Association Studies

▪   Besides its obvious intrinsic value, knowledge of population history, and of the demographic and evolutionary changes that accompany it, has proven fundamental to address applied research in human genetics. In this review we place current European genetic diversity in the context of the global human genome diversity and review the evidence supporting a recent African origin of the Europeans. We then discuss the results and the interpretation of genetic studies attempting to quantify the relative importance of various gene flow processes, both within Europe and from Asia into Europe, focusing especially on the initial, Paleolithic colonization of the continent, and on later, Paleolithic postglacial and Neolithic dispersals. Finally, we discuss how knowledge of the patterns of genetic diversity in Europe, and of their inferred generating processes, can be extremely useful in planning health care and in biomedical research.

■ Abstract Besides its obvious intrinsic value, knowledge of population history, and of the demographic and evolutionary changes that accompany it, has proven funda- mental to address applied research in human,genetics. In this review we place current European genetic diversity in the context of the global human,genome,diversity and review,the evidence,supporting,a recent African origin of the Europeans. We then discuss the results and the interpretation of genetic studies attempting to quantify the relative importance of various gene flow processes, both within Europe and from Asia into Europe, focusing especially on the initial, Paleolithic colonization of the continent, and on later, Paleolithic postglacial and Neolithic dispersals. Finally, we discuss how knowledge of the patterns of genetic diversity in Europe, and of their inferred gen- erating processes, can be extremely useful in planning health care and in biomedical research.

Mitochondrial dysfunction has been proposed to play a role in the pathogenesis of Parkinson's disease (PD). Supportive of this hypothesis, several genetic variants that regulate mitochondrial function and homeostasis have been described to alter PD susceptibility. A recent report demonstrated association of a single nucleotide polymorphism in the mitochondrial translation initiation factor 3 (MTIF3) gene with PD risk. The protein encoded by this nuclear gene is essential for initiation complex formation on the mitochondrial 55S ribosome and regulates translation of proteins within the mitochondria. Changes in the function or expression of the MTIF3 protein may result in altered mitochondrial function, ATP production or formation of reactive oxygen species thereby affecting susceptibility to PD. We examined the association of rs7669 with sporadic PD in three Caucasian case control series (n=2434). A significant association was observed in the largest series (Norwegian; n=1650) when comparing CC vs. CT/TT genotypes, with the Irish and US series having a similar but non-significant trend. The combined series also revealed an association with risk of PD (P=0.01), supporting the possible involvement of this gene in PD etiology.

BACKGROUND AND OBJECTIVE: Studies have suggested that HLA-G is involved in protecting the fetus against the mother's immune system, and upstream polymorphisms of this gene may influence pregnancy success by effecting its expression. The aim of this study was to evaluate the association of upstream HLA-G gene polymorphism, rs1736933, with recurrent spontaneous abortion in East Azerbaijan women population.
METHODS: This case-control study was performed on 80 women with at least one child and without any history of abortion, and 100 women with at least two recurrent spontaneous abortions which were diagnosed by gynecologist. 2 ml of blood was obtained from the participants and after DNA extraction, a segment of the HLA-G gene promoter was amplified by PCR and analyzed by agarose gel electrophoresis. PCR products were sequenced and genotyped. Allelic and genotypic frequencies of patient and control groups were compared.
FINDINGS: Frequency of AA, CA, CC genotypes in the patient group were 8(8%), 37(37%), 55(55%) and in the control group were 16(20%), 33(41.25%), 31(38.75%) respectively. Comparison of genotypic frequencies between the two groups showed that CC homozygous genotype was associated with recurrent abortion (p= 0.015). Statistical analysis also showed a significant difference between the allelic frequencies of the two groups (p= 0.019).
CONCLUSION: The results of this study showed that the upstream HLA-G gene polymorphism, rs1736933, is associated with the recurrent abortion in East Azerbaijan women population.

Power and sample size calculations are critical parts of any research design for genetic association. We present a method that utilizes haplotype frequency information and average marker-marker linkage disequilibrium on SNPs typed in and around all genes on a chromosome. The test statistic used is the classic likelihood ratio test applied to haplotypes in case/control populations. Haplotype frequencies are computed through specification of genetic model parameters. Power is determined by computation of the test's non-centrality parameter. Power per gene is computed as a weighted average of the power assuming each haplotype is associated with the trait. We apply our method to genotype data from dense SNP maps across three entire chromosomes (6, 21, and 22) for three different human populations (African-American, Caucasian, Chinese), three different models of disease (additive, dominant, and multiplicative) and two trait allele frequencies (rare, common). We perform a regression analysis using these factors, average marker-marker disequilibrium, and the haplotype diversity across the gene region to determine which factors most significantly affect average power for a gene in our data. Also, as a 'proof of principle' calculation, we perform power and sample size calculations for all genes within 100 kb of the PSORS1 locus (chromosome 6) for a previously published association study of psoriasis. Results of our regression analysis indicate that four highly significant factors that determine average power to detect association are: disease model, average marker-marker disequilibrium, haplotype diversity, and the trait allele frequency. These findings may have important implications for the design of well-powered candidate gene association studies. Our power and sample size calculations for the PSORS1 gene appear consistent with published findings, namely that there is substantial power (>0.99) for most genes within 100 kb of the PSORS1 locus at the 0.01 significance level.

Genotype/phenotype association analyses (Treescan) with plasma lipid levels and functional site prediction methods (TreeSAAP and PolyPhen) were performed using sequence data for ANGPTL4 from 3,551 patients in the Dallas Heart Study. Biological assays of rare variants in phenotypic tails and results from a Treescan analysis were used as "known" variants to assess the site prediction abilities of PolyPhen and TreeSAAP. The E40K variant in European Americans and the R278Q variant in African Americans were significantly associated with multiple lipid phenotypes. Combining TreeSAAP and PolyPhen performed well to predict "known" functional variants while reducing noise from false positives.