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BIRS Workshop Lecture Videos

Detection of de novo copy number deletions from targeted sequencing of trios Ruczinski, Ingo


De novo copy number deletions have been implicated in many diseases, but no formal methods existed that identify de novo deletions in parent-offspring trios from capture-based sequencing platforms. We developed Minimum Distance for Targeted Sequencing (MDTS) to fill this void. MDTS has similar sensitivity (recall), but a much lower false positive rate compared to less specific CNV callers, resulting in a much higher positive predictive value (precision). MDTS also exhibited much better scalability. We applied our method to 1,305 case-parent trios with targeted sequencing data of regions previously implicated in oral cleft. Across the 6.3Mb of capture, we detected one de novo deletion in gene TRAF3IP3, in addition to one rare inherited deletion and 2 copy number polymorphic regions.

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