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


METHODS
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.


RESULTS
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.


CONCLUSION
Robust identification of CNVs by GS is possible within a clinical testing environment.
['Gross|Andrew M|AM|', 'Ajay|Subramanian S|SS|', 'Rajan|Vani|V|', 'Brown|Carolyn|C|', 'Bluske|Krista|K|', 'Burns|Nicole J|NJ|', 'Chawla|Aditi|A|', 'Coffey|Alison J|AJ|', 'Malhotra|Alka|A|', 'Scocchia|Alicia|A|', 'Thorpe|Erin|E|', 'Dzidic|Natasa|N|', 'Hovanes|Karine|K|', 'Sahoo|Trilochan|T|', 'Dolzhenko|Egor|E|', 'Lajoie|Bryan|B|', 'Khouzam|Amirah|A|', 'Chowdhury|Shimul|S|', 'Belmont|John|J|', 'Roller|Eric|E|', 'Ivakhno|Sergii|S|', 'Tanner|Stephen|S|', 'McEachern|Julia|J|', 'Hambuch|Tina|T|', 'Eberle|Michael|M|', 'Hagelstrom|R Tanner|RT|', 'Bentley|David R|DR|', 'Perry|Denise L|DL|', 'Taft|Ryan J|RJ|']
D000293:Adolescent D002648:Child D002675:Child, Preschool D002874:Chromosome Mapping D015331:Cohort Studies D056915:DNA Copy Number Variations D005260:Female D005820:Genetic Testing D015894:Genome, Human D023281:Genomics D006801:Humans D007223:Infant D008297:Male D035583:Rare Diseases D000080842:Undiagnosed Diseases D000073336:Whole Genome Sequencing D055815:Young Adult
rare and undiagnosed disease microarray copy number variation (CNV) structural variation (SV) whole genome sequencing (WGS)