Characterization of somatically-acquired copy number alterations in chronic lymphocytic leukaemia using shallow whole genome sequencing

Strefford, Jonathan, Parker, Helen and Bryant, Dean (2019) Characterization of somatically-acquired copy number alterations in chronic lymphocytic leukaemia using shallow whole genome sequencing. In, Malek, Sami (ed.) Chronic Lymphocytic Leukemia. (Methods in Molecular Biology, 1881) New York, NY. Humana Press, pp. 327-353. (doi:10.1007/978-1-4939-8876-1_23).

Record type: Book Section

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.

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