Normal breast tissues harbour rare populations of aneuploid epithelial cells – Nature
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).
Google Scholar
Hassiotou, F. & Geddes, D. Anatomy of the human mammary gland: current status of knowledge. Clin. Anat. 26, 29–48 (2013).
Google Scholar
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).
Google Scholar
Martincorena, I. et al. Tumor evolution. High burden and pervasive positive selection of somatic mutations in normal human skin. Science 348, 880–886 (2015).
Google Scholar
Martincorena, I. et al. Somatic mutant clones colonize the human esophagus with age. Science 362, 911–917 (2018).
Google Scholar
Lee-Six, H. et al. The landscape of somatic mutation in normal colorectal epithelial cells. Nature 574, 532–537 (2019).
Google Scholar
Brunner, S. F. et al. Somatic mutations and clonal dynamics in healthy and cirrhotic human liver. Nature 574, 538–542 (2019).
Google Scholar
Blokzijl, F. et al. Tissue-specific mutation accumulation in human adult stem cells during life. Nature 538, 260–264 (2016).
Google Scholar
Li, R. et al. Macroscopic somatic clonal expansion in morphologically normal human urothelium. Science 370, 82–89 (2020).
Google Scholar
Moore, L. et al. The mutational landscape of normal human endometrial epithelium. Nature 580, 640–646 (2020).
Google Scholar
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).
Google Scholar
Li, R. et al. A body map of somatic mutagenesis in morphologically normal human tissues. Nature 597, 398–403 (2021).
Google Scholar
McConnell, M. J. et al. Mosaic copy number variation in human neurons. Science 342, 632–637 (2013).
Google Scholar
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).
Google Scholar
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).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Gawad, C., Koh, W. & Quake, S. R. Single-cell genome sequencing: current state of the science. Nat. Rev. Genet. 17, 175–188 (2016).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Yu, X. et al. TUSC3: a novel tumour suppressor gene and its functional implications. J. Cell. Mol. Med. 21, 1711–1718 (2017).
Google Scholar
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).
Google Scholar
Ren, L. et al. Caveolin-1 is a prognostic marker and suppresses the proliferation of breast cancer. Transl. Cancer Res. 10, 3797–3810 (2021).
Google Scholar
Kaufmann, T. L. et al. MEDICC2: whole-genome doubling aware copy-number phylogenies for cancer evolution. Genome Biol. 23, 241 (2022).
Google Scholar
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).
Google Scholar
Gao, R. et al. Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes. Nat. Biotechnol. 39, 599–608 (2021).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Machiela, M. J. et al. Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome. Nat. Commun. 7, 11843 (2016).
Google Scholar
Yates, L. R. et al. Subclonal diversification of primary breast cancer revealed by multiregion sequencing. Nat. Med. 21, 751–759 (2015).
Google Scholar
Minussi, D. C. et al. Breast tumours maintain a reservoir of subclonal diversity during expansion. Nature 592, 302–308 (2021).
Google Scholar
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).
Google Scholar
Haupt, S. et al. The role of MDM2 and MDM4 in breast cancer development and prevention. J. Mol. Cell. Biol. 9, 53–61 (2017).
Google Scholar
Bose, S. et al. Reduced expression of PTEN correlates with breast cancer progression. Hum. Pathol. 33, 405–409 (2002).
Google Scholar
McCart Reed, A. E. et al. The genomic landscape of lobular breast cancer. Cancers 13, 1950 (2021).
Google Scholar
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).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Huang, X. & Huang, Y. Cellsnp-lite: an efficient tool for genotyping single cells. Bioinformatics 37, 4569–4571 (2021).
Google Scholar
Funnell, T. et al. Single-cell genomic variation induced by mutational processes in cancer. Nature 612, 106–115 (2022).
Google Scholar
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Google Scholar
Granja, J. M. et al. ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis. Nat. Genet. 53, 403–411 (2021).
Google Scholar
Granja, J. M. et al. Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia. Nat. Biotechnol. 37, 1458–1465 (2019).
Google Scholar
Korsunsky, I. et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat. Methods 16, 1289–1296 (2019).
Google Scholar
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).
Google Scholar
Thennavan, A. et al. Molecular analysis of TCGA breast cancer histologic types. Cell Genom. 1, 100067 (2021).
Google Scholar