Cited by 1,967Cancer Genomics and DiagnosticsBreast Cancer Treatment StudiesBRCA gene mutations in cancer

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The clonal and mutational evolution spectrum of primary triple-negative breast cancers

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Shah, Sohrab P., Roth, Andrew, Goya, Rodrigo, Oloumi, Arusha, Ha, Gavin, Zhao, Yongjun, Turashvili, Gulisa, Ding, Jiarui, Tse, Kane, Haffari, Gholamreza, Bashashati, Ali, Prentice, Leah M., Khattra, Jaswinder, Burleigh, Angela, Yap, Damian, Bernard, Virginie, McPherson, Andrew, Shumansky, Karey, Crisan, Anamaria, Giuliany, Ryan, Heravi-Moussavi, Alireza, Rosner, Jamie, Lai, Daniel, Birol, Inanc, Varhol, Richard, Tam, Angela, Dhalla, Noreen, Zeng, Thomas, Ma, Kevin, Chan, Simon K., Griffith, Malachi, Moradian, Annie, Cheng, S.-W. Grace, Morin, Gregg B., Watson, Peter, Gelmon, Karen, Chia, Stephen, Chin, Suet-Feung, Curtis, Christina, Rueda, Oscar M., Pharoah, Paul D., Damaraju, Sambasivarao, Mackey, John, Hoon, Kelly, Harkins, Timothy, Tadigotla, Vasisht, Sigaroudinia, Mahvash, Gascard, Philippe, Tlsty, Thea, Costello, Joseph F., Meyer, Irmtraud M., Eaves, Connie J., Wasserman, Wyeth W., Jones, Steven, Huntsman, David, Hirst, Martin, Caldas, Carlos, Marra, Marco A., Aparicio, Samuel·2012·Nature

DOI 10.1038/nature10933PMC PMC3863681

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Abstract

Primary triple-negative breast cancers (TNBCs), a tumour type defined by lack of oestrogen receptor, progesterone receptor and ERBB2 gene amplification, represent approximately 16% of all breast cancers. Here we show in 104 TNBC cases that at the time of diagnosis these cancers exhibit a wide and continuous spectrum of genomic evolution, with some having only a handful of coding somatic aberrations in a few pathways, whereas others contain hundreds of coding somatic mutations. High-throughput RNA sequencing (RNA-seq) revealed that only approximately 36% of mutations are expressed. Using deep re-sequencing measurements of allelic abundance for 2,414 somatic mutations, we determine for the first time-to our knowledge-in an epithelial tumour subtype, the relative abundance of clonal frequencies among cases representative of the population. We show that TNBCs vary widely in their clonal frequencies at the time of diagnosis, with the basal subtype of TNBC showing more variation than non-basal TNBC. Although p53 (also known as TP53), PIK3CA and PTEN somatic mutations seem to be clonally dominant compared to other genes, in some tumours their clonal frequencies are incompatible with founder status. Mutations in cytoskeletal, cell shape and motility proteins occurred at lower clonal frequencies, suggesting that they occurred later during tumour progression. Taken together, our results show that understanding the biology and therapeutic responses of patients with TNBC will require the determination of individual tumour clonal genotypes.

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Authors: Shah, S. P., Roth, A., Goya, R., Oloumi, A., Ha, G., Zhao, Y., Turashvili, G., Ding, J., Tse, K., Haffari, G., Bashashati, A., Prentice, L. M., Khattra, J., Burleigh, A., Yap, D., Bernard, V., McPherson, A., Shumansky, K., Crisan, A., Giuliany, R., Heravi-Moussavi, A., Rosner, J., Lai, D., Birol, I., Varhol, R., Tam, A., Dhalla, N., Zeng, T., Ma, K., Chan, S. K., Griffith, M., Moradian, A., Cheng, S.-W. G., Morin, G. B., Watson, P., Gelmon, K., Chia, S., Chin, S.-F., Curtis, C., Rueda, O. M., Pharoah, P. D., Damaraju, S., Mackey, J., Hoon, K., Harkins, T., Tadigotla, V., Sigaroudinia, M., Gascard, P., Tlsty, T., Costello, J. F., Meyer, I. M., Eaves, C. J., Wasserman, W. W., Jones, S., Huntsman, D., Hirst, M., Caldas, C., Marra, M. A., & Aparicio, S.
Affiliations: University of British Columbia (CA)
Canada's Michael Smith Genome Sciences Centre (CA)
BC Cancer Agency (CA)
University of Cambridge (GB)
University of Southern California (US)
Cancer Research UK (GB)
University of Alberta (CA)
University of California, San Francisco (US)
Corresponding author: Shah, Sohrab P.
Caldas, Carlos
Marra, Marco A.
Aparicio, Samuel
ORCID: Shah, Sohrab P.
Roth, Andrew
Ha, Gavin
Zhao, Yongjun
Turashvili, Gulisa
Ding, Jiarui
Haffari, Gholamreza
Bashashati, Ali
Prentice, Leah M.
Burleigh, Angela
Yap, Damian
McPherson, Andrew
Crisan, Anamaria
Rosner, Jamie
Lai, Daniel
Varhol, Richard
Tam, Angela
Griffith, Malachi
Moradian, Annie
Cheng, S.-W. Grace
Morin, Gregg B.
Watson, Peter
Gelmon, Karen
Chia, Stephen
Chin, Suet-Feung
Curtis, Christina
Rueda, Oscar M.
Pharoah, Paul D.
Damaraju, Sambasivarao
Mackey, John
Harkins, Timothy
Gascard, Philippe
Tlsty, Thea
Costello, Joseph F.
Meyer, Irmtraud M.
Eaves, Connie J.
Wasserman, Wyeth W.
Jones, Steven
Huntsman, David
Hirst, Martin
Caldas, Carlos
Marra, Marco A.
Aparicio, Samuel
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2012-04-04
Volume: 486
Issue: 7403
Pages: 395-399
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature10933
PMC: PMC3863681
OpenAlex: W2063382533
Cited by: 1,967
References: 23
Citations by year: 2026: 40 · 2025: 61 · 2024: 71 · 2023: 131 · 2022: 132 · 2021: 119 · 2020: 131 · 2019: 120 · 2018: 135 · 2017: 173 · 2016: 179 · 2015: 198 · 2014: 199 · 2013: 201 · 2012: 76
FWCI: 71.57
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
eScholarship (California Digital Library) (submittedVersion)
RePEc: Research Papers in Economics (submittedVersion)
MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (submittedVersion)
eSpace (Curtin University) (submittedVersion)
Funders: U.S. Department of Defense
Memorial Sloan-Kettering Cancer Center
Canada's Michael Smith Genome Sciences Centre
Canadian Breast Cancer Research Alliance
Michael Smith Health Research BC
Cancer Research UK
National Institute for Health and Care Research (NF-SI-0611-10154)
Cure Brain Cancer Foundation
BC Cancer Foundation
National Institutes of Health
Imperial Experimental Cancer Medicine Centre
BC Cancer Agency
National Institute of General Medical Sciences (R01GM084875)
National Institute of Environmental Health Sciences (U01ES017154)
Congressionally Directed Medical Research Programs
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Breast Cancer Treatment Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › BRCA gene mutations in cancer
Keywords: triple-negative breast cancer, clonal evolution, somatic mutations, copy number variation, cancer genomics, TP53 mutation, PIK3CA mutation, PTEN mutation, basal subtype, tumor progression, founder mutation, clonal heterogeneity
MeSH terms: Alleles, Breast Neoplasms, Clone Cells, DNA Mutational Analysis, Female, Genotype, Humans, Mutation, Reproducibility of Results, Gene Expression Regulation, Neoplastic, Point Mutation, Sequence Analysis, RNA, Disease Progression, Evolution, Molecular, Gene Expression Profiling, INDEL Mutation, DNA Copy Number Variations, Precision Medicine, High-Throughput Nucleotide Sequencing

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The clonal and mutational evolution spectrum of primary triple-negative breast cancers

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