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SVCurator: A Crowds...
SVCurator: A Crowdsourcing app to visualize evidence of structural variants for the human genome
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- Chapman, Lesley M (author)
- National Institute of Standards and Technology (NIST)
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- Spies, Noah (author)
- National Institute of Standards and Technology (NIST)
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- Pai, Patrick (author)
- University of Maryland
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- Lim, Chun Shen (author)
- University of Otago
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Carroll, Andrew (author)
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Narzisi, Giuseppe (author)
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- Watson, Christopher M (author)
- St James's University Hospital
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- Proukakis, Christos (author)
- University College London
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Clarke, Wayne E (author)
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Nariai, Naoki (author)
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- Dawson, Eric (author)
- National Cancer Institute, NCI
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Jones, Garan (author)
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Blankenberg, Daniel (author)
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- Brueffer, Christian (author)
- Lund University,Lunds universitet,Bröstcancer-genetik,Sektion I,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,Translational Oncogenomics,Forskargrupper vid Lunds universitet,Breastcancer-genetics,Section I,Department of Clinical Sciences, Lund,Faculty of Medicine,Lund University Research Groups
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- Xiao, Chunlin (author)
- National Institutes of Health, United States
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Kolora, Sree Rohit Raj (author)
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Alexander, Noah (author)
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Wolujewicz, Paul (author)
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Ahmed, Azza E. (author)
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Smith, Graeme (author)
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Shehreen, Saadlee (author)
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Wenger, Aaron M (author)
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Salit, Marc (author)
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- Zook, Justin M (author)
- National Institute of Standards and Technology (NIST)
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(creator_code:org_t)
- Cold Spring Harbor Laboratory, 2019
- English 35 s.
- Related links:
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http://dx.doi.org/10... (free)
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https://journals.plo...
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https://doi.org/10.1...
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Abstract
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- 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 yet to be defined. In this study, we manually curated 1235 SVs which can ultimately be used to evaluate SV callers ortrain machine learning models. We developed a crowdsourcing app - SVCurator - to help curators manually review large indels and SVs within the human genome, and report their genotype and size accuracy.SVCurator is a Python Flask-based web platform that 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. The crowdsourced results were highly concordant with 37 out ofthe 61 curators having at least 78% concordance with a set of ‘expert’ curators, where there was 93% concordance amongst ‘expert’ curators. This produced high confidence labels for 935 events. When compared to the heuristic-based draft benchmark SV callset from GIAB, the SVCurator crowdsourced labels were 94.5% concordant with the benchmark set. We found that curators can successfully evaluate putative SVs when given evidence from multiple sequencing technologies.
Subject headings
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
Keyword
- Bioinformatics
- Genomics
- Structural variants
- Benchmark datasets
Publication and Content Type
- ovr (subject category)
- vet (subject category)
To the university's database
- By the author/editor
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Chapman, Lesley ...
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Spies, Noah
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Pai, Patrick
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Lim, Chun Shen
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Carroll, Andrew
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Narzisi, Giusepp ...
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show more...
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Watson, Christop ...
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Proukakis, Chris ...
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Clarke, Wayne E
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Nariai, Naoki
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Dawson, Eric
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Jones, Garan
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Blankenberg, Dan ...
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Brueffer, Christ ...
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Xiao, Chunlin
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Kolora, Sree Roh ...
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Alexander, Noah
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Wolujewicz, Paul
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Ahmed, Azza E.
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Smith, Graeme
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Shehreen, Saadle ...
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Wenger, Aaron M
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Salit, Marc
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Zook, Justin M
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show less...
- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Computer and Inf ...
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and Bioinformatics
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Bioinformatics a ...
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Medical Genetics
- By the university
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Lund University