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, Ezekiel J. Maier, Emily Boja, 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

Forskningsoutput: Working paper/PreprintPreprint (i preprint-arkiv)

Sammanfattning

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.
Originalspråkengelska
UtgivarebioRxiv
DOI
StatusPublished - 2020 nov. 15

Ämnesklassifikation (UKÄ)

  • Bioinformatik och systembiologi
  • Bioinformatik (beräkningsbiologi)
  • Medicinsk genetik

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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., Boja, E., Maier, E. J., 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 andra, 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, 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., 2022 maj 11, I: Cell Genomics. 2, 5, s. 1-12 100129.

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskriftPeer review

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