Balkan Journal of Medical Genetics

ALTERATIONS OF COPY NUMBER OF METHYLATION PATTERN IN MISMATCH REPAIR GENES BY METHYLATION SPECIFIC-MULTIPLEX LIGATION-DEPENDENT PROBE AMPLIFICATION IN CASES OF COLON CANCER
Onrat ST1*, Çeken I2, Ellidokuz E3, Kupelioğlu A4
*Corresponding Author: Serap Tutgun Onrat, Department of Medical Genetics, Afyon Kocatepe University Medical Faculty, ANS Arastırma Uygulama Hastanesi, Morfoloji Binası, Ozdilek yolu, Afyonkarahisar, 03200, Turkey; Tel.: +90-272-246-3301, Fax: +90-272-246-3300, E-mail: tutgunonrat@ yahoo.com, sonrat@aku.edu.tr
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RESULTS

The methylation status of MS-MLPA probes is calculated by dividing: a) the intra-normalized ratio of each MS-MLPA probe obtained on the digested sample with b) the intra-normalized ratio of each MSMLPA probe obtained on the undigested [–] sample. Multiplying this value with 100 gives an estimation of the percentage of methylation. Aberrant methylation can be identified by the appearance of a signal peak after HhaI digestion that was absent in the digested [+] reference DNA. Rates of methylation of all genes in a sample of each of the numerical values at the average methylation percentages were compared to controls and study groups in Table 1. This after comparison with a high rate of methylation in genes in the study groups where there was methylation, as is shown in the methylation [+] and non methylation [–], marked in Supplementary tables S1 and S2, and Figures 1 and 2. The MMR genes methylation ratio was determined in the pathological findings in all cases of subjects with colon cancer in our study (Table S2). According to the results of our study, the highest rate of methylation was in the MLH1 gene 68/70 (97.14%) gene, and the rate was not so high in the MSH2 17/70 (24.28%) gene. Comparison of the diagnosis is given by gender, age groups and clinopathological characteristics in Tables 2, 3 and 4. Therefore, patients with adenocarcinomas (56.1%) and adenomas (43.9%) were male, while patients with adenocarcinomas (89.7) and adenomas (10.3%) were females; the difference between the two groups was statistically significant (χ2 = 9.10, p = 0.003<0.05). Those patients under 60 years of age with adenocarcinomas (60.5%) and adenomas (39.5%), and over 60 years of age with adenocarcinomas (81.3%) and adenomas (18.8%) (χ2 = 3.55, p = 0.059>0.05). We obtained the following methylation rates: MLH1 (97.14%), MGMT (82.85%), MSH3 (78.57%), MLH3 (75.71%), MSH6 (67.14%), PMS2 (65.71%), MSH2 (24.28%). The methylation percentage distribution by sex is given in Table 5. There was no difference observed between methylation for all genes and the percentages of the gender groups (p >0.05). The high percentage of methylation for PMS2 was 68.3% in males and 62.1% for females. The percentage rate for MSH6 was 61.0% for males and 75.9% for females; MLH1 percentage rate was 90.2% for males and 86.2% for females; MSH2 percentage rate was 22.0% in males and 27.6% for females; MGMT percentage rate was 80.5% for males and 86.2% females; MSH3 percentage rate was 73.2% for males and 86.2% for females, and the MLH3 percentage rate was 70.7% for males and 82.8% for females.

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