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Exploring the feasibility and utility of exome‐scale tumour sequencing in a clinical setting
Author(s) -
Lee Belinda,
Tran Ben,
Hsu Arthur L.,
Taylor Graham R.,
Fox Stephen B.,
Fellowes Andrew,
Marquis Renata,
Mooi Jennifer,
Desai Jayesh,
Doig Ken,
Ekert Paul,
Gaff Clara,
Herath Dishan,
Hamilton Anne,
James Paul,
Roberts Andrew,
Snyder Ray,
Waring Paul,
McArthur Grant
Publication year - 2018
Publication title -
internal medicine journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.596
H-Index - 70
eISSN - 1445-5994
pISSN - 1444-0903
DOI - 10.1111/imj.13806
Subject(s) - medicine , exome sequencing , germline , druggability , precision medicine , exome , dna sequencing , germline mutation , cancer , oncology , computational biology , bioinformatics , genetics , gene , mutation , pathology , biology
Abstract Background Technology has progressed from single gene panel to large‐scale genomic sequencing. This is raising expectations from clinicians and patients alike. The utility and performance of this technology in a clinical setting needs to be evaluated. Aim This pilot study investigated the feasibility of using exome‐scale sequencing (ESS) to identify molecular drivers within cancers in real‐time for Precision Oncology in the clinic. Methods Between March 2014 and March 2015, the Victorian Comprehensive Cancer Centre Alliance explored the feasibility and utility of ESS in a pilot study. DNA extracted from the tumour specimens underwent both ESS and targeted ‘hotspot’ sequencing (TS). Blood was taken for germline analysis. A multi‐disciplinary molecular tumour board determined the clinical relevance of identified mutations; in particular, whether they were ‘actionable’ and/or ‘druggable’. Results Of 23 patients screened, 15 (65%) met the tissue requirements for genomic analysis. TS and ESS were successful in all cases. ESS identified pathogenic somatic variants in 73% (11/15 cases) versus 53% (8/15 cases) using TS. Clinically focused ESS identified 63 variants, consisting of 30 somatic variants (including all 13 identified by TS) and 33 germline variants. Overall, there were 48 unique variants. ESS had a clinical impact in 53% (8/15 cases); 47% (7/15 cases) were referred to the familial cancer clinic, and ‘druggable’ targets were identified in 53% (8/15 cases). Conclusion ESS of tumour DNA impacted clinical decision‐making in 53%, with 20% more pathogenic variants identified through ESS than TS. The identification of germline variants in 47% was an unexpected finding.