Molecular role of non-exonic variants in CALPAIN 10 gene in polycystic ovarian syndrome in Saudi women

Abstract

IntroductionNon-diabetic women with polycystic ovarian syndrome (PCOS) often have abnormal insulin regulation. Calpain 10 (CALP10) is a biomarker of type 2 diabetes mellitus, with some of its single-nucleotide polymorphisms (SNPs) influencing PCOS development.MethodsIn this case-control study on 90 women each with and without PCOS, we explored the molecular role of five CALP10 SNPs using biochemical parameters and Sanger sequencing analyses.ResultsDifferent genetic models, genotypes, and allele frequencies were significantly associated with UCSNP-19 (rs3842570; p=0.01), UCSNP-44 (rs2975760; p=0.009), UCSNP-56 (rs2975762; p<0.0001), and UCSNP-63 (rs5030952; p=0.0003) in women with PCOS. The multiple logistic regression model showed a strong association of CALP10 SNPs with fasting blood glucose (p<0.001). ANOVA showed significant associations with various biochemical parameters such as FSH (p=0.0001) in UCSNP-19 (rs3842570), FI (p=0.002), TG (p=0.01) in UCSNP-56 (rs2975762) and FBG (p=0.001), FI (p=0.004), FSH (p=0.02) & LDLc (p=0.04) in UCSNP-63 (rs5030952) SNPs. Haplotype analysis also revealed significant associations between different combinations of alleles in the studied 5 SNPs in women with PCOS (p<0.05). Generalized multifactor dimensionality reduction analysis showed the best gene–gene interactions among the five SNPs in CALP10I (p<0.05). However, dendrogram and graphical depletion models found no strong association in women with PCOS.ConclusionIn conclusion, this study confirms rs3842570, rs2975760, rs2975767, and rs5030952 SNPs in CALP10 gene is associated in diagnosed PCOS women in the Saudi Arabia.

FOXP3 gene polymorphisms increase the risk of systemic lupus erythematosus in a Han Chinese population

“…The haplotype analysis and LD testing was based on the online SHEsis ( http://analysis.bio-x.cn/myAnalysis.php ). SNP–SNP interactions were studied using the generalized multifactor dimensionality reduction (MDR) model with three SNPs [ 31 ], and functional annotation was assessed by the Encyclopedia of DNA Elements tool HaploReg v4.2 [ 32 ] to predict the potential SNP functions. The risk associated with individual genotypes or alleles was calculated as the odds ratio (OR) with 95% confidence intervals (95% CIs).…”

Usefulness of the Sympto-Thermal Method with Standardized Cervical Mucus Assessment (InVivo Method) for Evaluating the Monthly Cycle in Women with Polycystic Ovary Syndrome (PCOS)

“…PCOS may clinically manifest as hyperandrogenism (HA), oligoanovulation (OA), and polycystic ovary morphology (PCOM). Women with PCOS are categorized into four phenotypes: HA + OA + PCOM, phenotype-A; HA + OA, phenotype-B; HA + PCOM, phenotype-C; and OA + PCOM, phenotype D [ 8 ].…”