Haplotype Relative Risk Research Articles

Lack of association or linkage disequilibrium between schizophrenia and polymorphisms in the 5-HT1Dalpha and 5-HT1Dbeta autoreceptor genes: family-based association study.

Genetic factors play a major role in the etiology of schizophrenia and disturbances of serotonergic pathways have been implicated in this disorder. The aim of the present study was to examine genetic association between schizophrenia and polymorphisms in the 5-HT1Dalpha (TaqI) and 5-HT1Dbeta (T261G and G861C) autoreceptor genes in ninety trios from Portugal. No association or linkage disequilibrium was obtained between schizophrenia and 5-HT1Dalpha and 5-HT1Dbeta autoreceptor genes with both haplotype relative risk (HRR) and transmission disequilibrium test (TDT). Concerning 5-HT1Dbeta autoreceptor gene, also negative results was obtained in the analysis of the haplotypes with transmit. Thus, our data provide no support for the hypothesis that polymorphisms at 5-HT1Dalpha (TaqI) and 5-HT1Dbeta (T261G and G861C) genes contributes to susceptibility to schizophrenia in the Portuguese population.

PedSplit: pedigree management for stratified analysis.

PedSplit facilitates pedigree management for gene-gene interaction and sex specific tests for increased homogeneity within subgroups. PedSplit also provides a simple approach for calculating haplotype relative risk and generating internal 'controls'. Executables, C++ source code and documentation for PedSplit can be downloaded from http://www.pharmacogenetics.ca in the links and software section.

Family association study between DRD2 and DRD3 gene polymorphisms and schizophrenia in a Portuguese population

Schizophrenia is a highly heritable condition, as demonstrated in family, twin and adoption studies. Candidate genes from the dopaminergic system have long been hypothesized to be involved in the etiology of this disorder. In the present study, we investigated the genetic association between polymorphisms in the D2 and D3 dopamine receptor (DRD2, DRD3) genes and schizophrenia. We examined 90 trios from Portugal, and negative results were obtained from association studies with both Haplotype Relative Risk (HRR) and Transmission Disequilibrium Test (TDT), as well as TRANSMIT. Therefore, we conclude that neither the DRD2 nor the DRD3 gene polymorphisms investigated are associated with schizophrenia in our sample.

Analysis of childhood absence epilepsy using haplotype-based haplotype relative risk and transmission disequilibrium test.

The authors performed haplotype-based haplotype relative risk (HHRR) and transmission disequilibrium test (TDT) analysis of childhood absence epilepsy in 30 trios families, using gene typing technology based on microsatellite polymorphic marker. The five microsatellite DNA markers (D8S554, D8S1753, D8S534, D8S1100, D8S1783) used in the study are on chromosome 8q24. HHRR shows D8S554(4) (chi2 = 5.939, P < 0.05), D8S1100(3) (chi2 = 5.081, P < 0.05), D8S1783(6) (chi2 = 4.308, P < 0.05), TDT shows D8S554(4) (chi2 = 4.455, P < 0.05), D8S1783(6) (chi2 = 4, P < 0.05), some signs of association and disequilibrium between these loci and CAE. A suspected association of childhood absence epilepsy in the Chinese population to chromosome 8q24 has been proposed. In addition, it is hypothesized that the CAE gene might have a genetic heterogeneity in the population from a different race.

Analysis of childhood absence epilepsy using haplotype-based haplotype relative risk and transmission disequilibrium test

The authors performed haplotype-based haplotype relative risk (HHRR) and transmission disequilibrium test (TDT) analysis of childhood absence epilepsy in 30 trios families, using gene typing technology based on microsatellite polymorphic marker. The five microsatellite DNA markers (D8S554, D8S1753, D8S534, D8S1100, D8S1783) used in the study are on chromosome 8q24. HHRR shows D8S554 4 ( χ 2=5.939, P<0.05), D8S1100 3 ( χ 2=5.081, P<0.05), D8S1783 6 ( χ 2=4.308, P<0.05), TDT shows D8S554 4 ( χ 2=4.455, P<0.05), D8S1783 6 ( χ 2=4, P<0.05), some signs of association and disequilibrium between these loci and CAE. A suspected association of childhood absence epilepsy in the Chinese population to chromosome 8q24 has been proposed. In addition, it is hypothesized that the CAE gene might have a genetic heterogeneity in the population from a different race.

Alpha-adducin gene polymorphism is associated with essential hypertension in Chinese: a case-control and family-based study.

A polymorphism at position 460(G <-- W) of the alpha-adducin gene was found to be associated with essential hypertension in some but not all studies. The aim of the present study was to further investigate the association of the alpha-adducin 460W allele with essential hypertension in Chinese population. Individuals from a population-based sample (n = 748) and 95 nuclear families and 47 discordant sibships were studied by questionnaire as well as by physical examination and biochemical analyses. The alpha-adducin gene G460W polymorphism was determined by polymerase chain reaction and restriction enzyme digestion. Chi-square test, one-way analysis of variance, logistic regression, linear regression, haplotype-based haplotype relative risk and transmission/disequilibrium test analyses were used to determine the association between the alpha-adducin G460W polymorphism and essential hypertension. In the case-control study, the prevalence of hypertension was higher in individuals with the WW genotype (40.0%) as compared with those with the GW and GG genotype (31.7%) (chi2 = 4.768, P = 0.029, odds ratio = 1.43). Adjusted for the conventional risk factors of hypertension, alpha-adducin polymorphism still plays an independent role on systolic blood pressure. We confirmed the results of our case-control study by observing a significant preferential transmission of the 460W allele of the alpha-adducin to the affected subjects in another northern Chinese population (for haplotype-based haplotype relative risk, chi2 = 6.24, P = 0.01; and for the transmission/disequilibrium test, chi2 = 4.69, P = 0.03). The present findings show a positive association between the alpha-adducin G460W polymorphism and essential hypertension in a northern Chinese population. This evidence indicates that the alpha-adducin gene may be a susceptible gene to essential hypertension.

Family-based association study of the serotonin-6 receptor gene (C267T polymorphism) in schizophrenia.

The expression of serotonin type 6 receptor (5-HT(6)) in limbic and cortical regions of the brain, and its high affinity for atypical antipsychotics suggest that its encoding gene may play a role in the pathogenesis of schizophrenia. We firstly performed a meta-analysis of the C267T polymorphism of the 5-HT(6) gene in schizophrenia, based on four different case/control studies, and showed that the allelic distribution is not significantly different between patients and controls, even when taking into account the role of between samples heterogeneity. We then recruited 103 trios (patients with Diagnostic and Statistical Manual Mental Disorders, 4th ed. (DSM-IV) diagnosis of schizophrenia and their parents), and investigated the C267T polymorphism of the 5-HT(6) receptor gene with regard to family-based association study approach (haplotype relative risk (HRR) and transmission disequilibrium test (TDT)). We found no excess of transmission of one allele from the parents to their affected children, using the HRR (P = 0.60), as well as no evidence for linkage between C267T polymorphism and schizophrenia, using the TDT (P = 0.71). Furthermore, the 267T allele frequency was comparable in the different subgroups defined on age at onset, family history of schizophrenia, treatment response, and subtypes of patients based on positive versus negative predominant symptoms. These data do not support the idea that the 5-HT(6) receptor gene plays a major role in the etiopathogenesis of schizophrenia.

No evidence of association or linkage disequilibrium between polymorphisms in the 5' upstream and coding regions of the dopamine D4 receptor gene and schizophrenia in a Portuguese population.

Alterations in dopaminergic system have been implicated in the pathophysiology of this disease for many years, and this study was performed to assess the possible involvement of the dopamine D4 receptor (DRD4) gene polymorphisms either in the 5' upstream or in the coding regions, in the etiology of schizophrenia. The approach included an association study with 90 Portuguese trios by doing the analysis of the individual alleles and the haplotypes. For the polymorphisms in the 5' upstream region (-C616G and -C521T) and in the coding region (48 bp repeat) of the DRD4 gene, negative results were obtained with both haplotype relative risk (HRR) and transmission disequilibrium test (TDT), as well as transmit. These data suggest that polymorphisms (-C616G, -C521T, and 48 bp repeat) at the DRD4 gene do not have a minor effect in the susceptibility to schizophrenia in our sample.

Association study of cannabinoid receptor gene (CNR1) alleles and anorexia nervosa: differences between restricting and binging/purging subtypes.

Anorexia nervosa (AN) is a severe and disabling psychiatric disorder, characterized by profound weight loss and body image disturbance. Family and twin studies indicate a significant genetic contribution to this disorder although no genetic mutation has yet been identified. The endocannabinoid system has recently been implicated in many physiological functions including appetite regulation. We, therefore, undertook a family based study to test the hypothesis whether a polymorphism of the CNR1 gene, which encodes human CB1 receptor, a subclass of the central cannabinoid receptor, contributes to the susceptibility to AN. Fifty two families (parents with one or two affected siblings) were genotyped for the (AAT) trinucleotide repeat of CNR1 gene. Using the haplotype relative risk (HRR) method, the distribution of alleles transmitted to the patients was not found to be significantly different from the non-transmitted parental alleles. However, upon dividing the samples to restricting and binging/purging subtypes of AN, the extended transmission disequilibrium test (ETDT) revealed that there is preferential transmission of different alleles in each of the subtypes. The 14 repeat allele was preferentially transmitted in the binging/purging AN group (P = 0.05) but not in the restricting AN group, whereas the 13 repeat allele was preferentially transmitted in the restricting AN group (almost significant, P = 0.07) but not in the binging/purging AN group. Our study suggests that restricting AN and binging/purging AN may be associated with different alleles of the CNR1 gene.

Is the alpha-2A adrenergic receptor gene (ADRA2A) associated with attention-deficit/hyperactivity disorder?

Attention-Deficit/Hyperactivity Disorder (ADHD) is a complex childhood-onset psychiatric disorder characterized by marked symptoms of inattention, hyperactivity, and impulsivity. The role of genetic factors in its etiology is strongly supported by family, adoption, and twin studies. Although most of the molecular studies have investigated the dopamine D4 receptor gene (DRD4) and the dopamine transporter gene (DAT1) genes in its etiology, pharmacological and brain imaging evidences seem to indicate that genes of the adrenergic system could also be attractive for association studies. We investigated a sample of 96 Brazilian ADHD children and adolescents and their parents for the ADRA2A MspI polymorphism. Although no association with either MspI allele was observed through the haplotype relative risk (HRR) analysis, effects of the ADRA2A gene on inattention and combined (inattention + hyperactivity/impulsivity) symptom scores were detected (U = 222.5, z = 2.19, P = 0.03; and U = 208.5, z = 2.32, P = 0.02, respectively). Our results suggest that the ADRA2A gene might have a small effect on ADHD susceptibility or that this gene might modulate the severity of the disorder. They are also consistent with the noradrenergic theories of ADHD, suggesting a role for the alpha2A adrenergic receptors in the disorder.

A family-based association study of T1945C polymorphism in the proline dehydrogenase gene and schizophrenia in the Chinese population

Previous studies have reported genetic linkage evidence for a candidate gene of schizophrenia on chromosome 22q11 but no genes in this region have been really confirmed to be involved in the etiology of schizophrenia so far. Very recently, the proline dehydrogenase gene ( PRODH), located in the most centromeric part of the 22q11 microdeletion region, has been reported to be strongly associated with schizophrenia from three sets of independent samples and the most significant evidence for association was derived from a single nucleotide polymorphism- PRODH*1945(T/C). We genotyped this polymorphism in 166 Chinese family trios with schizophrenia from East China. No evidence for preferential transmission of the PRODH*1945 alleles from parents to affected offsprings was found using either Transmission Disequilibrium Test ( P=0.4) or Haplotype-based Haplotype Relative Risk analysis ( P=0.35). Our results suggest that the 1945(T/C) polymorphism of the proline dehydrogenase gene is unlikely to play a major role in the susceptibility to schizophrenia in the Chinese population.

Analysis of the peptidylarginine deiminase V gene in rheumatoid arthritis

A number of rheumatoid arthritis (RA) sera contain antibodies specific for peptides in which arginine is substituted by the deiminated form citrulline (AKA). These antibodies are a marker of RA, as they are absent in other disorders. The enzyme responsible for the generation of citrulline residues, peptidylarginine deiminase (PAD), has different isoforms, with a specific tissue distribution. PAD V, expressed in monocytes, might be responsible for the deimination of arginine residues of synovial proteins and thus be involved in the generation of epitopes for RA-specific antibodies. The ECRAF genome scan showed suggestive linkage evidence at PAD V locus on chromosome 1 (P < 0.005). We decided to analyze PAD V as a candidate gene for RA, studying a cohort of 100 RA patients (tested for AKA) and their unaffected parents. Investigation (by single-strand conformation polymorphism [SSCP] analysis and sequencing) of the 16 exons, 5' and 3' regions of the PAD V gene provided polymorphisms in the 5', exons 3, 4, and 7 and 3' regions. Analysis used the transmission disequilibrium test and the haplotype relative risk for alleles and haplotypes with Analyze and Genhunter2 programs. We found an association between RA and one PAD V haplotype (38% in RA versus 17% in controls) (P < 0.007). The association was also observed in the AKA+ RA subgroup (41%) (P < 0.03). In conclusion, the PAD V gene may be considered one of the genetic factors that confer susceptibility to RA. Studies are in progress to clarify the relationship between the PAD V haplotypes, the enzyme activity and the production of anticitrulline antibodies.

Association and linkage disequilibrium between a functional polymorphism of the dopamine-2 receptor gene and schizophrenia in a genetically homogeneous Portuguese population

A functional polymorphism in the promoter region of the DRD2 gene has been found to be associated with schizophrenia in Japanese(1,2) and Swedish populations.(3) We attempted to replicate these findings in a genetically homogeneous Portuguese population using a family-based study design. Analysis of 78 trios revealed evidence for association between the -141 C Ins allele and schizophrenia using the haplotype relative risk (HRR) method (chi(2) = 9.30, P = 0.0023). Further examination of this sample using an alternative family-based association analysis method, the transmission disequilibrium test (TDT), of 33 informative matings from the Portuguese trios provided evidence for an allelic association and linkage disequilibrium between the insertion allele and schizophrenia (chi(2) = 8.76, P = 0.0031). These consistent results using two alternative family-based association analysis methods replicate the findings of previous reports, and thus further implicate a potential role for the dopamine-2 receptor in the genetic etiology of schizophrenia.

Evidence to suggest biased phenotypes in children with Attention Deficit Hyperactivity Disorder from completely ascertained trios.

The transmission disequilibrium test (TDT) is widely used as a robust statistical method to test for genetic association due to linkage based upon analysis of parent-proband trios. The TDT and other family-based tests (eg haplotype relative risk method) are commonly used in association studies including those of ADHD because of concerns that the case-control design has a strong tendency for false positives due to poor matching between cases and controls. Unfortunately, it is not always possible to obtain DNA from both parents in studies of this design, even where the onset of disorder is in childhood, and usually the missing parent is the father. Despite the fact that methods exist for analysis where one parent is missing, many family-based studies are based on the collection or analysis of complete trios only. However this selection process might potentially introduce bias, particularly for studies of behavioural phenotypes like ADHD because the phenotype of proband or parents might influence family stability and therefore complete parental ascertainment. We set out to examine whether children with ADHD and for whom DNA samples from fathers were missing ('duos') differed phenotypically from children for whom genotype information was available from both parents ('trios'). Children from duos showed a significantly higher frequency of DMS-IV ADHD-combined type, significantly more co-morbid conduct disorder and conduct disorder symptoms, and a trend for higher total ADHD symptom scores. Excluding duos from sample collection and analysis may result in systematic bias. If comorbid conduct disorder and ADHD-combined type index increased genetic liability, exclusion of duos could further reduce the power of the TDT (and similar tests) to detect susceptibility genes for ADHD, or replicate effects detected by case-control analysis.

Association of mu-opioid receptor subunit gene and idiopathic generalized epilepsy.

To replicate and extend the previously reported association between the opioid receptor mu subunit gene (OPRM1) and idiopathic absence epilepsy (IAE), using a sample of 230 probands with idiopathic generalized epilepsy (IGE). In humans and in animal models, several lines of evidence implicate opioid receptors with seizures. The G118 allele of OPRM1 was associated with IAE (p = 0.019). Three single nucleotide polymorphisms (SNP) of OPRM1 were investigated by association studies with IGE using a case/control design, one of which also used a within-family design. Association was found for G118 with IGE (p = 0.00027, odds ratio [OR] = 1.86), replicating the previous association. Within-family tests of linkage and association (haplotype-based haplotype relative risk and transmission disequilibrium test) confirmed this result. Further evidence for involvement of OPRM1 in IGE was provided by an association with G-172T, located in the 5' untranslated region (p = 0.0015, OR = 2.36). Haplotypes of the two SNPs were associated with IGE with a greater level of significance (p = 0.000087) suggesting that both SNPs might be in linkage disequilibrium with a single functional variant. Analysis of the results by subgroups of IGE showed association with all subgroups tested. These results confirm the previous association and support the hypothesis of a role for OPRM1 in IGE, including absence syndromes. However, the authors found no evidence for a specific association between OPRM1 and idiopathic absence epilepsy. The data suggest that the functional variant predisposing to IGE is located within 60kb of exon 1.

Antisocial alcoholism and serotonin-related polymorphisms: association tests.

Central serotonin dysfunction appears to be related to a subtype of alcoholism with antisocial impulsive features (type II; antisocial alcoholism). The serotonergic deficit may be associated with greater impulsivity, which in turn facilitates both alcohol dependence and antisocial behavior. The present study tested association of antisocial impulsive alcoholism with candidate genes related to serotonergic neurotransmission, using families. Eight markers were assayed using polymerase chain reaction: tryptophan hydroxylase (intron 7), the serotonin transporter SLC6A4 (VNTR 9/12), HTTLPR, the three serotonin receptor types HTR1B (G861C), HTR2A (T102C) and HTR2C (Cys23Ser), monoamine oxidase A (T1460C), and (CA)(n). Eligible probands had early age of onset of alcoholism, child conduct disorder, and two or more symptoms of adult Antisocial Personality Disorder. This sample included 35 probands, their parents, and some siblings (n = 116). Association tests were conducted using the Haplotype Relative Risk method for antisocial alcoholism diagnosis and the George-Elston regression method (the S.A.G.E. program ASSOC) for quantitative antisocial alcoholism severity. Haplotype Relative Risk analyses were not significant at the 0.05 level for any of the markers. Trends suggestive for future research occurred for tryptophan hydroxylase and HTR2A. Quantitative ASSOC analyses showed significant marker effects (P < 0.05) for both monoamine oxidase A markers, which were in linkage disequilibrium. Antisocial alcoholism symptom severity was higher with monoamine oxidase A C homozygotes or hemizygotes, indicating that low monoamine oxidase activity may be important. Future studies are needed to examine joint and interactive effects of serotonin-related markers.

Association between tumor necrosis factor receptor II and familial, but not sporadic, rheumatoid arthritis: evidence for genetic heterogeneity.

Tumor necrosis factor alpha (TNFalpha) binds the receptors TNFRI and TNFRII. Results of genome scans have suggested that TNFR2 is a candidate rheumatoid arthritis (RA) locus. A case-control study in a UK Caucasian population has shown an association between a TNFR2 genotype (196R/R in exon 6) and familial, but not sporadic, RA. The present study was undertaken to test this association in the French Caucasian population. To test for an association in sporadic RA, 100 families were genotyped for the 196M/R polymorphism and analyzed using the transmission disequilibrium test and haplotype relative risk. To test for an association in familial RA, RA index cases from 100 affected sibpair (ASP) families were genotyped for 196M/R. Linkage analysis was performed with 3 TNFR2 microsatellite markers. The TNFR2 196R/R genotype was not associated with sporadic RA (odds ratio [OR] 0.59, P = 0.72), but was associated with familial RA (OR 4.0, P = 0.026). The association was most marked in the context of TNFR2 "twin-like" RA sibs (affected sibs sharing both TNFR2 haplotypes) (OR 9.2, P = 0.0017). Linkage analysis results were consistent with the association; most of the TNFR2 linkage evidence was found in the subgroup of families with 196R/R ASP index cases. This study is the first to replicate evidence of the involvement of TNFR2 in RA genetic heterogeneity. Our data refine the initial hypothesis, to suggest that a TNFR2 recessive factor, in linkage disequilibrium with the 196R allele, plays a major role in a subset of families with multiple cases of RA.

Serotonergic system and attention deficit hyperactivity disorder (ADHD): a potential susceptibility locus at the 5-HT1B receptor gene in 273 nuclear families from a multi-centre sample

Attention deficit hyperactivity disorder (ADHD) is a highly heritable and heterogeneous disorder, which usually becomes apparent during the first few years of childhood. Imbalance in dopamine neurotransmission has been suggested as a factor predisposing to ADHD. However, evidence has suggested an interaction between dopamine and serotonin systems in the pathophysiology of the disorder. Studies using selective agonists of the different 5-HT receptors microinjected into selected brain structures have shown a positive modulating effect on the functional activities of the mesotelencephalic dopaminergic system. This suggests that some of the genetic predisposition to ADHD might be due to DNA variation at serotonin system genes. In this study, we investigated polymorphisms in HTR(1B) and HTR(2A) (which encode the serotonin receptors 5-HT(1B) and 5-HT(2A) respectively) in a European ADHD sample. Using haplotype based haplotype relative risk (HHRR) and transmission disequilibrium test (TDT) analyses, we observed significant preferential transmission of the allele 861G of the HTR(1B) in the total sample (for HHRR; chi(2) = 7.4, P = 0.0065 and TDT; (chi(2) = 6.4, P = 0.014). Analysis of HTR(2A) failed to reveal evidence of association or linkage between the His452Tyr polymorphism and ADHD in the total sample. However, a significantly increased transmission of the allele 452His was observed in the Irish sample alone (chi(2) = 4.9, P = 0.026). These preliminary data suggest an important role for the serotonin system in the development of ADHD. Further studies, preferentially including different ethnic groups are required to substantiate these findings.

Possible association of a cholecystokinin promoter variant to schizophrenia.

Several lines of research indicate a cholecystokinin (CCK) deficit in schizophrenia patients. A C to T substitution was found in the promoter region of the CCK gene. We investigated this promoter variant in patients with schizophrenia and geographically-matchedcontrols. The T allele was detected in 24% of the 85 schizophrenics and 16% of the 247 controls. No significant difference in the T allele frequency was found between patients and controls (chi(2) = 2.77, P > 0.1). The schizophrenia sample was analyzed further along the dimensions of positive and negative symptoms. The patients with prominent negative symptoms presented a statistically significant association to the T allele (chi(2) = 4.13, P < 0.04). However, the significance disappeared after the Bonferroni correction (P > 0.15). Since the case-control analysis may present incorrect ethnic match between cases and controls, we applied the family-based tests to verify the above findings. Both transmission disequilibrium test (TDT; chi(2) = 5.33, P < 0.025 in 12 trios) and haplotype relative risk (HRR; chi(2) = 3.844, P < 0.05 in 60 trios) indicated a significantly high transmission of T allele to schizophrenia offspring probands from their parents. While our family-based tests seem to support the CCK involvement in schizophrenia, no definite conclusion can be drawn based on such a small sample size. This preliminary finding is subjected to future investigations.

A Bayesian partition model for case-control studies on highly polymorphic candidate genes.

We present a new statistical model for the analysis of case-control or cohort studies examining a highly polymorphic candidate disease susceptibility gene. Many genotypes are possible for such a gene. Consequently, the average number of subjects having each genotype will be modest. If analyzed separately, the risks associated with most genotypes will be estimated imprecisely. Our Bayesian partition model clusters genotypes according to risk, only allowing partitions that satisfy a particular assumption about the joint effect of the two alleles making up a genotype. This assumption is genetically plausible, imposes structure on the set of genotype risks, and still leaves a highly flexible model. By Bayesian model averaging over partitions, the model becomes, in effect, a semiparametric model for genotype risk. It allows borrowing of strength, i.e., estimates of risk for one genotype are informed by the risk estimates of all the genotypes. We present the results of fitting the model to two datasets, one simulated and one genuine case-control study of the NAT1 gene and lung cancer, and compare it in a simulation study with a haplotype relative risk model. The partition model enables genotype risks to be estimated more accurately and the alleles to be ranked according to risk.