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 Nathan D. Olson
A1 Justin Wagner
A1 Jennifer McDaniel
A1 Sarah H. Stephens
A1 Samuel T. Westreich
A1 Anish G. Prasanna
A1 Elaine Johanson
A1 Emily Boja
A1 Ezekiel J. Maier
A1 Omar Serang
A1 David Jáspez
A1 José M. Lorenzo-Salazar
A1 Adrián Muñoz-Barrera
A1 Luis A. Rubio-Rodríguez
A1 Carlos Flores
A1 Konstantinos Kyriakidis
A1 Andigoni Malousi
A1 Kishwar Shafin
A1 Trevor Pesout
A1 Miten Jain
A1 Benedict Paten
A1 Pi-Chuan Chang
A1 Alexey Kolesnikov
A1 Maria Nattestad
A1 Gunjan Baid
A1 Sidharth Goel
A1 Howard Yang
A1 Andrew Carroll
A1 Robert Eveleigh
A1 Mathieu Bourgey
A1 Guillaume Bourque
A1 Gen Li
A1 MA ChouXian
A1 LinQi Tang
A1 DU YuanPing
A1 ShaoWei Zhang
A1 Jordi Morata
A1 Raúl Tonda
A1 Genís Parra
A1 Jean-Rémi Trotta
A1 Christian Brueffer
A1 Sinem Demirkaya-Budak
A1 Duygu Kabakci-Zorlu
A1 Deniz Turgut
A1 Özem Kalay
A1 Gungor Budak
A1 Kübra Narcı
A1 Elif Arslan
A1 Richard Brown
A1 Ivan J Johnson
A1 Alexey Dolgoborodov
A1 Vladimir Semenyuk
A1 Amit Jain
A1 H. Serhat Tetikol
A1 Varun Jain
A1 Mike Ruehle
A1 Bryan Lajoie
A1 Cooper Roddey
A1 Severine Catreux
A1 Rami Mehio
A1 Umair Ahsan
A1 Qian Liu
A1 Kai Wang
A1 Sayed Mohammad Ebrahim Sahraeian
A1 Li Tai Fang
A1 Marghoob Mohiyuddin
A1 Calvin Hung
A1 Chirag Jain
A1 Hanying Feng
A1 Zhipan Li
A1 Luoqi Che
A1 Fritz J. Sedlazeck
A1 Justin M. Zook
YR 2020
UL http://biorxiv.org/content/early/2020/11/15/2020.11.13.380741.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, 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.