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Bioinformatics Tools in Clinical Genomics

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Genomic Applications in Pathology

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Abstract

The field of DNA sequencing experienced a transformational shift beginning in 2005 with the introduction of the first high-throughput, massively parallel DNA sequencing platform that ushered in the era of “next-generation sequencing.” Initially, next-generation sequencing (NGS) platforms generated millions of bases per instrument run which steadily progressed to the now routine output of billions of bases. These unprecedented data volumes have driven a renaissance in bioinformatics research and development resulting in a proliferation of open-source and commercial software algorithms to support the computational processing, analysis, and interpretation of NGS results. These efforts have facilitated a broad dissemination of NGS into every facet of biomedical research and into a growing list of clinical diagnostic applications from targeted multigene panels to whole-genome sequencing.

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Abbreviations

BAM:

Binary Alignment Mapping file format

BWA:

Burrows-Wheeler aligner

BWT:

Burrows-Wheeler transform

GATK:

Genome Analysis Tool Kit

HGMD:

Human Gene Mutation Database

IGV:

Integrative Genomics Viewer

NGS:

next-generation sequencing

OMIM:

Online Mendelian Inheritance in Man

TVC:

Torrent Variant Caller

VCF:

Variant Call File format

VUS:

variant of uncertain significance

WGS:

whole-genome sequencing

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Authors and Affiliations

  1. ARUP Laboratories, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA

    David K. Crockett, Karl V. Voelkerding, Alan F. Brown & Rachel L. Stewart

  2. Department of Pathology and Laboratory Medicine, University of Kentucky College of Medicine, Lexington, KY, USA

    Rachel L. Stewart

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  1. David K. Crockett
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  2. Karl V. Voelkerding
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  3. Alan F. Brown
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  4. Rachel L. Stewart
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Correspondence to Karl V. Voelkerding .

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Editors and Affiliations

  1. Professor and Chair of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA

    George Jabboure Netto

  2. Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Clinical Professor of Pathology, University of Chicago Pritzker School of Medicine, Evanston, IL, USA

    Karen L. Kaul

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Crockett, D.K., Voelkerding, K.V., Brown, A.F., Stewart, R.L. (2019). Bioinformatics Tools in Clinical Genomics. In: Netto, G., Kaul, K. (eds) Genomic Applications in Pathology. Springer, Cham. https://doi.org/10.1007/978-3-319-96830-8_14

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