Abstract
Mapping loss of heterozygosity (LOH) regions in the genomes of tumor tissues is a practical approach for identifying genes whose loss is related to tumorigenesis. Conventional LOH analyses using microsatellite or single nucleotide polymorphism (SNP) markers require the simultaneous examination of tumor- and matched normal-DNA. Here, we improved the previously developed SNP-based LOH assay using single strand conformation polymorphism (SSCP) analysis, so that LOH in tumor samples heavily contaminated with normal DNA can now be precisely estimated, even when matched normal DNA is not available. We demonstrate the reliability of the improved SSCP-based LOH detection method, called the LOH estimation by quantitative SSCP analysis using averaged control (LOQUS-AC), by comparing the results with those of the previous "LOH estimated bv quantitative SSCP assay" (LOQUS) method. Using the LOQUS-AC assay, LOH was detected at a high consistency (98.1%) with the previous LOQUS method. We then applied this new method to characterize LOH profiles in 130 meningiomas, using 68 SNPs (i.e., a mean inter-SNP interval of 441 kbp) that are evenly distributed throughout chromosome 1p36. Benign, atypical and anaplastic meningiomas exhibited 1p36 LOH at frequencies of 48.39, 84.62 and 100.00%, respectively, using LOQUS-AC. Subsequently, we detected a candidate common LOH region on 1p36.11 that might harbor tumor suppressor genes related to malignant progression of meningioma.
| Original language | English |
|---|---|
| Pages (from-to) | 1820-1826 |
| Number of pages | 7 |
| Journal | International Journal of Cancer |
| Volume | 122 |
| Issue number | 8 |
| DOIs | |
| Publication status | Published - Apr 15 2008 |
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All Science Journal Classification (ASJC) codes
- Oncology
- Cancer Research
Cite this
Narrowing of the regions of allelic losses of chromosome 1p36 in meningioma tissues by an improved SSCP analysis. / Guan, Yanlei; Hata, Nobuhiro; Kuga, Daisuke; Yoshimoto, Koji; Mizoguchi, Masahiro; Shono, Tadahisa; Suzuki, Satoshi; Tahira, Tomoko; Kukita, Yoji; Higasa, Koichiro; Yokoyama, Nobuhiko; Nagata, Shinji; Iwaki, Toru; Sasaki, Tomio; Hayashi, Kenshi.
In: International Journal of Cancer, Vol. 122, No. 8, 15.04.2008, p. 1820-1826.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Narrowing of the regions of allelic losses of chromosome 1p36 in meningioma tissues by an improved SSCP analysis
AU - Guan, Yanlei
AU - Hata, Nobuhiro
AU - Kuga, Daisuke
AU - Yoshimoto, Koji
AU - Mizoguchi, Masahiro
AU - Shono, Tadahisa
AU - Suzuki, Satoshi
AU - Tahira, Tomoko
AU - Kukita, Yoji
AU - Higasa, Koichiro
AU - Yokoyama, Nobuhiko
AU - Nagata, Shinji
AU - Iwaki, Toru
AU - Sasaki, Tomio
AU - Hayashi, Kenshi
PY - 2008/4/15
Y1 - 2008/4/15
N2 - Mapping loss of heterozygosity (LOH) regions in the genomes of tumor tissues is a practical approach for identifying genes whose loss is related to tumorigenesis. Conventional LOH analyses using microsatellite or single nucleotide polymorphism (SNP) markers require the simultaneous examination of tumor- and matched normal-DNA. Here, we improved the previously developed SNP-based LOH assay using single strand conformation polymorphism (SSCP) analysis, so that LOH in tumor samples heavily contaminated with normal DNA can now be precisely estimated, even when matched normal DNA is not available. We demonstrate the reliability of the improved SSCP-based LOH detection method, called the LOH estimation by quantitative SSCP analysis using averaged control (LOQUS-AC), by comparing the results with those of the previous "LOH estimated bv quantitative SSCP assay" (LOQUS) method. Using the LOQUS-AC assay, LOH was detected at a high consistency (98.1%) with the previous LOQUS method. We then applied this new method to characterize LOH profiles in 130 meningiomas, using 68 SNPs (i.e., a mean inter-SNP interval of 441 kbp) that are evenly distributed throughout chromosome 1p36. Benign, atypical and anaplastic meningiomas exhibited 1p36 LOH at frequencies of 48.39, 84.62 and 100.00%, respectively, using LOQUS-AC. Subsequently, we detected a candidate common LOH region on 1p36.11 that might harbor tumor suppressor genes related to malignant progression of meningioma.
AB - Mapping loss of heterozygosity (LOH) regions in the genomes of tumor tissues is a practical approach for identifying genes whose loss is related to tumorigenesis. Conventional LOH analyses using microsatellite or single nucleotide polymorphism (SNP) markers require the simultaneous examination of tumor- and matched normal-DNA. Here, we improved the previously developed SNP-based LOH assay using single strand conformation polymorphism (SSCP) analysis, so that LOH in tumor samples heavily contaminated with normal DNA can now be precisely estimated, even when matched normal DNA is not available. We demonstrate the reliability of the improved SSCP-based LOH detection method, called the LOH estimation by quantitative SSCP analysis using averaged control (LOQUS-AC), by comparing the results with those of the previous "LOH estimated bv quantitative SSCP assay" (LOQUS) method. Using the LOQUS-AC assay, LOH was detected at a high consistency (98.1%) with the previous LOQUS method. We then applied this new method to characterize LOH profiles in 130 meningiomas, using 68 SNPs (i.e., a mean inter-SNP interval of 441 kbp) that are evenly distributed throughout chromosome 1p36. Benign, atypical and anaplastic meningiomas exhibited 1p36 LOH at frequencies of 48.39, 84.62 and 100.00%, respectively, using LOQUS-AC. Subsequently, we detected a candidate common LOH region on 1p36.11 that might harbor tumor suppressor genes related to malignant progression of meningioma.
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U2 - 10.1002/ijc.23297
DO - 10.1002/ijc.23297
M3 - Article
VL - 122
SP - 1820
EP - 1826
JO - International Journal of Cancer
JF - International Journal of Cancer
SN - 0020-7136
IS - 8
ER -