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Characterization of Somatically-Acquired Copy Number Alterations in Chronic Lymphocytic Leukaemia Using Shallow Whole Genome Sequencing

  • Helen Parker
  • Louise Carr
  • Sharma Syeda
  • Dean Bryant
  • Jonathan C. StreffordEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1881)

Abstract

Shallow whole genome sequencing (sWGS) is a simple, robust, and cost-effective technique recently optimized for the identification of copy number aberrations (CNAs) in tumor samples. This multiplexed methodology sequences 50 bp from one end of the DNA molecule, generating ˜0.1× coverage, and utilizes the observed sequence depth across the genome to infer copy number. It is amenable to low quantities of input DNA, sequencing costs are modest, processing is compatible with low-output instruments, and downstream analysis is simplified by the use of freely available bioinformatics tools and a data analysis package written especially for the analysis of sWGS data. It is the aim of this chapter to introduce the fundamental concepts of sWGS and to provide an overview of the steps involved in a successful sWGS experiment.

Key words

Copy number alterations Chromosomal imbalances Shallow whole genome sequencing Next-generation sequencing Bioinformatics QDNAseq 

Notes

Acknowledgments

H.P., L.C., S.S., D.B., and J.C.S. wrote and reviewed the manuscript. This work was funded by Bloodwise (11052, 12036), the Kay Kendall Leukaemia Fund (873) and Cancer Research UK (C34999/A18087, ECMC C24563/A15581).

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Helen Parker
    • 1
  • Louise Carr
    • 1
  • Sharma Syeda
    • 1
  • Dean Bryant
    • 1
  • Jonathan C. Strefford
    • 1
    • 2
    Email author
  1. 1.Cancer Genomics, Academic Unit of Cancer Sciences, Faculty of MedicineUniversity of SouthamptonSouthamptonUK
  2. 2.Southampton General HospitalSouthamptonUK

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