Copy Number Analysis by Low Coverage Whole Genome Sequencing Using Ultra Low-input DNA from Formalin-fixed Paraffin Embedded Tumor Tissue

Overview

Journal Genome Med

Publisher Biomed Central

Specialty Genetics

Date 2016 Nov 17

PMID 27846907

Citations 24

Authors

Tanjina Kader

David L Goode

Stephen Q Wong

Jacquie Connaughton

Simone M Rowley

Lisa Devereux

David Byrne

Stephen B Fox

Gisela Mir Arnau

Richard W Tothill

Ian G Campbell

Kylie L Gorringe

Affiliations

Soon will be listed here.

Abstract

Unlocking clinically translatable genomic information, including copy number alterations (CNA), from formalin-fixed paraffin-embedded (FFPE) tissue is challenging due to low yields and degraded DNA. We describe a robust, cost-effective low-coverage whole genome sequencing (LC WGS) method for CNA detection using 5 ng of FFPE-derived DNA. CN profiles using 100 ng or 5 ng input DNA were highly concordant and comparable with molecular inversion probe (MIP) array profiles. LC WGS improved CN profiles of samples that performed poorly using MIP arrays. Our technique enables identification of driver and prognostic CNAs in archival patient samples previously deemed unsuitable for genomic analysis due to DNA limitations.

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