eprintid: 10205418 rev_number: 7 eprint_status: archive userid: 699 dir: disk0/10/20/54/18 datestamp: 2025-03-06 15:29:12 lastmod: 2025-03-06 15:29:12 status_changed: 2025-03-06 15:29:12 type: article metadata_visibility: show sword_depositor: 699 creators_name: Loennstedt, Ingrid M creators_name: Caramia, Franco creators_name: Li, Jason creators_name: Fumagalli, Debora creators_name: Salgado, Roberto creators_name: Rowan, Andrew creators_name: Salm, Max creators_name: Kanu, Nnennaya creators_name: Savas, Peter creators_name: Horswell, Stuart creators_name: Gade, Stephan creators_name: Loibl, Sibylle creators_name: Neven, Patrick creators_name: Sotiriou, Christos creators_name: Swanton, Charles creators_name: Loi, Sherene creators_name: Speed, Terence P title: Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data ispublished: pub divisions: UCL divisions: B02 divisions: C10 divisions: D19 divisions: G99 keywords: Science & Technology, Life Sciences & Biomedicine, Biotechnology & Applied Microbiology, Genetics & Heredity, COPY NUMBER ANALYSIS, EVOLUTION, HETEROGENEITY, MUTATIONS, ALIGNMENT, CANCER, TOOL note: Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. abstract: Intra-tumor heterogeneity concerns the existence of genetically different subclones within the same tumor. Single sample quantification of heterogeneity relies on precise determination of chromosomal copy numbers throughout the genome, and an assessment of whether identified mutation variant allele fractions match clonal or subclonal copy numbers. We discuss these issues using data from SNP arrays, whole exome sequencing and pathologist purity estimates on several breast cancers characterized by ERBB2 amplification. We show that chromosomal copy numbers can only be estimated from SNP array signals or sequencing depths for subclonal tumor samples with simple subclonal architectures under certain assumptions. date: 2014 date_type: published publisher: BMC official_url: https://doi.org/10.1186/preaccept-9755896761283690 oa_status: green full_text_type: pub language: eng primo: open primo_central: open_green verified: verified_manual elements_id: 982571 doi: 10.1186/s13059-014-0470-7 medium: Electronic pii: s13059-014-0470-7 lyricists_name: Swanton, Robert lyricists_name: Kanu, Nnennaya lyricists_id: CSWAN79 lyricists_id: NKANU55 actors_name: Kanu, Nnennaya actors_id: NKANU55 actors_role: owner funding_acknowledgements: 278659 [European Union]; [Cancer Council Victoria]; [NHMRC Australia Fellowship]; G0701935 [MRC] full_text_status: public publication: Genome Biology volume: 15 number: 9 article_number: 470 pages: 23 event_location: England issn: 1474-760X citation: Loennstedt, Ingrid M; Caramia, Franco; Li, Jason; Fumagalli, Debora; Salgado, Roberto; Rowan, Andrew; Salm, Max; ... Speed, Terence P; + view all <#> Loennstedt, Ingrid M; Caramia, Franco; Li, Jason; Fumagalli, Debora; Salgado, Roberto; Rowan, Andrew; Salm, Max; Kanu, Nnennaya; Savas, Peter; Horswell, Stuart; Gade, Stephan; Loibl, Sibylle; Neven, Patrick; Sotiriou, Christos; Swanton, Charles; Loi, Sherene; Speed, Terence P; - view fewer <#> (2014) Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data. Genome Biology , 15 (9) , Article 470. 10.1186/s13059-014-0470-7 <https://doi.org/10.1186/s13059-014-0470-7>. Green open access document_url: https://discovery.ucl.ac.uk/id/eprint/10205418/1/Deciphering%20clonality%20in%20aneuploid%20breast%20tumors%20using%20SNP%20array%20and%20sequencing%20data.pdf