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

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

Research output: Contribution to journalArticlepeer-review

Abstract

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.
Original languageEnglish
Article number100129
Pages (from-to)1-12
JournalCell Genomics
Volume2
Issue number5
DOIs
Publication statusPublished - 2022 May 11

Subject classification (UKÄ)

  • Bioinformatics and Systems Biology
  • Bioinformatics (Computational Biology)
  • Medical Genetics

Free keywords

  • DNA
  • variant
  • shot-read sequencing
  • long-read sequencing
  • benchmark

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

    Olson, N. D., Wagner, J., McDaniel, J., Stephens, S. H., Westreich, S. T., Prasanna, A. G., Johanson, E., Maier, E. J., Boja, E., Serang, O., Jáspez, D., Lorenzo-Salazar, J. M., Muñoz-Barrera, A., Rubio-Rodríguez, L. A., Flores, C., Kyriakidis, K., Malousi, A., Shafin, K., Pesout, T., Jain, M., & 53 othersPaten, 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, C., Tang, L., DU, Y., Zhang, S., 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, I. J., Dolgoborodov, A., Semenyuk, V., Jain, A., Tetikol, H. S., Jain, V., Ruehle, M., Lajoie, B., Roddey, C., Catreux, S., Mehio, R., Ahsan, M. U., Liu, Q., Wang, K., Sahraeian, S. M. E., Fang, L. T., Mohiyuddin, M., Hung, C., Jain, C., Feng, H., Li, Z., Chen, L., Sedlazeck, F. J. & Zook, J. M., 2020 Nov 15, bioRxiv.

    Research output: Working paper/PreprintPreprint (in preprint archive)

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