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CrowdVariant: a crowdsourcing approach to classify copy number variants

Peyton Greenside
Justin Zook
Marc Salit
Madeleine Cule
Mark DePristo
BioRxiv (2016)


Copy number variants (CNVs) are an important type of genetic variation and play a causal role in many diseases. However, they are also notoriously difficult to identify accurately from next-generation sequencing (NGS) data. For larger CNVs, genotyping arrays provide reasonable benchmark data, but NGS allows us to assay a far larger number of small (< 10kbp) CNVs that are poorly captured by array-based methods. The lack of high quality benchmark callsets of small-scale CNVs has limited our ability to assess and improve CNV calling algorithms for NGS data. To address this issue we developed a crowdsourcing framework, called CrowdVariant, that leverages Google's high-throughput crowdsourcing platform to create a high confidence set of copy number variants for NA24385 (NIST HG002/RM 8391), an Ashkenazim reference sample developed in partnership with the Genome In A Bottle Consortium. In a pilot study we show that crowdsourced classifications, even from non-experts, can be used to accurately assign copy number status to putative CNV calls and thereby identify a high-quality subset of these calls. We then scale our framework genome-wide to identify 1,781 high confidence CNVs, which multiple lines of evidence suggest are a substantial improvement over existing CNV callsets, and are likely to prove useful in benchmarking and improving CNV calling algorithms. Our crowdsourcing methodology may be a useful guide for other genomics applications.

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