Curtis, C. et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 486, 346–352 (2012).
The Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature 490, 61–70 (2012).
Hassiotou, F. & Geddes, D. Anatomy of the human mammary gland: current status of knowledge. Clin. Anat. 26, 29–48 (2013).
Kumar, T. et al. A spatially resolved single-cell genomic atlas of the adult human breast. Nature 620, 181–191 (2023).
Wang, Y. & Navin, N. E. Advances and applications of single-cell sequencing technologies. Mol. Cell 58, 598–609 (2015).
Martincorena, I. et al. Tumor evolution. High burden and pervasive positive selection of somatic mutations in normal human skin. Science 348, 880–886 (2015).
Martincorena, I. et al. Somatic mutant clones colonize the human esophagus with age. Science 362, 911–917 (2018).
Lee-Six, H. et al. The landscape of somatic mutation in normal colorectal epithelial cells. Nature 574, 532–537 (2019).
Brunner, S. F. et al. Somatic mutations and clonal dynamics in healthy and cirrhotic human liver. Nature 574, 538–542 (2019).
Blokzijl, F. et al. Tissue-specific mutation accumulation in human adult stem cells during life. Nature 538, 260–264 (2016).
Li, R. et al. Macroscopic somatic clonal expansion in morphologically normal human urothelium. Science 370, 82–89 (2020).
Moore, L. et al. The mutational landscape of normal human endometrial epithelium. Nature 580, 640–646 (2020).
Nishimura, T. et al. Evolutionary histories of breast cancer and related clones. Nature 620, 607–614 (2023).
Park, S. et al. Clonal dynamics in early human embryogenesis inferred from somatic mutation. Nature 597, 393–397 (2021).
Li, R. et al. A body map of somatic mutagenesis in morphologically normal human tissues. Nature 597, 398–403 (2021).
McConnell, M. J. et al. Mosaic copy number variation in human neurons. Science 342, 632–637 (2013).
Wang, J., Fan, H. C., Behr, B. & Quake, S. R. Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell 150, 402–412 (2012).
Liu, L. et al. Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling. Genome Res. 32, 44–54 (2022).
Zhou, Y. et al. Single-cell multiomics sequencing reveals prevalent genomic alterations in tumor stromal cells of human colorectal cancer. Cancer Cell 38, 818–828 e815 (2020).
Knouse, K. A., Wu, J., Whittaker, C. A. & Amon, A. Single cell sequencing reveals low levels of aneuploidy across mammalian tissues. Proc. Natl Acad. Sci. USA 111, 13409–13414 (2014).
Gawad, C., Koh, W. & Quake, S. R. Single-cell genome sequencing: current state of the science. Nat. Rev. Genet. 17, 175–188 (2016).
Wang, K. et al. Archival single-cell genomics reveals persistent subclones during DCIS progression. Cell 186, 3968–3982 (2023).
Mermel, C. H. et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12, R41 (2011).
Koon, H. B., Ippolito, G. C., Banham, A. H. & Tucker, P. W. FOXP1: a potential therapeutic target in cancer. Expert Opin. Ther. Targets 11, 955–965 (2007).
Yu, X. et al. TUSC3: a novel tumour suppressor gene and its functional implications. J. Cell. Mol. Med. 21, 1711–1718 (2017).
Chen, W. X., Cheng, L., Xu, L. Y., Qian, Q. & Zhu, Y. L. Bioinformatics analysis of prognostic value of TRIM13 gene in breast cancer. Biosci. Rep. 39, BSR20190285 (2019).
Ren, L. et al. Caveolin-1 is a prognostic marker and suppresses the proliferation of breast cancer. Transl. Cancer Res. 10, 3797–3810 (2021).
Kaufmann, T. L. et al. MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution. Genome Biol. 23, 241 (2022).
Wang, K. et al. Single cell genome and epigenome co-profiling reveals hardwiring and plasticity in breast cancer. Preprint at bioRxiv https://doi.org/10.1101/2024.09.06.611519 (2024).
Pervolarakis, N. et al. Integrated single-cell transcriptomics and chromatin accessibility analysis reveals regulators of mammary epithelial cell identity. Cell Rep. 33, 108273 (2020).
Gao, R. et al. Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes. Nat. Biotechnol. 39, 599–608 (2021).
Butler, A., Hoffman, P., Smibert, P., Papalexi, E. & Satija, R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat. Biotechnol. 36, 411–420 (2018).
McGuire, A., Brown, J. A., Malone, C., McLaughlin, R. & Kerin, M. J. Effects of age on the detection and management of breast cancer. Cancers 7, 908–929 (2015).
Machiela, M. J. et al. Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome. Nat. Commun. 7, 11843 (2016).
Yates, L. R. et al. Subclonal diversification of primary breast cancer revealed by multiregion sequencing. Nat. Med. 21, 751–759 (2015).
Minussi, D. C. et al. Breast tumours maintain a reservoir of subclonal diversity during expansion. Nature 592, 302–308 (2021).
Leighton, J., Hu, M., Sei, E., Meric-Bernstam, F. & Navin, N. E. Reconstructing mutational lineages in breast cancer by multi-patient-targeted single-cell DNA sequencing. Cell Genom. 3, 100215 (2023).
Haupt, S. et al. The role of MDM2 and MDM4 in breast cancer development and prevention. J. Mol. Cell. Biol. 9, 53–61 (2017).
Bose, S. et al. Reduced expression of PTEN correlates with breast cancer progression. Hum. Pathol. 33, 405–409 (2002).
McCart Reed, A. E. et al. The genomic landscape of lobular breast cancer. Cancers 13, 1950 (2021).
Pearson, A. et al. Inactivating NF1 mutations are enriched in advanced breast cancer and contribute to endocrine therapy resistance. Clin. Cancer Res. 26, 608–622 (2020).
Karaayvaz-Yildirim, M. et al. Aneuploidy and a deregulated DNA damage response suggest haploinsufficiency in breast tissues of BRCA2 mutation carriers. Sci. Adv. 6, eaay2611 (2020).
Minussi, D. C. et al. Resolving clonal substructure from single cell genomic data using CopyKit. Preprint at bioRxiv https://doi.org/10.1101/2022.03.09.483497 (2022).
Delaneau, O., Marchini, J. & Zagury, J. F. A linear complexity phasing method for thousands of genomes. Nat. Methods 9, 179–181 (2011).
Huang, X. & Huang, Y. Cellsnp-lite: an efficient tool for genotyping single cells. Bioinformatics 37, 4569–4571 (2021).
Funnell, T. et al. Single-cell genomic variation induced by mutational processes in cancer. Nature 612, 106–115 (2022).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Granja, J. M. et al. ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis. Nat. Genet. 53, 403–411 (2021).
Granja, J. M. et al. Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia. Nat. Biotechnol. 37, 1458–1465 (2019).
Korsunsky, I. et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat. Methods 16, 1289–1296 (2019).
Lun, A. T., McCarthy, D. J. & Marioni, J. C. A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor. F1000Res 5, 2122 (2016).
Thennavan, A. et al. Molecular analysis of TCGA breast cancer histologic types. Cell Genom. 1, 100067 (2021).