Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection

Autor: Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, Bare JC, P'ng C, Waggott D, Sabelnykova VY, ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants, Kellen MR, Norman TC, Haussler D, Friend SH, Stolovitzky G, Margolin AA, Stuart JM, Boutros PC

Publikováno v: NATURE METHODS
r-CIPF. Repositorio Institucional Producción Científica del Centro de Investigación Principe Felipe (CIPF)
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r-CIPF: Repositorio Institucional Producción Científica del Centro de Investigación Principe Felipe (CIPF)
Centro de Investigación Principe Felipe (CIPF)

The detection of somatic mutations from cancer genome sequences is key to understanding the genetic basis of disease progression, patient survival and response to therapy. Benchmarking is needed for tool assessment and improvement but is complicated

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::5db1278a634204af0f22ca080337984e
https://fundanet.cipf.es/Publicaciones/ProdCientif/PublicacionFrw.aspx?id=1813

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An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences.

Autor: Gurun B; Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA. gurundem@ohsu.edu.; School of Medicine, Oregon Health and Science University, Portland, OR, USA. gurundem@ohsu.edu., Horton W; Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA., Murugan D; Department of Cell, Developmental & Cancer Biology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA., Zhu B; Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA., Leyshock P; Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA., Kumar S; Department of Cell, Developmental & Cancer Biology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA., Byrne KT; Department of Cell, Developmental & Cancer Biology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA., Vonderheide RH; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA., Margolin AA; NextVivo, Palo Alto, CA, USA., Mori M; Department of Biostatistics, St. Jude's Children's Research Hospital, Memphis, TN, USA., Spellman PT; Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA. spellmap@ohsu.edu., Coussens LM; Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA. coussenl@ohsu.edu.; Department of Cell, Developmental & Cancer Biology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA. coussenl@ohsu.edu., Speed TP; Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. terry@wehi.edu.au.; School of Mathematics and Statistics, University of Melbourne, Parkville, VIC, 3010, Australia. terry@wehi.edu.au.

Publikováno v: BMC genomics [BMC Genomics] 2023 Jun 26; Vol. 24 (1), pp. 349. Date of Electronic Publication: 2023 Jun 26.