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PrecisionFDA Truth ...
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Olson, Nathan D.National Institute of Standards and Technology (NIST)
(author)
PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions
- Article/chapterEnglish2022
Publisher, publication year, extent ...
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LIBRIS-ID:oai:lup.lub.lu.se:321a29e2-0c7d-4659-90cc-e5a073131432
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https://lup.lub.lu.se/record/321a29e2-0c7d-4659-90cc-e5a073131432URI
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https://doi.org/10.1016/j.xgen.2022.100129DOI
Supplementary language notes
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Language:English
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Summary in:English
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Subject category:art swepub-publicationtype
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Subject category:ref swepub-contenttype
Notes
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The precisionFDA Truth Challenge V2 aimed to assess the state of the art of variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied their variant-calling pipelines and submitted 64 variant call sets for one or more sequencing technologies (Illumina, PacBio HiFi, and Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with updated Genome in a Bottle benchmark sets and genome stratifications. Challenge submissions included numerous innovative methods, with graph-based and machine learning methods scoring best for short-read and long-read datasets, respectively. With machine learning approaches, combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.
Subject headings and genre
Added entries (persons, corporate bodies, meetings, titles ...)
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Wagner, JustinNational Institute of Standards and Technology (NIST)
(author)
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McDaniel, JenniferNational Institute of Standards and Technology (NIST)
(author)
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Stephens, Sarah H.Booz Allen Hamilton, Inc.
(author)
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Westreich, Samuel T.DNAnexus
(author)
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Prasanna, Anish G.Booz Allen Hamilton, Inc.
(author)
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Johanson, ElaineUnited States Food and Drug Administration
(author)
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Boja, EmilyUnited States Food and Drug Administration
(author)
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Maier, Ezekiel J.Booz Allen Hamilton, Inc.
(author)
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Serang, OmarDNAnexus
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Jáspez, David
(author)
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Lorenzo-Salazar, José M.
(author)
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Muñoz-Barrera, Adrián
(author)
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Rubio-Rodríguez, Luis A.
(author)
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Flores, Carlos
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Kyriakidis, Konstantinos
(author)
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Malousi, Andigoni
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Shafin, Kishwar
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Pesout, Trevor
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Jain, Miten
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Paten, Benedict
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Chang, Pi-Chuan
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Kolesnikov, Alexey
(author)
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Nattestad, Maria
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Baid, Gunjan
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Goel, Sidharth
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Yang, Howard
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Carroll, Andrew
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Eveleigh, Robert
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Bourgey, Mathieu
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Bourque, Guillaume
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Li, Gen
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MA, ChouXian
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Tang, LinQi
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DU, YuanPing
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Zhang, ShaoWei
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Morata, Jordi
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Tonda, Raúl
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Parra, Genís
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Trotta, Jean-Rémi
(author)
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Brueffer, ChristianLund University,Lunds universitet,Translational Oncogenomics,Forskargrupper vid Lunds universitet,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments(Swepub:lu)med-csb
(author)
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Demirkaya-Budak, Sinem
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Kabakci-Zorlu, Duygu
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Turgut, Deniz
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Kalay, Özem
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Budak, Gungor
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Narcı, Kübra
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Arslan, Elif
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Brown, Richard
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Johnson, Ivan J.
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Dolgoborodov, Alexey
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Semenyuk, Vladimir
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Jain, Amit
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Tetikol, H. Serhat
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Jain, Varun
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Ruehle, Mike
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Lajoie, Bryan
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Roddey, Cooper
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Catreux, Severine
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Mehio, Rami
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Ahsan, Mian Umair
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Liu, Qian
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Wang, Kai
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Sahraeian, Sayed Mohammad Ebrahim
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Fang, Li Tai
(author)
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Mohiyuddin, Marghoob
(author)
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Hung, Calvin
(author)
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Jain, Chirag
(author)
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Feng, Hanying
(author)
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Li, Zhipan
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Chen, Luoqi
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Sedlazeck, Fritz J.
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Zook, Justin M
(author)
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National Institute of Standards and Technology (NIST)Booz Allen Hamilton, Inc.
(creator_code:org_t)
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In:Cell Genomics: Elsevier BV2:5, s. 1-122666-979X
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Olson, Nathan D.
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Wagner, Justin
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McDaniel, Jennif ...
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Stephens, Sarah ...
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Westreich, Samue ...
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Prasanna, Anish ...
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show more...
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Johanson, Elaine
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Boja, Emily
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Maier, Ezekiel J ...
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Serang, Omar
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Jáspez, David
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Lorenzo-Salazar, ...
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Muñoz-Barrera, A ...
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Rubio-Rodríguez, ...
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Flores, Carlos
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Kyriakidis, Kons ...
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Malousi, Andigon ...
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Shafin, Kishwar
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Pesout, Trevor
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Jain, Miten
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Paten, Benedict
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Chang, Pi-Chuan
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Kolesnikov, Alex ...
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Nattestad, Maria
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Baid, Gunjan
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Goel, Sidharth
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Yang, Howard
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Carroll, Andrew
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Eveleigh, Robert
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Bourgey, Mathieu
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Bourque, Guillau ...
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Li, Gen
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MA, ChouXian
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Tang, LinQi
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DU, YuanPing
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Zhang, ShaoWei
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Morata, Jordi
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Tonda, Raúl
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Parra, Genís
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Trotta, Jean-Rém ...
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Brueffer, Christ ...
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Demirkaya-Budak, ...
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Kabakci-Zorlu, D ...
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Turgut, Deniz
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Kalay, Özem
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Budak, Gungor
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Narcı, Kübra
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Arslan, Elif
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Brown, Richard
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Johnson, Ivan J.
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Dolgoborodov, Al ...
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Semenyuk, Vladim ...
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Jain, Amit
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Lajoie, Bryan
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Roddey, Cooper
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Catreux, Severin ...
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Mehio, Rami
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Ahsan, Mian Umai ...
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Liu, Qian
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Wang, Kai
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Sahraeian, Sayed ...
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Fang, Li Tai
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Mohiyuddin, Marg ...
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Cell Genomics
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Lund University