April 21, 2020  |  

Copy-number variants in clinical genome sequencing: deployment and interpretation for rare and undiagnosed disease.

Authors: Gross, Andrew M and Ajay, Subramanian S and Rajan, Vani and Brown, Carolyn and Bluske, Krista and Burns, Nicole J and Chawla, Aditi and Coffey, Alison J and Malhotra, Alka and Scocchia, Alicia and Thorpe, Erin and Dzidic, Natasa and Hovanes, Karine and Sahoo, Trilochan and Dolzhenko, Egor and Lajoie, Bryan and Khouzam, Amirah and Chowdhury, Shimul and Belmont, John and Roller, Eric and Ivakhno, Sergii and Tanner, Stephen and McEachern, Julia and Hambuch, Tina and Eberle, Michael and Hagelstrom, R Tanner and Bentley, David R and Perry, Denise L and Taft, Ryan J

Current diagnostic testing for genetic disorders involves serial use of specialized assays spanning multiple technologies. In principle, genome sequencing (GS) can detect all genomic pathogenic variant types on a single platform. Here we evaluate copy-number variant (CNV) calling as part of a clinically accredited GS test.We performed analytical validation of CNV calling on 17 reference samples, compared the sensitivity of GS-based variants with those from a clinical microarray, and set a bound on precision using orthogonal technologies. We developed a protocol for family-based analysis of GS-based CNV calls, and deployed this across a clinical cohort of 79 rare and undiagnosed cases.We found that CNV calls from GS are at least as sensitive as those from microarrays, while only creating a modest increase in the number of variants interpreted (~10 CNVs per case). We identified clinically significant CNVs in 15% of the first 79 cases analyzed, all of which were confirmed by an orthogonal approach. The pipeline also enabled discovery of a uniparental disomy (UPD) and a 50% mosaic trisomy 14. Directed analysis of select CNVs enabled breakpoint level resolution of genomic rearrangements and phasing of de novo CNVs.Robust identification of CNVs by GS is possible within a clinical testing environment.

Journal: Genetics in medicine
DOI: 10.1038/s41436-018-0295-y
Year: 2019

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