hapmap.ncbi.nlm.nih.gov). These SNPs were selected because they are predicted to tag SNPs across the entirety of each gene, plus 5?kb upstream and downstream of the gene. These SNPs capture 34 of 41 (83%) of the white HapMap SNP alleles at r2?>?0.8 for all four genes. The 13 SNPs were genotyped using Applied Biosystems Taqman Assays on Demand, following the manufacturer��s instructions. The program Haploview?v4.1 (Broad Institute, Cambridge, MA, USA) was used to calculate linkage disequilibrium (LD, the D�� statistic) between each pairwise combination of SNPs, and to determine haplotypes and their frequencies.9 The solid spine of the LD algorithm in Haploview was used to determine haplotype blocks. Only women whose haplotype assignment was >95% certain were used in the analyses. www.selleckchem.com/products/DAPT-GSI-IX.html
Unpaired Student��s t-tests and chi-square tests were used to compare clinical characteristics between women with and without PCOS: quantitative trait values were log- or square root-transformed, as appropriate, to reduce non-normality. Data are expressed as medians (interquartile ranges). The association of SNPs or haplotypes with the presence/absence of PCOS and qualitative traits was evaluated using logistic regression, adjusting for recruitment site, age, and body mass index Fulvestrant
(BMI). Within the group of women with PCOS, an association with quantitative phenotypic traits was evaluated using analysis of covariance (ANCOVA), again adjusting for recruitment site, age, and BMI in all analyses, except those in which BMI was the dependent variable, wherein analyses were adjusted for recruitment site and age only. To handle multiple testing, the significance of each analysis was taken as P?<?0.003(=?0.05/16), considering that we analysed four linkage disequilibrium groups of SNPs against four families of traits (PCOS diagnosis, androgens, metabolic traits, and reproductive end points), yielding a Bonferroni��s correction factor of 16 (i.e. 16 independent comparisons). The sample size of 335 cases and 198 controls has excellent power (��90%) to detect the association of risk alleles of frequency <a href="http://www.selleckchem.com/hydroxysteroid-dehydrogenase-hsd.html
">Selleck IDH inhibitor ��0.2 with PCOS at odds ratios ��1.75, and has fair-to-good power (40�C80%) to detect an association at an odds ratio of 1.5. The detailed power calculations listed in Table?S2 reveal a lower power to detect the association of rare risk alleles (frequency ��0.1) with PCOS at odds ratios of less than 1.75. We genotyped five SNPs spanning GDF9 (Figure?1A). SNP frequencies are shown in Table?S3. All markers were in Hardy�CWeinberg equilibrium. Linkage disequilibrium among these markers (D��) ranged from 0.40 to 1.0 (with an average pairwise D�� of 0.90). The common haplotypes are listed in Table?S4. GDF9 SNPs and haplotypes were not associated with PCOS susceptibility.