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Hereditary cancers are thought to account for between 5 and 20% of cancers.  Large duplications and deletions are not uncommon in hereditary cancer syndromes, accounting for 2% to 45% of cases depending on the gene tested. Comprehensive laboratory investigation of a patient with a hereditary cancer syndrome requires that duplications and deletions be screened for at exon-level resolution.  Of the various genes implicated in hereditary cancer syndromes, screening of 14 highly-penetrant genes makes up ~90-95% of the genes tested by the Hereditary Cancer Program.  Of these 14 genes, only 4 are currently screened at the BC Cancer Agency for copy number alterations (CNA) using an expensive and laborious technique, with the rest either being sent to external labs at great cost or not tested at all.

The overall goal of the project was to develop and validate an assay that will be able to detect exon level CNA in all 14 genes of interest in order to: (1) increase the diagnostic yield by providing comprehensive cancer genetic screening to all eligible BC patients; (2) shorten the time to diagnosis by 50%; (3) lower the cost per patient by ~56% by avoiding sending out assays to out-of-province labs; and (4) provide proof-of-concept for development of CNA assays for other clinical indications.

Since the CNA assay was successfully developed, the MLPA send-out assays can be eliminated from HCP routine testing. With its development, BC patients eligible for HCP screening will be offered this comprehensive test increasing the diagnostic yield.  The time to diagnosis has been decreased since the CNA assay is run in parallel with the HCP assay resulting in a total turnaround time of 8 weeks.  The cost per patient has also been decreased by eliminating the MLPA send-out tests.