Fixation of a Deleterious Allele under Mutation Pressure and Finite Selection Intensity

The mean fixation time of a deleterious mutant allele is studied beyond the diffusion approximation. As in Kimura's classical work [M. Kimura, Proc. Natl. Acad. Sci. U.S.A. Vol.77, 522 (1980)], that was motivated by the problem of fixation in the presence of amorphic or hypermorphic mutations, we consider a diallelic model at a single locus comprising a wild-type A and a mutant allele A' produced irreversibly from A at small uniform rate v. The relative fitnesses of the mutant homozygotes A'A', mutant heterozygotes A'A and wild-type homozygotes AA are 1-s, 1-h and 1, respectively, where it is assumed that v<< s. Here, we adopt an approach based on the direct treatment of the underlying Markov chain (birth-death process) obeyed by the allele frequency (whose dynamics is prescribed by the Moran model), which allows to accurately account for the effects of large fluctuations. After a general description of the theory, we focus on the case of a deleterious mutant allele (i.e. s>0) and discuss three situations: when the mutant is (i) completely dominant (s=h); (ii) completely recessive (h=0), and (iii) semi-dominant (h=s/2). Our theoretical predictions for the mean fixation time and the quasi-stationary distribution of the mutant population in the coexistence state, are shown to be in excellent agreement with numerical simulations. Furthermore, when s is finite, we demonstrate that our results are superior to those of the diffusion theory that is shown to be an accurate approximation only when N_e s^2 << 1, where N_e is the effective population size.Comment: 26 pages, 5 figures. Accepted by the Journal of Theoretical Biolog

PPAR alpha L162V underlies variation in serum triglycerides and subcutaneous fat volume in young males

Background: Of the five sub-phenotypes defining metabolic syndrome, all are known to have strong genetic components ( typically 50 - 80% of population variation). Studies defining genetic predispositions have typically focused on older populations with metabolic syndrome and/or type 2 diabetes. We hypothesized that the study of younger populations would mitigate many confounding variables, and allow us to better define genetic predisposition loci for metabolic syndrome. Methods: We studied 610 young adult volunteers ( average age 24 yrs) for metabolic syndrome markers, and volumetric MRI of upper arm muscle, bone, and fat pre- and post-unilateral resistance training. Results: We found the PPARa L162V polymorphism to be a strong determinant of serum triglyceride levels in young White males, where carriers of the V allele showed 78% increase in triglycerides relative to L homozygotes ( LL = 116 +/- 11 mg/ dL, LV = 208 +/- 30 mg/ dL; p = 0.004). Men with the V allele showed lower HDL ( LL = 42 +/- 1 mg/ dL, LV = 34 +/- 2 mg/ dL; p = 0.001), but women did not. Subcutaneous fat volume was higher in males carrying the V allele, however, exercise training increased fat volume of the untrained arm in V carriers, while LL genotypes significantly decreased in fat volume ( LL = - 1,707 +/- 21 mm(3), LV = 17,617 +/- 58 mm(3); p = 0.002), indicating a systemic effect of the V allele on adiposity after unilateral training. Our study suggests that the primary effect of PPARa L162V is on serum triglycerides, with downstream effects on adiposity and response to training. Conclusion: Our results on association of PPARa and triglycerides in males showed a much larger effect of the V allele than previously reported in older and less healthy populations. Specifically, we showed the V allele to increase triglycerides by 78% ( p = 0.004), and this single polymorphism accounted for 3.8% of all variation in serum triglycerides in males ( p = 0.0037)

Detection of FXIII gene V34L and fibrinogen β-gene -455G/A polymorphisms among Saudi Arabia population via polymerase chain reaction-reverse hybridization technique

FXIII gene Val34Leu variant appears to be associated with decreased risk of myocardial infarction and venous thromboembolism as well as with increased risk of intracerebral hemorrhage. Fibrinogen β-gene SNP -455G/A are associated with differences in the plasma levels of fibrinogen and severity of arterial disease. The aim of the present work was to study the prevalence of FXIII gene V34L and Fibrinogen β-gene -455G/A SNPs in Saudi population. Among 200 blood samples randomly collected from unrelated healthy Saudi subjects, FXIII gene V34L and Fibrinogen β-gene -455G/A SNPs were genotyped via cardiovascular disease (CVD) StripAssay (ViennaLab, Austria. Homozygous (V/V) and heterozygous (V/L) genotypes were detected with 96 and 4%, respectively, among FXIII gene V34L genotypes, whereas (L/L) genotype was not found. The allele frequency was 0.98 for V allele and 0.02 for L allele. Three genotypes of Fibrinogen β-gene -455G/A SNP (GG, GA and AA) were obtained and its prevalence (%) was 70, 25 and 5, respectively. The frequency of G allele was 0.825 and 0.175 for A allele. Prevalence of FXIII gene Vl34L polymorphism and its allele frequency are in line with other Asian populations. Distribution of β-gene -455G/A genotypes and allele frequency are in accordance with previous reports in different ethnic groups. This is the first time to report these polymorphisms in Saudi Arabia population. This study provides valuable information on Saudi genetic background in comparison with other populations. In addition, it serves as a template for future clinical research involving cardiovascular and cerebrovascular diseases.Key words: FXIII gene V34L, fibrinogen β-gene -455G/A, polymorphisms, Saudi Arabia

PPARα L162V underlies variation in serum triglycerides and subcutaneous fat volume in young males

<p>Abstract</p> <p>Background</p> <p>Of the five sub-phenotypes defining metabolic syndrome, all are known to have strong genetic components (typically 50–80% of population variation). Studies defining genetic predispositions have typically focused on older populations with metabolic syndrome and/or type 2 diabetes. We hypothesized that the study of younger populations would mitigate many confounding variables, and allow us to better define genetic predisposition loci for metabolic syndrome.</p> <p>Methods</p> <p>We studied 610 young adult volunteers (average age 24 yrs) for metabolic syndrome markers, and volumetric MRI of upper arm muscle, bone, and fat pre- and post-unilateral resistance training.</p> <p>Results</p> <p>We found the PPARα L162V polymorphism to be a strong determinant of serum triglyceride levels in young White males, where carriers of the V allele showed 78% increase in triglycerides relative to L homozygotes (LL = 116 ± 11 mg/dL, LV = 208 ± 30 mg/dL; p = 0.004). Men with the V allele showed lower HDL (LL = 42 ± 1 mg/dL, LV = 34 ± 2 mg/dL; p = 0.001), but women did not. Subcutaneous fat volume was higher in males carrying the V allele, however, exercise training increased fat volume of the untrained arm in V carriers, while LL genotypes significantly decreased in fat volume (LL = -1,707 ± 21 mm³, LV = 17,617 ± 58 mm³; p = 0.002), indicating a systemic effect of the V allele on adiposity after unilateral training. Our study suggests that the primary effect of PPARα L162V is on serum triglycerides, with downstream effects on adiposity and response to training.</p> <p>Conclusion</p> <p>Our results on association of PPARα and triglycerides in males showed a much larger effect of the V allele than previously reported in older and less healthy populations. Specifically, we showed the V allele to increase triglycerides by 78% (p = 0.004), and this single polymorphism accounted for 3.8% of all variation in serum triglycerides in males (p = 0.0037).</p

Association of the tumour necrosis factor alpha -308 but not the interleukin 10 -627 promoter polymorphism with genetic susceptibility to primary sclerosing cholangitis

BACKGROUND AND AIMS Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease of unknown aetiology. Abnormalities in immune regulation and genetic associations suggest that PSC is an immune mediated disease. Several polymorphisms within the tumour necrosis factor α (TNF-α) and interleukin 10 (IL-10) promoter genes have been described which influence expression of these cytokines. This study examines the possible association between polymorphisms at the −308 and −627 positions in the TNF-α and IL-10 promoter genes, respectively, and susceptibility to PSC. METHODS TNF-α −308 genotypes were studied by polymerase chain reaction (PCR) in 160 PSC patients from Norway and the UK compared with 145 ethnically matched controls. IL-10 −627 genotypes were studied by PCR in 90 PSC patients compared with 84 ethnically matched controls. RESULTS A total of 16% of Norwegian PSC patients and 12% of British PSC patients were homozygous for the TNF2 allele compared with 3% and 6% of respective controls. The TNF2 allele was present in 60% of PSC patients versus 30% of controls (ORcombined data=3.2 (95% confidence intervals (CI) 1.8–4.5); pcorr=10−5). The association between the TNF2 allele and susceptibility to PSC was independent of the presence of concurrent inflammatory bowel disease (IBD) in the PSC patients; 61% of PSC patients without IBD had TNF2 compared with 30% of controls (ORcombined data=3.2 (95% CI 1.2–9.0); pcorr=0.006 ). There was no difference in the −627 IL-10 polymorphism distributions between patients and controls in either population. The increase in TNF2 allele in PSC patients only occurs in the presence of DRB1*0301 (DR3) and B8. In the combined population data, DRB1*0301 showed a stronger association with susceptibility to PSC than both the TNF2 and B8 alleles (ORcombined data=3.8, pcorr=10−6 v ORcombined data=3.2, pcorr=10−5 vORcombined data =3.41, pcorr=10−4, respectively). CONCLUSIONS This study identified a significant association between possession of the TNF2 allele, a G→A substitution at position −308 in the TNF-α promoter, and susceptibility to PSC. This association was secondary to the association of PSC with the A1-B8-DRB1*0301-DQA1*0501-DQB1*0201 haplotype. No association was found between the IL-10 −627 promoter polymorphism and PSC

Association study between brain-derived neurotrophic factor gene polymorphisms and methamphetamine abusers in Japan

Several lines of evidence suggest that genetic factors might contribute to drug abuse vulnerability. Recent genomic scans for association demonstrated that the brain-derived neurotrophic factor (BDNF) gene was associated with drug abuse vulnerability. In this study, we analyzed association of two BDNF gene single nucleotide polymorphisms (SNPs), 132C>T (C270T named formerly) in the noncoding region of exon V and 196G >A (val66met) in the coding region of exon XIIIA, with methamphetamine (MAP) abuse in Japan. No significant differences were found in the frequency of the genotype or allele in these two SNPs between MAP abusers and controls (132C>T in exon V: genotype, p = 0.586, allele, p = 0.594; 196G>A (val66met) in exon XIIIA: genotype, p = 0.889, allele, p = 0.713). Furthermore, there was no difference between clinical parameters (e.g. prognosis psychosis, spontaneous relapse, or poly-substance abuse) and the two SNPs of BDNF gene. These results suggest that the two SNPs (132C>T in exon V and 196G>A (val66met) in exon XIIIA) of the BDNF gene may not be associated with Japanese MAP abusers

Comparative frequency of Coagulation Factor II and Coagulation Factor V Alleles among new-born and senior citizens

Resistance to activated protein C is one of the most common inherited disorders associated with hereditary thrombophilia. A missense mutation in the gene coding for coagulation factor V (CF V Leiden) and which renders this procoagulant factor resistant to inactivation by activated protein C results in an inherited risk for venous thrombosis. Recently, another mutation has been identified in the prothrombin gene (CF II G20210A) which was also associated with increased risk for venous thrombosis. In this study, we sought to establish the frequency of the two alleles in a random sample of Maltese newborn and compare these with the frequencies of the same alleles among senior citizens and patients with clinical thrombophilia. The control population of 554 newborn samples processed for the same point mutations gave 13 (2.3%) who were CF V Leiden heterozygotes and 7 (2.7%) who were CF II G20210A heterozygotes. Neither homozygotes nor trans-heterozygotes (i.e. CF V Leden and CF II2 0210A heterozygotes) were observed. The 348 senior citizens gave 9 (2.6%) CF V Leiden heterozygotes and 8 (2.4%) CF II G20210A heterozygotes. Neither homozygotes nor trans-heterozygotes (i.e. CF V Leden and CF II20210A heterozygotes) were observed. The 328 patients referred to the Laboratory of Molecular Genetics, University of Malta, with clinical thrombosis gave 23 (7.01%) CF V Leiden heterozygotes and 24 (7.31%) CF II G20210A heterozygous. One patient was found to be trans-heterozygous for the two mutations. The data suggested that although CF V G1691A and CF II G20210A may increase risk for thrombophilia, they do not impact on the survival of the carriers, but the transheterozygozity may also confer increased risk. The high allele frequency may be best explained by positive natural selection.peer-reviewe