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  • Chapman, Lesley MNational Cancer Institute, USA (author)

A crowdsourced set of curated structural variants for the human genome

  • Article/chapterEnglish2020

Publisher, publication year, extent ...

  • 2020-06-19
  • Public Library of Science (PLoS),2020

Numbers

  • LIBRIS-ID:oai:lup.lub.lu.se:cdd6cd98-734f-4c7e-a60f-4fb91fe81fca
  • https://lup.lub.lu.se/record/cdd6cd98-734f-4c7e-a60f-4fb91fe81fcaURI
  • https://doi.org/10.1371/journal.pcbi.1007933DOI

Supplementary language notes

  • Language:English
  • Summary in:English

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  • Subject category:art swepub-publicationtype
  • Subject category:ref swepub-contenttype

Notes

  • A high quality benchmark for small variants encompassing 88 to 90% of the reference genome has been developed for seven Genome in a Bottle (GIAB) reference samples. However a reliable benchmark for large indels and structural variants (SVs) is more challenging. In this study, we manually curated 1235 SVs, which can ultimately be used to evaluate SV callers or train machine learning models. We developed a crowdsourcing app - SVCurator - to help GIAB curators manually review large indels and SVs within the human genome, and report their genotype and size accuracy. SVCurator displays images from short, long, and linked read sequencing data from the GIAB Ashkenazi Jewish Trio son [NIST RM 8391/HG002]. We asked curators to assign labels describing SV type (deletion or insertion), size accuracy, and genotype for 1235 putative insertions and deletions sampled from different size bins between 20 and 892,149 bp. 'Expert' curators were 93% concordant with each other, and 37 of the 61 curators had at least 78% concordance with a set of 'expert' curators. The curators were least concordant for complex SVs and SVs that had inaccurate breakpoints or size predictions. After filtering events with low concordance among curators, we produced high confidence labels for 935 events. The SVCurator crowdsourced labels were 94.5% concordant with the heuristic-based draft benchmark SV callset from GIAB. We found that curators can successfully evaluate putative SVs when given evidence from multiple sequencing technologies.

Subject headings and genre

Added entries (persons, corporate bodies, meetings, titles ...)

  • Spies, NoahStanford University (author)
  • Pai, PatrickUniversity of Maryland, Baltimore (author)
  • Lim, Chun ShenUniversity of Otago (author)
  • Carroll, Andrew (author)
  • Narzisi, Giuseppe (author)
  • Watson, Christopher M (author)
  • Proukakis, Christos (author)
  • Clarke, Wayne E (author)
  • Nariai, Naoki (author)
  • Dawson, Eric (author)
  • Jones, Garan (author)
  • Blankenberg, Daniel (author)
  • Brueffer, ChristianLund University,Lunds universitet,Translational Oncogenomics,Forskargrupper vid Lunds universitet,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Transl onkogenomik,Sektion I,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments,Transl oncogenomics,Section I,Department of Clinical Sciences, Lund,Faculty of Medicine(Swepub:lu)med-csb (author)
  • Xiao, Chunlin (author)
  • Kolora, Sree Rohit Raj (author)
  • Alexander, Noah (author)
  • Wolujewicz, Paul (author)
  • Ahmed, Azza E. (author)
  • Smith, Graeme (author)
  • Shehreen, Saadlee (author)
  • Wenger, Aaron M (author)
  • Salit, MarcNational Institute of Standards and Technology (NIST) (author)
  • Zook, Justin MNational Institute of Standards and Technology (NIST) (author)
  • National Cancer Institute, USAStanford University (creator_code:org_t)

Related titles

  • In:PLoS Computational Biology: Public Library of Science (PLoS)16:61553-7358

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