[1] Nowell P C. The clonal evolution of tumor cell populations [J]. Science, 1976, 194(4260): 23-28.
[2] Merlo L M F, Pepper J W, Reid B J, et al. Cancer as an evolutionary and ecological process [J]. Nature Reviews Cancer, 2006, 6(12): 924-935.
[3] Greaves M, Maley C C. Clonal evolution in cancer [J]. Nature, 2012, 481(7381): 306-313.
[4] Cairns J. Mutation selection and the natural history of cancer [J]. Nature, 1975, 255(5505): 197-200.
[5] Nik-Zainal S, Van Loo P, Wedge D C, et al. The life history of 21 breast cancers [J]. Cell, 2012, 149(5): 994-1007.
[6] Marusyk A, Janiszewska M, Polyak K. Intratumor heterogeneity: The Rosetta stone of therapy resistance [J]. Cancer Cell, 2020, 37(4): 471-484.
[7] Gao J J, Aksoy B A, Dogrusoz U, et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal [J]. Science Signaling, 2013, 6(269): pl1.
[8] Funnell T, O’Flanagan C H, Williams M J, et al. Single-cell genomic variation induced by mutational processes in cancer [J]. Nature, 2022, 612(7938): 106-115.
[9] Cosenza M R, Rodriguez-Martin B, Korbel J O. Structural variation in cancer: Role, prevalence, and mechanisms [J]. Annual Review of Genomics and Human Genetics, 2022, 23: 123-152.
[10] Dentro S C, Leshchiner I, Haase K, et al. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes [J]. Cell, 2021, 184(8): 2239-2254. e39.
[11] McGranahan N, Swanton C. Clonal heterogeneity and tumor evolution: Past, present, and the future [J]. Cell, 2017, 168(4): 613-628.
[12] Unni A M, Lockwood W W, Zejnullahu K, et al. Evidence that synthetic lethality underlies the mutual exclusivity of oncogenic KRAS and EGFR mutations in lung adenocarcinoma [J]. eLife, 2015, 4: e06907.
[13] Huang L M, Guo Z X, Wang F, et al. KRAS mutation: From undruggable to druggable in cancer [J]. Signal Transduction and Targeted Therapy, 2021, 6: 386.
[14] Lourenço F C, Sadien I D, Wong K, et al. Decay of driver mutations shapes the landscape of intestinal transformation [J]. Nature, 2026, 649(8097): 729-738.
[15] Kumar S, Warrell J, Li S T, et al. Passenger mutations in more than 2, 500 cancer genomes: Overall molecular functional impact and consequences [J]. Cell, 2020, 180(5): 915-927.e16.
[16] Shen X K, Song S L, Li C, et al. Synonymous mutations in representative yeast genes are mostly strongly non-neutral [J]. Nature, 2022, 606(7915): 725-731.
[17] Dagogo-Jack I, Shaw A T. Tumour heterogeneity and resistance to cancer therapies [J]. Nature Reviews Clinical Oncology, 2018, 15(2): 81-94.
[18] Bailey C, Black J R M, Reading J L, et al. Tracking cancer evolution through the disease course [J]. Cancer Discovery, 2021, 11(4): 916-932.
[19] Yates L R, Campbell P J. Evolution of the cancer genome [J]. Nature Reviews Genetics, 2012, 13(11): 795-806.
[20] Savy T, Flanders L, Karpanasamy T, et al. Cancer evolution: From Darwin to the extended evolutionary synthesis [J]. Trends in Cancer, 2025, 11(3): 204-215.
[21] Al Bakir M, Reading J L, Gamble S, et al. Clonal driver neoantigen loss under EGFR TKI and immune selection pressures [J]. Nature, 2025, 639(8056): 1052-1059.
[22] Fernandez-Mateos J, Cresswell G D, Trahearn N, et al. Tumor evolution metrics predict recurrence beyond 10 years in locally advanced prostate cancer [J]. Nature Cancer, 2024, 5(9): 1334-1351.
[23] van den Berg N I, Swanton C, Turajlic S. TRACERx as an optimized paradigm for understanding cancer evolution [J]. Annual Review of Cancer Biology, 2025. https://doi.org/10.1146/annurev-cancerbio-070824-125326.
[24] Tarabichi M, Salcedo A, Deshwar A G, et al. A practical guide to cancer subclonal reconstruction from DNA sequencing [J]. Nature Methods, 2021, 18(2): 144-155.
[25] Martincorena I, Raine K M, Gerstung M, et al. Universal patterns of selection in cancer and somatic tissues [J]. Cell, 2018, 173(7): 1823.
[26] Shih J, Sarmashghi S, Zhakula-Kostadinova N, et al. Cancer aneuploidies are shaped primarily by effects on tumour fitness [J]. Nature, 2023, 619(7971): 793-800.
[27] Curtius K, Wright N A, Graham T A. An evolutionary perspective on field cancerization [J]. Nature Reviews Cancer, 2018, 18(1): 19-32.
[28] Bozic I, Antal T, Ohtsuki H, et al. Accumulation of driver and passenger mutations during tumor progression [J]. Proceedings of the National Academy of Sciences of the United States of America, 2010, 107(43): 18545-18550.
[29] Jindal K, Adil M T, Yamaguchi N, et al. Single-cell lineage capture across genomic modalities with CellTag-multi reveals fate-specific gene regulatory changes [J]. Nature Biotechnology, 2024, 42(6): 946-959.
[30] Karlsson K, Przybilla M J, Kotler E, et al. Deterministic evolution and stringent selection during preneoplasia [J]. Nature, 2023, 618(7964): 383-393.
[31] Howland K K, Brock A. Cellular barcoding tracks heterogeneous clones through selective pressures and phenotypic transitions [J]. Trends in Cancer, 2023, 9(7): 591-601.
[32] Li L, Bowling S, McGeary S E, et al. A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells [J]. Cell, 2023, 186(23): 5183-5199.e22.
[33] Davis A, Gao R L, Navin N. Tumor evolution: Linear, branching, neutral or punctuated? [J]. Biochimica et Biophysica Acta Reviews on Cancer, 2017, 1867(2): 151-161.
[34] Williams M J, Sottoriva A, Graham T A. Measuring clonal evolution in cancer with genomics [J]. Annual Review of Genomics and Human Genetics, 2019, 20: 309-329.
[35] Sottoriva A, Kang H, Ma Z C, et al. A Big Bang model of human colorectal tumor growth [J]. Nature Genetics, 2015, 47(3): 209-216.
[36] Williams M J, Werner B, Barnes C P, et al. Identification of neutral tumor evolution across cancer types [J]. Nature Genetics, 2016, 48(3): 238-244.
[37] Tang J, Tu K L, Lu K Y, et al. Single-cell exome sequencing reveals multiple subclones in metastatic colorectal carcinoma [J]. Genome Medicine, 2021, 13(1): 148.
[38] Wang Y, Waters J, Leung M L, et al. Clonal evolution in breast cancer revealed by single nucleus genome sequencing [J]. Nature, 2014, 512(7513): 155-160.
[39] Guo L, Yi X F, Chen L, et al. Single-cell DNA sequencing reveals punctuated and gradual clonal evolution in hepatocellular carcinoma [J]. Gastroenterology, 2022, 162(1): 238-252.
[40] Hoadley K A, Yau C, Hinoue T, et al. Cell-of-origin patterns dominate the molecular classification of 10,000 tumors from 33 types of cancer [J]. Cell, 2018, 173(2): 291-304. e6.
[41] Williams M J, Werner B, Heide T, et al. Quantification of subclonal selection in cancer from bulk sequencing data [J]. Nature Genetics, 2018, 50(6): 895-903.
[42] Miller C A, White B S, Dees N D, et al. SciClone: Inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution [J]. PLoS Computational Biology, 2014, 10(8): e1003665.
[43] Roth A, Khattra J, Yap D, et al. PyClone: Statistical inference of clonal population structure in cancer [J]. Nature Methods, 2014, 11(4): 396-398.
[44] Caravagna G, Heide T, Williams M J, et al. Subclonal reconstruction of tumors by using machine learning and population genetics [J]. Nature Genetics, 2020, 52(9): 898-907.
[45] Lim B, Lin Y Y, Navin N. Advancing cancer research and medicine with single-cell genomics [J]. Cancer Cell, 2020, 37(4): 456-470.
[46] Jamal-Hanjani M, Wilson G A, McGranahan N, et al. Tracking the evolution of non–small-cell lung cancer [J]. New England Journal of Medicine, 2017, 376(22): 2109-2121.
[47] Turajlic S, Xu H, Litchfield K, et al. Tracking cancer evolution reveals constrained routes to metastases: TRACERx renal [J]. Cell, 2018, 173(3): 581-594. e12.
[48] Hu Z, Li Z, Ma Z C, et al. Multi-cancer analysis of clonality and the timing of systemic spread in paired primary tumors and metastases [J]. Nature Genetics, 2020, 52(7): 701-708.
[49] Sariipek N, van Galen P. Insights into leukemia from single-cell genomics [J]. Annual Review of Cancer Biology, 2025, 9: 267-284.
[50] Gerlinger M, Rowan A J, Horswell S, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing [J]. New England Journal of Medicine, 2012, 366(10): 883-892.
[51] Sun R P, Hu Z, Sottoriva A, et al. Between-region genetic divergence reflects the mode and tempo of tumor evolution [J]. Nature Genetics, 2017, 49(7): 1015-1024.
[52] Ling S P, Hu Z, Yang Z Y, et al. Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution [J]. Proceedings of the National Academy of Sciences of the United States of America, 2015, 112(47): E6496-E6505.
[53] Alves J M, Prieto T, Posada D. Multiregional tumor trees are not phylogenies [J]. Trends in Cancer, 2017, 3(8): 546-550.
[54] Miles L A, Bowman R L, Merlinsky T R, et al. Single-cell mutation analysis of clonal evolution in myeloid malignancies [J]. Nature, 2020, 587(7834): 477-482.
[55] Turajlic S, Sottoriva A, Graham T, et al. Resolving genetic heterogeneity in cancer [J]. Nature Reviews Genetics, 2019, 20(7): 404-416.
[56] Huang L, Ma F, Chapman A, et al. Single-cell whole-genome amplification and sequencing: Methodology and applications [J]. Annual Review of Genomics and Human Genetics, 2015, 16: 79-102.
[57] Stuart T, Satija R. Integrative single-cell analysis [J]. Nature Reviews Genetics, 2019, 20(5): 257-272.
[58] Dong X, Zhang L, Milholland B, et al. Accurate identification of single-nucleotide variants in whole-genome-amplified single cells [J]. Nature Methods, 2017, 14(5): 491-493.
[59] Navin N, Kendall J, Troge J, et al. Tumour evolution inferred by single-cell sequencing [J]. Nature, 2011, 472(7341): 90-94.
[60] McPherson A, Vázquez-García I, Myers M A, et al. Ongoing genome doubling shapes evolvability and immunity in ovarian cancer [J]. Nature, 2025, 644(8078): 1078-1087.
[61] Leung M L, Davis A, Gao R L, et al. Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer [J]. Genome Research, 2017, 27(8): 1287-1299.
[62] McPherson A, Roth A, Laks E, et al. Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer [J]. Nature Genetics, 2016, 48(7): 758-767.
[63] Gawad C, Koh W, Quake S R. Dissecting the clonal origins of childhood acute lymphoblastic leukemia by single-cell genomics [J]. Proceedings of the National Academy of Sciences of the United States of America, 2014, 111(50): 17947-17952.
[64] Lohr J G, Adalsteinsson V A, Cibulskis K, et al. Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer [J]. Nature Biotechnology, 2014, 32(5): 479-484.
[65] Wang K L, Ye R, Bai S S, et al. Coalescing single-cell genomes and transcriptomes to decode breast cancer progression [J]. Cell, 2025, 188(22): 6355-6369.e16.
[66] Wang K L, Kumar T, Wang J K, et al. Archival single-cell genomics reveals persistent subclones during DCIS progression [J]. Cell, 2023, 186(18): 3968-3982.e15.
[67] Minussi D C, Nicholson M D, Ye H H, et al. Breast tumours maintain a reservoir of subclonal diversity during expansion [J]. Nature, 2021, 592(7853): 302-308.
[68] Kim C, Gao R L, Sei E, et al. Chemoresistance evolution in triple-negative breast cancer delineated by single-cell sequencing [J]. Cell, 2018, 173(4): 879-893.e13.
[69] Casasent A K, Schalck A, Gao R L, et al. Multiclonal invasion in breast tumors identified by topographic single cell sequencing [J]. Cell, 2018, 172(1/2): 205-217.e12.
[70] Navin N E. Cancer genomics: One cell at a time [J]. Genome Biology, 2014, 15(8): 452.
[71] Estévez-Gómez N, Prieto T, Tomás L, et al. Differential performance of strategies for single-cell whole-genome amplification [J]. Cell Reports Methods, 2025, 5(4): 101025.
[72] Evrony G D, Hinch A G, Luo C Y. Applications of single-cell DNA sequencing [J]. Annual Review of Genomics and Human Genetics, 2021, 22: 171-197.
[73] Malikic S, Jahn K, Kuipers J, et al. Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data [J]. Nature Communications, 2019, 10: 2750.
[74] De Jonghe J, Opzoomer J W, Vilas-Zornoza A, et al. scTrends: A living review of commercial single-cell and spatial 'omic technologies [J]. Cell Genomics, 2024, 4(12): 100723.
[75] Gonzalez-Pena V, Natarajan S, Xia Y T, et al. Accurate genomic variant detection in single cells with primary template-directed amplification [J]. Proceedings of the National Academy of Sciences of the United States of America, 2021, 118(24): e2024176118.
[76] Chen C Y, Xing D, Tan L Z, et al. Single-cell whole-genome analyses by linear amplification via transposon insertion (LIANTI) [J]. Science, 2017, 356(6334): 189-194.
[77] Su X B, Zhao L N, Shi Y, et al. Clonal evolution in liver cancer at single-cell and single-variant resolution [J]. Journal of Hematology & Oncology, 2021, 14: 22.
[78] Duan M, Hao J F, Cui S J, et al. Diverse modes of clonal evolution in HBV-related hepatocellular carcinoma revealed by single-cell genome sequencing [J]. Cell Research, 2018, 28(3): 359-373.
[79] Su X B, Bai S H, Xie G C, et al. Accurate tumor clonal structures require single-cell analysis [J]. Annals of the New York Academy of Sciences, 2022, 1517(1): 213-224.
[80] Andel D, Viergever B J, Peters N A, et al. Pre-existing subclones determine radioresistance in rectal cancer organoids [J]. Cell Reports, 2024, 43(2): 113735.
[81] Stangis M M, Chen Z Y, Min J M, et al. The hallmarks of precancer [J]. Cancer Discovery, 2024, 14(4): 683-689.
[82] Van Egeren D, Schenck R O, Khan A, et al. Polyclonal origins of human premalignant colorectal lesions [J]. Nature, 2026, 650(8103): 1017-1024.
[83] Lu Z L, Mo S L, Xie D, et al. Polyclonal-to-monoclonal transition in colorectal precancerous evolution [J]. Nature, 2024, 636(8041): 233-240.
[84] Suda K, Nakaoka H, Yoshihara K, et al. Clonal expansion and diversification of cancer-associated mutations in endometriosis and normal endometrium [J]. Cell Reports, 2018, 24(7): 1777-1789.
[85] Martincorena I, Roshan A, Gerstung M, et al. High burden and pervasive positive selection of somatic mutations in normal human skin [J]. Science, 2015, 348(6237): 880-886.
[86] Moore L, Leongamornlert D, Coorens T H H, et al. The mutational landscape of normal human endometrial epithelium [J]. Nature, 2020, 580(7805): 640-646.
[87] Martincorena I, Fowler J C, Wabik A, et al. Somatic mutant clones colonize the human esophagus with age [J]. Science, 2018, 362(6417): 911-917.
[88] Lee-Six H, Olafsson S, Ellis P, et al. The landscape of somatic mutation in normal colorectal epithelial cells [J]. Nature, 2019, 574(7779): 532-537.
[89] Ogawa H, Horitani K, Izumiya Y, et al. Somatic mosaicism in biology and disease [J]. Annual Review of Physiology, 2022, 84: 113-133.
[90] Shao D D, Kriz A J, Snellings D A, et al. Advances in single-cell DNA sequencing enable insights into human somatic mosaicism [J]. Nature Reviews Genetics, 2025, 26(11): 761-774.
[91] Vijg J, Dong X. Pathogenic mechanisms of somatic mutation and genome mosaicism in aging [J]. Cell, 2020, 182(1): 12-23.
[92] Vijg J, Schumacher B, Abakir A, et al. Mitigating age-related somatic mutation burden [J]. Trends in Molecular Medicine, 2023, 29(7): 530-540.
[93] Coorens T H H, Oh J W, Choi Y A, et al. The somatic mosaicism across human tissues network [J]. Nature, 2025, 643(8070): 47-59.
[94] Pich O, Ward S, Rowan A, et al. Somatic evolution following cancer treatment in normal tissue[J]. Nature, 2025. https://doi.org/10.1038/s41586-025-09792-4.
[95] ROOD J E, WYNNE S, ROBSON L, HUPALOWSKA A, RANDELL J, TEICHMANN S A, REGEV A. The Human Cell Atlas from a cell census to a unified foundation model [J]. Nature, 2025, 637(8048): 1065-71.
[95] Rood J E, Wynne S, Robson L, et al. The Human Cell Atlas from a cell census to a unified foundation model [J]. Nature, 2025, 637(8048): 1065-1071.
[96] Svensson V, Vento-Tormo R, Teichmann S A. Exponential scaling of single-cell RNA-seq in the past decade [J]. Nature Protocols, 2018, 13(4): 599-604.
[97] Su X B, Shi Y, Zou X, et al. Single-cell RNA-Seq analysis reveals dynamic trajectories during mouse liver development [J]. BMC Genomics, 2017, 18(1): 946.
[98] Tang F C, Barbacioru C, Wang Y Z, et al. mRNA-Seq whole-transcriptome analysis of a single cell [J]. Nature Methods, 2009, 6(5): 377-382.
[99] Macosko E Z, Basu A, Satija R, et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets [J]. Cell, 2015, 161(5): 1202-1214.
[100] Cheng S, Zou Y H, Zhang M, et al. Single-cell RNA sequencing reveals the heterogeneity and intercellular communication of hepatic stellate cells and macrophages during liver fibrosis [J]. MedComm, 2023, 4(5): e378.
[101] Trapnell C, Cacchiarelli D, Grimsby J, et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells [J]. Nature Biotechnology, 2014, 32(4): 381-386.
[102] Qiu X J, Mao Q, Tang Y, et al. Reversed graph embedding resolves complex single-cell trajectories [J]. Nature Methods, 2017, 14(10): 979-982.
[103] Cao J Y, Spielmann M, Qiu X J, et al. The single-cell transcriptional landscape of mammalian organogenesis [J]. Nature, 2019, 566(7745): 496-502.
[104] Patel A P, Tirosh I, Trombetta J J, et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma [J]. Science, 2014, 344(6190): 1396-1401.
[105] Tirosh I, Izar B, Prakadan S M, et al. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq [J]. Science, 2016, 352(6282): 189-196.
[106] Su X B, Long Q, Bo J J, et al. Mutational and transcriptomic landscapes of a rare human prostate basal cell carcinoma [J]. The Prostate, 2020, 80(6): 508-517.
[107] Bai S H, Su X B, Chen Z Y, et al. De novo detection of clonal structure and evolution in single-cell and spatial transcriptomes [J]. International Journal of Molecular Sciences, 2025, 26(23): 11428.
[108] Ren X W, Zhang L, Zhang Y Y, et al. Insights gained from single-cell analysis of immune cells in the tumor microenvironment [J]. Annual Review of Immunology, 2021, 39: 583-609.
[109] Elhanani O, Ben-Uri R, Keren L. Spatial profiling technologies illuminate the tumor microenvironment [J]. Cancer Cell, 2023, 41(3): 404-420.
[110] Mo C K, Liu J X, Chen S Q, et al. Tumour evolution and microenvironment interactions in 2D and 3D space [J]. Nature, 2024, 634(8036): 1178-1186.
[111] Lybaert L, Lefever S, Fant B, et al. Challenges in neoantigen-directed therapeutics [J]. Cancer Cell, 2023, 41(1): 15-40.
[112] Shi Y, Guo Z H, Su X B, et al. DeepAntigen: A novel method for neoantigen prioritization via 3D genome and deep sparse learning [J]. Bioinformatics, 2020, 36(19): 4894-4901.
[113] Lakatos E, Williams M J, Schenck R O, et al. Evolutionary dynamics of neoantigens in growing tumors [J]. Nature Genetics, 2020, 52(10): 1057-1066.
[114] Nam A S, Chaligne R, Landau D A. Integrating genetic and non-genetic determinants of cancer evolution by single-cell multi-omics [J]. Nature Reviews Genetics, 2021, 22(1): 3-18.
[115] Vandereyken K, Sifrim A, Thienpont B, et al. Methods and applications for single-cell and spatial multi-omics [J]. Nature Reviews Genetics, 2023, 24(8): 494-515.
[116] Baysoy A, Bai Z L, Satija R, et al. The technological landscape and applications of single-cell multi-omics [J]. Nature Reviews Molecular Cell Biology, 2023, 24(10): 695-713.
[117] MacAulay I C, Haerty W, Kumar P, et al. G&T-seq: Parallel sequencing of single-cell genomes and transcriptomes [J]. Nature Methods, 2015, 12(6): 519-522.
[118] Seferbekova Z, Lomakin A, Yates L R, et al. Spatial biology of cancer evolution [J]. Nature Reviews Genetics, 2023, 24(5): 295-313.
[119] Gong D, Arbesfeld-Qiu J M, Perrault E, et al. Spatial oncology: Translating contextual biology to the clinic [J]. Cancer Cell, 2024, 42(10): 1653-1675.
[120] Xiao J, Yu X Y, Meng F L, et al. Integrating spatial and single-cell transcriptomics reveals tumor heterogeneity and intercellular networks in colorectal cancer [J]. Cell Death & Disease, 2024, 15: 326.
[121] You R, Shen Q L, Lin C, et al. Single-cell and spatial transcriptomics reveal mechanisms of radioresistance and immune escape in recurrent nasopharyngeal carcinoma [J]. Nature Genetics, 2025, 57(8): 1950-1965.
[122] Hunter M V, Moncada R, Weiss J M, et al. Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface [J]. Nature Communications, 2021, 12: 6278.
[123] Lomakin A, Svedlund J, Strell C, et al. Spatial genomics maps the structure, nature and evolution of cancer clones [J]. Nature, 2022, 611(7936): 594-602.
[124] Jones M G, Yang D, Weissman J S. New tools for lineage tracing in cancer in vivo [J]. Annual Review of Cancer Biology, 2023, 7: 111-129.
[125] Wagner D E, Klein A M. Lineage tracing meets single-cell omics: Opportunities and challenges [J]. Nature Reviews Genetics, 2020, 21(7): 410-427.
[126] Gabbutt C, Wright N A, Baker A M, et al. Lineage tracing in human tissues [J]. The Journal of Pathology, 2022, 257(4): 501-512.
[127] Xue Y, Su Z Z, Lin X Y, et al. Single-cell lineage tracing with endogenous markers [J]. Biophysical Reviews, 2024, 16(1): 125-139.
[128] Yang D, Jones M G, Naranjo S, et al. Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution [J]. Cell, 2022, 185(11): 1905-1923.e25.
[129] Weber T S, Biben C, Miles D C, et al. LoxCode in vivo barcoding reveals epiblast clonal fate bias to fetal organs [J]. Cell, 2025, 188(14): 3882-3896.e19.
[130] Pan X H, Li H C, Putta P, et al. LinRace: Cell division history reconstruction of single cells using paired lineage barcode and gene expression data [J]. Nature Communications, 2023, 14: 8388.
[131] Boscenco S, Cumming E M, Kim M, et al. Single-cell technologies for studying the evolution and function of mitochondrial DNA heteroplasmy in cancer [J]. Annual Review of Cancer Biology, 2025, 9: 161-180.
[132] Árnadóttir E R, Moore K H S, Guðmundsdóttir V B, et al. The rate and nature of mitochondrial DNA mutations in human pedigrees [J]. Cell, 2024, 187(15): 3904-3918.e8.
[133] Scherer M, Singh I, Braun M M, et al. Clonal tracing with somatic epimutations reveals dynamics of blood ageing [J]. Nature, 2025, 643(8071): 478-487.
[134] Chen M Y, Fu R J, Chen Y Q, et al. High-resolution, noninvasive single-cell lineage tracing in mice and humans based on DNA methylation epimutations [J]. Nature Methods, 2025, 22(3): 488-498.
[135] Liu M, Yue Y Z, Chen X B, et al. Genome-coverage single-cell histone modifications for embryo lineage tracing [J]. Nature, 2025, 640(8059): 828-839.
[136] Xiao Y, Jin W, Ju L G, et al. Tracking single-cell evolution using clock-like chromatin accessibility loci [J]. Nature Biotechnology, 2025, 43(5): 784-798.
[137] Liberali P, Schier A F. The evolution of developmental biology through conceptual and technological revolutions [J]. Cell, 2024, 187(14): 3461-3495.
[138] Muter J, Lynch V J, McCoy R C, et al. Human embryo implantation [J]. Development, 2023, 150(10): dev201507.
[139] Kreso A, Dick J E. Evolution of the cancer stem cell model [J]. Cell Stem Cell, 2014, 14(3): 275-291.
[140] Haniffa M, Taylor D, Linnarsson S, et al. A roadmap for the human developmental cell atlas [J]. Nature, 2021, 597(7875): 196-205.
[141] Su X, Zhao L, Shi Y, et al. Single-cell and single-variant resolution analysis of clonal evolution in human liver cancer [PP/OL]. bioRxiv (2021-01-02) [2025-12-29]. https://doi.org/10.1101/2020.12.30.424907.
[142] Logsdon G A, Vollger M R, Eichler E E. Long-read human genome sequencing and its applications [J]. Nature Reviews Genetics, 2020, 21(10): 597-614.
[143] van Dijk E L, Naquin D, Gorrichon K, et al. Genomics in the long-read sequencing era [J]. Trends in Genetics, 2023, 39(9): 649-671.
[144] Liu M H, Costa B M, Bianchini E C, et al. DNA mismatch and damage patterns revealed by single-molecule sequencing [J]. Nature, 2024, 630(8017): 752-761.
[145] Warburton P E, Sebra R P. Long-read DNA sequencing: Recent advances and remaining challenges [J]. Annual Review of Genomics and Human Genetics, 2023, 24: 109-132.
[146] Salk J J, Schmitt M W, Loeb L A. Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations [J]. Nature Reviews Genetics, 2018, 19(5): 269-285.
