Salcedo, Adriana, Tarabichi, Maxime ORCID: 0000-0002-1635-2348, Espiritu, Shadrielle Melijah G., Deshwar, Amit G., David, Matei, Wilson, Nathan M., Dentro, Stefan, Wintersinger, Jeff A., Liu, Lydia Y., Ko, Minjeong, Sivanandan, Srinivasan, Zhang, Hongjiu, Zhu, Kaiyi, Ou Yang, Tai-Hsien, Chilton, John M., Buchanan, Alex, Lalansingh, Christopher M., P'ng, Christine, Anghel, Catalina V., Umar, Imaad, Lo, Bryan, Zou, William, Simpson, Jared T., Stuart, Joshua M., Anastassiou, Dimitris, Guan, Yuanfang ORCID: 0000-0001-8275-2852, Ewing, Adam D., Ellrott, Kyle, Wedge, David C., Morris, Quaid, Van Loo, Peter, Boutros, Paul C., Jha, Alokkumar, Huang, Tanxiao, Yang, Tsun-Po, Peifer, Martin, Sahinalp, Cenk, Malikic, Salem, Vazquez-Garcia, Ignacio, Mustonen, Ville, Yang, Hsih-Te, Lee, Ken-Ray, Ji, Yuan, Sengupta, Subhajit, Rudewicz, Justine, Nikolski, Macha, Schaeverbeke, Quentin ORCID: 0000-0002-6262-085X, Yuan, Ke, Markowetz, Florian, Macintyre, Geoff, Cmero, Marek, Chaudhary, Belal, Leshchiner, Ignaty, Livitz, Dimitri, Getz, Gad, Loher, Phillipe, Yu, Kaixian, Wang, Wenyi ORCID: 0000-0003-0617-9438 and Zhu, Hongtu (2020). A community effort to create standards for evaluating tumor subclonal reconstruction. Nat. Biotechnol., 38 (1). S. 97 - 113. BERLIN: NATURE RESEARCH. ISSN 1546-1696

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Abstract

Methods for reconstructing tumor evolution are benchmarked in the DREAM Somatic Mutation Calling Tumour Heterogeneity Challenge. Tumor DNA sequencing data can be interpreted by computational methods that analyze genomic heterogeneity to infer evolutionary dynamics. A growing number of studies have used these approaches to link cancer evolution with clinical progression and response to therapy. Although the inference of tumor phylogenies is rapidly becoming standard practice in cancer genome analyses, standards for evaluating them are lacking. To address this need, we systematically assess methods for reconstructing tumor subclonality. First, we elucidate the main algorithmic problems in subclonal reconstruction and develop quantitative metrics for evaluating them. Then we simulate realistic tumor genomes that harbor all known clonal and subclonal mutation types and processes. Finally, we benchmark 580 tumor reconstructions, varying tumor read depth, tumor type and somatic variant detection. Our analysis provides a baseline for the establishment of gold-standard methods to analyze tumor heterogeneity.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Salcedo, AdrianaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Tarabichi, MaximeUNSPECIFIEDorcid.org/0000-0002-1635-2348UNSPECIFIED
Espiritu, Shadrielle Melijah G.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Deshwar, Amit G.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
David, MateiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wilson, Nathan M.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Dentro, StefanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wintersinger, Jeff A.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Liu, Lydia Y.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ko, MinjeongUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Sivanandan, SrinivasanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zhang, HongjiuUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zhu, KaiyiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ou Yang, Tai-HsienUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Chilton, John M.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Buchanan, AlexUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lalansingh, Christopher M.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
P'ng, ChristineUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Anghel, Catalina V.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Umar, ImaadUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lo, BryanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zou, WilliamUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Simpson, Jared T.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Stuart, Joshua M.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Anastassiou, DimitrisUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Guan, YuanfangUNSPECIFIEDorcid.org/0000-0001-8275-2852UNSPECIFIED
Ewing, Adam D.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ellrott, KyleUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wedge, David C.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Morris, QuaidUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Van Loo, PeterUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Boutros, Paul C.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Jha, AlokkumarUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Huang, TanxiaoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Yang, Tsun-PoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Peifer, MartinUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Sahinalp, CenkUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Malikic, SalemUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Vazquez-Garcia, IgnacioUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Mustonen, VilleUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Yang, Hsih-TeUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lee, Ken-RayUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ji, YuanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Sengupta, SubhajitUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Rudewicz, JustineUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Nikolski, MachaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Schaeverbeke, QuentinUNSPECIFIEDorcid.org/0000-0002-6262-085XUNSPECIFIED
Yuan, KeUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Markowetz, FlorianUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Macintyre, GeoffUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Cmero, MarekUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Chaudhary, BelalUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Leshchiner, IgnatyUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Livitz, DimitriUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Getz, GadUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Loher, PhillipeUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Yu, KaixianUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wang, WenyiUNSPECIFIEDorcid.org/0000-0003-0617-9438UNSPECIFIED
Zhu, HongtuUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-351684
DOI: 10.1038/s41587-019-0364-z
Journal or Publication Title: Nat. Biotechnol.
Volume: 38
Number: 1
Page Range: S. 97 - 113
Date: 2020
Publisher: NATURE RESEARCH
Place of Publication: BERLIN
ISSN: 1546-1696
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
SOMATIC POINT MUTATIONS; GENOME SIMULATION; CANCER; HETEROGENEITY; EVOLUTION; IDENTIFICATIONMultiple languages
Biotechnology & Applied MicrobiologyMultiple languages
URI: http://kups.ub.uni-koeln.de/id/eprint/35168

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