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A robust benchmark for detection of germline large deletions and insertions.

ABSTRACT: New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine research and clinical practice, we developed a sequence-resolved benchmark set for identification of both false-negative and false-positive germline large insertions and deletions. To create this benchmark for a broadly consented son in a Personal Genome Project trio with broadly available cells and DNA, the Genome in a Bottle Consortium integrated 19 sequence-resolved variant calling methods from diverse technologies. The final benchmark set contains 12,745 isolated, sequence-resolved insertion (7,281) and deletion (5,464) calls ≥50 base pairs (bp). The Tier 1 benchmark regions, for which any extra calls are putative false positives, cover 2.51 Gbp and 5,262 insertions and 4,095 deletions supported by ≥1 diploid assembly. We demonstrate that the benchmark set reliably identifies false negatives and false positives in high-quality SV callsets from short-, linked- and long-read sequencing and optical mapping.

SUBMITTER: Zook JM 

PROVIDER: S-EPMC8454654 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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A robust benchmark for detection of germline large deletions and insertions.

Zook Justin M JM   Hansen Nancy F NF   Olson Nathan D ND   Chapman Lesley L   Mullikin James C JC   Xiao Chunlin C   Sherry Stephen S   Koren Sergey S   Phillippy Adam M AM   Boutros Paul C PC   Sahraeian Sayed Mohammad E SME   Huang Vincent V   Rouette Alexandre A   Alexander Noah N   Mason Christopher E CE   Hajirasouliha Iman I   Ricketts Camir C   Lee Joyce J   Tearle Rick R   Fiddes Ian T IT   Barrio Alvaro Martinez AM   Wala Jeremiah J   Carroll Andrew A   Ghaffari Noushin N   Rodriguez Oscar L OL   Bashir Ali A   Jackman Shaun S   Farrell John J JJ   Wenger Aaron M AM   Alkan Can C   Soylev Arda A   Schatz Michael C MC   Garg Shilpa S   Church George G   Church George G   Marschall Tobias T   Chen Ken K   Fan Xian X   English Adam C AC   Rosenfeld Jeffrey A JA   Zhou Weichen W   Mills Ryan E RE   Sage Jay M JM   Davis Jennifer R JR   Kaiser Michael D MD   Oliver John S JS   Catalano Anthony P AP   Chaisson Mark J P MJP   Spies Noah N   Sedlazeck Fritz J FJ   Salit Marc M  

Nature biotechnology 20200615 11

New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine research and clinical practice, we developed a sequence-resolved benchmark set for identification of both false-negative and false-positive germline large insertions and deletions. To create this benchmark for a broadly consented son in a Personal Genome Project trio with broadly available c  ...[more]

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