Journal article

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

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

GENOME MEDICINE | BMC | Published : 2016


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..

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Awarded by Australian National Health and Medical Research Council (NHMRC)

Awarded by Peter MacCallum Cancer Foundation

Awarded by NHMRC Early Career Fellowship

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).