Identification of possible genetic alterations in the breast cancer cell line MCF-7 using high-density SNP genotyping microarray.
BACKGROUND
Cancer cell lines are used extensively in various research. Knowledge of genetic alterations in these lines is important for understanding mechanisms underlying their biology. However, since paired normal tissues are usually unavailable for comparison, precisely determining genetic alterations in cancer cell lines is difficult. To address this issue, a highly efficient and reliable method is developed.


OBJECTIVE
Establishing a highly efficient and reliable experimental system for genetic profiling of cell lines.


METHODS
A widely used breast cancer cell line, MCF-7, was genetically profiled with 4,396 single nucleotide polymorphisms (SNPs) spanning 11 whole chromosomes and two other small regions using a newly developed high-throughput multiplex genotyping approach.


RESULTS
The fractions of homozygous SNPs in MCF-7 (13.3%) were significantly lower than those in the control cell line and in 24 normal human individuals (25.1% and 27.4%, respectively). Homozygous SNPs in MCF-7 were found in clusters. The sizes of these clusters were significantly larger than the expected based on random allelic combination. Fourteen such regions were found on chromosomes 1p, 1q, 2q, 6q, 13, 15q, 16q, 17q and 18p in MCF-7 and two in the small regions.


CONCLUSIONS
These results are generally concordant with those obtained using different approaches but are better in defining their chromosomal positions. The used approach provides a reliable way to detecting possible genetic alterations in cancer cell lines without paired normal tissues.
Wang
Hui-Yun
HY
Department of Molecular Genetics, Microbiology and Immunology/The Cancer Institute of New Jersey, Piscataway, New Jersey, 08854, USA.
Greenawalt
Danielle
D
Cui
Xiangfeng
X
Tereshchenko
Irina V
IV
Luo
Minjie
M
Yang
Qifeng
Q
Azaro
Marco A
MA
Hu
Guohong
G
Chu
Yi
Y
Li
James Y
JY
Shen
Li
L
Lin
Yong
Y
Zhang
Lianjun
L
Li
Honghua
H