Luminal breast epithelial cells of BRCA1 or BRCA2 mutation carriers and noncarriers harbor common breast cancer copy number alterations
Open accessAbstract
The prevalence and nature of somatic copy number alterations (CNAs) in breast epithelium and their role in tumor initiation and evolution remain poorly understood. Using single-cell DNA sequencing (49,238 cells) of epithelium from BRCA1 and BRCA2 carriers or wild-type individuals, we identified recurrent CNAs (for example, 1q-gain and 7q, 10q, 16q and 22q-loss) that are present in a rare population of cells across almost all samples (n = 28). In BRCA1/BRCA2 carriers, these occur before loss of heterozygosity (LOH) of wild-type alleles. These CNAs, common in malignant tumors, are enriched in luminal cells but absent in basal myoepithelial cells. Allele-specific analysis of prevalent CNAs reveals that they arose by independent mutational events, consistent with convergent evolution. BRCA1/BRCA2 carriers contained a small percentage of cells with extreme aneuploidy, featuring loss of TP53, BRCA1/BRCA2 LOH and multiple breast cancer-associated CNAs. Our findings suggest that CNAs arising in normal luminal breast epithelium are precursors to clonally expanded tumor genomes.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
A group of already transformed tumors can remain stable and controlled for years before progressing into symptomatic disease.
“This evidence reinforces the idea that a group of already transformed tumors can remain stable and controlled for years before progressing into symptomatic disease.21,100,101”
From Evolution of Multiple Myeloma from a Genomic Perspective (2026) · cites this paper as [100]
The Results identify rare cancer-like cells, and the Discussion suggests they may come from microscopic premalignant lesions. Neither section establishes that already transformed tumors remain stable and controlled for years before becoming symptomatic; searches for long-term stability and progression found no such passage. Page numbers were unavailable in our copy. (LLM, conf=0.76)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Comprehensive molecular portraits of human breast tumours
The Cancer Genome Atlas Network (2012) · Nature · doi:10.1038/nature11412 · Cited by 12,129 · see citing works
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
METABRIC Group, Curtis, C., Shah, S. P., Chin, S.-F., Turashvili, G., Rueda, O. M., Dunning, M. J., Speed, D., Lynch, A. G., Samarajiwa, S., et al. (2012) · Nature · doi:10.1038/nature10983 · Cited by 6,097 · see citing works
Self-citationPan-cancer analysis of whole genomes
The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S.-M., Aikata, H., et al. (2020) · Nature · doi:10.1038/s41586-020-1969-6 · Cited by 3,064 · see citing works
Self-citationInduction of apoptosis in fibroblasts by c-myc protein
Evan, G. I., Wyllie, A. H., Gilbert, C. S., Littlewood, T. D., Land, H., Brooks, M. W., Waters, C. M., Penn, L. Z., & Hancock, D. C. (1992) · Cell · doi:10.1016/0092-8674(92)90123-t · Cited by 2,941 · see citing works
Landscape of somatic mutations in 560 breast cancer whole-genome sequences
Nik-Zainal, S., Davies, H., Staaf, J., Ramakrishna, M., Glodzik, D., Zou, X., Martincorena, I., Alexandrov, L. B., Martin, S., Wedge, D. C., et al. (2016) · Nature · doi:10.1038/nature17676 · Cited by 2,218 · see citing works
High burden and pervasive positive selection of somatic mutations in normal human skin
Martincorena, I., Roshan, A., Gerstung, M., Ellis, P., Van Loo, P., McLaren, S., Wedge, D. C., Fullam, A., Alexandrov, L. B., Tubio, J. M., et al. (2015) · Science · doi:10.1126/science.aaa6806 · Cited by 1,770 · see citing works
The landscape of cancer genes and mutational processes in breast cancer
Stephens, P. J., Tarpey, P. S., Davies, H. R., Loo, P. V., Greenman, C., Wedge, D. C., Nik‐Zainal, S., Martin, S., Varela, I., Bignell, G. R., et al. (2012) · Nature · doi:10.1038/nature11017 · Cited by 1,686 · see citing works
Self-citationPurification and unique properties of mammary epithelial stem cells
Stingl, J., Eirew, P. D., Ricketson, I., Shackleton, M. J., Vaillant, F., Choi, D., Li, H. I., & Eaves, C. J. (2006) · Nature · doi:10.1038/nature04496 · Cited by 1,562 · see citing works
Davoli, T., Uno, H., Wooten, E. C., & Elledge, S. J. (2017) · Science · doi:10.1126/science.aaf8399 · Cited by 1,325 · see citing works
Genomic and transcriptional aberrations linked to breast cancer pathophysiologies
Chin, K., DeVries, S., Fridlyand, J., Spellman, P. T., Roydasgupta, R., Kuo, W.-L., Lapuk, A. V., Neve, R. M., Qian, Z., Ryder, T., et al. (2006) · Cancer Cell · doi:10.1016/j.ccr.2006.10.009 · Cited by 1,288 · see citing works
Somatic mutant clones colonize the human esophagus with age
Martincorena, I., Fowler, J. C., Wabik, A., Lawson, A. R. J., Abascal, F., Hall, M. W. J., Cagan, A., Murai, K., Mahbubani, K., Stratton, M. R., et al. (2018) · Science · doi:10.1126/science.aau3879 · Cited by 1,113 · see citing works
HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures
Davies, H., Glodzik, D., Morganella, S., Yates, L. R., Staaf, J., Zou, X., Ramakrishna, M., Martin, S., Boyault, S., Sieuwerts, A. M., et al. (2017) · Nature Medicine · doi:10.1038/nm.4292 · Cited by 1,086 · see citing works
Punctuated equilibrium comes of age
Gould, S. J., & Eldredge, N. (1993) · Nature · doi:10.1038/366223a0 · Cited by 957 · see citing works
Novel primitive lymphoid tumours induced in transgenic mice by cooperation between myc and bcl-2
Strasser, A., Harris, A. W., Bath, M. L., & Cory, S. (1990) · Nature · doi:10.1038/348331a0 · Cited by 905 · see citing works
Askew, D. S., Ashmun, R. A., Simmons, B. C., & Cleveland, J. L. (1991) · PubMed · Cited by 867 · see citing works
Patterns of somatic structural variation in human cancer genomes
Li, Y., Roberts, N. D., Wala, J. A., Shapira, O., Schumacher, S. E., Kumar, K., Khurana, E., Waszak, S., Korbel, J. O., Haber, J. E., et al. (2020) · Nature · doi:10.1038/s41586-019-1913-9 · Cited by 867 · see citing works
Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing
Cortés-Ciriano, I., Lee, J. J.-K., Xi, R., Jain, D., Jung, Y. L., Yang, L., Gordenin, D., Klimczak, L. J., Zhang, C.-Z., Pellman, D. S., et al. (2020) · Nature Genetics · doi:10.1038/s41588-019-0576-7 · Cited by 712 · see citing works
Intra-tumour diversification in colorectal cancer at the single-cell level
Roerink, S. F., Sasaki, N., Lee-Six, H., Young, M. D., Alexandrov, L. B., Behjati, S., Mitchell, T. J., Großmann, S., Lightfoot, H. W., Egan, D. A., et al. (2018) · Nature · doi:10.1038/s41586-018-0024-3 · Cited by 547 · see citing works
Molecular evolution of breast cancer
Simpson, P. T., Reis-Filho, J. S., Gale, T., & Lakhani, S. R. (2005) · The Journal of Pathology · doi:10.1002/path.1691 · Cited by 520 · see citing works
In situ identification of bipotent stem cells in the mammary gland
Rios, A. C., Fu, N. Y., Lindeman, G. J., & Visvader, J. E. (2014) · Nature · doi:10.1038/nature12948 · Cited by 511 · see citing works
Somatic mutation landscapes at single-molecule resolution
Abascal, F., Harvey, L. M. R., Mitchell, E., Lawson, A. R. J., Lensing, S. V., Ellis, P., Russell, A. J. C., Alcantara, R. E., Baez‐Ortega, A., Wang, Y., et al. (2021) · Nature · doi:10.1038/s41586-021-03477-4 · Cited by 508 · see citing works
Somatic copy number mosaicism in human skin revealed by induced pluripotent stem cells
Abyzov, A. S., Mariani, J., Palejev, D., Zhang, Y., Haney, M. S., Tomasini, L., Ferrandino, A. F., Belmaker, L. R., Szekely, A. M., Wilson, M., et al. (2012) · Nature · doi:10.1038/nature11629 · Cited by 378 · see citing works
Tirkkonen, M., Johannsson, O. T., Agnarsson, B. A., Olsson, H. L., Ingvarsson, S., Karhu, R., Tanner, M., Isola, J. J., Barkardottir, R. B., Borg, Å., et al. (1997) · PubMed · Cited by 354 · see citing works
Breast cancer precursors revisited: molecular features and progression pathways
López‐García, M. Á., Geyer, F. C., Lacroix‐Triki, M., Marchiò, C., & Reis-Filho, J. S. (2010) · Histopathology · doi:10.1111/j.1365-2559.2010.03568.x · Cited by 344 · see citing works
A new genome‐driven integrated classification of breast cancer and its implications
Dawson, S., Rueda, O. M., Aparicio, S. A. J. R., & Caldas, C. (2013) · The EMBO Journal · doi:10.1038/emboj.2013.19 · Cited by 299 · see citing works
Self-citationRosenbluth, J. M., Schackmann, R. C. J., Gray, G. K., Selfors, L. M., Li, C. M.-C., Boedicker, M., Kuiken, H. J., Richardson, A. L., Brock, J. E., Garber, J. E., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15548-7 · Cited by 277 · see citing works
Self-citationSomatic mutations reveal asymmetric cellular dynamics in the early human embryo
Ju, Y. S., Martincorena, I., Gerstung, M., Petljak, M., Alexandrov, L. B., Rahbari, R., Wedge, D. C., Davies, H. R., Ramakrishna, M., Fullam, A., et al. (2017) · Nature · doi:10.1038/nature21703 · Cited by 272 · see citing works
Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing
Laks, E., McPherson, A., Zahn, H., Lai, D., Steif, A., Brimhall, J., Biele, J., Wang, B., Masud, T., Ting, J., et al. (2019) · Cell · doi:10.1016/j.cell.2019.10.026 · Cited by 247 · see citing works
Self-citationOncogenic properties of PPM1D located within a breast cancer amplification epicenter at 17q23
Li, J., Yang, Y., Yue, P., Austin, R. J., van Eyndhoven, W., Nguyen, K. C. Q., Gabriele, T., McCurrach, M. E., Marks, J. R., Hoey, T. C., et al. (2002) · Nature Genetics · doi:10.1038/ng888 · Cited by 246 · see citing works
Inherent mosaicism and extensive mutation of human placentas
Coorens, T. H. H., Oliver, T. R. W., Sanghvi, R., Sovio, U., Cook, E., Vento‐Tormo, R., Haniffa, M. A., Young, M. D., Rahbari, R., Sebire, N. J., et al. (2021) · Nature · doi:10.1038/s41586-021-03345-1 · Cited by 213 · see citing works
Scalable whole-genome single-cell library preparation without preamplification
Zahn, H., Steif, A., Laks, E., Eirew, P. D., VanInsberghe, M. A., Shah, S. P., Aparicio, S. A. J. R., & Hansen, C. L. (2017) · Nature Methods · doi:10.1038/nmeth.4140 · Cited by 195 · see citing works
Self-citationFemale chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome
Machiela, M. J., Zhou, W., Karlins, E., Sampson, J. N., Freedman, N. D., Yang, Q., Hicks, B. D., Dagnall, C. L., Hautman, C., Jacobs, K. B., et al. (2016) · Nature Communications · doi:10.1038/ncomms11843 · Cited by 163 · see citing works
Evolutionary Pathways in BRCA1-Associated Breast Tumors
Martins, F. C., De, S., Almendro, V., Gönen, M., Park, S. Y., Blum, J. L., Herlihy, W. G., Ethington, G., Schnitt, S. J., Tung, N., et al. (2012) · Cancer Discovery · doi:10.1158/2159-8290.cd-11-0325 · Cited by 155 · see citing works
Self-citationA human breast atlas integrating single-cell proteomics and transcriptomics
Gray, G. K., Li, C. M.-C., Rosenbluth, J. M., Selfors, L. M., Girnius, N., Lin, J., Schackmann, R. C. J., Goh, W. L., Moore, K., Shapiro, H., et al. (2022) · Developmental Cell · doi:10.1016/j.devcel.2022.05.003 · Cited by 151 · see citing works
Self-citationGenomic Architecture Characterizes Tumor Progression Paths and Fate in Breast Cancer Patients
Russnes, H. G., Vollan, H. K. M., Lingjærde, O. C., Krasnitz, A., Lundin, P., Naume, B., Sørlie, T., Borgen, E., Rye, I. H., Langerød, A., et al. (2010) · Science Translational Medicine · doi:10.1126/scitranslmed.3000611 · Cited by 150 · see citing works
Oncogene-like addiction to aneuploidy in human cancers
Girish, V., Lakhani, A. A., Thompson, S. L., Scaduto, C. M., Brown, L. M., Hagenson, R. A., Sausville, E. L., Mendelson, B. E., Kandikuppa, P. K., Lukow, D. A., et al. (2023) · Science · doi:10.1126/science.adg4521 · Cited by 146 · see citing works
Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencingPreprint
Cortés‐Ciriano, I., Lee, J. J.-K., Xi, R., Jain, D. S., Jung, Y. L., Yang, L., Gordenin, D. A., Klimczak, L. J., Zhang, C., Pellman, D. S., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/333617 · Cited by 137 · see citing works
Sedic, M., Skibinski, A., Brown, N. E., Gallardo, M., Mulligan, P., Martínez, P., Keller, P. J., Glover, E., Richardson, A. L., Cowan, J. M., et al. (2015) · Nature Communications · doi:10.1038/ncomms8505 · Cited by 137 · see citing works
Chromosome Segregation Fidelity in Epithelia Requires Tissue Architecture
Knouse, K. A., Lopez, K. E., Bachofner, M., & Amon, A. (2018) · Cell · doi:10.1016/j.cell.2018.07.042 · Cited by 134 · see citing works
Single-cell genomic variation induced by mutational processes in cancer
Funnell, T., O’Flanagan, C. H., Williams, M. J., McPherson, A., McKinney, S. E., Kabeer, F., Lee, H., Salehi, S., Vázquez-Garćıa, I., Shi, H., et al. (2022) · Nature · doi:10.1038/s41586-022-05249-0 · Cited by 131 · see citing works
Self-citationRejection of immunogenic tumor clones is limited by clonal fraction
Gejman, R. S., Chang, A. Y., Jones, H. F., DiKun, K. M., Hakimi, A. A., Schietinger, A., & Scheinberg, D. A. (2018) · eLife · doi:10.7554/elife.41090 · Cited by 127 · see citing works
Nuclear chromosome locations dictate segregation error frequencies
Klaasen, S. J., Truong, M. A., van Jaarsveld, R. H., Koprivec, I., Štimac, V., de Vries, S. G., Risteski, P., Kodba, S., Vukušić, K., de Luca, K. L., et al. (2022) · Nature · doi:10.1038/s41586-022-04938-0 · Cited by 124 · see citing works
ERα-associated translocations underlie oncogene amplifications in breast cancer
Lee, J. J.-K., Jung, Y. L., Cheong, T.-C., Valle-Inclán, J. E., Chu, C., Gulhan, D., Ljungström, V., Jin, H., Viswanadham, V., Watson, E. V., et al. (2023) · Nature · doi:10.1038/s41586-023-06057-w · Cited by 123 · see citing works
Notch1 mutations drive clonal expansion in normal esophageal epithelium but impair tumor growth
Abby, E., Dentro, S. C., Hall, M. W. J., Fowler, J. C., Ong, S. H., Sood, R., Herms, A., Piedrafita, G., Abnizova, I., Siebel, C. W., et al. (2023) · Nature Genetics · doi:10.1038/s41588-022-01280-z · Cited by 121 · see citing works
Non-random Mis-segregation of Human Chromosomes
Worrall, J. T., Tamura, N., Mazzagatti, A., Shaikh, N., van Lingen, T., Bakker, B., Spierings, D. C. J., Vladimirou, E., Foijer, F., & McClelland, S. E. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.05.047 · Cited by 113 · see citing works
Lips, E. H., Kumar, T., Megalios, A., Visser, L. L., Sheinman, M., Fortunato, A., Shah, V., Hoogstraat, M., Sei, E., Mallo, D., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01082-3 · Cited by 98 · see citing works
New paradigms in clonal evolution: punctuated equilibrium in cancer
Cross, W. C. H., Graham, T. A., & Wright, N. A. (2016) · The Journal of Pathology · doi:10.1002/path.4757 · Cited by 86 · see citing works
Evolutionary histories of breast cancer and related clones
Nishimura, T., Kakiuchi, N., Yoshida, K., Sakurai, T., Kataoka, T. R., Kondoh, E., Chigusa, Y., Kawai, M., Sawada, M., Inoue, T., et al. (2023) · Nature · doi:10.1038/s41586-023-06333-9 · Cited by 85 · see citing works
A glycolytic metabolite bypasses “two-hit” tumor suppression by BRCA2
Kong, L. R., Gupta, K., Wu, A., Perera, D., Iványi-Nagy, R., Ahmed, S. M., Tan, T. Z., Tan, S. L.-W., Fuddin, A., Sundaramoorthy, E., et al. (2024) · Cell · doi:10.1016/j.cell.2024.03.006 · Cited by 74 · see citing works
Archival single-cell genomics reveals persistent subclones during DCIS progression
Wang, K., Kumar, T., Wang, J., Minussi, D. C., Sei, E., Li, J., Tran, T. M., Thennavan, A., Hu, M. S., Casasent, T. D., et al. (2023) · Cell · doi:10.1016/j.cell.2023.07.024 · Cited by 61 · see citing works
SCOPIT: sample size calculations for single-cell sequencing experiments
Davis, A., Gao, R., & Navin, N. E. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-3167-9 · Cited by 57 · see citing works
Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns
Watson, E. V., Lee, J. J.-K., Gulhan, D., Melloni, G. E. M., Venev, S. V., Magesh, R. Y., Frederick, A., Chiba, K., Wooten, E. C., Naxerova, K., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01665-2 · Cited by 51 · see citing works
Jakubek, Y. A., Chang, K., Sivakumar, S., Yu, Y., Giordano, M. R., Fowler, J., Huff, C., Kadara, H. N., Vilar, E., & Scheet, P. A. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0297-6 · Cited by 44 · see citing works
Cancer phylogenetic tree inference at scale from 1000s of single cell genomes
Salehi, S., Dorri, F., Chern, K., Kabeer, F., Rusk, N., Funnell, T., Williams, M. J., Lai, D., Andronescu, M., Campbell, K. R., et al. (2023) · Peer Community Journal · doi:10.24072/pcjournal.292 · Cited by 39 · see citing works
Self-citationThe origins and functional effects of postzygotic mutations throughout the human life span
Rockweiler, N. B., Ramu, A., Nagirnaja, L., Wong, W., Noordam, M. J., Drubin, C. W., Huang, N., Miller, B., Todres, E. Z., Vigh‐Conrad, K. A., et al. (2023) · Science · doi:10.1126/science.abn7113 · Cited by 35 · see citing works
Privitera, A. P., Barresi, V., & Condorelli, D. F. (2021) · Cancers · doi:10.3390/cancers13071585 · Cited by 23 · see citing works
Farabegoli, F., Hermsen, M. A. J. A., Ceccarelli, C., Santini, D., Weiss, M. M., Meijer, G. A., & van Diest, P. J. (2004) · Modern Pathology · doi:10.1038/modpathol.3800059 · Cited by 23 · see citing works
A pan-tissue survey of mosaic chromosomal alterations in 948 individuals
Gao, T., Kastriti, M., Ljungström, V., Heinzel, A., Tischler, A. S., Oberbauer, R., Loh, P.-R., Adameyko, I., Park, P. J., & Kharchenko, P. (2023) · Nature Genetics · doi:10.1038/s41588-023-01537-1 · Cited by 21 · see citing works
Shi, H., Williams, M. J., Satas, G., Weiner, A. C., McPherson, A., & Shah, S. P. (2024) · Nature Communications · doi:10.1038/s41467-024-46710-0 · Cited by 20 · see citing works
Self-citationDisentangling oncogenic amplicons in esophageal adenocarcinoma
Ng, A. W. T., McClurg, D. P., Wesley, B., Zamani, S. A., Black, E. L., Miremadi, A., Giger, O., ten Hoopen, R., Devonshire, G., Redmond, A. M., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-47619-4 · Cited by 20 · see citing works
Self-citationRye, I. H., Lundin, P., Månér, S., Fjelldal, R., Naume, B., Wigler, M. H., Hicks, J. B., Børresen‐Dale, A., Zetterberg, A., & Russnes, H. G. (2014) · Genes Chromosomes and Cancer · doi:10.1002/gcc.22237 · Cited by 20 · see citing works
The mutational landscape of the adult healthy parous and nulliparous human breast
Cereser, B., Yiu, A., Tabassum, N., Belluz, L. D. B., Zagorac, S., Ancheta, K., Zhong, R., Miere, C., Jeffries-Jones, A. R., Moderau, N., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-40608-z · Cited by 19 · see citing works
Daniel Lai, G. H. (2017) · NCI BioConductor · doi:10.18129/b9.bioc.hmmcopy · Cited by 14 · see citing works
Ongoing genome doubling promotes evolvability and immune dysregulation in ovarian cancerPreprint
McPherson, A., Vázquez-Garćıa, I., Myers, M. A., Zatzman, M., Al-Rawi, D. H., Weiner, A. C., Freeman, S. S., Mohibullah, N., Satas, G., Williams, M. J., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.11.602772 · Cited by 10 · see citing works
Self-citationWilliams, M. J., Vázquez-Garćıa, I., Tam, G. K., Wu, M., Varice, N., Havasov, E., Shi, H., Satas, G., Lees, H., Lee, J. J.-K., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.21.609031 · Cited by 8 · see citing works
Self-citationWilliams, M., & Funnell, T. (2022) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.6642341 · Cited by 2 · see citing works
Self-citationWilliams, M. J. (2024) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.13645601 · Cited by 1 · see citing works
Self-citationmarcjwilliams1/normal_brca_scdna: v0.1.0
Williams, M. J. (2024) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.13904325 · Cited by 1 · see citing works
Self-citation
Flagged first, then by citations
Research works printed but not linked: 2
- [10]PCAWG Transcriptome Core Group et al. Genomic basis for RNA alterations in cancer. Nature578, 129–136 (2020). PMC7054216 32025019
- [59]Davis, A., Gao, R. & Navin, N. Tumor evolution: linear, branching, neutral or punctuated? Biochim. Biophys. Acta 1867, 151–161 (2017). PMC5558210 28110020
Cited by
Sorted by citations
The end of the genetic paradigm of cancer
Huang, S., Soto, A. M., & Sonnenschein, C. (2025) · PLoS Biology · doi:10.1371/journal.pbio.3003052 · Cited by 66 · see citing works
Tracking clonal evolution during treatment in ovarian cancer using cell-free DNA
Williams, M. J., Vázquez-Garćıa, I., Tam, G. K., Wu, M. K. Y., Varice, N., Havasov, E., Shi, H., Al-Rawi, D. H., Satas, G., Lees, H., et al. (2025) · Nature · doi:10.1038/s41586-025-09580-0 · Cited by 32 · see citing works
Self-citationLandragin, C., Saichi, M., Laisné, M., Durand, A., Prompsy, P., Leclère, R., Mesple, J., Borgman, K. J. E., Trouchet, A., Faraldo, M. M., et al. (2025) · Molecular Cancer · doi:10.1186/s12943-025-02331-9 · Cited by 13 · see citing works
Thirty Years of BRCA1: Mechanistic Insights and Their Impact on Mutation Carriers
Moser, S. C., & Jonkers, J. (2025) · Cancer Discovery · doi:10.1158/2159-8290.cd-24-1326 · Cited by 12 · see citing works
Evolution of Multiple Myeloma from a Genomic Perspective
Maura, F., Samur, M., & Munshi, N. (2026) · Blood · doi:10.1182/blood.2024026313 · Cited by 8 · see citing works
Pal, T., Christopher, J., Astiazarán-Symonds, E., Foulkes, W. D., James, P., Klugman, S. D., Kurian, A. W., Mak, J. S., Monteiro, A. N., Robson, M. E., et al. (2026) · Genetics in Medicine · doi:10.1016/j.gim.2025.101659 · Cited by 8 · see citing works
Unraveling the role of withanolides as key modulators in breast cancer mitigation
Hameed, H., Afzal, M., Khan, M. A., Javaid, L., Shahzad, M., & Abrar, K. (2025) · Molecular Biology Reports · doi:10.1007/s11033-025-10442-1 · Cited by 6 · see citing works
Single-cell spatial atlas of the aging human breast
Gupta, P., Lee, E., Masqué‐Soler, N., Schrader, E., Wang, X. Q., Mayer, S., Flores, C. C., Beatty, S., Roth, A., Aparicio, S. A. J. R., et al. (2026) · Nature Aging · doi:10.1038/s43587-026-01104-3 · Cited by 4 · see citing works
Self-citationKrings, G., Shamir, E. R., Hwang, E., & Chen, Y. (2025) · Modern Pathology · doi:10.1016/j.modpat.2025.100820 · Cited by 3 · see citing works
Of Barriers and Loops—How Evolution Limits Most Cancer Risks to Older Ages
Dominici, M. D., & DeGregori, J. V. (2026) · Cancer Discovery · doi:10.1158/2159-8290.cd-25-0779 · Cited by 3 · see citing works
Zhang, G., Lin, W., Guo, L., Li, Z., Xiang, Y., Wang, L., & Yan, X. (2026) · iScience · doi:10.1016/j.isci.2026.115356 · Cited by 3 · see citing works
A single-cell lens into the co-evolution of genotypes and phenotypes in cancer
Izzo, F., Prieto, T., Potenski, C. J., & Landau, D. A. (2026) · Nature reviews. Cancer · doi:10.1038/s41568-026-00970-8 · Cited by 2 · see citing works
BMI and Breast Subcutaneous Fat
Wang, S., Zhou, J., Huang, Y., Zheng, D., Hou, R., & Zhou, S. (2025) · Journal of Ultrasound in Medicine · doi:10.1002/jum.70096 · Cited by 2 · see citing works
Echidna: A Bayesian framework for quantifying gene dosage effect impacting phenotypic plasticityPreprint
Fan, J. L., Zhang, M., O’Brien, W., Myers, J. D., Melms, J. C., Biermann, J., D’Souza, E. K., Tagore, S., Beltran-Velez, N., Hoffer-Hawlik, K., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.15.628568 · Cited by 2 · see citing works
High-speed cell partitioning through reactive machine learning-guided inkjet printing
Cheng, E., Chang, G., MacDonald, H., Ramirez, M., Hoodless, P. A., Coope, R., Steif, A., & Cheung, K. C. (2025) · Lab on a Chip · doi:10.1039/d5lc00514k · Cited by 1 · see citing works
Kolbeinsdóttir, S., Zachariadis, V., Sommerauer, C., Lohi, O., Heinäniemi, M., & Enge, M. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf919 · Cited by 1 · see citing works
Somatic mutations and clonal evolution in normal tissues and cancer development
Yoshida, K. (2025) · Experimental & Molecular Medicine · doi:10.1038/s12276-025-01592-0 · Cited by 1 · see citing works
Kader, T., Chen, Y., Hug, C. B., Lin, J., Muhlich, J. L., Coy, S., Jung, E., Schwartz, L. E., Fazio, T., Chiu, C., et al. (2026) · Cancer Discovery · doi:10.1158/2159-8290.cd-26-0171 · Cited by 1 · see citing works
Evidence that extra copies of chromosome 1q play a role in the early phases of pancreatic neoplasia
Douville, C. B., Parksong, J., Molin, M. D., Graham, S., Greipp, P. T., Knudson, R. A., Curtis, S. D., Wang, Y., Dobbyn, L., Popoli, M., et al. (2026) · Science Advances · doi:10.1126/sciadv.adx7501 · Cited by 1 · see citing works
Stem cells as an essential mediator of the exercise–tumorigenesis link
Zhuang, X., Wong, E. S. W., Tammela, T., & Jones, L. W. (2026) · Nature reviews. Cancer · doi:10.1038/s41568-026-00933-z · Cited by 1 · see citing works
Forecasting oncogene amplification and tumour suppressor deletionPreprint
Hernando, B., Fernández-Sanromán, Á., Cádiz, A., Santamaría, P., Gómez-Sánchez, D., Escobar-Rey, M., Chaves-Urbano, B., Thompson, J. S., Torres, M., Ponce, G. R. D. G., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.06.658212 · Cited by 1 · see citing works
Eyal-Lubling, Y., Vias, M., Kania, K., Kaludova, D., Hall, J., Crawford, R., Nyagumbo, R., Ward, S., Khoronenkova, S., Aparicio, S. A. J. R., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.26.746998 · Cited by 1 · see citing works
Self-citationBRCA1/2 germline sequencing in children and adolescents with cancer: it is the context that matters
Goudie, C. (2025) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/djae339
Redefining “normal”: discovery of aneuploid epithelial cells in healthy breast tissue
Chen, X., Liu, X., Xue, J., & Li, Z. (2025) · Frontiers in Oncology · doi:10.3389/fonc.2025.1558977
Timing the Onset of Homologous Recombination Deficiency Before Cancer DiagnosisPreprint
Andreopoulos, M., Niu, M., Zhang, Y., Viswanadham, V., Gulhan, D., Jin, H., Batalini, F., Wulf, G. M., Zong, C. C., Park, P. J., et al. (2025) · SSRN Electronic Journal · doi:10.2139/ssrn.5412800
Timing the onset of homologous recombination deficiency before breast cancer diagnosisPreprint
Andreopoulos, M., Niu, M., Zhang, Y., Viswanadham, V., Gulhan, D., Jin, H., Batalini, F., Wulf, G. M., Zong, C. C., Park, P. J., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.17.683157
Aneuploidy patterns in colorectal cancer
Zaalberg, I. C., Ketelaars, S. L. C., Jodal, H. C., Løberg, M., Kalager, M., Meijer, G. A., Carvalho, B. G., & Lens, S. M. A. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.116721
Quantifying rate-limiting genetic variation in breast and ovarian tumourigenesis
Houlahan, K. E., Bihie, M., Greatti, Y., Contreras, J. G., Fulop, D. J., López, G., Williams, M. J., Huang, H.-H., Loo, P. V., Boutros, P. C., et al. (2026) · EBioMedicine · doi:10.1016/j.ebiom.2026.106181
Self-citationCellular and spatial remodeling of aging breast tissue revealed
(2026) · Nature Aging · doi:10.1038/s43587-026-01111-4
Molecular evolution of mosaic chromosome 18 copy-number alterations from gametes to hepatoblastoma
Cendres, E., Cornet, M., Gautier, Z., Pire, A., Urvoy, N., Morcrette, G., Simaga, F., Guimier, A., Chardot, C., Capito, C., et al. (2026) · JHEP Reports · doi:10.1016/j.jhepr.2026.101862
Tissue-Specific Prevalence and Clonal Architecture of BRCA1/2 LOH-Inducing Chromosomal AneuploidyPreprint
Wang, X., Sisoudiya, S. D., Bihie, M., Greatti, Y., Contreras, J. G., Jun, T. W., Sivakumar, S., & Huang, K. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.17.718766
Epithelial mesenchymal transition initiates precancer states in BRCA1 mutation carriersPreprint
Bar-Hai, N., Ben-Yishay, R., Arbili-Yarhi, S., Bernstein‐Molho, R., Goldinger, G., Balint‐Lahat, N., Menes, T. S., Herman, N., Noy, V., Mansour, A., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.06.723061
A guide to understanding tumour evolution through the lens of population genetics
Caravagna, G., Graham, T. A., & Sottoriva, A. (2026) · Nature reviews. Cancer · doi:10.1038/s41568-026-00973-5
Protracted copy number alteration evolution in Barrett’s oesophagus leading to oesophageal cancerPreprint
Gabbutt, C., Fernández-Sanromán, Á., Grant, H. E., Milite, S., Cross, W. C. H., Wright, N. A., Maley, C. C., Sottoriva, A., Caravagna, G., Paulson, T. G., et al. (2026) · medRxiv · doi:10.64898/2026.10.16.26365037
- Authors
- Williams, M. J., Oliphant, M. U. J., Au, V., Liu, C., Baril, C., O’Flanagan, C., Lai, D., Beatty, S., Van Vliet, M., Yiu, J. C., O’Connor, L., Goh, W. L., Pollaci, A., Weiner, A. C., Grewal, D., McPherson, A., Norton, K., Moore, M., Prabhakar, V., Agarwal, S., Garber, J. E., Dillon, D. A., Shah, S. P., Brugge, J. S., & Aparicio, S.
- Affiliations
- Memorial Sloan Kettering Cancer Center (US)
- Harvard University (US)
- University of British Columbia (CA)
- Dana-Farber Cancer Institute (US)
- Brigham and Women's Hospital (US)
- Corresponding author
- Shah, Sohrab P.
- Brugge, Joan S.
- Aparicio, Samuel
- ORCID
- Venue
- Nature Genetics
- Published
- 2024-11-20
- Volume
- 56
- Issue
- 12
- Pages
- 2753-2762
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC11631757
- OpenAlex
- W4404566931
- Cited by
- 34
- References
- 68
- Citations by year
- 2026: 16 · 2025: 17 · 2024: 1
- FWCI
- 6.82
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature Genetics (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- National Human Genome Research Institute (RM1HG011014)
- National Cancer Institute (K99CA256508, P50CA247749, P30CA008748, R35CA242428, P50CA168504)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › BRCA gene mutations in cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- somatic copy number alterations, BRCA1 mutation carriers, BRCA2 mutation carriers, breast cancer, loss of heterozygosity, aneuploidy, p53 deficiency, convergent evolution, tumor initiation, clonal evolution, single-cell DNA sequencing
- MeSH terms
- Breast, Breast Neoplasms, Epithelial Cells, Female, Heterozygote, Humans, Mutation, BRCA1 Protein, Loss of Heterozygosity, BRCA2 Protein, DNA Copy Number Variations, Single-Cell Analysis
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review