Linkage Disequilibrium (linkage + disequilibrium)

Distribution by Scientific Domains
Distribution within Life Sciences

Kinds of Linkage Disequilibrium

  • complete linkage disequilibrium
  • high linkage disequilibrium
  • significant linkage disequilibrium
  • strong linkage disequilibrium

  • Terms modified by Linkage Disequilibrium

  • linkage disequilibrium analysis
  • linkage disequilibrium mapping
  • linkage disequilibrium pattern

  • Selected Abstracts

    Characterization of simple sequence repeat variants linked to candidate genes for behavioral phenotypes,,

    HUMAN MUTATION, Issue 1 2006
    Zoë Prichard
    Abstract Simple sequence repeats (SSRs) have traditionally been used as markers in gene mapping studies and typing for forensic purposes. Recently there has been some speculation that this type of genetic variation also plays a more direct role in influencing gene expression and hence complex phenotypic outcomes such as human behavior. For this reason it is interesting to investigate SSRs linked to candidate genes for various complex phenotypes. An economical multiplex PCR-based assay was designed to simultaneously genotype individuals at 15 loci across 10 candidate genes for human behavioural phenotypes, including seven loci previously unreported in Caucasians (five unreported in any population). All loci were tested for Hardy-Weinberg equilibrium and for two-locus Linkage Disequilibrium. Ewens-Watterson neutrality testing indicated possible selection at a previously unreported DRD2 locus. © 2005 Wiley-Liss, Inc. [source]

    The Impact of Incomplete Linkage Disequilibrium and Genetic Model Choice on the Analysis and Interpretation of Genome-wide Association Studies

    Mark M. Iles
    Summary When conducting a genetic association study, it has previously been observed that a multiplicative risk model tends to fit better at a disease-associated marker locus than at the ungenotyped causative locus. This suggests that, while overall risk decreases as linkage disequilibrium breaks down, non-multiplicative components are more affected. This effect is investigated here, in particular the practical consequences it has on testing for trait/marker associations and the estimation of mode of inheritance and risk once an associated locus has been found. The extreme significance levels required for genome-wide association studies define a restricted range of detectable allele frequencies and effect sizes. For such parameters there is little to be gained by using a test that models the correct mode of inheritance rather than the multiplicative; thus the Cochran-Armitage trend test, which assumes a multiplicative model, is preferable to a more general model as it uses fewer degrees of freedom. Equally when estimating risk, it is likely that a multiplicative risk model will provide a good fit to the data, regardless of the underlying mode of inheritance at the true susceptibility locus. This may lead to problems in interpreting risk estimates. [source]

    The Causal Element for the Lactase Persistence/ non-persistence Polymorphism is Located in a 1 Mb Region of Linkage Disequilibrium in Europeans

    M. Poulter
    Summary Expression of lactase in the intestine persists into adult life in some people and not others, and this is due to a cis -acting regulatory polymorphism. Previous data indicated that a mutation leading to lactase persistence had occurred on the background of a 60 kb 11-site LCT haplotype known as A (Hollox et al. 2001). Recent studies reported a 100% correlation of lactase persistence with the presence of the T allele at a CT SNP at ,14 kb from LCT, in individuals of Finnish origin, suggesting that this SNP may be causal of the lactase persistence polymorphism, and also reported a very tight association with a second SNP (GA ,22 kb) (Enattah et al. 2002). Here we report the existence of a one megabase stretch of linkage disequilibrium in the region of LCT and show that the ,14 kb T allele and the ,22 kb A allele both occur on the background of a very extended A haplotype. In a series of Finnish individuals we found a strong correlation (40/41 people) with lactose digestion and the presence of the T allele. The T allele was present in all 36 lactase persistent individuals from the UK (phenotyped by enzyme assay) studied, 31/36 of whom were of Northern European ancestry, but not in 11 non-persistent individuals who were mainly of non-UK ancestry. However, the CT heterozygotes did not show intermediate lactase enzyme activity, unlike those previously phenotyped by determining allelic transcript expression. Furthermore the one lactase persistent homozygote identified by having equally high expression of A and B haplotype transcripts, was heterozygous for CT at the ,14 kb site. SNP analysis across the 1 megabase region in this person showed no evidence of recombination on either chromosome between the ,14 kb SNP and LCT. The combined data shows that although the ,14 kb CT SNP is an excellent candidate for the cause of the lactase persistence polymorphism, linkage disequilibrium extends far beyond the region searched so far. In addition, the CT SNP does not, on its own, explain all the variation in expression of LCT, suggesting the possibility of genetic heterogeneity. [source]

    Peroxisome proliferator-activated receptor-, co-activator-1, (PGC-1,) gene polymorphisms and their relationship to Type 2 diabetes in Asian Indians

    DIABETIC MEDICINE, Issue 11 2005
    K. S. Vimaleswaran
    Abstract Aims The objective of the present investigation was to examine the relationship of three polymorphisms, Thr394Thr, Gly482Ser and +A2962G, of the peroxisome proliferator activated receptor-, co-activator-1 alpha (PGC-1,) gene with Type 2 diabetes in Asian Indians. Methods The study group comprised 515 Type 2 diabetic and 882 normal glucose tolerant subjects chosen from the Chennai Urban Rural Epidemiology Study, an ongoing population-based study in southern India. The three polymorphisms were genotyped using polymerase chain reaction,restriction fragment length polymorphism (PCR,RFLP). Haplotype frequencies were estimated using an expectation,maximization (EM) algorithm. Linkage disequilibrium was estimated from the estimates of haplotypic frequencies. Results The three polymorphisms studied were not in linkage disequilibrium. With respect to the Thr394Thr polymorphism, 20% of the Type 2 diabetic patients (103/515) had the GA genotype compared with 12% of the normal glucose tolerance (NGT) subjects (108/882) (P = 0.0004). The frequency of the A allele was also higher in Type 2 diabetic subjects (0.11) compared with NGT subjects (0.07) (P = 0.002). Regression analysis revealed the odds ratio for Type 2 diabetes for the susceptible genotype (XA) to be 1.683 (95% confidence intervals: 1.264,2.241, P = 0.0004). Age adjusted glycated haemoglobin (P = 0.003), serum cholesterol (P = 0.001) and low-density lipoprotein (LDL) cholesterol (P = 0.001) levels and systolic blood pressure (P = 0.001) were higher in the NGT subjects with the XA genotype compared with GG genotype. There were no differences in genotype or allelic distribution between the Type 2 diabetic and NGT subjects with respect to the Gly482Ser and +A2962G polymorphisms. Conclusions The A allele of Thr394Thr (G , A) polymorphism of the PGC-1 gene is associated with Type 2 diabetes in Asian Indian subjects and the XA genotype confers 1.6 times higher risk for Type 2 diabetes compared with the GG genotype in this population. [source]

    GENETIC STUDY: Association between the nociceptin receptor gene (OPRL1) single nucleotide polymorphisms and alcohol dependence

    ADDICTION BIOLOGY, Issue 1 2008
    Jia Huang
    ABSTRACT OPRL1 encodes the nociceptin receptor, which has been shown to be involved in alcohol dependence in previous studies. In the present study, we investigated the association between genetic polymorphisms of OPRL1 and alcohol dependence in a Scandinavian population. We genotyped 15 single nucleotide polymorphisms (SNPs) spanning the OPRL1 locus and found that SNP rs6010718 was significantly associated with both Type I and Type II alcoholics (P < 0.05). Linkage disequilibrium and haplotype analysis identified two haplotype blocks in this region. Furthermore, two haplotypes composed of five tag SNPs showed significant association with alcohol dependence. These findings suggest that genetic variants of the OPRL1 gene play a role in alcohol dependence in the Scandinavian population, warranting further investigation at the OPRL1 locus. [source]

    Association of estrogen receptor , polymorphisms with susceptibility to chronic hepatitis B virus infection

    HEPATOLOGY, Issue 2 2004
    Guohong Deng
    Several studies have demonstrated that estrogen receptor , (ESR1) participates in the pathogenesis of persistent hepatitis B virus (HBV) infection. To examine whether polymorphisms at the ESR1 gene locus are associated with persistent HBV infection, we resequenced ESR1 genomic region for single nucleotide polymorphisms (SNPs) in 27 unrelated Chinese. Two haplotype-tagged SNPs (htSNP), T29C and A252966G, were selected for genotyping in 1,277 persistent HBV-infected cases, 748 spontaneously recovered controls, and 293 nuclear families using polymerase chain reaction (PCR)-restriction fragment length polymorphism (PCR-RFLP) analysis. We observed that the subjects bearing ESR1 29T/T genotype had an increased susceptibility to persistent HBV infection compared to those bearing at least one 29C allele (odds ratio 1.41; 95% CI, 1.17-1.71, P < .001). Consistent with the results of population-based association study, a significantly greater than expected transmission of the 29T allele (56.4%) from heterozygous parents to offspring with persistent HBV infection was observed (,2 = 4.60, P = .033) using the transmission-disequilibrium test (TDT) in 293 nuclear families. Linkage disequilibrium (LD) mapping analysis indicated that the T29C polymorphism contained within a LD block located from promoter region to intron 3 of ESR1, suggesting that the strong association detected with T29C in ESR1 originated from ESR1 itself. In conclusion, our results suggest that the genetic variation at the ESR1 locus influences susceptibility to persistent HBV infection in a Chinese population. (HEPATOLOGY 2004;40:318,326.) [source]

    Identification of novel single nucleotide polymorphisms within the NOTCH4 gene and determination of association with MHC alleles

    R. Tazi-Ahnini
    Summary Mapping of disease susceptibility loci within the MHC has been partly hampered by the high degree of polymorphism of the HLA genes and the high level of linkage disequilibrium (LD) between markers within the MHC region. It is therefore important to identify new markers and determine the level of LD between HLA alleles and non-HLA genes. The NOTCH4 gene lies at the centromeric end of the MHC class III region, approximately 335 kb telomeric of the DRB1 locus. The encoded protein is an oncogene that is important in regulating vascular development and remodelling. A recent report has linked polymorphisms within NOTCH4 with risk of developing schizophrenia. We have investigated if coding polymorphisms exist within this gene and have identified three single nucleotide polymorphisms; a synonomous T to C transition at +1297 (HGBASE accession number SNP000064386), a synonomous A to G transition at +3061 (SNP000064387) and an A to G transition at +3063 which results in a replacement of glycine with aspartic acid at amino acid 279 (SNP000064388). The allele frequencies of +1297T, +3061A and +3063G were 0.65, 0.66 and 0.66, respectively. Linkage disequilibrium was detected both between these markers and with MHC alleles. These findings can be used in the fine mapping of disease susceptibility alleles within the MHC. [source]

    Contribution of the LRP5 Gene to Normal Variation in Peak BMD in Women,

    Daniel L Koller
    Abstract The role of the LRP5 gene in rare BMD-related traits has recently been shown. We tested whether variation in this gene might play a role in normal variation in peak BMD. Association between SNPs in LRP5 and hip and spine BMD was measured in 1301 premenopausal women. Only a small proportion of the BMD variation was attributable to LRP5 in our sample. Introduction: Mutations in the low-density lipoprotein receptor-related protein 5 (LRP5) gene have been implicated as the cause of multiple distinct BMD-related rare Mendelian phenotypes. We sought to examine whether the LRP5 gene contributes to the observed variation in peak BMD in the normal population. Materials and Methods: We genotyped 12 single nucleotide polymorphisms (SNPs) in LRP5 using allele-specific PCR and mass spectrometry methods. Linkage disequilibrium between the genotyped LRP5 SNPs was measured. We tested for association between these SNPs and both hip and spine BMD (adjusted for age and body weight) in 1301 healthy premenopausal women who took part in a sibling pair study aimed at identifying the genes underlying peak bone mass. Our study used both population-based (ANOVA) and family-based (quantitative transmission disequilibrium test) association methodology. Results and Conclusions: The linkage disequilibrium pattern and haplotype block structure within the LRP5 gene were consistent with that observed in other studies. Although significant evidence of association was found between LRP5 SNPs and both hip and spine BMD, only a small proportion of the total variation in these phenotypes was accounted for. The genotyped SNPs accounted for ,0.8% of the variation in femoral neck BMD and 1.1% of the variation in spine BMD. Results from our sample suggest that natural variation in and around LRP5 is not a major contributor to the observed variability in peak BMD at either the femoral neck or lumbar spine in white women. [source]

    Genetic variation in ORM1-like 3 (ORMDL3) and gasdermin-like (GSDML) and childhood asthma

    ALLERGY, Issue 4 2009
    H. Wu
    Background:, A genome-wide association study identified ORM1-like 3 (orosomucoid 1-like 3, ORMDL3) as an asthma candidate gene. Single nucleotide polymorphisms (SNPs) in the region including ORMDL3 on chromosome 17q21 were related to childhood asthma risk and ORMDL3 expression levels in Europeans. Objective:, We examined whether polymorphisms in ORMDL3 and the adjacent gasdermin-like (GSDML) gene associated with asthma in the genome-wide association study are related to childhood asthma and atopy in a Mexico City population. Methods:, We genotyped rs4378650 in ORMDL3 and rs7216389 in GSDML in 615 nuclear families consisting of asthmatic children aged 4,17 years and their parents. Atopy was determined by skin prick tests to 25 aeroallergens. Results:, Individuals carrying the C allele of rs4378650 or the T allele of rs7216389 had increased risk of asthma [relative risk (RR) = 1.73, 95% confidence interval (CI) 1.19,2.53, P = 0.003 for one or two copies of rs4378650 C, and RR = 1.64, 95% CI 1.12,2.38, P = 0.009 for one or two copies of rs7216389 T). Linkage disequilibrium between the two SNPs was high (r2 = 0.92). Neither of the SNPs was associated with the degree of atopy. A meta-analysis of five published studies on rs7216389 in nine populations gave an odds ratio for asthma of 1.44 (95% CI, 1.35,1.54, P < 0.00001). Conclusions:, Our results and the meta-analysis provide evidence to confirm the finding from a recent genome-wide association study that polymorphisms in ORMDL3 and the adjacent GSDML may contribute to childhood asthma. [source]

    Association of ERCC1 polymorphisms and susceptibility to nasopharyngeal carcinoma

    Zhi-Hui Yang
    Abstract The normal function of excision repair cross complementing group 1 (ERCC1) is essential for maintaining genomic integrity and preventing cellular neoplastic transformation, and multiple studies have reported an association between ERCC1 polymorphisms and increased risk of cancers. To test whether the genetic variants of ERCC1 gene modify the risk of nasopharyngeal carcinoma (NPC), we compared the 8092 C,>,A and 19007 C,>,T single nucleotide polymorphisms (SNPs) and the haplotypes of ERCC1 between 267 patients with NPC and 304 healthy controls. Linkage disequilibrium was observed between the two SNPs loci (D,,=,0.861). Significant differences of allele frequencies were found for ERCC1 8092C,>,A between the cases and controls. Individuals with 8092 C allele showed 1.411-fold (OR,=,1.411, 95% CI, 1.076,1.850, P,=,0.014) increased risk of developing NPC, and the CC haplotype was associated with a significantly increased risk of NPC (OR,=,1.712; 95% CI, 1.211,2.421; P,=,0.013). No interactions were found between 8092C,>,A polymorphism and genders, smoking status and alcohol consumption. These results suggested that the polymorphism of ERCC1 8092 C,>,A might be a contributing factor in the development of NPC in Chinese population. © 2008 Wiley-Liss, Inc. [source]

    Isolation of nine nuclear microsatellites in the common Mediterranean sea urchin, Paracentrotus lividus (Lamarck)

    Abstract Nine polymorphic microsatellite loci were isolated and characterized for the edible common sea urchin Paracentrotus lividus. Loci were obtained from two genomic libraries enriched with different di-, tri- and tetranucleotides. Most microsatellites obtained were imperfect dinucleotides. Allelic variation was screened for a total of 56 individuals from two populations from North-Western Mediterranean. Microsatellites showed a number of alleles ranging from 13 to 35. Linkage disequilibrium was not detected between any pair of loci, and all loci showed a significant departure from Hardy,Weinberg equilibrium which is not likely to be the result of null alleles, suggesting that demographic features may be acting upon this commercially interesting species. [source]

    Polymorphic microsatellite loci in Linum usitatissimum

    Abstract We report the characterization of 28 polymorphic microsatellite markers in Linum usitatissimum that allow distinguishing almost all cultivars of both flax and linseed. Polymorphism was low, ranging from two to 10 alleles per locus in the 93 cultivars screened. Linkage disequilibrium was found at about a third of the pairs of loci likely due to self-fertilization and strong selection by breeders. We tested these loci for cross-amplification in nine additional species of Linum and found that three species amplified a majority of loci. [source]

    Prion-like Doppel gene polymorphisms and scrapie susceptibility in portuguese sheep breeds

    ANIMAL GENETICS, Issue 3 2010
    P. Mesquita
    Summary The establishment of an association between prion protein gene (PRNP) polymorphisms and scrapie susceptibility in sheep has enabled the development of breeding programmes to increase scrapie resistance in the European Union. Intense selection for PRNP genotype may lead to correlated selection for genes linked to PRNP. We intended to investigate if any association exists between genetic variation in prion-like protein Doppel gene (PRND) and scrapie susceptibility, determined through PRNP genotyping. Sampling included 460 sheep from eight Portuguese breeds and the PRND gene coding region was analysed by multiple restriction fragment-single strand conformation polymorphism (MRF-SSCP), whereas PRNP genotyping was carried out by primer extension. A synonymous substitution (c.78G>A) was detected in codon 26 of the PRND gene, in all breeds except Churra Mondegueira. Linkage disequilibrium was found between the PRND and PRNP loci (P = 0.000). Specifically, PRND was monomorphic in the 45 animals with the more resistant ARR/ARR PRNP genotype (P = 0.003), whereas a higher frequency of PRND heterozygotes (GA) was associated with ARQ/AHQ (P = 0.029). These results constitute preliminary evidence of an association between a polymorphism in the PRND gene and scrapie susceptibility, and indicate that the possibility of undesirable consequences from widespread selection for PRNP genotype on genetic diversity and reproduction traits needs to be further investigated. [source]

    Detailed characterization of the porcine MC4R gene in relation to fatness and growth

    ANIMAL GENETICS, Issue 4 2009
    B. Fan
    Summary In contrast to the human MC4R gene, where multiple variants have been described, several of which are associated with appetite and obesity, few MC4R variants have been reported in the pig. The most interesting polymorphism reported to date in the pig is p.Asp298Asn, which is significantly associated with variation in growth and fatness traits in most breeds and crosses. However, some reports have seemingly failed to confirm this association. The discrepancy of p.Asp298Asn associations in some pig populations suggested that further discovery of SNPs in MC4R would be useful. Utilizing the recently released pig genome sequence information, we obtained the whole MC4R genome sequence and detected five additional SNPs, a variable (CA)n repeat and a C indel in the ISU Berkshire × Yorkshire pig resource family. Linkage disequilibrium (LD) analysis revealed that the additional five SNPs were not in strong LD with p.Asp298Asn, but single marker association analysis indicated that they were significantly (P < 0.05) associated with fatness measures and very highly significantly (P < 0.0001) associated with average daily gain on test (ADGTEST). Three major haplotypes were identified and the subsequent association analyses suggested that the two non-synonymous SNPs had different effects, e.g. p.Arg236His influenced back fat and growth on test while p.Asp298Asn was primarily associated with variation in growth rate in this population. An interaction effect between these two SNPs was found for ADGTEST, which may partly explain some of the previous discrepancies reported for MC4R in different pig populations. Examination of the p.Arg236His polymorphism in populations where the effect of p.Asp298Asn is limited is warranted. [source]

    Linkage disequilibrium in the North American Holstein population

    ANIMAL GENETICS, Issue 3 2009
    E.-S. Kim
    Summary Linkage disequilibrium was estimated using 7119 single nucleotide polymorphism markers across the genome and 200 animals from the North American Holstein cattle population. The analysis of maternally inherited haplotypes revealed strong linkage disequilibrium (r2 > 0.8) in genomic regions of ,50 kb or less. While linkage disequilibrium decays as a function of genomic distance, genomic regions within genes showed greater linkage disequilibrium and greater variation in linkage disequilibrium compared with intergenic regions. Identification of haplotype blocks could characterize the most common haplotypes. Although maximum haplotype block size was over 1 Mb, mean block size was 26,113 kb by various definitions, which was larger than that observed in humans (,10 kb). Effective population size of the dairy cattle population was estimated from linkage disequilibrium between single nucleotide polymorphism marker pairs in various haplotype ranges. Rapid reduction of effective population size of dairy cattle was inferred from linkage disequilibrium in recent generations. This result implies a loss of genetic diversity because of the high rate of inbreeding and high selection intensity in dairy cattle. The pattern observed in this study indicated linkage disequilibrium in the current dairy cattle population could be exploited to refine mapping resolution. Changes in effective population size during past generations imply a necessity of plans to maintain polymorphism in the Holstein population. [source]

    Variation in neighbouring genes of the dopaminergic and serotonergic systems affects feather pecking behaviour of laying hens

    ANIMAL GENETICS, Issue 2 2009
    K. Flisikowski
    Summary Feather pecking is a behavioural disorder of laying hens and has serious animal welfare and economic implications. One of the several aetiological hypotheses proposes that the disorder results from redirected exploratory behaviour. Variation in the gene encoding the dopamine D4 receptor (DRD4) has been shown to be associated with exploratory behaviour in several species, including in a passerine bird species. We therefore considered DRD4 as a candidate gene for feather pecking. We have annotated DRD4 in the chicken genome and have re-sequenced it in 140 animals belonging to: experimental layer lines divergently selected for high and low propensity to feather pecking; the unselected founder population; and two commercial lines with low and high propensity to feather pecking. We have identified two sub-haplotypes of DRD4 that are highly significantly associated with feather pecking behaviour in the experimental (P = 7.30 × 10,7) as well as in the commercial lines (P = 2.78 × 10,6). Linkage disequilibrium (LD) extends into a neighbouring gene encoding deformed epidermal autoregulatory factor 1 (DEAF1). The product of DEAF1 regulates the transcription of the gene encoding the serotonin (5-hydroxytryptamine) 1A receptor. Thus, DEAF1 represents another candidate gene for feather pecking. Re-sequencing of five animals homozygous for the ,low-pecking' sub-haplotype and of six animals homozygous for the ,high-pecking' sub-haplotype delineated an LD block of 14 833 bases spanning the two genes. None of the variants in the LD block is obviously functional. However, the haplotype information will be useful to select against the propensity to feather pecking in chicken and to elucidate the functional implications of the variants. [source]

    Haplotypes of the Human RET Proto-oncogene Associated with Hirschsprung Disease in the Italian Population Derive from a Single Ancestral Combination of Alleles

    F. Lantieri
    Summary The RET proto-oncogene is the major gene involved in the complex genetics of Hirschsprung disease (HSCR), or aganglionic megacolon, showing causative loss-of-function mutations in 15,30% of the sporadic cases. Several RET polymorphisms and haplotypes have been described in association with the disease, suggesting a role for this gene in HSCR predisposition, also in the absence of mutations in the coding region. Finally, the presence of a functional variant in intron 1 has repeatedly been proposed to explain such findings. Here we report a case-control study conducted on 97 Italian HSCR sporadic patients and 85 population matched controls, using 13 RET polymorphisms distributed throughout the gene, from the basal promoter to the 3,UTR. Linkage disequilibrium and haplotype analyses have shown increased recombination between the 5, and 3, portions of the gene and an over-representation, in the cases studied, of two haplotypes sharing a common allelic combination that extends from the promoter up to intron 5. We propose that these two disease-associated haplotypes derive from a single founding locus, extending up to intron 19 and successively rearranged in correspondence with a high recombination rate region located between the proximal and distal portions of the gene. Our results suggests the possibility that a common HSCR predisposing variant, in linkage disequilibrium with such haplotypes, is located further downstream than the previously suggested interval encompassing intron 1. [source]

    TRAF1 polymorphisms associated with rheumatoid arthritis susceptibility in Asians and in Caucasians

    ARTHRITIS & RHEUMATISM, Issue 9 2009
    Tae-Un Han
    Objective Recent genome-wide association scans and replication studies of European populations have disclosed several single-nucleotide polymorphisms (SNPs) associated with rheumatoid arthritis (RA) susceptibility. The aim of this study was to evaluate the RA-associated loci by genotyping previously reported SNPs and additional tag SNPs in a Korean population. Methods A total of 1,316 unrelated RA patients and 1,006 controls were genotyped for 12 SNPs identified in genome-wide scans and for 12 additional tag SNPs in IL2RB, OLIG3,TNFAIP3, PTPN22, and TRAF1,C5, and the findings were statistically compared. Results None of the SNPs tested was associated with RA susceptibility, except rs7021206 in TRAF1 intron 3 (P = 0.0032) and, among the SNPs previously reported, rs6457617 in HLA (P = 4.6 × 10,35). The association of rs7021206 was positive in patients who were seropositive for rheumatoid factor (P = 0.0051) or for anti,cyclic citrullinated peptide autoantibodies (P = 0.0062). However, Korean patients were negative for the association of rs3761847 in the TRAF1,C5 intergenic region previously reported in Caucasians. Linkage disequilibrium between rs3761847 and rs7021206 was not as high in Koreans (r2 = 0.37) as in Caucasians (r2 = 0.67), which explains the lack of association of rs3761847 in Koreans. Accordingly, RA susceptibility was localized to an extended haplotype marked by rs7021206 rather than rs3761847, and SNPs highly correlated with rs7021206 (r2 , 0.81) extended from rs1953126 in the PHF19,TRAF1 intergenic region to rs2900180 in the TRAF1,C5 intergenic region, spanning 66 kb. Conclusion Our results demonstrate that within and around TRAF1, excluding PHF19 and C5, SNPs highly correlated with rs7021206, but not those correlated with rs3761847, are associated with RA in both Asians and Caucasians and are possibly correlated with causative variations. [source]

    Linkage disequilibrium and natural selection for mimicry in the Batesian mimic Hypolimnas misippus (L.) (Lepidoptera: Nymphalidae) in the Afrotropics

    On two occasions, on opposite sides of the African continent (Cape Coast, Ghana, and Dar es Salaam, Tanzania), high adult population densities in the polymorphic butterfly Hypolimnas misippus (a presumed mimic of Danaus chrysippus) were followed by linkage disequilibrium in combinations of fore- and hindwing colour patterns. On both occasions, disequilibrium was caused by significant changes in morph frequencies favouring rarer and more mimetic forms. Recaptures were too few for analysis at Dar, although the changes there took place within a single generation and must have been the result of differential survival. Recapture rate data and survival rate estimates at Cape Coast support the hypothesis that selective predation was responsible, as does the observation of synchronous linkage disequilibrium at Dar in the model D. chrysippus, indicating parasitic mimicry. There was clear selection for the perfection of mimicry for forewings at Dar and for hindwings at Cape Coast. Disequilibrium is also reported for two other sites, Legon (Ghana) and Boksburg (South Africa) and, in all four sites, it was associated with an increase in the most mimetic forms. New chemical evidence is presented to support the contention that D. chrysippus is a defended model. Although all the evidence leads to the conclusion that H. misippus is a Batesian mimic of D. chrysippus, many questions remain, particularly with regard to the identity of predators, the episodic nature of selective predation events, and their apparent lack of lasting and significant impact on overall gene frequencies. We conclude that H. misippus presents both challenges and opportunities for studies on mimicry, and we suggest that linkage disequilibrium can be a useful generic indicator for Gestalt predation on polymorphic prey. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100, 180,194. [source]

    Association between renin,angiotensin,aldosterone system genotypes and haplotypes and risk of ischemic stroke of atherosclerotic etiology

    S. Saidi
    Objective,,, The association of renin C-4063T and angiotensinogen (AGT) T174M, AGT M235T and AGT A-6G polymorphisms with ischemic stroke of atherosclerotic etiology was investigated in 329 Tunisian patients with stroke and 444 controls. Materials and methods,,, Genotyping was performed using PCR-RFLP and the contributions of polymorphisms to the risk of stroke were analyzed using haplotype and multivariate regression analysis. Results,,, AGT 235T and AGT-6G allele and AGT 235T/T, AGT-6A/G and AGT-6G/G genotype frequencies were higher in patients. Linkage disequilibrium (LD) was noted for AGT174T with AGT235M and AGT(-6)A in patients, while AGT235M was in LD with AGT(-6)A in controls and AGT235T was in LD with AGT(-6)G in both groups. The AGT 174T/235T/-6A and AGT 174T/235M/-6G haplotypes were positively and negatively associated with stroke respectively. Multivariate regression analysis identified AGT 174T/235M/-6A, AGT 174T/235T/-6G, AGT 174T/235T/-6A and AGT 174M/235T/-6A haplotypes to be significantly associated with an increased risk of stroke. Conclusions,,, Renin,angiotensin,aldosterone system polymorphisms influence the risk of atherosclerotic stroke in Tunisians. [source]

    Association of HLA DQ4-DR8 haplotype with papillary thyroid carcinomas

    Teresa Porto
    Summary Objective, The association of the human leucocyte antigen (HLA) system with thyroid carcinomas is not clear. We sought to relate HLA alleles to susceptibility to papillary thyroid carcinoma (PTC) and also to clinical and pathological characteristics of PTC patients. Design and patients, The distribution of HLA in 181 unrelated Caucasian patients with PTC was compared to the HLA distribution in 315 normal controls, 31 patients with follicular carcinoma (FTC), 29 patients with lymphocytic thyroiditis (LT) and 50 patients with multinodular goitre (MNG), using a microlymphocytotoxicity assay. Results, Compared to normal controls, patients with PTC showed a significantly increased frequency of HLA-DQ4 [12·8%vs. 3·5%, P = 0·0005, Pcorrected (Pc) = 0·0032, odds ratio (OR) = 4·058, 95% confidence interval (95% CI) = 1·820,9·045] and HLA-DR8 (10·9%vs. 4·3%, P = 0·013, Pc > 0·05, OR = 2·752, 95% CI = 1·275,5·940). DQ4 and DR8 were also significantly increased in patients with MNG (DQ4, 16·3%; DR8, 16·3%) compared to controls (DQ4, P = 0·0019, Pc = 0·011, OR = 5·420, 95% CI = 1·978,14·852; DR8, P = 0·0044, Pc = 0·062). Linkage disequilibrium (LD) for these two alleles was present in controls (D = 0·0130, P = 9·7e-57) and in MNG patients (D = 0·0730, P = 4·6e-19) but not in PTC patients (D = 0·038, P > 0·05). In the subgroup of PTC subjects with concomitant nonthyroidal neoplasias (n = 27), there was a significant (P < 0·05) increase in the frequency of B57 (18·5%), DR11 (56·5%) and DQ3 (81·8%) compared to PTC patients without coexistent neoplasias (2·0%, 21% and 47%, respectively). No significant differences of HLA allele distribution was found in relation to PTC histology, age at diagnosis (> 45 or , 45 years), gender or tumour,node,metastasis (TNM) staging. In patients with FTC, the frequency of DR17 (FTC = 51·6%; controls = 22·5%; P = 0·0009; Pc = 0·0138) was significantly increased compared to controls. Patients with LT showed a higher frequency of the DR11 allele (48·3%) than controls (DR11 = 21·3%; P = 0·0028, Pc = 0·039, OR = 3·445, 95% CI = 1·568,7·567). Conclusions, We have typed the largest series of patients with thyroid carcinomas reported to date, and found that DR8 and DQ4 are independent susceptibility markers for PTC. [source]

    Identification of 25 new mutations in 40 unrelated Spanish Niemann-Pick type C patients: genotype-phenotype correlations

    CLINICAL GENETICS, Issue 3 2005
    EM Fernandez-Valero
    To better characterize Niemann-Pick type C (NPC) in Spain and improve genetic counselling, molecular analyses were carried out in 40 unrelated Spanish patients. The search identified 70/80 alleles (88%) involving 38 different NPC1 mutations, 26 of which are described for the first time. No patient with NPC2 mutations was identified. The novel NPC1 mutations include 14 amino acid substitutions [R372W (c.1114C > T), P434L (c.1301C > T), C479Y (c.1436G > A), K576R (c.1727G > A), V727F (c.2179G > T), M754K (c.2261T > A), S865L (c.2594C > T), A926T (c.2776G > A), D948H (c.2842G > C), V959E (c.2876T > A), T1036K (c.3107C > A), T1066N (c.3197C > A), N1156I (c.3467A > T) and F1224L (c.3672C > G)], four stop codon [W260X (c.780G > A), S425X (c.1274C > A), C645X (c.1935T > A) and R1059X (c.3175C > T)], two donor splice-site mutations [IVS7+1G > A (g.31432G > A) and IVS21+2insG (g.51871insG)], one in-frame mutation [N961_F966delinsS (c.2882del16bpins1bp)] and five frameshift mutations [V299fsX8 (c.895insT), A558fsX11 (c.1673insG), C778fsX10 (c.2334insT), G993fsX3 (c.2973_78delG) and F1221fsX20 (c.3662delT)]. We also identified three novel changes [V562V (c.1686G > A), A580A (c.1740C > G) and A1187A (c.3561G > T)] in three independent NPC patients and five polymorphisms that have been described previously. The combination of these polymorphisms gave rise to the establishment of different haplotypes. Linkage disequilibrium was detected between mutations C177Y and G993fsX3 and specific haplotypes, suggesting a unique origin for these mutations. In contrast, I1061T mutation showed at least two different origins. The most prevalent mutations in Spanish patients were I1061T, Q775P, C177Y and P1007A (10, 7, 7 and 5% of alleles, respectively). Our data in homozygous patients indicate that the Q775P mutation correlates with a severe infantile neurological form and the C177Y mutation with a late infantile clinical phenotype. [source]

    Polymorphisms in the interleukin-1 gene influence the stratum corneum interleukin-1, concentration in uninvolved skin of patients with chronic irritant contact dermatitis

    CONTACT DERMATITIS, Issue 5 2008
    Cindy M. DeJongh
    Background:, Interleukin (IL)-1, and its receptor antagonist IL-1ra play a role in skin inflammation. Several polymorphisms in the IL1 gene cluster, coding for IL-1,, IL-1ra, and IL-1,, influence their protein expression. Within this cluster, strong linkage disequilibrium has been shown. Objective:, We studied the association between the polymorphisms IL1A -889 (C,T) and IL1B -31 (T,C) and the concentration of IL-1, and IL-1ra in the stratum corneum (SC). Method:, In 124 patients with chronic irritant contact dermatitis, we genotyped the IL1A -889 and IL1B -31 polymorphisms and determined the amount of IL-1, and IL-1ra on tape strips obtained from uninvolved skin of the volar forearm. Results:, The SC IL-1, concentration was 23% and 47% lower in subjects with IL1A -889 C/T genotype and T/T genotype, respectively, compared with wild-type genotype. In subjects with IL1B -31 C/C genotype, the IL-1, concentration was 51% lower compared with C/T and T/T genotypes. The ratio IL-1ra/IL-1, increased twofold in IL1A -889 C/T genotype and threefold in T/T genotype compared with wild type. Conclusions:, We have shown a clear effect of IL1 genotype on protein expression in the SC. This altered expression may be responsible for the interindividual differences in the inflammatory response of the skin. [source]

    Effect of RBP4 gene variants on circulating RBP4 concentration and Type 2 diabetes in a Chinese population

    DIABETIC MEDICINE, Issue 1 2008
    C. Hu
    Abstract Aims Retinol binding protein 4 (RBP4) is a newly discovered adipokine, which plays a role in insulin resistance and obesity. The aim of this study was to determine the relationship between genetic variants of the RBP4 gene, circulating RBP4 concentrations and phenotypes related to glucose and lipid metabolism in the Chinese population. Methods We sequenced exons and the putative promoter region to identify single nucleotide polymorphisms (SNPs) in the RBP4 gene in 32 Chinese subjects. Additional SNPs were selected from a public database to increase marker density. Taking account of the pairwise linkage disequilibrium and minor allele frequencies, a subset of SNPs was further genotyped in 255 Type 2 diabetic patients and 372 normal control subjects. Circulating RBP4 concentrations and phenotypes related to glucose and lipid metabolism were measured. Results Ten SNPs were identified and five were further genotyped in the full sample. No individual SNP was significantly associated with Type 2 diabetes, but a rare haplotype CAA formed by +5388 C>T, +8201 T>A and +8204 T>A was more frequent in diabetic patients (P = 0.0343, empirical P = 0.0659 on 10 000 permutations). In both groups, non-coding SNPs were associated with circulating RBP4 concentrations (P < 0.05). In the normal control subjects, the SNP +5388 C>T was associated with serum C-peptide levels both fasting and 2 h after an oral glucose tolerance test (P = 0.0162 and P = 0.0075, respectively). Conclusion Our findings suggest that genetic variants in the RBP4 gene may be associated with circulating RBP4 concentration and phenotypes related to glucose metabolism. [source]

    Peroxisome proliferator-activated receptor-, co-activator-1, (PGC-1,) gene polymorphisms and their relationship to Type 2 diabetes in Asian Indians

    DIABETIC MEDICINE, Issue 11 2005
    K. S. Vimaleswaran
    Abstract Aims The objective of the present investigation was to examine the relationship of three polymorphisms, Thr394Thr, Gly482Ser and +A2962G, of the peroxisome proliferator activated receptor-, co-activator-1 alpha (PGC-1,) gene with Type 2 diabetes in Asian Indians. Methods The study group comprised 515 Type 2 diabetic and 882 normal glucose tolerant subjects chosen from the Chennai Urban Rural Epidemiology Study, an ongoing population-based study in southern India. The three polymorphisms were genotyped using polymerase chain reaction,restriction fragment length polymorphism (PCR,RFLP). Haplotype frequencies were estimated using an expectation,maximization (EM) algorithm. Linkage disequilibrium was estimated from the estimates of haplotypic frequencies. Results The three polymorphisms studied were not in linkage disequilibrium. With respect to the Thr394Thr polymorphism, 20% of the Type 2 diabetic patients (103/515) had the GA genotype compared with 12% of the normal glucose tolerance (NGT) subjects (108/882) (P = 0.0004). The frequency of the A allele was also higher in Type 2 diabetic subjects (0.11) compared with NGT subjects (0.07) (P = 0.002). Regression analysis revealed the odds ratio for Type 2 diabetes for the susceptible genotype (XA) to be 1.683 (95% confidence intervals: 1.264,2.241, P = 0.0004). Age adjusted glycated haemoglobin (P = 0.003), serum cholesterol (P = 0.001) and low-density lipoprotein (LDL) cholesterol (P = 0.001) levels and systolic blood pressure (P = 0.001) were higher in the NGT subjects with the XA genotype compared with GG genotype. There were no differences in genotype or allelic distribution between the Type 2 diabetic and NGT subjects with respect to the Gly482Ser and +A2962G polymorphisms. Conclusions The A allele of Thr394Thr (G , A) polymorphism of the PGC-1 gene is associated with Type 2 diabetes in Asian Indian subjects and the XA genotype confers 1.6 times higher risk for Type 2 diabetes compared with the GG genotype in this population. [source]

    Further evidence for an association between the gamma-aminobutyric acid receptor A, subunit 4 genes on chromosome 4 and Fagerström Test for Nicotine Dependence

    ADDICTION, Issue 3 2009
    Arpana Agrawal
    ABSTRACT Aims A previous association analysis identified polymorphisms in gamma-aminobutyric acid receptor A, subunit 4 (GABRA4) and GABRA2 to be associated with nicotine dependence, as assessed by a score of 4 or more on the Fagerström Test for Nicotine Dependence (FTND). In the present report, we extend the previous study by expanding our genotyping efforts significantly for these two genes. Design In 1049 cases (FTND of 4 or more) and 872 controls (smokers with FTND of 0) from the United States and Australia, we examine the association between 23 GABRA4 and 39 GABRA2 recently genotyped single nucleotide polymorphisms (SNPs) and nicotine dependence using logistic regression-based association analyses using the genomic analysis package PLINK. Results Two and 18 additional SNPs in GABRA4 and GABRA2, respectively, were associated with nicotine dependence. The SNPs identified in GABRA4 (P -value = 0.002) were restricted to introns 1 and 2, exon 1 and the 5, end of the gene, while those in GABRA2 localized to the 3, end of the gene and spanned introns 9,3, and were in moderate to high linkage disequilibrium (as measured by r2) with each other and with previously studied polymorphisms. Conclusion Our findings demonstrate consistently the role of GABRA4 and GABRA2 in nicotine dependence. However, further research is needed to identify the biological influence of these intronic variations and to isolate functionally relevant polymorphisms neighboring them. [source]

    The recent breakthroughs in the understanding of host genomics in hepatitis C

    Andri Rauch
    Eur J Clin Invest 2010; 40 (10): 950,959 Abstract Background, Hepatitis C Virus (HCV) infection is spontaneously resolved in about 30% of acutely infected individuals. In those who progress to chronic hepatitis C, HCV therapy permanently eradicates infection in about 40% of cases. It has long been suspected that host genetic factors are key determinants for the control of HCV infection. Design, We will review in this study four genome-wide association studies (GWAS) and two large candidate gene studies that assessed the role of host genetic variation for the natural and treatment-induced control of HCV infection. Results, The studies consistently identified genetic variation in interleukin 28B (IL28B) as the strongest predictor for the control of HCV infection. Importantly, single nucleotide polymorphisms (SNPs) in IL28B strongly predicted both spontaneous and treatment-induced HCV recovery. IL28B is located on chromosome 19 and encodes interferon-,, a type III interferon with antiviral activity, which is mediated through the JAK-STAT pathway by inducing interferon-stimulated genes. The SNPs identified in the GWAS are in high linkage disequilibrium with coding or functional non-coding SNPs that might modulate function and/or expression of IL28B. The role of the different IL28B alleles on gene expression and cytokine function has not yet been established. Conclusions, These findings provide strong genetic evidence for the influence of interferon-, for both the natural and treatment-induced control of HCV infection, and support the further investigation of interferon-, for the treatment of chronic hepatitis C. Furthermore, genetic testing before HCV therapy could provide important information towards an individualized HCV treatment. [source]

    PON1 L55M polymorphism is not a predictor of coronary atherosclerosis either alone or in combination with Q192R polymorphism in an Italian population

    M. Arca
    Abstract Background, The present study evaluated the role of the PON1 L55M polymorphism independently and in conjunction with the Q192R polymorphism on the risk of coronary atherosclerosis in an Italian population. Materials and methods, Three hundred and ninety-one subjects with significant coronary stenosis (> 50%) (coronary artery disease-positive; CAD+), 196 subjects with normal coronary arteries (< 10% stenosis) (CAD,) and 178 healthy controls were screened using a combination of polymerase chain reaction and restriction enzyme digestion. Results, In the pooled population, the frequencies of L and M alleles were 0·63 and 0·37, respectively; the most common haplotypes were QQ/LM (24·2%) and QR/LL (21·8%) and a strong linkage disequilibrium between L/55 and R/192 alleles was observed (D, = ,0·91; P < 0·0001). CAD+ subjects did not show any significant differences in the distribution of PON1,55 genotypes as compared to CAD, subjects and population controls (,2 = 1·5, P = 0·8). After controlling for other risk factors, the low-concentration M allele was not associated with a significant change of CAD risk (OR 1·02; 95% CI 0·80,1·29; P = 0·87). Moreover, the L55M polymorphism did not show any interaction with other risk factors such as smoking, diabetes, hypertension, low levels of high-density lipoprotein (HDL) or high ratios of low-density to high-density lipoproteins. The combination of L55M with the Q192R polymorphism did not show any effect on CAD risk. However, a marginal decrease in myocardial infarction risk was detected when QQ/MM carriers (OR 0·51; 95% CI 0·26,0·99; P = 0·048), but not LL/RR carriers, were compared with subjects not homozygous for an L or R allele. Conclusions, These findings did not indicate a major effect of the PON1 L55M polymorphism, either alone or in combination with the Q192R polymorphism, on CAD risk. Additional studies are needed for a better evaluation of the role of the 55/192 PON1 genotypes in combination on myocardial infarction risk. [source]

    GENETIC STUDY: H2 haplotype at chromosome 17q21.31 protects against childhood sexual abuse-associated risk for alcohol consumption and dependence

    ADDICTION BIOLOGY, Issue 1 2010
    Elliot C. Nelson
    ABSTRACT Animal research supports a central role for corticotropin-releasing factor (CRF) in actions of ethanol on brain function. An examination of alcohol consumption in adolescents reported a significant genotype × environment (G × E) interaction involving rs1876831, a corticotropin-releasing hormone receptor 1 (CRHR1) polymorphism, and negative events. CRHR1 and at least four other genes are located at 17q21.31 in an extremely large block of high linkage disequilibrium resulting from a local chromosomal inversion; the minor allele of rs1876831 is contained within the H2 haplotype. Here, we examine whether G × E interactions involving this haplotype and childhood sexual abuse (CSA) are associated with risk for alcohol consumption and dependence in Australian participants (n = 1128 respondents from 476 families) of the Nicotine Addiction Genetics project. Telephone interviews provided data on DSM-IV alcohol dependence diagnosis and CSA and enabled calculation of lifetime alcohol consumption factor score (ACFS) from four indices of alcohol consumption. Individuals reporting a history of CSA had significantly higher ACFS and increased risk for alcohol dependence. A significant G × E interaction was found for ACFS involving the H2 haplotype and CSA (P < 0.017). A similar G × E interaction was associated with protective effects against alcohol dependence risk (odds ratio 0.42; 95% confidence interval 0.20,0.89). For each outcome, no significant CSA-associated risk was observed in H2 haplotype carriers. These findings support conducting further investigation of the H2 haplotype to determine the gene(s) responsible. Our results also suggest that severe early trauma may prove to be an important clinical covariate in the treatment of alcohol dependence. [source]


    EVOLUTION, Issue 12 2009
    Alan Brelsford
    Hybrid zones between recently diverged taxa are natural laboratories for speciation research, allowing us to determine whether there is reproductive isolation between divergent forms and the causes of that isolation. We present a study of a classic avian hybrid zone in North America between two subspecies of the yellow-rumped warbler (Dendroica coronata). Although previous work has shown very little differentiation in mitochondrial DNA across this hybrid zone, we identified two nuclear loci (one sex-linked and one autosomal) that show fixed differences across the hybrid zone, in a close concordance with patterns of plumage variation. Temporal stability and limited width of the hybrid zone, along with substantial linkage disequilibrium between these two diagnostic markers in the center of the zone, indicate that there is moderate reproductive isolation between these populations, with an estimated strength of selection maintaining the zone of 18%. Pairing data indicate that assortative mating is either very weak or absent, suggesting that this reproductive isolation is largely due to postmating barriers. Thus, despite extensive hybridization the two forms are distinct evolutionary groups carrying genes for divergent adaptive peaks, and this situation appears relatively stable. [source]