J Korean Assoc Oral Maxillofac Surg.  2011 Dec;37(6):550-555. 10.5125/jkaoms.2011.37.6.550.

Analysis of copy number abnormality (CNA) and loss of heterozygosity (LOH) in the whole genome using single nucleotide polymorphism (SNP) genotyping arrays in tongue squamous cell carcinoma

• Tsukasa K
• Nobuharu Y
• Takeshi O
• Hiroki B
• Takashi Y
• Akira K
• Nobuo T
• Takahiko S

• KMID: 2136997
• DOI: http://doi.org/10.5125/jkaoms.2011.37.6.550

Abstract

Chromosomal loss of heterozygosity (LOH) is a common mechanism for the inactivation of tumor suppressor genes in human epithelial cancers. LOH patterns can be generated through allelotyping using polymorphic microsatellite markers; however, owing to the limited number of available microsatellite markers and the requirement for large amounts of DNA, only a modest number of microsatellite markers can be screened. Hybridization to single nucleotide polymorphism (SNP) arrays using Affymetarix GeneChip Mapping 10 K 2.0 Array is an efficient method to detect genome-wide cancer LOH. We determined the presence of LOH in oral SCCs using these arrays. DNA was extracted from tissue samples obtained from 10 patients with tongue SCCs who presented at the Hospital of Tokyo Dental College. We examined the presence of LOH in 3 of the 10 patients using these arrays. At the locus that had LOH, we examined the presence of LOH using microsatellite markers. LOH analysis using Affymetarix GeneChip Mapping 10K Array showed LOH in all patients at the 1q31.1. The LOH regions were detected and demarcated by the copy number 1 with the series of three SNP probes. LOH analysis of 1q31.1 using microsatellite markers (D1S1189, D1S2151, D1S2595) showed LOH in all 10 patients (100). Our data may suggest that a putative tumor suppressor gene is located at the 1q31.1 region. Inactivation of such a gene may play a role in tongue tumorigenesis.

Keyword

Tongue squamous cell carcinoma; Loss of heterozygosity; Copy number abnormality; Single nucleotide polymorphism; tumor suppressor gene

MeSH Terms

Carcinoma, Squamous Cell
Cell Transformation, Neoplastic
Chimera
Coat Protein Complex I
DNA
Genes, Tumor Suppressor
Genes, vif
Genome
Humans
Loss of Heterozygosity
Microsatellite Repeats
Polymorphism, Single Nucleotide
Tokyo
Tongue
Coat Protein Complex I
DNA

Figure

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  Fig. 1. DNA labeling, hybridization, washing and staining of the Affymetrix 10K SNP Mapping Array were performed according to the standard Single Primer GeneChip Mapping 10K Assay protocol (Affymetrix). The array was scanned with a GeneChip Scanner 3000, and the scanned array images were processed with GeneChip Operating software. Kuroiwa Tsukasa et al: Analysis of copy number abnormality (CNA) and loss of heterozygosity (LOH) in the whole genome using single nucleotide polymorphism (SNP) genotyping arrays in tongue squamous cell carcinoma. J Korean Assoc Oral Maxillofac Surg 2011

• 

  Fig. 2. Analysis of copy number abnormality (CNA) on 1q31.1 region. Physical positions of each SNP probe are shown at the vertical axis. The copy number of each SNP probe is shown at the horizontal axis. In the region of 1q31.1, genome copy numbers from 0.8 to 1.2 were confirmed from continual SNP probes in all of the 3 cases. Kuroiwa Tsukasa et al: Analysis of copy number abnormality (CNA) and loss of heterozygosity (LOH) in the whole genome using single nucleotide polymorphism (SNP) genotyping arrays in tongue squamous cell carcinoma. J Korean Assoc Oral Maxillofac Surg 2011

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  Fig. 3. Analysis of LOH using microsatellite markers (D1S1189, D1S2151, D1S2595). Case numbers are shown at the top and locus symbols on the left. Paired normal (N) and tumor (T) samples for all of 10 patients demonstrating loss of the upper allele (LOH). Kuroiwa Tsukasa et al: Analysis of copy number abnormality (CNA) and loss of heterozygosity (LOH) in the whole genome using single nucleotide polymorphism (SNP) genotyping arrays in tongue squamous cell carcinoma. J Korean Assoc Oral Maxillofac Surg 2011

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