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

Olson, Nathan D. (author)
National Institute of Standards and Technology (NIST)
Wagner, Justin (author)
National Institute of Standards and Technology (NIST)
McDaniel, Jennifer (author)
National Institute of Standards and Technology (NIST)
show more...
Stephens, Sarah H. (author)
Booz Allen Hamilton, Inc.
Westreich, Samuel T. (author)
DNAnexus
Prasanna, Anish G. (author)
Booz Allen Hamilton, Inc.
Johanson, Elaine (author)
United States Food and Drug Administration
Boja, Emily (author)
United States Food and Drug Administration
Maier, Ezekiel J. (author)
Booz Allen Hamilton, Inc.
Serang, Omar (author)
DNAnexus
Jáspez, David (author)
Lorenzo-Salazar, José M. (author)
Muñoz-Barrera, Adrián (author)
Rubio-Rodríguez, Luis A. (author)
Flores, Carlos (author)
Kyriakidis, Konstantinos (author)
Malousi, Andigoni (author)
Shafin, Kishwar (author)
Pesout, Trevor (author)
Jain, Miten (author)
Paten, Benedict (author)
Chang, Pi-Chuan (author)
Kolesnikov, Alexey (author)
Nattestad, Maria (author)
Baid, Gunjan (author)
Goel, Sidharth (author)
Yang, Howard (author)
Carroll, Andrew (author)
Eveleigh, Robert (author)
Bourgey, Mathieu (author)
Bourque, Guillaume (author)
Li, Gen (author)
MA, ChouXian (author)
Tang, LinQi (author)
DU, YuanPing (author)
Zhang, ShaoWei (author)
Morata, Jordi (author)
Tonda, Raúl (author)
Parra, Genís (author)
Trotta, Jean-Rémi (author)
Brueffer, Christian (author)
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 Environments
Demirkaya-Budak, Sinem (author)
Kabakci-Zorlu, Duygu (author)
Turgut, Deniz (author)
Kalay, Özem (author)
Budak, Gungor (author)
Narcı, Kübra (author)
Arslan, Elif (author)
Brown, Richard (author)
Johnson, Ivan J. (author)
Dolgoborodov, Alexey (author)
Semenyuk, Vladimir (author)
Jain, Amit (author)
Tetikol, H. Serhat (author)
Jain, Varun (author)
Ruehle, Mike (author)
Lajoie, Bryan (author)
Roddey, Cooper (author)
Catreux, Severine (author)
Mehio, Rami (author)
Ahsan, Mian Umair (author)
Liu, Qian (author)
Wang, Kai (author)
Sahraeian, Sayed Mohammad Ebrahim (author)
Fang, Li Tai (author)
Mohiyuddin, Marghoob (author)
Hung, Calvin (author)
Jain, Chirag (author)
Feng, Hanying (author)
Li, Zhipan (author)
Chen, Luoqi (author)
Sedlazeck, Fritz J. (author)
Zook, Justin M (author)
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National Institute of Standards and Technology (NIST) Booz Allen Hamilton, Inc (creator_code:org_t)
Elsevier BV, 2022
2022
English.
In: Cell Genomics. - : Elsevier BV. - 2666-979X. ; 2:5, s. 1-12
  • Journal article (peer-reviewed)
Abstract Subject headings
Close  
  • 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

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)
MEDICIN OCH HÄLSOVETENSKAP  -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
MEDICAL AND HEALTH SCIENCES  -- Basic Medicine -- Medical Genetics (hsv//eng)

Keyword

DNA
variant
shot-read sequencing
long-read sequencing
benchmark

Publication and Content Type

art (subject category)
ref (subject category)

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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...
About the subject
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
Articles in the publication
Cell Genomics
By the university
Lund University

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