Allelic losses of chromosome 10 in glioma tissues detected by quantitative single-strand conformation polymorphism analysis.
BACKGROUND
Detection of loss of heterozygosity (LOH) in clinical tissue samples is frequently difficult because samples are usually contaminated with noncancerous cells or because tumor cells in single tissues have genetic heterogeneity, and the precision of available techniques is insufficient for reliable analysis in such materials. We hypothesized that single-strand conformation polymorphism (SSCP) analysis can precisely quantify the gene dosage in mixed samples and is suitable for detection of LOH in clinical tissue samples.


METHODS
We assessed the accuracy of a fluorescent SSCP method for the quantification of single-nucleotide polymorphism (SNP) alleles, using DNAs that were composed of cancerous DNA mixed with noncancerous DNA at various ratios. We applied this method to precisely characterize LOH in glioma tissue samples, using 96 SNPs that were evenly distributed throughout chromosome 10.


RESULTS
LOH could be detected even in the cancerous DNA heavily contaminated (up to 80%) with noncancerous DNA. Using this method, we obtained LOH profiles of 56 gliomas with resolution at the SNP level (i.e., 1.5-Mbp interval). Anaplastic astrocytomas exhibited both 10p and 10q LOH, whereas diffuse astrocytomas frequently (63% of the cases) exhibited loss of 10p alone. We also found a possible new LOH region (around 10p13) in gliomas.


CONCLUSIONS
The present method is effective for precise mapping of LOH region in surgically obtained tumor tissues and could be applicable to the genetic diagnosis of cancers other than gliomas.
Hata
Nobuhiro
N
Department of Neurosurgery, Graduate School of Medical Sciences, Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
Yoshimoto
Koji
K
Yokoyama
Nobuhiko
N
Mizoguchi
Masahiro
M
Shono
Tadahisa
T
Guan
Yanlei
Y
Tahira
Tomoko
T
Kukita
Yoji
Y
Higasa
Koichiro
K
Nagata
Shinji
S
Iwaki
Toru
T
Sasaki
Tomio
T
Hayashi
Kenshi
K
D000483:Alleles; D001254:Astrocytoma / Q000235:genetics; D001932:Brain Neoplasms / Q000235:genetics*; D002879:Chromosomes, Human, Pair 10; D005910:Glioma / Q000235:genetics*; D006801:Humans; D019656:Loss of Heterozygosity; D020641:Polymorphism, Single Nucleotide; D018807:Polymorphism, Single-Stranded Conformational