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

TitlePrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions.
Publication TypeJournal Article
Year of Publication2022
AuthorsOlson, ND, Wagner, J, McDaniel, J, Stephens, SH, Westreich, ST, Prasanna, AG, Johanson, E, Boja, E, Maier, EJ, Serang, O, Jáspez, D, Lorenzo-Salazar, JM, Muñoz-Barrera, A, Rubio-Rodríguez, LA, Flores, C, Kyriakidis, K, Malousi, A, Shafin, K, Pesout, T, Jain, M, Paten, B, Chang, P-C, Kolesnikov, A, Nattestad, M, Baid, G, Goel, S, Yang, H, Carroll, A, Eveleigh, R, Bourgey, M, Bourque, G, Li, G, Ma, CX, Tang, LQ, Du, YP, Zhang, SW, Morata, J, Tonda, R, Parra, G, Trotta, J-R, Brueffer, C, Demirkaya-Budak, S, Kabakci-Zorlu, D, Turgut, D, Kalay, Ö, Budak, G, Narcı, K, Arslan, E, Brown, R, Johnson, IJ, Dolgoborodov, A, Semenyuk, V, Jain, A, H Tetikol, S, Jain, V, Ruehle, M, Lajoie, B, Roddey, C, Catreux, S, Mehio, R, Ahsan, MUmair, Liu, Q, Wang, K, Sahraeian, SMohammad E, Fang, LTai, Mohiyuddin, M, Hung, C, Jain, C, Feng, H, Li, Z, Chen, L, Sedlazeck, FJ, Zook, JM
JournalCell Genom
Date Published2022 May 11

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.

Alternate JournalCell Genom
PubMed ID35720974
PubMed Central IDPMC9205427
Grant ListR01 GM132713 / GM / NIGMS NIH HHS / United States
UM1 HG008898 / HG / NHGRI NIH HHS / United States