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Viktor A Adalsteinsson - One of the best experts on this subject based on the ideXlab platform.

  • scalable whole Exome Sequencing of cell free dna reveals high concordance with metastatic tumors
    Nature Communications, 2017
    Co-Authors: Viktor A Adalsteinsson, Gavin Ha, Samuel S Freeman, Atish D Choudhury, Daniel G Stover, Heather A Parsons, Gregory Gydush
    Abstract:

    Whole-Exome Sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome Sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-Exome Sequencing. Using whole-Exome Sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-Exome Sequencing. Identifying the mutational landscape of tumours from cell-free DNA in the blood could help diagnostics in cancer. Here, the authors present ichorCNA, software that quantifies tumour content in cell free DNA, and they demonstrate that cell-free DNA whole-Exome Sequencing is concordant with metastatic tumour whole-Exome Sequencing.

  • scalable whole Exome Sequencing of cell free dna reveals high concordance with metastatic tumors
    Nature Communications, 2017
    Co-Authors: Viktor A Adalsteinsson, Samuel S Freeman, Atish D Choudhury, Daniel G Stover, Heather A Parsons, Gregory Gydush, Sarah Reed, Denisse Rotem
    Abstract:

    Whole-Exome Sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome Sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-Exome Sequencing. Using whole-Exome Sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-Exome Sequencing.

Joris A. Veltman - One of the best experts on this subject based on the ideXlab platform.

  • Novel bioinformatic developments for Exome Sequencing
    Human Genetics, 2016
    Co-Authors: Stefan H. Lelieveld, Joris A. Veltman, Christian Gilissen
    Abstract:

    With the widespread adoption of next generation Sequencing technologies by the genetics community and the rapid decrease in costs per base, Exome Sequencing has become a standard within the repertoire of genetic experiments for both research and diagnostics. Although bioinformatics now offers standard solutions for the analysis of Exome Sequencing data, many challenges still remain; especially the increasing scale at which Exome data are now being generated has given rise to novel challenges in how to efficiently store, analyze and interpret Exome data of this magnitude. In this review we discuss some of the recent developments in bioinformatics for Exome Sequencing and the directions that this is taking us to. With these developments, Exome Sequencing is paving the way for the next big challenge, the application of whole genome Sequencing.

  • Exome Sequencing and whole genome Sequencing for the detection of copy number variation
    Expert Review of Molecular Diagnostics, 2015
    Co-Authors: Jayne Y Hehir-kwa, Rolph Pfundt, Joris A. Veltman
    Abstract:

    Many laboratories now use genomic microarrays as their first-tier diagnostic test for copy number variation (CNV) detection. In addition, whole Exome Sequencing is increasingly being offered as a diagnostic test for heterogeneous disorders. Although mostly used for the detection of point mutations and small insertion–deletions, Exome Sequencing can also be used to call CNVs, allowing combined small and large variant analysis. Whole genome Sequencing in addition to these advantages also offers the potential to characterize CNVs to unprecedented levels of accuracy, providing position and orientation information. In this review, we discuss the clinical potential of CNV identification in whole Exome Sequencing and whole genome Sequencing data and the implications this has on diagnostic laboratories.

  • Clinical Exome Sequencing in daily practice: 1,000 patients and beyond
    Genome medicine, 2014
    Co-Authors: Wendy A. G. Van Zelst-stams, Hans Scheffer, Joris A. Veltman
    Abstract:

    Diagnostic Exome Sequencing Using next-generation Sequencing technology to sequence the coding regions of all human genes, known as Exome Sequencing, has rapidly become one of the most successful methods for genetic disease research since its introduction in 2009 [1]. The possibility to investigate all genes for mutations in a single experiment holds great promise in the diagnostic arena, in particular for genetically heterogeneous disorders and clinically undiagnosed diseases. Laboratories, including our own, have now started to offer Exome Sequencing as a diagnostic test. In this article, we share our experience with diagnostic Exome Sequencing and discuss the impact of these novel diagnostic methods on medical practice, now and in the future.

  • Unlocking Mendelian disease using Exome Sequencing
    Genome Biology, 2011
    Co-Authors: Christian Gilissen, Alexander Hoischen, Han G Brunner, Joris A. Veltman
    Abstract:

    Exome Sequencing is revolutionizing Mendelian disease gene identification. This results in improved clinical diagnosis, more accurate genotype-phenotype correlations and new insights into the role of rare genomic variation in disease.

Samuel S Freeman - One of the best experts on this subject based on the ideXlab platform.

  • scalable whole Exome Sequencing of cell free dna reveals high concordance with metastatic tumors
    Nature Communications, 2017
    Co-Authors: Viktor A Adalsteinsson, Gavin Ha, Samuel S Freeman, Atish D Choudhury, Daniel G Stover, Heather A Parsons, Gregory Gydush
    Abstract:

    Whole-Exome Sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome Sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-Exome Sequencing. Using whole-Exome Sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-Exome Sequencing. Identifying the mutational landscape of tumours from cell-free DNA in the blood could help diagnostics in cancer. Here, the authors present ichorCNA, software that quantifies tumour content in cell free DNA, and they demonstrate that cell-free DNA whole-Exome Sequencing is concordant with metastatic tumour whole-Exome Sequencing.

  • scalable whole Exome Sequencing of cell free dna reveals high concordance with metastatic tumors
    Nature Communications, 2017
    Co-Authors: Viktor A Adalsteinsson, Samuel S Freeman, Atish D Choudhury, Daniel G Stover, Heather A Parsons, Gregory Gydush, Sarah Reed, Denisse Rotem
    Abstract:

    Whole-Exome Sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome Sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-Exome Sequencing. Using whole-Exome Sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-Exome Sequencing.

Steven G. Kernie - One of the best experts on this subject based on the ideXlab platform.

  • Rapid Exome Sequencing in PICU patients with new-onset metabolic or neurological disorders.
    Pediatric research, 2020
    Co-Authors: Abigail S. Carey, John P. Schacht, Christine Umandap, David A. Fasel, Chunhua Weng, Joshua Cappell, Wendy K. Chung, Steven G. Kernie
    Abstract:

    BACKGROUND Genomic assessment previously took months to result and was unable to impact clinical care in the pediatric intensive care unit (PICU). The advent of rapid Exome Sequencing potentially changes this. We investigated the impact of rapid Exome Sequencing in a pilot study on pediatric patients admitted to a single PICU with new-onset metabolic/neurologic disease. METHODS Rapid Exome Sequencing (7 days to verbal result) was performed on (n = 10) PICU patients age 

Gregory Gydush - One of the best experts on this subject based on the ideXlab platform.

  • scalable whole Exome Sequencing of cell free dna reveals high concordance with metastatic tumors
    Nature Communications, 2017
    Co-Authors: Viktor A Adalsteinsson, Gavin Ha, Samuel S Freeman, Atish D Choudhury, Daniel G Stover, Heather A Parsons, Gregory Gydush
    Abstract:

    Whole-Exome Sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome Sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-Exome Sequencing. Using whole-Exome Sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-Exome Sequencing. Identifying the mutational landscape of tumours from cell-free DNA in the blood could help diagnostics in cancer. Here, the authors present ichorCNA, software that quantifies tumour content in cell free DNA, and they demonstrate that cell-free DNA whole-Exome Sequencing is concordant with metastatic tumour whole-Exome Sequencing.

  • scalable whole Exome Sequencing of cell free dna reveals high concordance with metastatic tumors
    Nature Communications, 2017
    Co-Authors: Viktor A Adalsteinsson, Samuel S Freeman, Atish D Choudhury, Daniel G Stover, Heather A Parsons, Gregory Gydush, Sarah Reed, Denisse Rotem
    Abstract:

    Whole-Exome Sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome Sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-Exome Sequencing. Using whole-Exome Sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-Exome Sequencing.