Finding possible missed variant candidates through coverage comparison among varying sequencing technologies

Authors

• HB Fauni
• CJ Adams
• K Chao
• T Ten
• C Lau
• B Pusey
• D Adams
• W Gahl

Abstract

The NIH Undiagnosed Diseases Program (UDP) was started in 2008 with the goals of making diagnoses and conducting research for individuals with serious medical illnesses remaining undiagnosed despite extensive evaluation. Next-generation sequencing, both exome and genome, have been important tools for a subset of these families. Since the start of the UDP, more than 700 families have been studied with these techniques. Less than 10% of cases yield a clear diagnosis, a success rate that is expected given the extensive prior evaluations of study participants. Exome sequencing has evolved substantially from the time it was first employed for clinical diagnostics. Adequate coverage rates for genes known to be associated with human disease have improved from 80-85% to over 95%. We posited that exome coverage has improved during the last 5 years in the UDP. We sought to quantify the number of exonic base positions that remained unevaluated due to poor coverage in older UDP cases compared with the current cases. Such positions represent a potential pool of sources for new diagnoses in older UDP cases. We calculated the exome coverage of individuals that were sequenced using different exome capture kits. We evaluated coverage in 30,522 hg19 UCSC transcripts and stratified the number of transcripts into three categories: no coverage, 0

Scientific Focus Area: Computational Biology

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