Abstract
PurposeFresh-frozen (FF) tissue is the optimal source of DNA for whole-genome sequencing (WGS) of cancer patients. However, it is not always available, limiting the widespread application of WGS in clinical practice. We explored the viability of using formalin-fixed, paraffin-embedded (FFPE) tissues, available routinely for cancer patients, as a source of DNA for clinical WGS. MethodsWe conducted a prospective study using DNAs from matched FF, FFPE, and peripheral blood germ-line specimens collected from 52 cancer patients (156 samples) following routine diagnostic protocols. We compared somatic variants detected in FFPE and matching FF samples. ResultsWe found the single-nucleotide variant agreement reached 71% across the genome and somatic copy-number alterations (CNAs) detection from FFPE samples was suboptimal (0.44 median correlation with FF) due to nonuniform coverage. CNA detection was improved significantly with lower reverse crosslinking temperature in FFPE DNA extraction (80°C or 65°C depending on the methods). Our final data showed somatic variant detection from FFPE for clinical decision making is possible. We detected 98% of clinically actionable variants (including 30/31 CNAs). ConclusionWe present the first prospective WGS study of cancer patients using FFPE specimens collected in a routine clinical environment proving WGS can be applied in the clinic.
Highlights
With the progress in analytical capability and cost reduction, it is widely accepted that whole-genome sequencing (WGS) presents advantages over targeted platforms.[1,2] WGS, a single test, is valuable for investigating all variant types, including single-nucleotide variants (SNVs), small insertions/ deletions, and structural variants such as copynumber alterations (CNAs)
Previous studies have demonstrated the feasibility of WGS for cancer patients in the clinic[8] but focused on using high-quality nucleic acids extracted from fresh-frozen tissue (FF) specimens collected within a research infrastructure.[9]
We present the largest study to date evaluating WGS data sets obtained from 156 genomes from 52 matched FF tumor, FFPE tumor, and peripheral blood GL samples routinely collected as part of the diagnostic process
Summary
With the progress in analytical capability and cost reduction, it is widely accepted that whole-genome sequencing (WGS) presents advantages over targeted platforms.[1,2] WGS, a single test, is valuable for investigating all variant types, including single-nucleotide variants (SNVs), small insertions/ deletions (indels), and structural variants such as copynumber alterations (CNAs). The conventional multimodality testing currently employed in routine diagnostics can rapidly exhaust the low amount of material available from tumor specimens.[3,4] several targeted sequencing methods allow the detection of all classes of mutations, WGS presents an additional advantage of unbiased sequencing.[5,6,7] The comprehensive nature of WGS removes the need to redesign and validate additional tests. FF specimens are not routinely collected because formalin-fixed, Submitted 19 May 2017; accepted 6 November 2017; advance online publication 1 February 2018. doi:10.1038/gim.2017.241
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