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Gross, Andrew M; Ajay, Subramanian S; Rajan, Vani; Brown, Carolyn; Bluske, Krista; Burns, Nicole J; Chawla, Aditi; Coffey, Alison J; Malhotra, Alka; Scocchia, Alicia; Thorpe, Erin; Dzidic, Natasa; Hovanes, Karine; Sahoo, Trilochan; Dolzhenko, Egor; Lajoie, Bryan; Khouzam, Amirah; Chowdhury, Shimul; Belmont, John; Roller, Eric; Ivakhno, Sergii; Tanner, Stephen; McEachern, Julia; Hambuch, Tina; Eberle, Michael; Hagelstrom, R Tanner; Bentley, David R; Perry, Denise L; Taft, Ryan J
Genetics in medicine, 05/2019, Letnik: 21, Številka: 5Journal Article
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.
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JCR | SNIP | JCR | SNIP | JCR | SNIP | JCR | SNIP |
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Vir: Osebne bibliografije
in: SICRIS
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