A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

Table 1 List and description of 10 cancer cell lines and a normal reference cell line with % estimated copy number alterations (CNA) and an intra-tumor heterogeneity (ITH) value to indicate potential polyclonality of the cell line

Cell line	Name	Description	Comments	CNA % (est.)^a	ITH (Shannon’s index)
B	Male reference	Normal		~ 0	0
BLY	B lymphocyte	Myeloma	Mixed with TLY within study^b	~ 25%	43.2
BRA	Brain	Glioblastoma	Polyclonal	90%	21.0
BRE	Breast	Adenocarcinoma	Polyclonal	60%	100.0
CRV	Cervix	Adenocarcinoma	Polyclonal	70%	10.9
LIP	Soft tissue	Liposarcoma		90%	3.5
LIV	Liver	Hepatoblastoma		27%	2.5
MAC	Macrophage	Lymphoma	Polyclonal	80%	11.8
SKN	Skin	Melanoma		24%	0
TES	Testes	Carcinoma		72%	4.8
TLY	T lymphoblast	Leukemia	Inherently tetraploid^c with variations	22%	1.1

^a CNA were estimated using Agilent GenetiSure Cancer Research CGH + SNP Microarray (2 × 400K), G5975A and WES
^b Information of the mixture of the original BLY with TLY is provided in Supplementary Information
^c Establishment of the tetraploid nature of the TLY is provided in Supplementary Information

ISSN: 1474-760X