Abstract：
:Standardized benchmarking approaches are required to assess the accuracy of variants called from sequence data. Although variant-calling tools and the metrics used to assess their performance continue to improve, important challenges remain. Here, as part of the Global Alliance for Genomics and Health (GA4GH), we present a benchmarking framework for variant calling. We provide guidance on how to match variant calls with different representations, define standard performance metrics, and stratify performance by variant type and genome context. We describe limitations of high-confidence calls and regions that can be used as truth sets (for example, single-nucleotide variant concordance of two methods is 99.7% inside versus 76.5% outside high-confidence regions). Our web-based app enables comparison of variant calls against truth sets to obtain a standardized performance report. Our approach has been piloted in the PrecisionFDA variant-calling challenges to identify the best-in-class variant-calling methods within high-confidence regions. Finally, we recommend a set of best practices for using our tools and evaluating the results.
journal_name
Nat Biotechnoljournal_title
Nature biotechnologyauthors
Krusche P,Trigg L,Boutros PC,Mason CE,De La Vega FM,Moore BL,Gonzalez-Porta M,Eberle MA,Tezak Z,Lababidi S,Truty R,Asimenos G,Funke B,Fleharty M,Chapman BA,Salit M,Zook JM,Global Alliance for Genomics and Health Benchmadoi
10.1038/s41587-019-0054-xsubject
Has Abstractpub_date
2019-05-01 00:00:00pages
555-560issue
5eissn
1087-0156issn
1546-1696pii
10.1038/s41587-019-0054-xjournal_volume
37pub_type
杂志文章abstract：:Evolution of eukaryotes is mediated by sexual recombination of parental genomes. Crossovers occur in random, but homologous, positions at a frequency that depends on DNA length. As exons occupy only 1% of the human genome and introns about 24%, by far most of the crossovers occur between exons, rather than inside. The...
journal_title：Nature biotechnology
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abstract：:We have evaluated inhibition of the plasmid-born chloramphenicol acetyl transferase gene (CAT) by the hammerhead ribozyme and antisense RNA in Escherichia coli where the translation and transcription rates have been modified. Whereas neither antisense nor the hammerhead had an inhibitory effect on CAT activity in wild...
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abstract：:Field tests of corn co-expressing two new delta-endotoxins from Bacillus thuringiensis (Bt) have demonstrated protection from root damage by western corn rootworm (Diabrotica virgifera virgifera LeConte). The level of protection exceeds that provided by chemical insecticides. In the bacterium, these proteins form crys...
journal_title：Nature biotechnology
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abstract：:The recently decided eBay and MedImmune cases interject both reassurance and uncertainty into the present patent licensing landscape, affecting the strategic decisions to be considered during negotiations. ...
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pub_type： 杂志文章
doi：10.1038/nbt965
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更新日期：2017-07-01 00:00:00
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pub_type： 杂志文章,评审
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更新日期：2012-11-01 00:00:00
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