Table 1.

Studies on genetic alterations in CSCs.

Cancer Type	Materials	Methods	Main Conclusions	Reference
GBM	Primary tumor cells	SNP array, WES, single-cell analysis	CNAs found in primary tumor cells are also present in neurospheres in different subclones	Piccirillo S.M. et al., 2015 [11]
GBM	Primary tumor cells	aCGH	High similarity between GBM mass and spheroids	Pesenti C. et al., 2019 [12]
GBM	Primary tumor cells	SKY; SNP array	Cells cultured in serum-containing medium underwent genomic rearrangements, while spheroids did not	Lee J. et al., 2006 [13]
Breast	Primary tumor cells	WES; ultra-deep amplicon sequencing	Mutations are shared between tumor bulk and spheres	Klevebring D. et al., 2014 [14]
Breast	Tumor cells from pleural effusions	low-coverage WGS	Same alteration in sorted CSCs and bulk tumor	Tiran V. et al., 2017 [15]
Breast	MDA-MB-231 cell line	WGS; target deep sequencing	No differences in VAF between monolayer and spheres	Tong M. et al., 2018 [16]
HNSCC	Primary tumor cells	WES	From LOH analysis, it is hypothesized that CSCs may originate either from normal tissue or from tumor cell dedifferentiation	Salazar-Garcia L. et al., 2018 [17]
Bladder	One primary tumor and lymph node metastases	WES	SNPs are mainly shared by sorted CSCs and bulk tumor cells; a small number is enriched either in CSCs or in bulk cells	Prado K. et al., 2017 [18]
Various	Cell lines	SKY	More rearranged genotype of spheres compared to parental cell lines	Gasparini P. et al., 2010 [10]

Abbreviations: CSCs, cancer stem cell; GBM = glioblastoma multiforme; SNP = single nucleotide polymorphism; WES = whole exome sequencing; can = copy number alteration; aCGH = array comparative genomic hybridization; SKY = spectral karyotyping imaging; WGS = whole genome sequencing; VAF = variant allele frequency; HNSCC = head and neck squamous cell carcinoma; LOH = loss of heterozygosity.