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Implementation of Genome Sequencing Assays

  • Tina M. HambuchEmail author
  • Keith Nykamp
  • Carri-Lyn Rebecca Mead
Chapter

Abstract

The implementation of whole-genome sequencing (WGS) as a clinical test has been a source of speculation, anticipation, and anecdotes for many years. The first clinical (CLIA-certified, CAP-accredited) laboratory to offer this test launched the service in 2009, and despite several significant challenges that still surround the offering and use of WGS for clinical applications, it has largely been embraced by an enthusiastic community of physicians and clinical laboratorians. In this chapter, we discuss the many considerations, caveats, challenges, and opportunities that must be addressed when implementing clinical WGS. Approaches to this implementation are also discussed. The chapter is organized into sections on test definition, staffing and training, infrastructure, validations, and interpretation and reporting considerations.

Keywords

Genome sequencing Next-generation sequencing (NGS) Clinical genomics Diagnostics Molecular pathology Molecular genetics Diagnostic odyssey 

Glossary

Allele frequency

Proportion of a particular allele among all alleles for a gene

Disease prevalence

Proportion of a population to have a condition

Mendelian condition

A condition that is caused by variants within a single gene and that can be passed to offspring in an autosomal dominant or autosomal recessive pattern

Proband

Affected individual on whom testing is being performed

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2019

Authors and Affiliations

  • Tina M. Hambuch
    • 1
    Email author
  • Keith Nykamp
    • 1
  • Carri-Lyn Rebecca Mead
    • 2
  1. 1.Genetics, InvitaeSan FranciscoUSA
  2. 2.Emerging Technologies, IlluminaSan DiegoUSA

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