RT Journal
A1 Poonia, Sarita
A1 Goel, Anurag
A1 Chawla, Smriti
A1 Bhattacharya, Namrata
A1 Rai, Priyadarshini
A1 Lee, Yi Fang
A1 Yap, Yoon Sim
A1 West, Jay
A1 Bhagat, Ali Asgar
A1 Tayal, Juhi
A1 Mehta, Anurag
A1 Ahuja, Gaurav
A1 Majumdar, Angshul
A1 Ramalingam, Naveen
A1 Sengupta, Debarka
T1 Marker-free characterization of full-length transcriptomes of single live circulating tumor cells
JF Genome Research 
JO Genome Research 
YR 2023 
FD January 01 
VO 33 
IS 1 
SP 80 
OP 95 
DO 10.1101/gr.276600.122 
UL http://genome.cshlp.org/content/33/1/80.abstract 
AB The identification and characterization of circulating tumor cells (CTCs) are important for gaining insights into the biology of metastatic cancers, monitoring disease progression, and medical management of the disease. The limiting factor in the enrichment of purified CTC populations is their sparse availability, heterogeneity, and altered phenotypes relative to the primary tumor. Intensive research both at the technical and molecular fronts led to the development of assays that ease CTC detection and identification from peripheral blood. Most CTC detection methods based on single-cell RNA sequencing (scRNA-seq) use a mix of size selection, marker-based white blood cell (WBC) depletion, and antibodies targeting tumor-associated antigens. However, the majority of these methods either miss out on atypical CTCs or suffer from WBC contamination. We present unCTC, an R package for unbiased identification and characterization of CTCs from single-cell transcriptomic data. unCTC features many standard and novel computational and statistical modules for various analyses. These include a novel method of scRNA-seq clustering, named deep dictionary learning using k-means clustering cost (DDLK), expression-based copy number variation (CNV) inference, and combinatorial, marker-based verification of the malignant phenotypes. DDLK enables robust segregation of CTCs and WBCs in the pathway space, as opposed to the gene expression space. We validated the utility of unCTC on scRNA-seq profiles of breast CTCs from six patients, captured and profiled using an integrated ClearCell FX and Polaris workflow that works by the principles of size-based separation of CTCs and marker-based WBC depletion.