Search: id:"swepub:oai:lup.lub.lu.se:cdd6cd98-734f-4c7e-a60f-4fb91fe81fca" >
A crowdsourced set ...
A crowdsourced set of curated structural variants for the human genome
-
- Chapman, Lesley M (author)
- National Cancer Institute, USA
-
- Spies, Noah (author)
- Stanford University
-
- Pai, Patrick (author)
- University of Maryland, Baltimore
-
show more...
-
- Lim, Chun Shen (author)
- University of Otago
-
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, Christian (author)
- Lund 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
-
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, Marc (author)
- National Institute of Standards and Technology (NIST)
-
- Zook, Justin M (author)
- National Institute of Standards and Technology (NIST)
-
show less...
-
(creator_code:org_t)
- 2020-06-19
- 2020
- English.
-
In: PLoS Computational Biology. - : Public Library of Science (PLoS). - 1553-7358. ; 16:6
- Related links:
-
http://dx.doi.org/10... (free)
-
show more...
-
https://journals.plo...
-
https://lup.lub.lu.s...
-
https://doi.org/10.1...
-
show less...
Abstract
Subject headings
Close
- 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
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
Keyword
- Bioinformatics
- Computational Biology
- Structural variants
- Benchmark
- crowd sourcing
Publication and Content Type
- art (subject category)
- ref (subject category)
Find in a library
To the university's database
- By the author/editor
-
Chapman, Lesley ...
-
Spies, Noah
-
Pai, Patrick
-
Lim, Chun Shen
-
Carroll, Andrew
-
Narzisi, Giusepp ...
-
show more...
-
Watson, Christop ...
-
Proukakis, Chris ...
-
Clarke, Wayne E
-
Nariai, Naoki
-
Dawson, Eric
-
Jones, Garan
-
Blankenberg, Dan ...
-
Brueffer, Christ ...
-
Xiao, Chunlin
-
Kolora, Sree Roh ...
-
Alexander, Noah
-
Wolujewicz, Paul
-
Ahmed, Azza E.
-
Smith, Graeme
-
Shehreen, Saadle ...
-
Wenger, Aaron M
-
Salit, Marc
-
Zook, Justin M
-
show less...
- About the subject
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Biological Scien ...
-
and Bioinformatics a ...
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Computer and Inf ...
-
and Bioinformatics
-
- NATURAL SCIENCES
-
NATURAL SCIENCES
-
and Biological Scien ...
-
and Genetics
- Articles in the publication
-
PLoS Computation ...
- By the university
-
Lund University