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Erratum published on 19 January 2021, see J. Clin. Med. 2021, 10(2), 370.
Open AccessArticle

Integrative Analysis and Machine Learning Based Characterization of Single Circulating Tumor Cells

1
Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi 110020, India
2
Department of Computer Science and Engineering, Indraprastha Institute of Information Technology, New Delhi 110020, India
3
Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
4
Biolidics Limited, 81 Science Park Drive, 02-03 The Chadwick, Singapore 118257, Singapore
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Qualcomm Incorporated, 5775 Morehouse Drive, San Diego, CA 92121, USA
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National Cancer Centre Singapore, 11 Hospital Dr, Singapore 169610, Singapore
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Fluidigm Corporation, 2 Tower Place, Suite 2000, South San Francisco, CA 94080, USA
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School of Mathematics, Indian Institute of Science Education and Research, Thiruvananthapuram 695551, India
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Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
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Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore 117599, Singapore
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Guangzhou Regenerative Medicine and Health; Guangdong laboratory, Chinese Academy of Science, Guangzhou 510530, China
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Center for Artificial Intelligence, Indraprastha Institute of Information Technology, New Delhi 110020, India
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Current address: Department of Computational Biology, University of Lausanne (UNIL), Lausanne 1015, Switzerland.
§
Current address: BioSkryb Corporation, BioLabs, 701 W Main St, Suite 200, Durham, NC 27701, USA.
Current address: Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Engineering Drive 1, Singapore 117575, Singapore.
Current address: Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.
J. Clin. Med. 2020, 9(4), 1206; https://doi.org/10.3390/jcm9041206
Received: 23 February 2020 / Revised: 6 April 2020 / Accepted: 16 April 2020 / Published: 22 April 2020
We collated publicly available single-cell expression profiles of circulating tumor cells (CTCs) and showed that CTCs across cancers lie on a near-perfect continuum of epithelial to mesenchymal (EMT) transition. Integrative analysis of CTC transcriptomes also highlighted the inverse gene expression pattern between PD-L1 and MHC, which is implicated in cancer immunotherapy. We used the CTCs expression profiles in tandem with publicly available peripheral blood mononuclear cell (PBMC) transcriptomes to train a classifier that accurately recognizes CTCs of diverse phenotype. Further, we used this classifier to validate circulating breast tumor cells captured using a newly developed microfluidic system for label-free enrichment of CTCs. View Full-Text
Keywords: high-throughput sequencing; rare cell type; single-cell; RNA-seq; machine learning; CTC; blood high-throughput sequencing; rare cell type; single-cell; RNA-seq; machine learning; CTC; blood
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MDPI and ACS Style

Iyer, A.; Gupta, K.; Sharma, S.; Hari, K.; Lee, Y.F.; Ramalingam, N.; Yap, Y.S.; West, J.; Bhagat, A.A.; Subramani, B.V.; Sabuwala, B.; Tan, T.Z.; Thiery, J.P.; Jolly, M.K.; Ramalingam, N.; Sengupta, D. Integrative Analysis and Machine Learning Based Characterization of Single Circulating Tumor Cells. J. Clin. Med. 2020, 9, 1206. https://doi.org/10.3390/jcm9041206

AMA Style

Iyer A, Gupta K, Sharma S, Hari K, Lee YF, Ramalingam N, Yap YS, West J, Bhagat AA, Subramani BV, Sabuwala B, Tan TZ, Thiery JP, Jolly MK, Ramalingam N, Sengupta D. Integrative Analysis and Machine Learning Based Characterization of Single Circulating Tumor Cells. Journal of Clinical Medicine. 2020; 9(4):1206. https://doi.org/10.3390/jcm9041206

Chicago/Turabian Style

Iyer, Arvind; Gupta, Krishan; Sharma, Shreya; Hari, Kishore; Lee, Yi F.; Ramalingam, Neevan; Yap, Yoon S.; West, Jay; Bhagat, Ali A.; Subramani, Balaram V.; Sabuwala, Burhanuddin; Tan, Tuan Z.; Thiery, Jean P.; Jolly, Mohit K.; Ramalingam, Naveen; Sengupta, Debarka. 2020. "Integrative Analysis and Machine Learning Based Characterization of Single Circulating Tumor Cells" J. Clin. Med. 9, no. 4: 1206. https://doi.org/10.3390/jcm9041206

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