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

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]