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exome data  (Broad Clinical Labs)


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    Broad Clinical Labs exome data
    Exome Data, supplied by Broad Clinical Labs, used in various techniques. Bioz Stars score: 95/100, based on 311 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/exome+sequence+data/Whole+Exome+Sequencing/pm41444428-26-27-34
    Average 95 stars, based on 311 article reviews
    exome data - by Bioz Stars, 2026-11
    95/100 stars

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    Related Articles

    Sequencing:

    Article Title: Multiparameter prediction of myeloid neoplasia risk.
    Article Snippet: .. Whole-exome sequence data processing, CH mutation calling and filtering Whole-exome sequencing of blood DNA from 454,340 participants was used to identify somatic mutations using Mutect2 software (GATK version 4.1.3.0) through the DNAnexus platform using Docker image broadinstitute/gatk:4.1.3.0. ..

    Article Title: Genomic and transcriptomic profiling indicates the prognosis significance of mutational signature for TMB-high subtype in Chinese patients with gastric cancer
    Article Snippet: The expression of checkpoint molecules, CTL-related genes and T-cell inflammatory genes , , , and the proportion of tumor-infiltrating immune cells in the tumor microenvironment (TME) were analyzed to predict response to immunotherapy. .. The TCGA GC (STAD) cohort containing whole exome sequencing data (n = 437) and whole transcriptional sequencing data (n = 407) of gastric adenocarcinoma were available at the Broad GDAC Firehose website( https://gdac.broadinstitute.org/ ), in which the DNA sequencing data with survival information (n = 402) were used for molecular subtyping, mutational signature evaluation, and survival validation, while the corresponding RNA sequencing data (n = 375) were used for analyzing the distribution of tumor-infiltrating immunocytes and the expression of immune-related genes. ..

    Article Title: Genomic and transcriptomic profiling indicates the prognosis significance of mutational signature for TMB-high subtype in Chinese patients with gastric cancer.
    Article Snippet: .. The TCGA GC (STAD) cohort containing whole exome sequencing data (n = 437) and whole transcriptional sequencing data (n = 407) of gastric adenocarcinoma were available at the Broad GDAC Firehose website(https://gdac.broadinstitute.org/), in which the DNA sequencing data with survival information (n = 402) were used for molecular subtyping, mutational signature evaluation, and survival validation, while the corresponding RNA sequencing data (n = 375) were used for analyzing the distribution of tumorinfiltrating immunocytes and the expression of immune-related genes. ..

    Article Title: Identification of Candidate Genes of Familial Multiple Idiopathic Cervical Root Resorption.
    Article Snippet: Introduction: Multiple idiopathic cervical root resorption (MICRR) is a disease with an unknown etiology that causes invasive cervical root resorption in multiple teeth.. Although previous MICRR genomic studies have identified candidate gene variants, the etiology of the condition remains poorly understood.. In the present study, we investigated the genetic causality of MICRR to explore candidate variants.

    Article Title: BRCA1/Trp53 heterozygosity and replication stress drive esophageal cancer development in a mouse model
    Article Snippet: .. We also analyzed the WES sequencing data using GATK HaplotypeCaller ( ) in genomic vcf mode from the Broad Institute and confirmed results generated through our qPCR analysis. ..

    Article Title: Detection of heterogeneous resistance mechanisms to tyrosine kinase inhibitors from cell-free DNA.
    Article Snippet: .. The remainder of our genomic analysis relied on whole exome sequencing (WES) data generated by the Broad Institute Genomics Platform. .. WES on cfDNA samples employed a Twist bait set; for solid tissue samples an Agilent bait set was used.58 Reads were aligned to the GRCh37 reference using BWA-MEM with Picard MarkDuplicates.

    Article Title: U2AF1 mutation connects DNA damage to the alternative splicing of RAD51 in lung adenocarcinomas.
    Article Snippet: Funding information This work was supported by a grant from National Natural Science Foundation of China (81960008).. Abstract The recurrent mutation (S34F) in splicing factor U2AF1 is frequently observed in lung adenocarcinoma, but its function remains largely unknown.. To determine the mechanistic basis and consequences of U2AF1 mutations, we established non–small cell lung carcinoma A549 cell lines with exogenous expression of wildtype (U2AF1-WT) or mutant (U2AF1-S34F).

    Article Title: Detection of heterogeneous resistance mechanisms to tyrosine kinase inhibitors from cell-free DNA
    Article Snippet: .. The remainder of our genomic analysis relied on whole exome sequencing (WES) data generated by the Broad Institute Genomics Platform. .. WES on cfDNA samples employed a Twist bait set; for solid tissue samples an Agilent bait set was used.

    Mutagenesis:

    Article Title: Multiparameter prediction of myeloid neoplasia risk.
    Article Snippet: .. Whole-exome sequence data processing, CH mutation calling and filtering Whole-exome sequencing of blood DNA from 454,340 participants was used to identify somatic mutations using Mutect2 software (GATK version 4.1.3.0) through the DNAnexus platform using Docker image broadinstitute/gatk:4.1.3.0. ..

    Article Title: U2AF1 mutation connects DNA damage to the alternative splicing of RAD51 in lung adenocarcinomas.
    Article Snippet: Funding information This work was supported by a grant from National Natural Science Foundation of China (81960008).. Abstract The recurrent mutation (S34F) in splicing factor U2AF1 is frequently observed in lung adenocarcinoma, but its function remains largely unknown.. To determine the mechanistic basis and consequences of U2AF1 mutations, we established non–small cell lung carcinoma A549 cell lines with exogenous expression of wildtype (U2AF1-WT) or mutant (U2AF1-S34F).

    Software:

    Article Title: Multiparameter prediction of myeloid neoplasia risk.
    Article Snippet: .. Whole-exome sequence data processing, CH mutation calling and filtering Whole-exome sequencing of blood DNA from 454,340 participants was used to identify somatic mutations using Mutect2 software (GATK version 4.1.3.0) through the DNAnexus platform using Docker image broadinstitute/gatk:4.1.3.0. ..

    DNA Sequencing:

    Article Title: Genomic and transcriptomic profiling indicates the prognosis significance of mutational signature for TMB-high subtype in Chinese patients with gastric cancer
    Article Snippet: The expression of checkpoint molecules, CTL-related genes and T-cell inflammatory genes , , , and the proportion of tumor-infiltrating immune cells in the tumor microenvironment (TME) were analyzed to predict response to immunotherapy. .. The TCGA GC (STAD) cohort containing whole exome sequencing data (n = 437) and whole transcriptional sequencing data (n = 407) of gastric adenocarcinoma were available at the Broad GDAC Firehose website( https://gdac.broadinstitute.org/ ), in which the DNA sequencing data with survival information (n = 402) were used for molecular subtyping, mutational signature evaluation, and survival validation, while the corresponding RNA sequencing data (n = 375) were used for analyzing the distribution of tumor-infiltrating immunocytes and the expression of immune-related genes. ..

    Article Title: Genomic and transcriptomic profiling indicates the prognosis significance of mutational signature for TMB-high subtype in Chinese patients with gastric cancer.
    Article Snippet: .. The TCGA GC (STAD) cohort containing whole exome sequencing data (n = 437) and whole transcriptional sequencing data (n = 407) of gastric adenocarcinoma were available at the Broad GDAC Firehose website(https://gdac.broadinstitute.org/), in which the DNA sequencing data with survival information (n = 402) were used for molecular subtyping, mutational signature evaluation, and survival validation, while the corresponding RNA sequencing data (n = 375) were used for analyzing the distribution of tumorinfiltrating immunocytes and the expression of immune-related genes. ..

    Biomarker Discovery:

    Article Title: Genomic and transcriptomic profiling indicates the prognosis significance of mutational signature for TMB-high subtype in Chinese patients with gastric cancer
    Article Snippet: The expression of checkpoint molecules, CTL-related genes and T-cell inflammatory genes , , , and the proportion of tumor-infiltrating immune cells in the tumor microenvironment (TME) were analyzed to predict response to immunotherapy. .. The TCGA GC (STAD) cohort containing whole exome sequencing data (n = 437) and whole transcriptional sequencing data (n = 407) of gastric adenocarcinoma were available at the Broad GDAC Firehose website( https://gdac.broadinstitute.org/ ), in which the DNA sequencing data with survival information (n = 402) were used for molecular subtyping, mutational signature evaluation, and survival validation, while the corresponding RNA sequencing data (n = 375) were used for analyzing the distribution of tumor-infiltrating immunocytes and the expression of immune-related genes. ..

    Article Title: Genomic and transcriptomic profiling indicates the prognosis significance of mutational signature for TMB-high subtype in Chinese patients with gastric cancer.
    Article Snippet: .. The TCGA GC (STAD) cohort containing whole exome sequencing data (n = 437) and whole transcriptional sequencing data (n = 407) of gastric adenocarcinoma were available at the Broad GDAC Firehose website(https://gdac.broadinstitute.org/), in which the DNA sequencing data with survival information (n = 402) were used for molecular subtyping, mutational signature evaluation, and survival validation, while the corresponding RNA sequencing data (n = 375) were used for analyzing the distribution of tumorinfiltrating immunocytes and the expression of immune-related genes. ..

    RNA Sequencing:

    Article Title: Genomic and transcriptomic profiling indicates the prognosis significance of mutational signature for TMB-high subtype in Chinese patients with gastric cancer
    Article Snippet: The expression of checkpoint molecules, CTL-related genes and T-cell inflammatory genes , , , and the proportion of tumor-infiltrating immune cells in the tumor microenvironment (TME) were analyzed to predict response to immunotherapy. .. The TCGA GC (STAD) cohort containing whole exome sequencing data (n = 437) and whole transcriptional sequencing data (n = 407) of gastric adenocarcinoma were available at the Broad GDAC Firehose website( https://gdac.broadinstitute.org/ ), in which the DNA sequencing data with survival information (n = 402) were used for molecular subtyping, mutational signature evaluation, and survival validation, while the corresponding RNA sequencing data (n = 375) were used for analyzing the distribution of tumor-infiltrating immunocytes and the expression of immune-related genes. ..

    Article Title: Genomic and transcriptomic profiling indicates the prognosis significance of mutational signature for TMB-high subtype in Chinese patients with gastric cancer.
    Article Snippet: .. The TCGA GC (STAD) cohort containing whole exome sequencing data (n = 437) and whole transcriptional sequencing data (n = 407) of gastric adenocarcinoma were available at the Broad GDAC Firehose website(https://gdac.broadinstitute.org/), in which the DNA sequencing data with survival information (n = 402) were used for molecular subtyping, mutational signature evaluation, and survival validation, while the corresponding RNA sequencing data (n = 375) were used for analyzing the distribution of tumorinfiltrating immunocytes and the expression of immune-related genes. ..

    Expressing:

    Article Title: Genomic and transcriptomic profiling indicates the prognosis significance of mutational signature for TMB-high subtype in Chinese patients with gastric cancer
    Article Snippet: The expression of checkpoint molecules, CTL-related genes and T-cell inflammatory genes , , , and the proportion of tumor-infiltrating immune cells in the tumor microenvironment (TME) were analyzed to predict response to immunotherapy. .. The TCGA GC (STAD) cohort containing whole exome sequencing data (n = 437) and whole transcriptional sequencing data (n = 407) of gastric adenocarcinoma were available at the Broad GDAC Firehose website( https://gdac.broadinstitute.org/ ), in which the DNA sequencing data with survival information (n = 402) were used for molecular subtyping, mutational signature evaluation, and survival validation, while the corresponding RNA sequencing data (n = 375) were used for analyzing the distribution of tumor-infiltrating immunocytes and the expression of immune-related genes. ..

    Article Title: Genomic and transcriptomic profiling indicates the prognosis significance of mutational signature for TMB-high subtype in Chinese patients with gastric cancer.
    Article Snippet: .. The TCGA GC (STAD) cohort containing whole exome sequencing data (n = 437) and whole transcriptional sequencing data (n = 407) of gastric adenocarcinoma were available at the Broad GDAC Firehose website(https://gdac.broadinstitute.org/), in which the DNA sequencing data with survival information (n = 402) were used for molecular subtyping, mutational signature evaluation, and survival validation, while the corresponding RNA sequencing data (n = 375) were used for analyzing the distribution of tumorinfiltrating immunocytes and the expression of immune-related genes. ..

    Variant Assay:

    Article Title: Identification of Candidate Genes of Familial Multiple Idiopathic Cervical Root Resorption.
    Article Snippet: Introduction: Multiple idiopathic cervical root resorption (MICRR) is a disease with an unknown etiology that causes invasive cervical root resorption in multiple teeth.. Although previous MICRR genomic studies have identified candidate gene variants, the etiology of the condition remains poorly understood.. In the present study, we investigated the genetic causality of MICRR to explore candidate variants.

    Generated:

    Article Title: BRCA1/Trp53 heterozygosity and replication stress drive esophageal cancer development in a mouse model
    Article Snippet: .. We also analyzed the WES sequencing data using GATK HaplotypeCaller ( ) in genomic vcf mode from the Broad Institute and confirmed results generated through our qPCR analysis. ..

    Article Title: Detection of heterogeneous resistance mechanisms to tyrosine kinase inhibitors from cell-free DNA.
    Article Snippet: .. The remainder of our genomic analysis relied on whole exome sequencing (WES) data generated by the Broad Institute Genomics Platform. .. WES on cfDNA samples employed a Twist bait set; for solid tissue samples an Agilent bait set was used.58 Reads were aligned to the GRCh37 reference using BWA-MEM with Picard MarkDuplicates.

    Article Title: Detection of heterogeneous resistance mechanisms to tyrosine kinase inhibitors from cell-free DNA
    Article Snippet: .. The remainder of our genomic analysis relied on whole exome sequencing (WES) data generated by the Broad Institute Genomics Platform. .. WES on cfDNA samples employed a Twist bait set; for solid tissue samples an Agilent bait set was used.

    Real-time Polymerase Chain Reaction:

    Article Title: BRCA1/Trp53 heterozygosity and replication stress drive esophageal cancer development in a mouse model
    Article Snippet: .. We also analyzed the WES sequencing data using GATK HaplotypeCaller ( ) in genomic vcf mode from the Broad Institute and confirmed results generated through our qPCR analysis. ..

    Analysis:

    Article Title: BRCA1/Trp53 heterozygosity and replication stress drive esophageal cancer development in a mouse model
    Article Snippet: .. We also analyzed the WES sequencing data using GATK HaplotypeCaller ( ) in genomic vcf mode from the Broad Institute and confirmed results generated through our qPCR analysis. ..



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    Image Search Results


    Study design for patient cohorts and genomic analyses (A) Initial study criteria with study design based on sample availability and treatment timing. After whole-exome sequencing, PhylogicNDT and SignatureAnalyzer were used to identify clones and compare mutational signatures, respectively. Functional mutations were characterized based on existing evidence previously published or annotated in genomic databases, such as COSMIC, ClinVar, and OncoKB. (B) Signaling pathway landscape for paired-cohort participants ( n = 26) organized by time on tyrosine kinase treatment (days by sampled TKI) and acquired ( n = 8) or intrinsic ( n = 18) resistance. Known mechanisms in ERBB2 and PIK3CA are highlighted. Signaling pathways are depicted in decreasing frequency per number of mutations for the entire cohort of paired participants. Arrows indicate the subclonal trajectory as either growing, stable, or shrinking. The TP53 and ESR1+ regulator pathways were significantly mutated ( q < 0.05; MutSig, Fisher’s method). Stacked bar charts indicate relative contributions of mutational signatures identified by SignatureAnalyzer to the mutational spectrum of each participant. (C) Pathway-level comparison of mutation frequency between four cohorts: intrinsic ( n = 18), acquired ( n = 8), pre-TKI ( n = 55), and post-TKI ( n = 30). Pathways were included if they possessed at least one mutation. There were no significant differences in pathway-level mutation frequency between cohorts (Fisher’s exact test).

    Journal: Cell Genomics

    Article Title: Detection of heterogeneous resistance mechanisms to tyrosine kinase inhibitors from cell-free DNA

    doi: 10.1016/j.xgen.2025.100987

    Figure Lengend Snippet: Study design for patient cohorts and genomic analyses (A) Initial study criteria with study design based on sample availability and treatment timing. After whole-exome sequencing, PhylogicNDT and SignatureAnalyzer were used to identify clones and compare mutational signatures, respectively. Functional mutations were characterized based on existing evidence previously published or annotated in genomic databases, such as COSMIC, ClinVar, and OncoKB. (B) Signaling pathway landscape for paired-cohort participants ( n = 26) organized by time on tyrosine kinase treatment (days by sampled TKI) and acquired ( n = 8) or intrinsic ( n = 18) resistance. Known mechanisms in ERBB2 and PIK3CA are highlighted. Signaling pathways are depicted in decreasing frequency per number of mutations for the entire cohort of paired participants. Arrows indicate the subclonal trajectory as either growing, stable, or shrinking. The TP53 and ESR1+ regulator pathways were significantly mutated ( q < 0.05; MutSig, Fisher’s method). Stacked bar charts indicate relative contributions of mutational signatures identified by SignatureAnalyzer to the mutational spectrum of each participant. (C) Pathway-level comparison of mutation frequency between four cohorts: intrinsic ( n = 18), acquired ( n = 8), pre-TKI ( n = 55), and post-TKI ( n = 30). Pathways were included if they possessed at least one mutation. There were no significant differences in pathway-level mutation frequency between cohorts (Fisher’s exact test).

    Article Snippet: The remainder of our genomic analysis relied on whole exome sequencing (WES) data generated by the Broad Institute Genomics Platform.

    Techniques: Sequencing, Clone Assay, Functional Assay, Protein-Protein interactions, Comparison, Mutagenesis