Hypervariable intronic region in NCX1 is enriched in short insertion-deletion polymorphisms and showed association with cardiovascular traits

<p>Abstract</p> <p>Background</p> <p>Conserved non-coding regions (CNR) have been shown to harbor gene expression regulatory elements. Genetic variations in these regions may potentially contribute to complex disease susceptibility.</p> <p>Methods</p> <p>We targeted CNRs of cardiovascular disease (CVD) candidate gene, <it>Na(+)-Ca(2+) exchanger (NCX1) </it>with polymorphism screening among CVD patients (n = 46) using DHPLC technology. The flanking region (348 bp) of the 14 bp indel in intron 2 was further genotyped by DGGE assay in two Eastern-European CVD samples: essential hypertension (HYPEST; 470 cases, 652 controls) and coronary artery disease, CAD (CADCZ; 257 cases, controls 413). Genotype-phenotype associations were tested by regression analysis implemented in PLINK. Alignments of primate sequences were performed by ClustalW2.</p> <p>Results</p> <p>Nine of the identified <it>NCX1 </it>variants were either singletons or targeted by commercial platforms. The 14 bp intronic indel (rs11274804) was represented with substantial frequency in HYPEST (6.82%) and CADCZ (14.58%). Genotyping in Eastern-Europeans (n = 1792) revealed hypervariable nature of this locus, represented by seven alternative alleles. The alignments of human-chimpanzee-macaque sequences showed that the major human variant (allele frequency 90.45%) was actually a human-specific deletion compared to other primates. In humans, this deletion was surrounded by other short (5-43 bp) deletion variants and a duplication (40 bp) polymorphism possessing overlapping breakpoints. This indicates a potential indel hotspot, triggered by the initial deletion in human lineage. An association was detected between the carrier status of 14 bp indel ancestral allele and CAD (<it>P </it>= 0.0016, OR = 2.02; Bonferroni significance level alpha = 0.0045), but not with hypertension. The risk for the CAD development was even higher among the patients additionally diagnosed with metabolic syndrome (<it>P </it>= 0.0014, OR = 2.34). Consistent with the effect on metabolic processes, suggestive evidence for the association with heart rate, serum triglyceride and LDL levels was detected (<it>P </it>= 0.04).</p> <p>Conclusions</p> <p>Compared to SNPs targeted by large number of locus-specific and genome-wide assays, considerably less attention has been paid to short indel variants in the human genome. The data of genome dynamics, mutation rate and population genetics of short indels, as well as their impact on gene expressional profile and human disease susceptibility is limited. The characterization of <it>NCX1 </it>intronic hypervariable non-coding region enriched in human-specific indel variants contributes to this gap of knowledge.</p

N-acetyltransferase 8, a positional candidate for blood pressure and renal regulation: resequencing, association and in silico study

BACKGROUND: Kidneys have an important function in blood pressure (BP) regulation and elevated BP may lead to kidney failure. Chr2p12-p13 region linked to BP traits in multiple studies harbours a potential candidate for BP and renal function, N-acetyltransferase 8 (NAT8) expressed in embryonic and adult kidney and associated with nephrotoxicity response. METHODS/RESULTS: We report the first study exploring NAT8 as a potential candidate gene for blood pressure and kidney function. The resequencing (n = 42, random Estonian samples) identified 15 NAT8 polymorphisms, including 6 novel variants. The diversity of NAT8 5' upstream region (π/bp = 0.00320) exceeded up to 10 times the variation in the NAT8 genic region (π/bp = 0.00037) as well as the average variation (π/bp = 0.00040) for the promoters of 29 reference genes associated with hypertension. We suggest that a potential source for such high variation could be an active gene conversion process from NAT8B duplicate gene to NAT8. Similarly to NAT8, several reference genes with the most variable upstream regions have also duplicate copies. The NAT8 promoter SNPs were targeted with pilot quantitative association studies for blood pressure (n = 137, healthy unrelated individuals) and for the index of kidney function – estimated glomerular filtration rate (eGFR; n = 157 hypertensives with and without nephropathy). Minor alleles of these polymorphisms revealed a significant protective effect against elevated systolic BP as well as kidney failure in hypertension patients (p < 0.05; linear regression model, addictive effect). CONCLUSION: The full resequencing and pilot association study of a novel positional candidate gene for blood pressure and renal function, human N-acetyltransferase 8, suggested a contribution of highly variable NAT8 promoter polymorphisms in determination of systolic blood pressure and eGFR. Based on in silico analysis, we raise the hypothesis that the alternative SNP alleles of the NAT8 upstream region may have differential effect on gene expression

Chorionic Gonadotropin β-Gene Variants Are Associated with Recurrent Miscarriage in Two European Populations

CONTEXT: The incidence of recurrent miscarriage (RM; ≥3 consecutive pregnancy losses) is estimated as 1%-2% in fertile couples. Familial clustering of RM has suggested the contribution of a genetic component. OBJECTIVE: Low level of HCG in maternal serum during the first trimester of the pregnancy is a clinically accepted risk factor for miscarriage. We sought to study whether variation in Chorionic Gonadotropin beta subunit genes (CGB) expressed in placenta may contribute to the risk of RM. DESIGN: Resequencing of CGB5 and CGB8, the two most actively transcribed loci of the four HCG beta duplicate genes. SETTING: A case-control study involving two sample sets, from Estonia (n=194) and from Finland (n=185). PATIENTS: RM patients (n=184) and fertile controls (n=195). RESULTS: From 71 identified variants in CGB5 and CGB8, 48 SNPs were novel. Significant protective effect was associated with two SNPs located at identical positions in intron 2 in both CGB5 (p=0.007, OR=0.53) and CGB8 (p=0.042, OR=0.15); and with four CGB5 promoter variants (p<0.03; OR=0.54-0.58). The carriers of minor alleles had reduced risk of RM. The haplotype structure of the CGB8 promoter was consistent with balancing selection; a rare mutation in CGB8 initiator element was detected only among patients (n=3). In addition, three rare non-synonymous substitutions were identified among RM cases as possible variants increasing the risk of recurrent pregnancy loss. CONCLUSIONS: The findings encourage studying the functional effect of the identified variants on CGB expression and HCG hormone activity to further elucidate the role of CGB variation in RM

Upper white bar depicts the positions of identified SNPs (Table 2) relative to the location of gene ATG (A denoted as 1)

Singleton polymorphisms were excluded from calculations.<p><b>Copyright information:</b></p><p>Taken from ", a positional candidate for blood pressure and renal regulation: resequencing, association and study"</p><p>http://www.biomedcentral.com/1471-2350/9/25</p><p>BMC Medical Genetics 2008;9():25-25.</p><p>Published online 10 Apr 2008</p><p>PMCID:PMC2330028.</p><p></p

Arrows pointing at polymorphic amino acid positions (14 Arg-His, 73 Ala-Val, 121 Met-Thr, 130 Pro-Pro, 143 Phe-Ser)

<p><b>Copyright information:</b></p><p>Taken from ", a positional candidate for blood pressure and renal regulation: resequencing, association and study"</p><p>http://www.biomedcentral.com/1471-2350/9/25</p><p>BMC Medical Genetics 2008;9():25-25.</p><p>Published online 10 Apr 2008</p><p>PMCID:PMC2330028.</p><p></p

Increased Prevalance of the −211 T Allele of Follicle Stimulating Hormone (FSH) β Subunit Promoter Polymorphism and Lower Serum FSH in Infertile Men

Context: The human FSHB promoter polymorphism (rs10835638; −211 G/T) has been associated with serum FSH in a cohort of young Estonian men. The minor allele carriers had reduced serum FSH (15.7% in GT heterozygotes; 40% in TT homozygotes) compared with GG homozygotes