{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T14:40:24Z","timestamp":1792593624248,"version":"4.5.0"},"reference-count":65,"publisher":"Elsevier BV","issue":"10","license":[{"start":{"date-parts":[[2021,10,1]],"date-time":"2021-10-01T00:00:00Z","timestamp":1633046400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2021,10,1]],"date-time":"2021-10-01T00:00:00Z","timestamp":1633046400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2021,8,26]],"date-time":"2021-08-26T00:00:00Z","timestamp":1629936000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100009192","name":"Alberta Innovates","doi-asserted-by":"publisher","award":["RES0010334"],"award-info":[{"award-number":["RES0010334"]}],"id":[{"id":"10.13039\/501100009192","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010877","name":"Science, Technology and Innovation Commission of Shenzhen Municipality","doi-asserted-by":"publisher","award":["GJHZ20170314152701465"],"award-info":[{"award-number":["GJHZ20170314152701465"]}],"id":[{"id":"10.13039\/501100010877","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003453","name":"Natural Science Foundation of Guangdong Province","doi-asserted-by":"publisher","award":["U1601224"],"award-info":[{"award-number":["U1601224"]}],"id":[{"id":"10.13039\/501100003453","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Reports Medicine"],"published-print":{"date-parts":[[2021,10]]},"DOI":"10.1016\/j.xcrm.2021.100404","type":"journal-article","created":{"date-parts":[[2021,10,22]],"date-time":"2021-10-22T05:37:09Z","timestamp":1634881029000},"page":"100404","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":12,"title":["Genome profiles of pathologist-defined cell clusters by multiregional LCM and G&amp;T-seq in one triple-negative breast cancer patient"],"prefix":"10.1016","volume":"2","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1921-567X","authenticated-orcid":false,"given":"Zhongyi","family":"Zhu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiwei","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tracy","family":"Jordan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guibo","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sveta","family":"Silverman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Si","family":"Qiu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anil Abraham","family":"Joy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0990-5239","authenticated-orcid":false,"given":"Chao","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deanna L.","family":"Hockley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xi","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qing","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8088-4197","authenticated-orcid":false,"given":"Lynne M.","family":"Postovit","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiuqing","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong","family":"Hou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John R.","family":"Mackey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6108-5560","authenticated-orcid":false,"given":"Gane Ka-Shu","family":"Wong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.xcrm.2021.100404_bib1","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1159\/000292644","article-title":"The changing role of pathology in breast cancer diagnosis and treatment","volume":"78","author":"Leong","year":"2011","journal-title":"Pathobiology"},{"key":"10.1016\/j.xcrm.2021.100404_bib2","doi-asserted-by":"crossref","first-page":"1895","DOI":"10.1056\/NEJMp1508811","article-title":"The Path to Cancer--Three Strikes and You\u2019re Out","volume":"373","author":"Vogelstein","year":"2015","journal-title":"N.\u00a0Engl. J. Med."},{"key":"10.1016\/j.xcrm.2021.100404_bib3","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1126\/science.959840","article-title":"The clonal evolution of tumor cell populations","volume":"194","author":"Nowell","year":"1976","journal-title":"Science"},{"key":"10.1016\/j.xcrm.2021.100404_bib4","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1056\/NEJM198809013190901","article-title":"Genetic alterations during colorectal-tumor development","volume":"319","author":"Vogelstein","year":"1988","journal-title":"N.\u00a0Engl. J. Med."},{"key":"10.1016\/j.xcrm.2021.100404_bib5","doi-asserted-by":"crossref","first-page":"48625","DOI":"10.18632\/oncotarget.8015","article-title":"Evaluation and consequences of heterogeneity in the circulating tumor cell compartment","volume":"7","author":"Brouwer","year":"2016","journal-title":"Oncotarget"},{"key":"10.1016\/j.xcrm.2021.100404_bib6","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s40169-017-0145-6","article-title":"Single-cell sequencing and tumorigenesis: improved understanding of tumor evolution and metastasis","volume":"6","author":"Ellsworth","year":"2017","journal-title":"Clin. Transl. Med."},{"key":"10.1016\/j.xcrm.2021.100404_bib7","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1038\/nature15260","article-title":"Single-cell analysis reveals a stem-cell program in human metastatic breast cancer cells","volume":"526","author":"Lawson","year":"2015","journal-title":"Nature"},{"key":"10.1016\/j.xcrm.2021.100404_bib8","doi-asserted-by":"crossref","first-page":"3588","DOI":"10.1038\/s41467-018-06052-0","article-title":"Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq","volume":"9","author":"Karaayvaz","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.xcrm.2021.100404_bib9","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1038\/nature09807","article-title":"Tumour evolution inferred by single-cell sequencing","volume":"472","author":"Navin","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.xcrm.2021.100404_bib10","doi-asserted-by":"crossref","first-page":"2310","DOI":"10.1172\/JCI97449","article-title":"Coexisting genomic aberrations associated with lymph node metastasis in breast cancer","volume":"128","author":"Bao","year":"2018","journal-title":"J.\u00a0Clin. Invest."},{"key":"10.1016\/j.xcrm.2021.100404_bib11","doi-asserted-by":"crossref","first-page":"1110","DOI":"10.1016\/j.cell.2014.07.013","article-title":"Circulating tumor cell clusters are oligoclonal precursors of breast cancer metastasis","volume":"158","author":"Aceto","year":"2014","journal-title":"Cell"},{"key":"10.1016\/j.xcrm.2021.100404_bib12","doi-asserted-by":"crossref","first-page":"E854","DOI":"10.1073\/pnas.1508541113","article-title":"Polyclonal breast cancer metastases arise from collective dissemination of keratin 14-expressing tumor cell clusters","volume":"113","author":"Cheung","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xcrm.2021.100404_bib13","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1126\/science.aaf6546","article-title":"A collective route to metastasis: seeding by tumor cell clusters","volume":"352","author":"Cheung","year":"2016","journal-title":"Science"},{"key":"10.1016\/j.xcrm.2021.100404_bib14","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1038\/nmeth.3370","article-title":"G&T-seq: parallel sequencing of single-cell genomes and transcriptomes","volume":"12","author":"Macaulay","year":"2015","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xcrm.2021.100404_bib15","doi-asserted-by":"crossref","first-page":"eaaw0726","DOI":"10.1126\/science.aaw0726","article-title":"RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues","volume":"364","author":"Yizhak","year":"2019","journal-title":"Science"},{"key":"10.1016\/j.xcrm.2021.100404_bib16","doi-asserted-by":"crossref","first-page":"640","DOI":"10.1038\/s41586-020-2214-z","article-title":"The mutational landscape of normal human endometrial epithelium","volume":"580","author":"Moore","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.xcrm.2021.100404_bib17","doi-asserted-by":"crossref","first-page":"4947","DOI":"10.1073\/pnas.1524448113","article-title":"Clusters of circulating tumor cells traverse capillary-sized vessels","volume":"113","author":"Au","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xcrm.2021.100404_bib18","doi-asserted-by":"crossref","first-page":"1024","DOI":"10.1038\/nprot.2012.039","article-title":"Genome-wide copy number analysis of single cells","volume":"7","author":"Baslan","year":"2012","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.xcrm.2021.100404_bib19","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/nature13600","article-title":"Clonal evolution in breast cancer revealed by single nucleus genome sequencing","volume":"512","author":"Wang","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.xcrm.2021.100404_bib20","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1038\/ng1294-387","article-title":"Mutations in the BRCA1 gene in families with early-onset breast and ovarian cancer","volume":"8","author":"Castilla","year":"1994","journal-title":"Nat. Genet."},{"key":"10.1016\/j.xcrm.2021.100404_bib21","doi-asserted-by":"crossref","first-page":"1974","DOI":"10.1093\/annonc\/mdq072","article-title":"Prognosis and adjuvant treatment effects in selected breast cancer subtypes of very young women (<35 years) with operable breast cancer","volume":"21","author":"Cancello","year":"2010","journal-title":"Ann. Oncol."},{"issue":"Suppl 6","key":"10.1016\/j.xcrm.2021.100404_bib22","doi-asserted-by":"crossref","first-page":"vi13","DOI":"10.1093\/annonc\/mds188","article-title":"Understanding the biology of triple-negative breast cancer","volume":"23","author":"Criscitiello","year":"2012","journal-title":"Ann. Oncol."},{"key":"10.1016\/j.xcrm.2021.100404_bib23","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1038\/nmeth.4236","article-title":"SC3: consensus clustering of single-cell RNA-seq data","volume":"14","author":"Kiselev","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xcrm.2021.100404_bib24","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1038\/ng.3641","article-title":"Punctuated copy number evolution and clonal stasis in triple-negative breast cancer","volume":"48","author":"Gao","year":"2016","journal-title":"Nat. Genet."},{"key":"10.1016\/j.xcrm.2021.100404_bib25","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/nbt.2859","article-title":"The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells","volume":"32","author":"Trapnell","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.xcrm.2021.100404_bib26","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1038\/nmeth.4150","article-title":"Single-cell mRNA quantification and differential analysis with Census","volume":"14","author":"Qiu","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xcrm.2021.100404_bib27","doi-asserted-by":"crossref","first-page":"1523","DOI":"10.1038\/s41467-019-09234-6","article-title":"Metascape provides a biologist-oriented resource for the analysis of systems-level datasets","volume":"10","author":"Zhou","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.xcrm.2021.100404_bib28","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1007\/s10585-008-9170-6","article-title":"Epithelial mesenchymal transition traits in human breast cancer cell lines","volume":"25","author":"Blick","year":"2008","journal-title":"Clin. Exp. Metastasis"},{"key":"10.1016\/j.xcrm.2021.100404_bib29","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1016\/j.cmet.2016.09.008","article-title":"Macrophage Metabolism Controls Tumor Blood Vessel Morphogenesis and Metastasis","volume":"24","author":"Wenes","year":"2016","journal-title":"Cell Metab."},{"key":"10.1016\/j.xcrm.2021.100404_bib30","doi-asserted-by":"crossref","first-page":"e9266","DOI":"10.15252\/emmm.201809266","article-title":"Apelin inhibition prevents resistance and metastasis associated with anti-angiogenic therapy","volume":"11","author":"Uribesalgo","year":"2019","journal-title":"EMBO Mol. Med."},{"key":"10.1016\/j.xcrm.2021.100404_bib31","doi-asserted-by":"crossref","first-page":"4609","DOI":"10.1172\/JCI125890","article-title":"Stromal integrin \u03b111 regulates PDGFR-\u03b2 signaling and promotes breast cancer progression","volume":"129","author":"Primac","year":"2019","journal-title":"J.\u00a0Clin. Invest."},{"key":"10.1016\/j.xcrm.2021.100404_bib32","doi-asserted-by":"crossref","first-page":"1745","DOI":"10.12688\/f1000research.9118.1","article-title":"Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks","volume":"5","author":"Muetze","year":"2016","journal-title":"F1000Res."},{"key":"10.1016\/j.xcrm.2021.100404_bib33","doi-asserted-by":"crossref","first-page":"9227","DOI":"10.1038\/s41598-018-27521-y","article-title":"Validation of miRNA prognostic power in hepatocellular carcinoma using expression data of independent datasets","volume":"8","author":"Nagy","year":"2018","journal-title":"Sci. Rep."},{"key":"10.1016\/j.xcrm.2021.100404_bib34","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1038\/nrc.2017.104","article-title":"Ribosome biogenesis in cancer: new players and therapeutic avenues","volume":"18","author":"Pelletier","year":"2018","journal-title":"Nat. Rev. Cancer"},{"key":"10.1016\/j.xcrm.2021.100404_bib35","doi-asserted-by":"crossref","first-page":"D92","DOI":"10.1093\/nar\/gkt1248","article-title":"starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data","volume":"42","author":"Li","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.xcrm.2021.100404_bib36","doi-asserted-by":"crossref","first-page":"1287","DOI":"10.1038\/ncb1973","article-title":"Localized and reversible TGFbeta signalling switches breast cancer cells from cohesive to single cell motility","volume":"11","author":"Giampieri","year":"2009","journal-title":"Nat. Cell Biol."},{"key":"10.1016\/j.xcrm.2021.100404_bib37","doi-asserted-by":"crossref","first-page":"413","DOI":"10.1038\/nbt.2203","article-title":"Absolute quantification of somatic DNA alterations in human cancer","volume":"30","author":"Carter","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.xcrm.2021.100404_bib38","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1038\/nature25432","article-title":"Chromosomal instability drives metastasis through a cytosolic DNA response","volume":"553","author":"Bakhoum","year":"2018","journal-title":"Nature"},{"key":"10.1016\/j.xcrm.2021.100404_bib39","doi-asserted-by":"crossref","first-page":"e1002174","DOI":"10.1371\/journal.pmed.1002174","article-title":"Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases","volume":"13","author":"Hoadley","year":"2016","journal-title":"PLoS Med."},{"key":"10.1016\/j.xcrm.2021.100404_bib40","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1038\/nature20785","article-title":"Early dissemination seeds metastasis in breast cancer","volume":"540","author":"Hosseini","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.xcrm.2021.100404_bib41","doi-asserted-by":"crossref","first-page":"2486","DOI":"10.1056\/NEJMcibr1701388","article-title":"Timing of Metastasis in Breast Cancer","volume":"376","author":"Schwartz","year":"2017","journal-title":"N.\u00a0Engl. J. Med."},{"key":"10.1016\/j.xcrm.2021.100404_bib42","doi-asserted-by":"crossref","first-page":"1565","DOI":"10.1126\/science.1203486","article-title":"Cancer immunoediting: integrating immunity\u2019s roles in cancer suppression and promotion","volume":"331","author":"Schreiber","year":"2011","journal-title":"Science"},{"key":"10.1016\/j.xcrm.2021.100404_bib43","doi-asserted-by":"crossref","first-page":"1423","DOI":"10.1038\/nm.3394","article-title":"Microenvironmental regulation of tumor progression and metastasis","volume":"19","author":"Quail","year":"2013","journal-title":"Nat. Med."},{"key":"10.1016\/j.xcrm.2021.100404_bib44","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1016\/j.ccell.2016.09.011","article-title":"Characteristics and Significance of the Pre-metastatic Niche","volume":"30","author":"Liu","year":"2016","journal-title":"Cancer Cell"},{"key":"10.1016\/j.xcrm.2021.100404_bib45","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1002\/1878-0261.12095","article-title":"EMT and inflammation: inseparable actors of cancer progression","volume":"11","author":"Suarez-Carmona","year":"2017","journal-title":"Mol. Oncol."},{"key":"10.1016\/j.xcrm.2021.100404_bib46","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1016\/j.semcancer.2017.08.002","article-title":"Epithelial-mesenchymal transition and inflammation at the site of the primary tumor","volume":"47","author":"Dominguez","year":"2017","journal-title":"Semin. Cancer Biol."},{"key":"10.1016\/j.xcrm.2021.100404_bib47","doi-asserted-by":"crossref","first-page":"E496","DOI":"10.1073\/pnas.1614876114","article-title":"Regulatory module involving FGF13, miR-504, and p53 regulates ribosomal biogenesis and supports cancer cell survival","volume":"114","author":"Bublik","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xcrm.2021.100404_bib48","doi-asserted-by":"crossref","first-page":"168","DOI":"10.3389\/fimmu.2019.00168","article-title":"Cold Tumors: A Therapeutic Challenge for Immunotherapy","volume":"10","author":"Bonaventura","year":"2019","journal-title":"Front. Immunol."},{"key":"10.1016\/j.xcrm.2021.100404_bib49","doi-asserted-by":"crossref","first-page":"R83","DOI":"10.1530\/JME-18-0058","article-title":"Oncogenic kinases and perturbations in protein synthesis machinery and energetics in neoplasia","volume":"62","author":"Uchenunu","year":"2019","journal-title":"J.\u00a0Mol. Endocrinol."},{"key":"10.1016\/j.xcrm.2021.100404_bib50","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1126\/science.aai8515","article-title":"Origins of lymphatic and distant metastases in human colorectal cancer","volume":"357","author":"Naxerova","year":"2017","journal-title":"Science"},{"key":"10.1016\/j.xcrm.2021.100404_bib51","doi-asserted-by":"crossref","first-page":"102793","DOI":"10.1016\/j.ebiom.2020.102793","article-title":"Phylogenetic reconstruction of breast cancer reveals two routes of metastatic dissemination associated with distinct clinical outcome","volume":"56","author":"Venet","year":"2020","journal-title":"EBioMedicine"},{"key":"10.1016\/j.xcrm.2021.100404_bib56","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xcrm.2021.100404_bib60","doi-asserted-by":"crossref","first-page":"e164","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.xcrm.2021.100404_bib55","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol"},{"key":"10.1016\/j.xcrm.2021.100404_bib57","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xcrm.2021.100404_bib58","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res"},{"key":"10.1016\/j.xcrm.2021.100404_bib61","doi-asserted-by":"crossref","first-page":"141","DOI":"10.12688\/f1000research.4536.1","article-title":"Enrichment Map\u00a0- a Cytoscape app to visualize and explore OMICs pathway enrichment results","volume":"3","author":"Isserlin","year":"2014","journal-title":"F1000Res."},{"key":"10.1016\/j.xcrm.2021.100404_bib59","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"10.1016\/j.xcrm.2021.100404_bib62","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1038\/nmeth.3835","article-title":"Monovar: single-nucleotide variant detection in single cells","volume":"13","author":"Zafar","year":"2016","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xcrm.2021.100404_bib63","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1186\/1471-2105-12-323","article-title":"RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome","volume":"12","author":"Li","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.xcrm.2021.100404_bib64","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"Genome Project Data Processing S. The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xcrm.2021.100404_bib65","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/gigascience\/gix120","article-title":"SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data","volume":"7","author":"Chen","year":"2018","journal-title":"Gigascience"},{"key":"10.1016\/j.xcrm.2021.100404_bib52","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1101\/gr.188060.114","article-title":"Optimizing sparse sequencing of single cells for highly multiplex copy number profiling","volume":"25","author":"Baslan","year":"2015","journal-title":"Genome Res."},{"key":"10.1016\/j.xcrm.2021.100404_bib53","doi-asserted-by":"crossref","first-page":"e431","DOI":"10.1093\/bioinformatics\/btl238","article-title":"Integrating copy number polymorphisms into array CGH analysis using a robust HMM","volume":"22","author":"Shah","year":"2006","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xcrm.2021.100404_bib54","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1002\/sim.4780090710","article-title":"More powerful procedures for multiple significance testing","volume":"9","author":"Hochberg","year":"1990","journal-title":"Stat. Med."}],"container-title":["Cell Reports Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666379121002627?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666379121002627?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,11,12]],"date-time":"2025-11-12T22:50:00Z","timestamp":1762987800000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2666379121002627"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,10]]},"references-count":65,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2021,10]]}},"alternative-id":["S2666379121002627"],"URL":"https:\/\/doi.org\/10.1016\/j.xcrm.2021.100404","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/807156","asserted-by":"object"}]},"ISSN":["2666-3791"],"issn-type":[{"value":"2666-3791","type":"print"}],"subject":[],"published":{"date-parts":[[2021,10]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Genome profiles of pathologist-defined cell clusters by multiregional LCM and G&T-seq in one triple-negative breast cancer patient","name":"articletitle","label":"Article Title"},{"value":"Cell Reports Medicine","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.xcrm.2021.100404","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2021 The Author(s).","name":"copyright","label":"Copyright"}],"article-number":"100404"}}