A Statistical Analysis of SNPs, In-Dels, and Their Flanking Sequences in Human Genomic Regions

Due to the increasing interest in SNPs and mutational hot spots for disease traits, it is becoming more important to define and understand the relationship between SNPs and their flanking sequences. To study the effects of flanking sequences on SNPs, statistical approaches are necessary to assess bias in SNP data. In this study we mainly applied Markov chains for SNP sequences, particularly those located in intronic regions, and for analysis of in-del data. All of the pertaining sequences showed a significant tendency to generate particular SNP types. Most sequences flanking SNPs had lower complexities than average sequences, and some of them were associated with microsatellites. Moreover, many Alu repeats were found in the flanking sequences. We observed an elevated frequency of single-base-pair repeat-like sequences, mirror repeats, and palindromes in the SNP flanking sequence data. Alu repeats are hypothesized to be associated with C-to-T transition mutations or A-to-I RNA editing. In particular, the in-del data revealed an association between particular changes such as palindromes or mirror repeats. Results indicate that the mechanism of induction of in-del transitions is probably very different from that which is responsible for other SNPs. From a statistical perspective, frequent DNA lesions in some regions probably have effects on the occurrence of SNPs.

The correlation between simple anthropometric indices and abdominal visceral fat accumulation by computed tomography

BACKGROUND: A predominant accumulation of adipose tissue in abdominal region confers increased risk of cardiovascular disease. The best technology available for measurement of regional fat distribution is computed tomography. However, computed tomography is limited its use for clinical purposes by cost. The aim of this study is to identify the best simple anthropometric index of abdominal visceral fat accumulation. METHODS: To quantify the relationship between anthropometric indices of abdominal obesity(waist circumference, waist to hip ratio, waist to height ratio, body mass index, abdominal sagittal diameter) and abdominal(total, visceral, subcutaneous) fat areas measured by computed tomography, correlation and multiple regression analyses have been conducted. RESULTS: No significant difference for waist circumference, body mass index and sagittal diameter between men and women have been found. Mean value of waist to hip ratio is larger in women, but waist to height ratio is larger in men. The mean abdominal total fat area and mean subcutaneous fat area are higher in women. Interestingly, men, despite lower total fat area, have higher mean abdominal visceral area. Thus, the mean visceral fat to subcutaneous fat ratio is much higher in men. Abdominal sagittal diameter shows the highest correlation(men: 0.69, women: 0.76) with abdominal visceral fat area in both genders. Stepwise regression analyses have been performed to determine the best simple anthropometric index of abdominal visceral fat accumulation. In men, the significant indices are abdominal sagittal diameter, body mass index, and waist to height ratio. In women, abdominal sagittal diameter is the only significant index. CONCLUSION: Abdominal sagittal diameter, in comparison with the waist circumference, waist to hip ratio, waist to height ratio and body mass index, is the best predictor of the amount of abdominal visceral fat.