RT Journal Article
SR Electronic
T1 precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.11.13.380741
DO 10.1101/2020.11.13.380741
A1 Olson, Nathan D.
A1 Wagner, Justin
A1 McDaniel, Jennifer
A1 Stephens, Sarah H.
A1 Westreich, Samuel T.
A1 Prasanna, Anish G.
A1 Johanson, Elaine
A1 Boja, Emily
A1 Maier, Ezekiel J.
A1 Serang, Omar
A1 Jáspez, David
A1 Lorenzo-Salazar, José M.
A1 Muñoz-Barrera, Adrián
A1 Rubio-Rodríguez, Luis A.
A1 Flores, Carlos
A1 Kyriakidis, Konstantinos
A1 Malousi, Andigoni
A1 Shafin, Kishwar
A1 Pesout, Trevor
A1 Jain, Miten
A1 Paten, Benedict
A1 Chang, Pi-Chuan
A1 Kolesnikov, Alexey
A1 Nattestad, Maria
A1 Baid, Gunjan
A1 Goel, Sidharth
A1 Yang, Howard
A1 Carroll, Andrew
A1 Eveleigh, Robert
A1 Bourgey, Mathieu
A1 Bourque, Guillaume
A1 Li, Gen
A1 ChouXian, MA
A1 Tang, LinQi
A1 YuanPing, DU
A1 Zhang, ShaoWei
A1 Morata, Jordi
A1 Tonda, Raúl
A1 Parra, Genís
A1 Trotta, Jean-Rémi
A1 Brueffer, Christian
A1 Demirkaya-Budak, Sinem
A1 Kabakci-Zorlu, Duygu
A1 Turgut, Deniz
A1 Kalay, Özem
A1 Budak, Gungor
A1 Narcı, Kübra
A1 Arslan, Elif
A1 Brown, Richard
A1 Johnson, Ivan J
A1 Dolgoborodov, Alexey
A1 Semenyuk, Vladimir
A1 Jain, Amit
A1 Tetikol, H. Serhat
A1 Jain, Varun
A1 Ruehle, Mike
A1 Lajoie, Bryan
A1 Roddey, Cooper
A1 Catreux, Severine
A1 Mehio, Rami
A1 Ahsan, Umair
A1 Liu, Qian
A1 Wang, Kai
A1 Sahraeian, Sayed Mohammad Ebrahim
A1 Fang, Li Tai
A1 Mohiyuddin, Marghoob
A1 Hung, Calvin
A1 Jain, Chirag
A1 Feng, Hanying
A1 Li, Zhipan
A1 Chen, Luoqi
A1 Sedlazeck, Fritz J.
A1 Zook, Justin M.
YR 2020
UL http://biorxiv.org/content/early/2020/11/19/2020.11.13.380741.abstract
AB 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.Competing Interest StatementC.B. is an employee and shareholder of SAGA Diagnostics AB. A.C., P.C., A.K., M.N., G.B., S.G., and H.Y. are employees of Google and A.C. is a shareholder. S.D., D.K., D.T., O.K., G.B., K.N., E.A., R.B., I.J.J., A.D., V.S., A.J., and H.S.T. are employees of Seven Bridges Genomics. O.S. and S.T.W. are employees of DNAnexus. G.L, C.M, L.T., Y.D., and S.Z. are employees of Genetalks. V.J., M.R., B.L., C.R, S.C., and R.M are employees of Illumina. S.M.E.S., and M.M. are employees of Roche. C.H. is an employee of Wasai Technology. H.F., Z.L, and L.C. are employees of Sentieon Inc.