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Table 3 Summary of single-cell sequencing studies on primary tumors from a variety of human cancers

From: Single-cell sequencing and tumorigenesis: improved understanding of tumor evolution and metastasis

Tumor Tissue source (number of cells, patients/cell lines) Data type Results Reference
Breast
  TNBC (200, 2) CNV TNBC displays punctuated clonal evolution where CNVs are shared across single cells [6]
TNBC (66, 1), ER + HER2- (113, 1) CNV and SNV TNBC has a higher mutation rate than ER + HER2- tumors or normal cells; CNVs are an early event in tumorigenesis [39]
TNBC (1000, 12) CNV Supports theory of punctuated clonal evolution [40]
ER + (332, 2) CNV Supports theory of punctuated clonal evolution [41]
MDA-MB-231 and CN34 cell lines (44, 2) RNA-seq Rare cell populations with highly variable gene expression differences have increased metastatic capacity and ability to survive treatment [42]
MDA-MB-231 cell line (15, 1) RNA-seq Development of drug-resistance to paclitaxel is associated with unique mutations; gene expression changes not detectable in bulk tumors [43]
HER2 + (8, 2)a RNA-seq 404 genes differentially expressed in breast cancer stem cells, including CA12 which may be prognostic [37]
Lung
  Lung adenocarcinoma PDX (34, 1) RNA-seq Gene expression profiling identifies a subpopulation of PDX cells with poor prognosis [44]
Lung adenocarcinoma PDX (34, 1) RNA-seq and WES Identification of a subpopulation of KRAS+/low risk cells that were drug resistant [45]
LC2/ad and LC2/ad-R lung cancer cell lines (336, 7) RNA-seq Increased plasticity in gene expression among cells is associated with vandetanib resistance [46]
Brain
  EGFR amplified glioblastomas (50-60, 2) CNV Patterns of EGFR mutations differ among cells; heterogeneity may contribute to therapy resistance [48]
Glioblastomas (430, 5)a RNA-seq Variable EGFR CNVs and cells reflecting different subtypes are present in primary glioblastomas [38]
Colon
  Colon tumor and normal adjacent cells (63, 1) SNV Different mutational profiles found in two sub-clonal populations of cells may suggest bi-clonal origins [49]
HCT116 cell line (96, 1) RNA-seq SCS reveals cryptic mutations not detected in bulk tumor [50]
Bladder
  Muscle-invasive bladder transitional-cell carcinoma (66, 1) SNV Cell-lineage-specific mutations may initiate carcinogenesis and drive cancer progression [51]
Squamous cell carcinoma of the bladder (75, 1) RNA-seq Cell-to-cell heterogeneity in the expression of genes within cancer-related pathways may affect outcomes [52]
Kidney
  Clear cell renal cell carcinoma (20, 1) SNV ccRCC more genetically complex than predicted based on whole-tumor sequencing [53]
ccRCC primary carcinoma and paired metastasis propagated in PDX model (116, 1) RNA-seq Differential expression of targetable genes between cells supports multi-agent treatment strategy [54]
Blood     
Secondary AML (36, 3) SNV SCS identifies genomic complexity not seen in whole-tumor analysis and resolves clonal relationships [55]
Pediatric ALL (1479, 6) SNV CNVs precede somatic mutations; diversity of driver mutations affects clonal fitness [56]
B-cell ALL (276, 3) CNV CNVs not detected in bulk tumors are observed in single cells; CNVs develop in response to environmental stressors [57]
JAK2-negative myeloproliferative neoplasm (58, 1) SNV Lack of identifiable sub-clones suggests tumor is monoclonal, but large genetic distances exist between cells [58]
  1. TNBC triple negative breast cancer, CNV copy number variant, ER estrogen receptor, HER2 human epidermal growth factor receptor 2, SNV single nucleotide variant, RNA-seq RNA sequencing, PDX patient-derived xenograft, WES whole-exome sequencing KRAS Kirsten rat sarcoma viral oncogene homolog, EGFR epidermal growth factor receptor, SCS single-cell sequencing, ccRCC clear cell renal cell carcinoma, AML acute myeloid leukemia, ALL acute lymphoblastic leukemia, JAK2 Janus kinase 2
  2. aThese studies investigated transcriptomic differences in breast and glioblastoma stem cells isolated as single cells from the primary carcinomas