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Bioinformatics Tools in Clinical Genomics

  • David K. Crockett
  • Karl V. VoelkerdingEmail author
  • Alan F. Brown
  • Rachel L. Stewart
Chapter

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.

Keywords

Annotation Bioinformatics Database Gene variants Genomics Genotype Phenotype Pipeline Sequencing Next generation 

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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Copyright information

© Springer International Publishing AG, part of Springer Nature 2019

Authors and Affiliations

  • David K. Crockett
    • 1
  • Karl V. Voelkerding
    • 1
    Email author
  • Alan F. Brown
    • 1
  • Rachel L. Stewart
    • 1
    • 2
  1. 1.ARUP Laboratories, Department of PathologyUniversity of Utah School of MedicineSalt Lake CityUSA
  2. 2.Department of Pathology and Laboratory MedicineUniversity of Kentucky College of MedicineLexingtonUSA

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