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

Unlocking the vast volume of clinically translatable genomic information captured in formalin-fixed-paraffin-embedded (FFPE) archival cancer tissues in diagnostic pathology laboratories is a critical bottleneck for the development of novel cancer diagnostics and therapeutics. The intrinsic molecular phenotype of cancers is generally reflected in the type and number of copy number alterations (CNAs), but detecting CNAs is highly challenging from FFPE archival tumour tissue due to low DNA yields and degraded DNA. We describe a robust, cost effective low-coverage whole genome sequencing (LC WGS) method for CNA detection, using as little as 5 ng of FFPE-derived DNA. We show CN profiles obtained using 100 ng or 5 ng of input DNA are highly concordant. Low input LC WGS produced copy number profiles with accuracy and sensitivity comparable with those obtained from the current gold standard method, molecular inversion probe (MIP) arrays, while requiring 10 fold less input DNA. Importantly, LC WGS from low input DNA greatly improved the CN profile of a sample that performed poorly using MIP arrays. Our technique opens the possibility of identifying driver and prognostic CNAs in large cohorts of archival patient samples previously deemed unsuitable for genomic analysis due to insufficient and degraded DNA.