PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions

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MARC

Fältnamn	Indikatorer	Metadata
000		06215naa a2201249 4500
001		oai:lup.lub.lu.se:321a29e2-0c7d-4659-90cc-e5a073131432
003		SwePub
008		220514s2022 \| \|\|\|\|\|\|\|\|\|\|\|000 \|\|eng\|
024	7	a https://lup.lub.lu.se/record/321a29e2-0c7d-4659-90cc-e5a0731314322 URI
024	7	a https://doi.org/10.1016/j.xgen.2022.1001292 DOI
040		a (SwePub)lu
041		a engb eng
042		9 SwePub
072	7	a art2 swepub-publicationtype
072	7	a ref2 swepub-contenttype
100	1	a Olson, Nathan D.u National Institute of Standards and Technology (NIST)4 aut
245	1 0	a PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions
264	1	b Elsevier BV,c 2022
520		a 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.
650	7	a NATURVETENSKAPx Biologix Bioinformatik och systembiologi0 (SwePub)106102 hsv//swe
650	7	a NATURAL SCIENCESx Biological Sciencesx Bioinformatics and Systems Biology0 (SwePub)106102 hsv//eng
650	7	a NATURVETENSKAPx Data- och informationsvetenskapx Bioinformatik0 (SwePub)102032 hsv//swe
650	7	a NATURAL SCIENCESx Computer and Information Sciencesx Bioinformatics0 (SwePub)102032 hsv//eng
650	7	a MEDICIN OCH HÄLSOVETENSKAPx Medicinska och farmaceutiska grundvetenskaperx Medicinsk genetik0 (SwePub)301072 hsv//swe
650	7	a MEDICAL AND HEALTH SCIENCESx Basic Medicinex Medical Genetics0 (SwePub)301072 hsv//eng
653		a DNA
653		a variant
653		a shot-read sequencing
653		a long-read sequencing
653		a benchmark
700	1	a Wagner, Justinu National Institute of Standards and Technology (NIST)4 aut
700	1	a McDaniel, Jenniferu National Institute of Standards and Technology (NIST)4 aut
700	1	a Stephens, Sarah H.u Booz Allen Hamilton, Inc.4 aut
700	1	a Westreich, Samuel T.u DNAnexus4 aut
700	1	a Prasanna, Anish G.u Booz Allen Hamilton, Inc.4 aut
700	1	a Johanson, Elaineu United States Food and Drug Administration4 aut
700	1	a Boja, Emilyu United States Food and Drug Administration4 aut
700	1	a Maier, Ezekiel J.u Booz Allen Hamilton, Inc.4 aut
700	1	a Serang, Omaru DNAnexus4 aut
700	1	a Jáspez, David4 aut
700	1	a Lorenzo-Salazar, José M.4 aut
700	1	a Muñoz-Barrera, Adrián4 aut
700	1	a Rubio-Rodríguez, Luis A.4 aut
700	1	a Flores, Carlos4 aut
700	1	a Kyriakidis, Konstantinos4 aut
700	1	a Malousi, Andigoni4 aut
700	1	a Shafin, Kishwar4 aut
700	1	a Pesout, Trevor4 aut
700	1	a Jain, Miten4 aut
700	1	a Paten, Benedict4 aut
700	1	a Chang, Pi-Chuan4 aut
700	1	a Kolesnikov, Alexey4 aut
700	1	a Nattestad, Maria4 aut
700	1	a Baid, Gunjan4 aut
700	1	a Goel, Sidharth4 aut
700	1	a Yang, Howard4 aut
700	1	a Carroll, Andrew4 aut
700	1	a Eveleigh, Robert4 aut
700	1	a Bourgey, Mathieu4 aut
700	1	a Bourque, Guillaume4 aut
700	1	a Li, Gen4 aut
700	1	a MA, ChouXian4 aut
700	1	a Tang, LinQi4 aut
700	1	a DU, YuanPing4 aut
700	1	a Zhang, ShaoWei4 aut
700	1	a Morata, Jordi4 aut
700	1	a Tonda, Raúl4 aut
700	1	a Parra, Genís4 aut
700	1	a Trotta, Jean-Rémi4 aut
700	1	a Brueffer, Christianu Lund 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 Environments4 aut0 (Swepub:lu)med-csb
700	1	a Demirkaya-Budak, Sinem4 aut
700	1	a Kabakci-Zorlu, Duygu4 aut
700	1	a Turgut, Deniz4 aut
700	1	a Kalay, Özem4 aut
700	1	a Budak, Gungor4 aut
700	1	a Narcı, Kübra4 aut
700	1	a Arslan, Elif4 aut
700	1	a Brown, Richard4 aut
700	1	a Johnson, Ivan J.4 aut
700	1	a Dolgoborodov, Alexey4 aut
700	1	a Semenyuk, Vladimir4 aut
700	1	a Jain, Amit4 aut
700	1	a Tetikol, H. Serhat4 aut
700	1	a Jain, Varun4 aut
700	1	a Ruehle, Mike4 aut
700	1	a Lajoie, Bryan4 aut
700	1	a Roddey, Cooper4 aut
700	1	a Catreux, Severine4 aut
700	1	a Mehio, Rami4 aut
700	1	a Ahsan, Mian Umair4 aut
700	1	a Liu, Qian4 aut
700	1	a Wang, Kai4 aut
700	1	a Sahraeian, Sayed Mohammad Ebrahim4 aut
700	1	a Fang, Li Tai4 aut
700	1	a Mohiyuddin, Marghoob4 aut
700	1	a Hung, Calvin4 aut
700	1	a Jain, Chirag4 aut
700	1	a Feng, Hanying4 aut
700	1	a Li, Zhipan4 aut
700	1	a Chen, Luoqi4 aut
700	1	a Sedlazeck, Fritz J.4 aut
700	1	a Zook, Justin M4 aut
710	2	a National Institute of Standards and Technology (NIST)b Booz Allen Hamilton, Inc.4 org
773	0	t Cell Genomicsd : Elsevier BVg 2:5, s. 1-12q 2:5<1-12x 2666-979X
856	4	u http://dx.doi.org/10.1016/j.xgen.2022.100129x freey FULLTEXT
856	4 8	u https://lup.lub.lu.se/record/321a29e2-0c7d-4659-90cc-e5a073131432
856	4 8	u https://doi.org/10.1016/j.xgen.2022.100129

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By the author/editor: Olson, Nathan D.; Wagner, Justin; McDaniel, Jennif ...; Stephens, Sarah ...; Westreich, Samue ...; Prasanna, Anish ...; show more...; Johanson, Elaine; Boja, Emily; Maier, Ezekiel J ...; Serang, Omar; Jáspez, David; Lorenzo-Salazar, ...; Muñoz-Barrera, A ...; Rubio-Rodríguez, ...; Flores, Carlos; Kyriakidis, Kons ...; Malousi, Andigon ...; Shafin, Kishwar; Pesout, Trevor; Jain, Miten; Paten, Benedict; Chang, Pi-Chuan; Kolesnikov, Alex ...; Nattestad, Maria; Baid, Gunjan; Goel, Sidharth; Yang, Howard; Carroll, Andrew; Eveleigh, Robert; Bourgey, Mathieu; Bourque, Guillau ...; Li, Gen; MA, ChouXian; Tang, LinQi; DU, YuanPing; Zhang, ShaoWei; Morata, Jordi; Tonda, Raúl; Parra, Genís; Trotta, Jean-Rém ...; Brueffer, Christ ...; Demirkaya-Budak, ...; Kabakci-Zorlu, D ...; Turgut, Deniz; Kalay, Özem; Budak, Gungor; Narcı, Kübra; Arslan, Elif; Brown, Richard; Johnson, Ivan J.; Dolgoborodov, Al ...; Semenyuk, Vladim ...; Jain, Amit; Tetikol, H. Serh ...; Jain, Varun; Ruehle, Mike; Lajoie, Bryan; Roddey, Cooper; Catreux, Severin ...; Mehio, Rami; Ahsan, Mian Umai ...; Liu, Qian; Wang, Kai; Sahraeian, Sayed ...; Fang, Li Tai; Mohiyuddin, Marg ...; Hung, Calvin; Jain, Chirag; Feng, Hanying; Li, Zhipan; Chen, Luoqi; Sedlazeck, Fritz ...; Zook, Justin M; show less...

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NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Bioinformatics a ...

NATURAL SCIENCES: NATURAL SCIENCES; and Computer and Inf ...; and Bioinformatics

MEDICAL AND HEALTH SCIENCES: MEDICAL AND HEAL ...; and Basic Medicine; and Medical Genetics

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By the university: Lund University

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