A robust benchmark for detection of germline large deletions and insertions
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A robust benchmark for detection of germline large deletions and insertions. / Zook, Justin M.; Hansen, Nancy F.; Olson, Nathan D.; Chapman, Lesley; Mullikin, James C.; Xiao, Chunlin; Sherry, Stephen; Koren, Sergey; Phillippy, Adam M.; Boutros, Paul C.; Sahraeian, Sayed Mohammad E.; Huang, Vincent; Rouette, Alexandre; Alexander, Noah; Mason, Christopher E.; Hajirasouliha, Iman; Ricketts, Camir; Lee, Joyce; Tearle, Rick; Fiddes, Ian T.; Barrio, Alvaro Martinez; Wala, Jeremiah; Carroll, Andrew; Ghaffari, Noushin; Rodriguez, Oscar L.; Bashir, Ali; Jackman, Shaun; Farrell, John J.; Wenger, Aaron M.; Alkan, Can; Soylev, Arda; Schatz, Michael C.; Garg, Shilpa; Church, George; Marschall, Tobias; Chen, Ken; Fan, Xian; English, Adam C.; Rosenfeld, Jeffrey A.; Zhou, Weichen; Mills, Ryan E.; Sage, Jay M.; Davis, Jennifer R.; Kaiser, Michael D.; Oliver, John S.; Catalano, Anthony P.; Chaisson, Mark J. P.; Spies, Noah; Sedlazeck, Fritz J.; Salit, Marc.
In: Nature Biotechnology, Vol. 38, No. 11, 11.2020, p. 1347-+.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - A robust benchmark for detection of germline large deletions and insertions
AU - Zook, Justin M.
AU - Hansen, Nancy F.
AU - Olson, Nathan D.
AU - Chapman, Lesley
AU - Mullikin, James C.
AU - Xiao, Chunlin
AU - Sherry, Stephen
AU - Koren, Sergey
AU - Phillippy, Adam M.
AU - Boutros, Paul C.
AU - Sahraeian, Sayed Mohammad E.
AU - Huang, Vincent
AU - Rouette, Alexandre
AU - Alexander, Noah
AU - Mason, Christopher E.
AU - Hajirasouliha, Iman
AU - Ricketts, Camir
AU - Lee, Joyce
AU - Tearle, Rick
AU - Fiddes, Ian T.
AU - Barrio, Alvaro Martinez
AU - Wala, Jeremiah
AU - Carroll, Andrew
AU - Ghaffari, Noushin
AU - Rodriguez, Oscar L.
AU - Bashir, Ali
AU - Jackman, Shaun
AU - Farrell, John J.
AU - Wenger, Aaron M.
AU - Alkan, Can
AU - Soylev, Arda
AU - Schatz, Michael C.
AU - Garg, Shilpa
AU - Church, George
AU - Marschall, Tobias
AU - Chen, Ken
AU - Fan, Xian
AU - English, Adam C.
AU - Rosenfeld, Jeffrey A.
AU - Zhou, Weichen
AU - Mills, Ryan E.
AU - Sage, Jay M.
AU - Davis, Jennifer R.
AU - Kaiser, Michael D.
AU - Oliver, John S.
AU - Catalano, Anthony P.
AU - Chaisson, Mark J. P.
AU - Spies, Noah
AU - Sedlazeck, Fritz J.
AU - Salit, Marc
PY - 2020/11
Y1 - 2020/11
N2 - Detection of structural variants in the human genome is facilitated by a benchmark set of large deletions and insertions.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.
AB - Detection of structural variants in the human genome is facilitated by a benchmark set of large deletions and insertions.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.
KW - STRUCTURAL VARIATION
KW - HUMAN GENOME
KW - VARIANTS
KW - RESOURCE
KW - SNP
U2 - 10.1038/s41587-020-0538-8
DO - 10.1038/s41587-020-0538-8
M3 - Journal article
C2 - 32541955
VL - 38
SP - 1347-+
JO - Nature Biotechnology
JF - Nature Biotechnology
SN - 1087-0156
IS - 11
ER -
ID: 257032178