subclonal SSNVs detected in WES of cfDNA and confirmed in WES of tumor biopsies. For 18 patients with WES of cfDNA at a second time point t2, SSNVs not detected in the matched tumor biopsy but confirmed at t2 are indicated with black. c Analysis of clonal dynamics in an ER+ breast cancer patient diagnosed with metastatic disease 1.5 years (yrs) prior to biopsy and cfDNA collection (t1, Day 0). Clustering analysis of CCF for SSNVs between matched tumor biopsy and cfDNA (t1) is shown in the left panel. The right panel shows the CCF of four mutation clusters, one containing ESR1 L536P (Subclonal Cluster 1, orange) and the other containing ESR1 D538G (Subclonal Cluster 2, light blue), at t1 and t2 (51 days apart) from a patient with ER+ metastatic breast cancer being treated with a SERD. The lymph node biopsy was taken at the same time as cfDNA t1. Mutations were clustered by the CCFs for each pair of samples using Phylogic39 (“Methods”). Error bars represent the 95% credible interval of the joint posterior density of the clusters. Mutations, excluding indels, having ≥90% estimated power based on coverage in both samples are shown; clusters with fewer than three mutations are excluded. The number of mutations in each cluster is indicated in the legend in parentheses
Customized Cellprofiler 3.1.8 Pipeline, supplied by Broad Institute Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


Fig. 2 Comparison of whole-exome sequencing of cfDNA to whole-exome sequencing of matched tumor biopsies. a Fraction of clonal (≥0.9 cancer cell fraction, CCF) and subclonal (<0.9 CCF) SSNVs detected by MuTect in WES of tumor biopsies and confirmed (i.e., supported by ≥3 variant reads) in WES of cfDNA. Sites with <3 reads that had power <0.9 for mutation calling were not included when computing the fraction of SNVs confirmed (“Methods”). b Fraction of clonal and subclonal SSNVs detected in WES of cfDNA and confirmed in WES of tumor biopsies. For 18 patients with WES of cfDNA at a second time point t2, SSNVs not detected in the matched tumor biopsy but confirmed at t2 are indicated with black. c Analysis of clonal dynamics in an ER+ breast cancer patient diagnosed with metastatic disease 1.5 years (yrs) prior to biopsy and cfDNA collection (t1, Day 0). Clustering analysis of CCF for SSNVs between matched tumor biopsy and cfDNA (t1) is shown in the left panel. The right panel shows the CCF of four mutation clusters, one containing ESR1 L536P (Subclonal Cluster 1, orange) and the other containing ESR1 D538G (Subclonal Cluster 2, light blue), at t1 and t2 (51 days apart) from a patient with ER+ metastatic breast cancer being treated with a SERD. The lymph node biopsy was taken at the same time as cfDNA t1. Mutations were clustered by the CCFs for each pair of samples using Phylogic39 (“Methods”). Error bars represent the 95% credible interval of the joint posterior density of the clusters. Mutations, excluding indels, having ≥90% estimated power based on coverage in both samples are shown; clusters with fewer than three mutations are excluded. The number of mutations in each cluster is indicated in the legend in parentheses

Journal: Nature communications

Article Title: Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.

doi: 10.1038/s41467-017-00965-y

Figure Lengend Snippet: Fig. 2 Comparison of whole-exome sequencing of cfDNA to whole-exome sequencing of matched tumor biopsies. a Fraction of clonal (≥0.9 cancer cell fraction, CCF) and subclonal (<0.9 CCF) SSNVs detected by MuTect in WES of tumor biopsies and confirmed (i.e., supported by ≥3 variant reads) in WES of cfDNA. Sites with <3 reads that had power <0.9 for mutation calling were not included when computing the fraction of SNVs confirmed (“Methods”). b Fraction of clonal and subclonal SSNVs detected in WES of cfDNA and confirmed in WES of tumor biopsies. For 18 patients with WES of cfDNA at a second time point t2, SSNVs not detected in the matched tumor biopsy but confirmed at t2 are indicated with black. c Analysis of clonal dynamics in an ER+ breast cancer patient diagnosed with metastatic disease 1.5 years (yrs) prior to biopsy and cfDNA collection (t1, Day 0). Clustering analysis of CCF for SSNVs between matched tumor biopsy and cfDNA (t1) is shown in the left panel. The right panel shows the CCF of four mutation clusters, one containing ESR1 L536P (Subclonal Cluster 1, orange) and the other containing ESR1 D538G (Subclonal Cluster 2, light blue), at t1 and t2 (51 days apart) from a patient with ER+ metastatic breast cancer being treated with a SERD. The lymph node biopsy was taken at the same time as cfDNA t1. Mutations were clustered by the CCFs for each pair of samples using Phylogic39 (“Methods”). Error bars represent the 95% credible interval of the joint posterior density of the clusters. Mutations, excluding indels, having ≥90% estimated power based on coverage in both samples are shown; clusters with fewer than three mutations are excluded. The number of mutations in each cluster is indicated in the legend in parentheses

Article Snippet: Matched tumor biopsies were processed and sequenced through the Broad Institute Genomics Platform’s Research Whole Exome Sequencing deep coverage pipeline (http://genomics.broadinstitute.org/data-sheets/DTS_WES_1Page_52016_0.pdf).

Techniques: Comparison, Sequencing, Variant Assay, Mutagenesis