{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T03:00:56Z","timestamp":1760238056367,"version":"build-2065373602"},"reference-count":87,"publisher":"MDPI AG","issue":"14","license":[{"start":{"date-parts":[[2020,7,8]],"date-time":"2020-07-08T00:00:00Z","timestamp":1594166400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>The comparison of the landscape of somatic alterations in circulating tumor cells (CTCs) versus metastases is challenging. Here, we comprehensively characterized the somatic landscape in bulk (amplified and non-amplified), spike-in breast cancer cells, CTCs, and metastases from breast cancer patients using whole-exome sequencing (WES). We determined the level of genomic concordance for somatic nucleotide variants (SNVs), copy number alterations (CNAs), and structural variants (SVs). The variant allele fractions (VAFs) of somatic variants were remarkably similar between amplified and non-amplified cell line samples as technical replicates. In clinical samples, a significant fraction of somatic variants had low VAFs in CTCs compared to metastases. The most frequently recurrent gene mutations in clinical samples were associated with an elevated C &gt; T mutational signature. We found complex rearrangement patterns including intra- and inter-chromosomal rearrangements, singleton, and recurrent gene fusions, and tandem duplications. We observed high molecular discordance for somatic alterations between paired samples consistent with marked heterogeneity of the somatic landscape. The most prevalent copy number calls were focal deletion events in CTCs and metastases. Our results demonstrate the feasibility of an integrated workflow for the identification of a complete repertoire of somatic alterations and highlight the intrapatient genomic differences that occur between CTCs and metastases.<\/jats:p>","DOI":"10.3390\/ijms21144826","type":"journal-article","created":{"date-parts":[[2020,7,8]],"date-time":"2020-07-08T11:47:46Z","timestamp":1594208866000},"page":"4826","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["A Pilot Study for the Feasibility of Exome-Sequencing in Circulating Tumor Cells Versus Single Metastatic Biopsies in Breast Cancer"],"prefix":"10.3390","volume":"21","author":[{"given":"Pushpinder","family":"Kaur","sequence":"first","affiliation":[{"name":"Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA"},{"name":"University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Campo","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tania B.","family":"Porras","sequence":"additional","affiliation":[{"name":"Cancer and Blood Disease Institute, Children Hospital Los Angeles, University of Southern California, Los Angeles, CA 90027, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander","family":"Ring","sequence":"additional","affiliation":[{"name":"Department of Oncology and Hematology, Universit\u00e4tsSpital Z\u00fcrich, R\u00e4mistrasse 100, 8091 Z\u00fcrich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Janice","family":"Lu","sequence":"additional","affiliation":[{"name":"University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA"},{"name":"Division of Medical Oncology, Department of Medicine and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA 90033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yvonne","family":"Chairez","sequence":"additional","affiliation":[{"name":"Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yunyun","family":"Su","sequence":"additional","affiliation":[{"name":"Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA"},{"name":"University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Irene","family":"Kang","sequence":"additional","affiliation":[{"name":"University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA"},{"name":"Division of Medical Oncology, Department of Medicine and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA 90033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7534-6124","authenticated-orcid":false,"given":"Julie E.","family":"Lang","sequence":"additional","affiliation":[{"name":"Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA"},{"name":"University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2020,7,8]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1324","DOI":"10.1016\/S1470-2045(15)00188-6","article-title":"Molecularly targeted therapy based on tumour molecular profiling versus conventional therapy for advanced cancer (SHIVA): A multicentre, open-label, proof-of-concept, randomised, controlled phase 2 trial","volume":"16","author":"Delord","year":"2015","journal-title":"Lancet Oncol."},{"key":"ref_2","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":"ref_3","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1111\/joim.12240","article-title":"The challenge of intratumour heterogeneity in precision medicine","volume":"276","author":"Seoane","year":"2014","journal-title":"J. Intern. Med."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1038\/nature08987","article-title":"International network of cancer genome projects","volume":"464","author":"Hudson","year":"2010","journal-title":"Nature"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1158\/2159-8290.CD-15-1483","article-title":"Clinical Applications of Circulating Tumor Cells and Circulating Tumor DNA as Liquid Biopsy","volume":"6","author":"Pantel","year":"2016","journal-title":"Cancer Discov."},{"key":"ref_6","first-page":"1","article-title":"Circulating tumor cells as a marker of prognosis","volume":"26","author":"Paoletti","year":"2012","journal-title":"Princ. Pract. Oncol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1007\/978-3-319-22909-6_11","article-title":"Circulating Plasma Tumor DNA","volume":"882","author":"Parsons","year":"2016","journal-title":"Adv. Exp. Med. Biol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"180ra148","DOI":"10.1126\/scitranslmed.3005109","article-title":"The identification and characterization of breast cancer CTCs competent for brain metastasis","volume":"5","author":"Zhang","year":"2013","journal-title":"Sci. Transl. Med."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1038\/s41568-019-0180-2","article-title":"Unravelling tumour heterogeneity by single-cell profiling of circulating tumour cells","volume":"19","author":"Keller","year":"2019","journal-title":"Nat. Rev. Cancer"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1056\/NEJMoa040766","article-title":"Circulating tumor cells, disease progression, and survival in metastatic breast cancer","volume":"351","author":"Cristofanilli","year":"2004","journal-title":"N. Engl. J. Med."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"6403","DOI":"10.1158\/1078-0432.CCR-05-1769","article-title":"Circulating tumor cells versus imaging-predicting overall survival in metastatic breast cancer","volume":"12","author":"Budd","year":"2006","journal-title":"Clin. Cancer Res. Off. J. Am. Assoc. Cancer Res."},{"key":"ref_12","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":"ref_13","doi-asserted-by":"crossref","first-page":"468","DOI":"10.1093\/annonc\/mdw619","article-title":"Circulating tumor markers: Harmonizing the yin and yang of CTCs and ctDNA for precision medicine","volume":"28","author":"Batth","year":"2017","journal-title":"Ann. Oncol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"12748","DOI":"10.18632\/oncotarget.7220","article-title":"Classification of large circulating tumor cells isolated with ultra-high throughput microfluidic Vortex technology","volume":"7","author":"Che","year":"2016","journal-title":"Oncotarget"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1827","DOI":"10.1101\/gad.305805.117","article-title":"A conduit to metastasis: Circulating tumor cell biology","volume":"31","author":"Micalizzi","year":"2017","journal-title":"Genes Dev."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"18575","DOI":"10.1038\/s41598-019-54960-y","article-title":"New Labyrinth Microfluidic Device Detects Circulating Tumor Cells Expressing Cancer Stem Cell Marker and Circulating Tumor Microemboli in Hepatocellular Carcinoma","volume":"9","author":"Wan","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1216","DOI":"10.1038\/onc.2015.192","article-title":"The biology of circulating tumor cells","volume":"35","author":"Pantel","year":"2016","journal-title":"Oncogene"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1016\/j.cell.2012.02.028","article-title":"Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm","volume":"148","author":"Hou","year":"2012","journal-title":"Cell"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1622","DOI":"10.1126\/science.1229164","article-title":"Genome-wide detection of single-nucleotide and copy-number variations of a single human cell","volume":"338","author":"Zong","year":"2012","journal-title":"Science"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"6086","DOI":"10.1158\/1078-0432.CCR-17-1173","article-title":"Detection of Activating Estrogen Receptor Gene (ESR1) Mutations in Single Circulating Tumor Cells","volume":"23","author":"Paolillo","year":"2017","journal-title":"Clin. Cancer Res. Off. J. Am. Assoc. Cancer Res."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"4530","DOI":"10.1158\/0008-5472.CAN-17-0688","article-title":"Quantitative Whole Genome Sequencing of Circulating Tumor Cells Enables Personalized Combination Therapy of Metastatic Cancer","volume":"77","author":"Gulbahce","year":"2017","journal-title":"Cancer Res."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"85349","DOI":"10.18632\/oncotarget.13350","article-title":"Enumeration and targeted analysis of KRAS, BRAF and PIK3CA mutations in CTCs captured by a label-free platform: Comparison to ctDNA and tissue in metastatic colorectal cancer","volume":"7","author":"Liu","year":"2016","journal-title":"Oncotarget"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"2965","DOI":"10.1158\/0008-5472.CAN-12-4140","article-title":"Complex tumor genomes inferred from single circulating tumor cells by array-CGH and next-generation sequencing","volume":"73","author":"Heitzer","year":"2013","journal-title":"Cancer Res."},{"key":"ref_24","unstructured":"(2020, January 30). Available online: https:\/\/www.atcc.org\/~\/media\/03E3D0D9F0C74FE593CE7D010F982CA2.ashx."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"3197","DOI":"10.1172\/JCI60517","article-title":"FAM83B mediates EGFR- and RAS-driven oncogenic transformation","volume":"122","author":"Cipriano","year":"2012","journal-title":"J. Clin. Investig."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1158\/0008-5472.CAN-11-2266","article-title":"Monoallelic expression determines oncogenic progression and outcome in benign and malignant brain tumors","volume":"72","author":"Walker","year":"2012","journal-title":"Cancer Res."},{"key":"ref_27","unstructured":"(2020, February 06). Available online: https:\/\/cancer.sanger.ac.uk\/census."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"R9","DOI":"10.1186\/bcr1370","article-title":"Comprehensive copy number profiles of breast cancer cell model genomes","volume":"8","author":"Shadeo","year":"2006","journal-title":"Breast Cancer Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1002\/gcc.20438","article-title":"High-resolution genomic profiles of breast cancer cell lines assessed by tiling BAC array comparative genomic hybridization","volume":"46","author":"Jonsson","year":"2007","journal-title":"Geneschromosomes Cancer"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Martin-Pardillos, A., Valls Chiva, A., Bande Vargas, G., Hurtado Blanco, P., Pineiro Cid, R., Guijarro, P.J., Hummer, S., Bejar Serrano, E., Rodriguez-Casanova, A., and Diaz-Lagares, A. (2019). The role of clonal communication and heterogeneity in breast cancer. BMC Cancer, 19.","DOI":"10.1186\/s12885-019-5883-y"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s41236-020-0010-1","article-title":"Detecting heterogeneity in and between breast cancer cell lines","volume":"4","author":"Shen","year":"2020","journal-title":"Cancer Converg."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/S0002-9440(10)64706-2","article-title":"Isolation by size of epithelial tumor cells: A new method for the immunomorphological and molecular characterization of circulatingtumor cells","volume":"156","author":"Vona","year":"2000","journal-title":"Am. J. Pathol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"18392","DOI":"10.1073\/pnas.1012539107","article-title":"Isolation of circulating tumor cells using a microvortex-generating herringbone-chip","volume":"107","author":"Stott","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"179ra147","DOI":"10.1126\/scitranslmed.3005616","article-title":"Inertial focusing for tumor antigen-dependent and -independent sorting of rare circulating tumor cells","volume":"5","author":"Ozkumur","year":"2013","journal-title":"Sci. Transl. Med."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1549","DOI":"10.1158\/1538-7445.AM2016-1549","article-title":"Abstract 1549: Molecular profiling of circulating tumor cells as a surrogate for distant metastasis in stage IV breast cancer","volume":"76","author":"Ring","year":"2016","journal-title":"Cancer Res."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"3492","DOI":"10.1158\/0008-5472.CAN-11-4037","article-title":"Ultrasensitive measurement of hotspot mutations in tumor DNA in blood using error-suppressed multiplexed deep sequencing","volume":"72","author":"Narayan","year":"2012","journal-title":"Cancer Res."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"4613","DOI":"10.1158\/1078-0432.CCR-13-3063","article-title":"Noninvasive diagnosis of actionable mutations by deep sequencing of circulating free DNA in lung cancer from never-smokers: A proof-of-concept study from BioCAST\/IFCT-1002","volume":"20","author":"Couraud","year":"2014","journal-title":"Clin. Cancer Res. Off. J. Am. Assoc. Cancer Res."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.1373\/clinchem.2015.241414","article-title":"Diagnostic Accuracy of Noninvasive Genotyping of EGFR in Lung Cancer Patients by Deep Sequencing of Plasma Cell-Free DNA","volume":"61","author":"Uchida","year":"2015","journal-title":"Clin. Chem."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1002\/humu.22825","article-title":"Evaluation of Hybridization Capture Versus Amplicon-Based Methods for Whole-Exome Sequencing","volume":"36","author":"Samorodnitsky","year":"2015","journal-title":"Hum. Mutat."},{"key":"ref_40","first-page":"513","article-title":"Capture-based high-coverage NGS: A powerful tool to uncover a wide spectrum of mutation types","volume":"18","author":"Wang","year":"2016","journal-title":"Genet. Med. Off. J. Am. Coll. Med. Genet."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"3494","DOI":"10.1038\/srep03494","article-title":"Targeted-capture massively-parallel sequencing enables robust detection of clinically informative mutations from formalin-fixed tumours","volume":"3","author":"Wong","year":"2013","journal-title":"Sci. Rep."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1038\/nprot.2009.86","article-title":"Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm","volume":"4","author":"Kumar","year":"2009","journal-title":"Nat. Protoc."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/nmeth0410-248","article-title":"A method and server for predicting damaging missense mutations","volume":"7","author":"Adzhubei","year":"2010","journal-title":"Nat. Methods"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1038\/nbt.2681","article-title":"Systematic investigation of cancer-associated somatic point mutations in SNP databases","volume":"31","author":"Jung","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"2238","DOI":"10.1093\/bioinformatics\/btt395","article-title":"OncodriveCLUST: Exploiting the positional clustering of somatic mutations to identify cancer genes","volume":"29","author":"Tamborero","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1016\/j.cell.2012.04.024","article-title":"Mutational processes molding the genomes of 21 breast cancers","volume":"149","author":"Alexandrov","year":"2012","journal-title":"Cell"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1038\/nature11017","article-title":"The landscape of cancer genes and mutational processes in breast cancer","volume":"486","author":"Stephens","year":"2012","journal-title":"Nature"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1038\/ng1335","article-title":"Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer","volume":"36","author":"Mitelman","year":"2004","journal-title":"Nat. Genet."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"4845","DOI":"10.1038\/onc.2014.406","article-title":"The landscape and therapeutic relevance of cancer-associated transcript fusions","volume":"34","author":"Yoshihara","year":"2015","journal-title":"Oncogene"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"7727","DOI":"10.18632\/oncotarget.3115","article-title":"TP53 intron 1 hotspot rearrangements are specific to sporadic osteosarcoma and can cause Li-Fraumeni syndrome","volume":"6","author":"Ribi","year":"2015","journal-title":"Oncotarget"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"e50267","DOI":"10.7554\/eLife.50267","article-title":"CNApp, a tool for the quantification of copy number alterations and integrative analysis revealing clinical implications","volume":"9","author":"Bassaganyas","year":"2020","journal-title":"eLife"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1482","DOI":"10.1038\/s41598-018-37574-8","article-title":"Comparison of TCGA and GENIE genomic datasets for the detection of clinically actionable alterations in breast cancer","volume":"9","author":"Kaur","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Xu, L., Mao, X., Imrali, A., Syed, F., Mutsvangwa, K., Berney, D., Cathcart, P., Hines, J., Shamash, J., and Lu, Y.-J. (2015). Optimization and Evaluation of a Novel Size Based Circulating Tumor Cell Isolation System. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0138032"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"812","DOI":"10.18632\/oncotarget.22549","article-title":"Efficient leukocyte depletion by a novel microfluidic platform enables the molecular detection and characterization of circulating tumor cells","volume":"9","author":"Obermayr","year":"2017","journal-title":"Oncotarget"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1126\/science.1228522","article-title":"Circulating breast tumor cells exhibit dynamic changes in epithelial and mesenchymal composition","volume":"339","author":"Yu","year":"2013","journal-title":"Science"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.canlet.2009.06.027","article-title":"Circulating tumor cells with a putative stem cell phenotype in peripheral blood of patients with breast cancer","volume":"288","author":"Theodoropoulos","year":"2010","journal-title":"Cancer Lett."},{"key":"ref_57","first-page":"1641","article-title":"A preliminary investigation of the relationship between circulating tumor cells and cancer stem cells in patients with breast cancer","volume":"58","author":"Wang","year":"2012","journal-title":"Cell. Mol. Biol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/nbt.2576","article-title":"Identification of a population of blood circulating tumor cells from breast cancer patients that initiates metastasis in a xenograft assay","volume":"31","author":"Baccelli","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Polioudaki, H., Agelaki, S., Chiotaki, R., Politaki, E., Mavroudis, D., Matikas, A., Georgoulias, V., and Theodoropoulos, P.A. (2015). Variable expression levels of keratin and vimentin reveal differential EMT status of circulating tumor cells and correlation with clinical characteristics and outcome of patients with metastatic breast cancer. BMC Cancer, 15.","DOI":"10.1186\/s12885-015-1386-7"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/s13058-016-0687-3","article-title":"In patients with metastatic breast cancer the identification of circulating tumor cells in epithelial-to-mesenchymal transition is associated with a poor prognosis","volume":"18","author":"Bulfoni","year":"2016","journal-title":"Breast Cancer Res."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"2163","DOI":"10.1038\/s41467-019-10122-2","article-title":"Hydro-Seq enables contamination-free high-throughput single-cell RNA-sequencing for circulating tumor cells","volume":"10","author":"Cheng","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1038\/nbt.2892","article-title":"Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer","volume":"32","author":"Lohr","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"1110","DOI":"10.1158\/0008-5472.CAN-17-2686","article-title":"Comprehensive Mutation and Copy Number Profiling in Archived Circulating Breast Cancer Tumor Cells Documents Heterogeneous Resistance Mechanisms","volume":"78","author":"Paoletti","year":"2018","journal-title":"Cancer Res."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"885","DOI":"10.1038\/s41598-017-01005-x","article-title":"Novel metrics to measure coverage in whole exome sequencing datasets reveal local and global non-uniformity","volume":"7","author":"Wang","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"883","DOI":"10.1056\/NEJMoa1113205","article-title":"Intratumor heterogeneity and branched evolution revealed by multiregion sequencing","volume":"366","author":"Gerlinger","year":"2012","journal-title":"N. Engl. J. Med."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1038\/nature19328","article-title":"HER2 expression identifies dynamic functional states within circulating breast cancer cells","volume":"537","author":"Jordan","year":"2016","journal-title":"Nature"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1038\/s41467-017-00196-1","article-title":"Molecular characterization of breast cancer CTCs associated with brain metastasis","volume":"8","author":"Boral","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"P6-05-08","DOI":"10.1158\/1538-7445.SABCS15-P6-05-08","article-title":"Abstract P6-05-08: Integrating whole exome sequencing data with RNAseq and quantitative proteomics to better inform clinical treatment decisions in patients with metastatic triple negative breast cancer","volume":"76","author":"Rabizadeh","year":"2016","journal-title":"Cancer Res."},{"key":"ref_69","first-page":"683","article-title":"DNA breakpoint assay reveals a majority of gross duplications occur in tandem reducing VUS classifications in breast cancer predisposition genes","volume":"21","author":"Richardson","year":"2019","journal-title":"Genet. Med. Off. J. Am. Coll. Med. Genet."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"850","DOI":"10.1038\/nrc928","article-title":"New aspects of natural-killer-cell surveillance and therapy of cancer","volume":"2","author":"Smyth","year":"2002","journal-title":"Nat. Rev. Cancer"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"5473","DOI":"10.1073\/pnas.1418631112","article-title":"Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants","volume":"112","author":"Belkadi","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1002\/humu.22813","article-title":"Comparison of Exome and Genome Sequencing Technologies for the Complete Capture of Protein-Coding Regions","volume":"36","author":"Lelieveld","year":"2015","journal-title":"Hum. Mutat."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1007\/s00439-015-1631-9","article-title":"Clinical sequencing: Is WGS the better WES?","volume":"135","author":"Meienberg","year":"2016","journal-title":"Hum. Genet."},{"key":"ref_74","doi-asserted-by":"crossref","unstructured":"Meynert, A.M., Ansari, M., FitzPatrick, D.R., and Taylor, M.S. (2014). Variant detection sensitivity and biases in whole genome and exome sequencing. BMC Bioinform., 15.","DOI":"10.1186\/1471-2105-15-247"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"908","DOI":"10.1038\/nbt.1975","article-title":"Performance comparison of exome DNA sequencing technologies","volume":"29","author":"Clark","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Kelley, R.K., Magbanua, M.J., Butler, T.M., Collisson, E.A., Hwang, J., Sidiropoulos, N., Evason, K., McWhirter, R.M., Hameed, B., and Wayne, E.M. (2015). Circulating tumor cells in hepatocellular carcinoma: A pilot study of detection, enumeration, and next-generation sequencing in cases and controls. BMC Cancer, 15.","DOI":"10.1186\/s12885-015-1195-z"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"44781","DOI":"10.18632\/oncotarget.6330","article-title":"A comparison of isolated circulating tumor cells and tissue biopsies using whole-genome sequencing in prostate cancer","volume":"6","author":"Jiang","year":"2015","journal-title":"Oncotarget"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"26107","DOI":"10.18632\/oncotarget.8431","article-title":"Mutational analysis of single circulating tumor cells by next generation sequencing in metastatic breast cancer","volume":"7","author":"Rotunno","year":"2016","journal-title":"Oncotarget"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"2349","DOI":"10.18632\/oncotarget.1946","article-title":"Unique molecular signatures as a hallmark of patients with metastatic breast cancer: Implications for current treatment paradigms","volume":"5","author":"Wheler","year":"2014","journal-title":"Oncotarget"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"886","DOI":"10.1016\/j.cell.2012.02.025","article-title":"Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor","volume":"148","author":"Xu","year":"2012","journal-title":"Cell"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"1928","DOI":"10.1038\/s41591-019-0652-7","article-title":"High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants","volume":"25","author":"Razavi","year":"2019","journal-title":"Nat. Med."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"1631","DOI":"10.1200\/JCO.2017.76.8671","article-title":"Circulating Tumor DNA Analysis in Patients with Cancer: American Society of Clinical Oncology and College of American Pathologists Joint Review","volume":"36","author":"Merker","year":"2018","journal-title":"J. Clin. Oncol."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_84","unstructured":"Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv."},{"key":"ref_85","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":"ref_86","doi-asserted-by":"crossref","first-page":"1747","DOI":"10.1101\/gr.239244.118","article-title":"Maftools: Efficient and comprehensive analysis of somatic variants in cancer","volume":"28","author":"Mayakonda","year":"2018","journal-title":"Genome Res."},{"key":"ref_87","first-page":"405","article-title":"Standards and guidelines for the interpretation of sequence variants: A joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology","volume":"17","author":"Richards","year":"2015","journal-title":"Genet. Med. Off. J. Am. Coll. Med. Genet."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/21\/14\/4826\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T09:48:55Z","timestamp":1760176135000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/21\/14\/4826"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,7,8]]},"references-count":87,"journal-issue":{"issue":"14","published-online":{"date-parts":[[2020,7]]}},"alternative-id":["ijms21144826"],"URL":"https:\/\/doi.org\/10.3390\/ijms21144826","relation":{},"ISSN":["1422-0067"],"issn-type":[{"type":"electronic","value":"1422-0067"}],"subject":[],"published":{"date-parts":[[2020,7,8]]}}}