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

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Fältnamn	Indikatorer	Metadata
000		06207nam a2201249 4500
001		oai:lup.lub.lu.se:5798e0a5-a5ee-4d5f-87ed-c78692ff514c
003		SwePub
008		201212s2020 \| \|\|\|\|\|\|\|\|\|\|\|000 \|\|eng\|
024	7	a https://lup.lub.lu.se/record/5798e0a5-a5ee-4d5f-87ed-c78692ff514c2 URI
024	7	a https://doi.org/10.1101/2020.11.13.3807412 DOI
040		a (SwePub)lu
041		a engb eng
042		9 SwePub
072	7	a ovr2 swepub-publicationtype
072	7	a vet2 swepub-contenttype
100	1	a Olson, Nathan D.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 Cold Spring Harbor Laboratory,c 2020
520		a The precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and the Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20 challenge participants applied their variant calling pipelines and submitted 64 variant callsets for one or more sequencing technologies (~35X Illumina, ~35X PacBio HiFi, and ~50X Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with the new GIAB benchmark sets and genome stratifications. Challenge submissions included a number of innovative methods for all three technologies, with graph-based and machine-learning methods scoring best for short-read and long-read datasets, respectively. New methods out-performed the 2016 Truth Challenge winners, and new 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 short-read sequencing
653		a long-read sequencing
653		a benchmark
700	1	a Wagner, Justin4 aut
700	1	a McDaniel, Jennifer4 aut
700	1	a Stephens, Sarah H.4 aut
700	1	a Westreich, Samuel T.4 aut
700	1	a Prasanna, Anish G.4 aut
700	1	a Johanson, Elaine4 aut
700	1	a Maier, Ezekiel J.4 aut
700	1	a Boja, Emily4 aut
700	1	a Serang, Omar4 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,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 Medicine4 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 Translational Oncogenomicsb Forskargrupper vid Lunds universitet4 org
856	4	u http://dx.doi.org/10.1101/2020.11.13.380741x freey FULLTEXT
856	4	u https://www.biorxiv.org/content/biorxiv/early/2021/02/03/2020.11.13.380741.full.pdf
856	4 8	u https://lup.lub.lu.se/record/5798e0a5-a5ee-4d5f-87ed-c78692ff514c
856	4 8	u https://doi.org/10.1101/2020.11.13.380741

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Av författaren/redakt...: Olson, Nathan D.; Wagner, Justin; McDaniel, Jennif ...; Stephens, Sarah ...; Westreich, Samue ...; Prasanna, Anish ...; visa fler...; Johanson, Elaine; Maier, Ezekiel J ...; Boja, Emily; 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; visa färre...

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