Whole genome loss of heterozygosity profiling on oral squamous cell carcinoma by high-density single nucleotide polymorphic allele (SNP) array

Zhou, Xiaofeng; Li, Cheng; Mok, Samuel C.; Chen, Zugen; Wong, David T.

doi:10.1016/j.cancergencyto.2003.11.010

Cited by 26 publications

(17 citation statements)

References 16 publications

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“…While minimum allelic imbalance was observed for the normal keratinocytes, several frequent LOH regions were identified for HNSCC cases (Table 1). Chromosome arms 3p, 4p, 4q, 5q, 8p, 9p, 10p, 11q, 17p exhibit the frequent LOH, which is in agreement with various previous finds [6,11,24]. The complete LOH profile for chromosome 8 was shown in Figure 1, where a region of approximately 7 Mb at 8p22−8p21.3 exhibits the most frequent allelic imbalance.…”

Section: Resultssupporting

confidence: 90%

“…The SNP array assay was performed as described previously [11][12][13]. In brief, the genomic DNAs were isolated from cultured cell lines using the Qiagen genomic DNA isolation kit (see Supplement Table 1 for the descriptions on the cell lines).…”

Section: Methodsmentioning

confidence: 99%

“…The recent advances in high-density single nucleotide polymorphic allele (SNP) array platform provide unique opportunity to generate LOH profile with high resolution. Our previous studies demonstrated the feasibility of using the Affymetrix 10K SNP Mapping Array for genome-wide LOH profiling [11][12][13].…”

Section: Introductionmentioning

confidence: 99%

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Genomic assessments of the frequent loss of heterozygosity region on 8p21.3∼p22 in head and neck squamous cell carcinoma

Pungpravat

Huang

et al. 2007

Cancer Genetics and Cytogenetics

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Most human cancers are characterized by genetic instabilities. Chromosomal aberrations include segments of allelic imbalance identifiable by loss of heterozygosity (LOH) at polymorphic loci, which may be used to implicate regions harboring tumor suppressor genes. Here we performed whole genome LOH profiling on over 40 human head and neck squamous cell carcinoma (HNSCC) cell lines. Several frequent LOH regions have been identified on chromosomal arms 3p, 4p, 4q, 5q, 8p, 9p, 10p, 11q, and 17p. A genomic region of ∼7 Mb located at 8p22-p21.3 exhibits the most frequent LOH (87.9%), which suggested that this region harbors important tumor suppressor gene(s). Mitochondrial tumor suppressor gene 1 (MTUS1) is a recently identified candidate tumor suppressor gene that resides in this region. Consistent down-regulation in expression was observed in HNSCC for MTUS1 as measured by real-time quantitative RT-PCR. Sequence analysis of MTUS1 gene in HNSCC revealed several important sequence variants in the exon regions of this gene. Thus, our results suggested that MTUS1 is one of the candidate tumor suppressor gene(s) reside in 8p22-p21.3 for HNSCC. The identification of these candidate genes will facilitate the understanding of tumorigenesis of HNSCC. Further studies are needed to functionally evaluate those candidate genes.

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Section: Resultssupporting

confidence: 90%

Section: Methodsmentioning

confidence: 99%

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Genomic assessments of the frequent loss of heterozygosity region on 8p21.3∼p22 in head and neck squamous cell carcinoma

Pungpravat

Huang

et al. 2007

Cancer Genetics and Cytogenetics

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“…Our studies suggested that allelic deletions of the 2q, 3p, and 21q loci played a role in oral SCC progression (2). However, because of the limited number of available microsatellite markers, the rather tedious and labor-intensive procedure, and the requirement for large amounts of DNA, only a modest number of microsatellite markers could be screened (3).…”

Section: Introductionmentioning

confidence: 89%

Expression of the FAM5C in tongue squamous cell carcinoma

Kuroiwa

Yamamoto²,

Onda³

et al. 2009

Oncol Rep

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Abstract. The purpose of this study was to perform a wholegenome analysis of loss of heterozygosity (LOH) in tongue squamous cell carcinoma (SCC) using the Affymetrix 10K SNP Mapping Array. In the gene which had been identified by whole-genome analysis of LOH, we analyzed allelic imbalance to identify the role of the gene. We applied wholegenome analysis of LOH in the specimens from the 5 cases of tongue SCC using this array. In the chromosomal region which had been identified by whole-genome analysis of LOH, we reconfirmed the existence of LOH in 30 cases using microsatellite markers. The expression levels of the mRNA in the region were examined in 15 cases and in 5 tongue SCC-derived cell lines by real-time quantitative RT-PCR analysis. LOH was observed in all of the 5 cases in the 1q31.1 region. Only 3 microsatellite markers (D1S1189, D1S2151, and D1S2595) existed in the 1q31.1 region. A high frequency of LOH was found at the D1S1189 locus in 18/30 (60%), D1S2151 locus in 16/30 (53%) and D1S2595 locus in 21/30 (70%). Only the Family with sequence similarity 5, member C (FAM5C) gene was located in the 1q31.1 region. There was statistically significant difference in the FAM5C mRNA expression levels between tongue SCC and normal tissues. All tongue SCC-derived cell lines decreased FAM5C mRNA expression compared with normal oral keratinocytes (NOKs). We conclude that FAM5C may be a novel tumor suppressor gene (TSG) in tongue SCC.

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“…It facilitates precise iden-tification of deleted chromosomal regions and their positional candidate genes associated with growth advantage and clonal expansion of in situ preneoplasia. [12][13][14] Here, we concentrate on the technological aspects of this approach referred to as highresolution whole-organ mapping with SNPs and present the pattern of losses associated with clonal expansion of in situ bladder preneoplasia in two model tumor suppressor gene loci (RB1 and p53).…”

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confidence: 99%

High-resolution whole-organ mapping with SNPs and its significance to early events of carcinogenesis

Tuziak

Lee

Majewski

et al. 2005

Laboratory Investigation

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We attempted to identify deleted segments in two model tumor suppressor gene loci on chromosomes 13q14 and 17p13 that were associated with clonal expansion of in situ bladder preneoplasia using single nucleotide polymorphisms (SNPs)-based whole-organ histologic and genetic mapping. For mapping with SNPs, the sequence-based maps spanning approximately 27 and 5 Mb centered around RB1 and p53, respectively, were assembled. The integrated gene and SNP maps of the regions were used to select 661 and 960 SNPs, which were genotyped by pyrosequencing. Genotyping of SNPs was performed on DNA samples corresponding to histologic maps of the entire bladder mucosa in human cystectomy specimens with invasive urothelial carcinoma. By using this approach, we have identified deleted regions associated with clonal expansion of intraurothelial neoplasia; which ranged from 0.001 to 4.3 Mb (average 0.67 Mb) and formed clusters of discontinuous deleted segments. The high resolution of such maps is a prerequisite for future positional targeting of genes involved in early phases of bladder neoplasia. This approach also permits analysis of the overall genomic landscape of the involved region and discloses that a unique composition of noncoding DNA characterized by a high concentration of repetitive sequences may predispose to deletions. Laboratory Investigation (2005) 85, 689-701. doi:10.1038/labinvest.3700270Keywords: single nucleotide polymorphic site; bladder cancer; genetic mapping; clonal expansion of preneoplasia Cancer develops via multiple, complex steps, many of which precede the development of microscopically recognizable preneoplastic conditions. 1-3 Recent studies indicate that common human malignancies, including bladder cancer, begin as clonal in situ expansion of phenotypically normal cells, which may form large plaques involving the affected mucosa. 4,5 Identification of chromosomal regions and their target genes involved in the development of such clinically and microscopically occult preneoplastic lesions may provide valuable clues to the incipient events of human carcinogenesis. 6,7 Ultimately, the results could lead to the development of novel markers for early cancer detection and prevention.We have previously reported the identification of several putative tumor suppressor gene loci involved in early preinvasive phases of human bladder cancer. [8][9][10][11] These loci were found by searching for allelic imbalances using DNA hypervariable markers and a whole-organ histologic and genetic mapping strategy developed in our laboratory. The ultimate identification of genes mapping to the deleted regions was hampered by the low resolution of the original recombination-based maps and the absence of continuous genome sequence maps, which were not available in the early phases of the human genome project.In this paper, we present the strategy that combines whole-organ histologic maps and highresolution genetic mapping using single nucleotide polymorphic (SNP) sites. It facilitates precise iden-

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Whole genome loss of heterozygosity profiling on oral squamous cell carcinoma by high-density single nucleotide polymorphic allele (SNP) array

Cited by 26 publications

References 16 publications

Genomic assessments of the frequent loss of heterozygosity region on 8p21.3∼p22 in head and neck squamous cell carcinoma

Genomic assessments of the frequent loss of heterozygosity region on 8p21.3∼p22 in head and neck squamous cell carcinoma

Expression of the FAM5C in tongue squamous cell carcinoma

High-resolution whole-organ mapping with SNPs and its significance to early events of carcinogenesis

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