Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue

T Kader; DL Goode; SQ Wong; J Connaughton; SM Rowley; L Devereux; D Byrne; SB Fox; G Mir Arnau; RW Tothill; IG Campbell; KL Gorringe

Journal article

Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue

T Kader, DL Goode, SQ Wong, J Connaughton, SM Rowley, L Devereux, D Byrne, SB Fox, G Mir Arnau, RW Tothill, IG Campbell, KL Gorringe

Genome Medicine | BMC | Published : 2016

DOI: 10.1186/s13073-016-0375-z

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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 5ng of FFPE-derived DNA. CN profiles using 100ng or 5ng 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..

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University of Melbourne Researchers

David Goode Author

Lisa Devereux Author

Richard Tothill Author

Kylie Gorringe Author

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Grants

Awarded by National Health and Medical Research Council

Funding Acknowledgements

This study was funded by the Australian National Health and Medical Research Council (NHMRC APP1063092), the National Breast Cancer Foundation, and Peter MacCallum Cancer Foundation (1448). TK was supported by Melbourne International Research Scholarship and Melbourne International Fee Remission Scholarship and DLG was supported by a NHMRC Early Career Fellowship (APP1052904).