An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays.
Changes in DNA copy number contribute to cancer pathogenesis. We now show that high-density single nucleotide polymorphism (SNP) arrays can detect copy number alterations. By hybridizing genomic representations of breast and lung carcinoma cell line and lung tumor DNA to SNP arrays, and measuring locus-specific hybridization intensity, we detected both known and novel genomic amplifications and homozygous deletions in these cancer samples. Moreover, by combining genotyping with SNP quantitation, we could distinguish loss of heterozygosity events caused by hemizygous deletion from those that occur by copy-neutral events. The simultaneous measurement of DNA copy number changes and loss of heterozygosity events by SNP arrays should strengthen our ability to discover cancer-causing genes and to refine cancer diagnosis.
Zhao
Xiaojun
X
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.
Li
Cheng
C
Paez
J Guillermo
JG
Chin
Koei
K
Jänne
Pasi A
PA
Chen
Tzu-Hsiu
TH
Girard
Luc
L
Minna
John
J
Christiani
David
D
Leo
Chris
C
Gray
Joe W
JW
Sellers
William R
WR
Meyerson
Matthew
M
D000483:Alleles; D001943:Breast Neoplasms / Q000235:genetics*; D004273:DNA, Neoplasm / Q000032:analysis / Q000235:genetics*; D018628:Gene Dosage; D006720:Homozygote; D006801:Humans; D019656:Loss of Heterozygosity; D008175:Lung Neoplasms / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide
D004273:DNA, Neoplasm