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Implementation of Genome Sequencing Assays

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Genomic Applications in Pathology

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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.

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Author information

Authors and Affiliations

  1. Illumina Clinical Services Laboratory, San Diego, CA, USA

    Tina M. Hambuch & Carri-Lyn Mead

Authors
  1. Tina M. Hambuch
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  2. Carri-Lyn Mead
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Editor information

Editors and Affiliations

  1. Departments of Pathology, Oncology and Urology, Johns Hopkins University, Baltimore, Maryland, USA

    George Jabboure Netto

  2. Department of Pathology, Stanford University School of Medicine, Stanford, California, USA

    Iris Schrijver

Glossary

Proband 

Affected individual on whom testing is being performed.

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.

Disease prevalence 

Proportion of a population to have a condition.

Allele frequency 

Proportion of a particular allele among all alleles for a gene.

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© 2015 Springer Science+Business Media New York

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Hambuch, T.M., Mead, CL. (2015). Implementation of Genome Sequencing Assays. In: Netto, G., Schrijver, I. (eds) Genomic Applications in Pathology. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-0727-4_17

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  • DOI: https://doi.org/10.1007/978-1-4939-0727-4_17

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  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-4939-0726-7

  • Online ISBN: 978-1-4939-0727-4

  • eBook Packages: MedicineMedicine (R0)

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