Three major haplotypes of the beta2 adrenergic receptor define psychological profile, blood pressure, and the risk for development of a common musculoskeletal pain disorder.

Adrenergic receptor beta(2) (ADRB2) is a primary target for epinephrine. It plays a critical role in mediating physiological and psychological responses to environmental stressors. Thus, functional genetic variants of ADRB2 will be associated with a complex array of psychological and physiological phenotypes. These genetic variants should also interact with environmental factors such as physical or emotional stress to produce a phenotype vulnerable to pathological states. In this study, we determined whether common genetic variants of ADRB2 contribute to the development of a common chronic pain condition that is associated with increased levels of psychological distress and low blood pressure, factors which are strongly influenced by the adrenergic system. We genotyped 202 female subjects and examined the relationships between three major ADRB2 haplotypes and psychological factors, resting blood pressure, and the risk of developing a chronic musculoskeletal pain condition-Temporomandibular Joint Disorder (TMD). We propose that the first haplotype codes for lower levels of ADRB2 expression, the second haplotype codes for higher ADRB2 expression, and the third haplotype codes for higher receptor expression and rapid agonist-induced internalization. Individuals who carried one haplotype coding for high and one coding for low ADRB2 expression displayed the highest positive psychological traits, had higher levels of resting arterial pressure, and were about 10 times less likely to develop TMD. Thus, our data suggest that either positive or negative imbalances in ADRB2 function increase the vulnerability to chronic pain conditions such as TMD through different etiological pathways that imply the need for tailored treatment options.     

No significance of the COMT valmet polymorphism in restless legs syndrome

The catechol-O-methyltransferase (COMT) val¹⁵⁸met polymorphism, which codes for the substitution of valine (val) by methionine (met) leading to a reduced COMT activity in homo- or heterozygous individuals, is associated with individual pain sensitivity and dopaminergic responses in Parkinson's disease as well as with various chronic painful diseases. Recent investigations support the notion of an alteration of the medial pain pathway as well as of the descending inhibitory control system in restless legs syndrome (RLS), that both involve dopaminergic transmission as well. Thus, the distribution of the COMT val¹⁵⁸met polymorphism was assessed in 298 RLS patients and compared with 135 healthy controls in relation to sex, age of onset and family history. The data revealed no significant differences in the distribution of the COMT val¹⁵⁸met polymorphism in RLS patients compared with the control group, also when the heterozygous and the homozygous group containing the ¹⁵⁸met allele were combined. In addition, sex, age of onset and family history were not associated with the COMT val¹⁵⁸met polymorphism in this German population of RLS patients. The present study adds to previous mostly negative investigations on the genetic determination of dopaminergic transmission in RLS, which have – so far – only detected an association of the MAO-A activity and RLS in females in a French-Canadian population. Further investigations assessing the different COMT haplotypes and experimental and clinical parameters are nevertheless warranted.     

A Preliminary Investigation of Human Frontal Cortex Under Noxious Thermal Stimulation Over the Temporomandibular Joint Using Functional Near Infrared Spectroscopy

Functional near infrared spectroscopy (fNIRS) was used to explore hemodynamic responses in the human frontal cortex to noxious thermal stimulation over the right temporomandibular joint (TMJ). fNIRS experiments were performed on nine healthy volunteers under both low‐pain stimulation (LPS) and high‐pain stimulation (HPS), using a temperature‐controlled thermal stimulator. By analyzing the temporal profiles of changes in oxy‐hemoglobin concentration (HbO) using cluster‐based statistical tests, several regions of interest in the prefrontal cortex, such as the dorsolateral prefrontal cortex and the anterior prefrontal cortex, were identified, where significant differences (p < .05) between HbO responses to LPS and HPS were shown. In order to classify these two levels of pain, a neural network‐based classification algorithm was utilized. With leave‐one‐out cross‐validation, the two levels of pain were identified with 99% mean accuracy to high pain. Furthermore, the “internal mentation hypothesis” and the default‐mode network were introduced to explain our observations of the contrasting trend, as well as the rise and fall of HbO responses to HPS and LPS.     

A low COMT activity haplotype is associated with recurrent preeclampsia in a Norwegian population cohort (HUNT2)

The etiology of preeclampsia is complex, with susceptibility being attributable to multiple environmental factors and a large genetic component. Although many candidate genes for preeclampsia have been suggested and studied, the specific causative genes still remain to be identified. Catechol-O-methyltransferase (COMT) is an enzyme involved in catecholamine and estrogen degradation and has recently been ascribed a role in development of preeclampsia. In the present study, we have examined the COMT gene by genotyping the functional Val108/158Met polymorphism (rs4680) and an additional single-nucleotide polymorphism, rs6269, predicting COMT activity haplotypes in a large Norwegian case/control cohort (n(cases)= 1135, n(controls)= 2262). A low COMT activity haplotype is associated with recurrent preeclampsia in our cohort. This may support the role of redox-regulated signaling and oxidative stress in preeclampsia pathogenesis as suggested by recent studies in a genetic mouse model. The COMT gene might be a genetic risk factor shared between preeclampsia and cardiovascular diseases.     

An association study between cathechol-O-methyltransferase gene and mental retardation in the Chinese Han population

Cathechol-O-methyltransferase (COMT) regulates the amount of dopamine in the prefrontal cortex (PFC). Substantial studies indicate a close relationship between COMT and several human psychotic disorders. The case-control method was used to study the association between mental retardation (MR) and genetic variants of COMT. Three single nucleotide polymorphisms (SNPs: rs4680, rs165656 and rs165774), in the cathechol-O-methyltransferase (COMT) gene, were genotyped by PCR-RFLP method. Individual SNP analysis shows significant differences only at SNP rs165656 for both genotype and allele frequency when comparing MR cases and controls (p=0.023, 0.011, respectively). Further haplotype analysis indicates that there are two haplotype sets, rs165656-rs4680 and rs165656-rs165774, which show statistical differences between MR cases and controls (global p=0.047, p=0.033, respectively). Our results suggest a positive association between the genetic variants of the COMT gene and MR in the Chinese Han population in the Qinba region.     

Human growth hormone 1 (GH1) gene expression: complex haplotype-dependent influence of polymorphic variation in the proximal promoter and locus control region

The proximal promoter region of the human pituitary expressed growth hormone (GH1) gene is highly polymorphic, containing at least 15 single nucleotide polymorphisms (SNPs). This variation is manifest in 40 different haplotypes, the high diversity being explicable in terms of gene conversion, recurrent mutation, and selection. Functional analysis showed that 12 haplotypes were associated with a significantly reduced level of reporter gene expression whereas 10 haplotypes were associated with a significantly increased level. The former tend to be more prevalent in the general population than the latter (p<0.01), possibly as a consequence of selection. Although individual SNPs contributed to promoter strength in a highly interactive and non-additive fashion, haplotype partitioning was successful in identifying six SNPs as major determinants of GH1 gene expression. The prediction and functional testing of hitherto unobserved super-maximal and sub-minimal promoter haplotypes was then used to test the efficacy of the haplotype partitioning approach. Electrophoretic mobility shift assays demonstrated that five SNP sites exhibit allele-specific protein binding. An association was noted between adult height and the mean in vitro expression value corresponding to an individual's GH1 promoter haplotype combination (p=0.028) although only 3.3% of the variance of adult height was found to be explicable by reference to this parameter. Three additional SNPs, identified within sites I and II of the upstream locus control region (LCR), were ascribed to three distinct LCR haplotypes. A series of LCR-GH1 proximal promoter constructs were used to demonstrate that 1) the LCR enhanced proximal promoter activity by up to 2.8-fold depending upon proximal promoter haplotype, and that 2) the activity of a given proximal promoter haplotype was also differentially enhanced by different LCR haplotypes. The genetic basis of inter-individual differences in GH1 gene expression thus appears to be extremely complex.     

Variations in catechol-O-methyltransferase gene interact with parenting to influence attention in early development

Attention influences many aspects of cognitive development. Variations in the catechol-O-methyltransferase (COMT) gene, known to affect dopamine neurotransmission, have frequently been found to influence attention in adults and older children. In this paper we examined 2 year old children and found that variation in the COMT gene influenced attention in a task involving looking to a sequence of visual stimuli. Because the influence of another dopamine-related gene (DRD4) has been shown to interact with parenting quality at this age, we explored parenting in relation to variations in the COMT gene. Variations in COMT interacted with parenting quality to influence our attention measure. The Val^108/158Met polymorphism of COMT is commonly used to determine allelic groups, but recently haplotypes of several polymorphisms within this gene have been shown to be more strongly associated with perceived pain. Since attention and pain both involve the activation of the anterior cingulate gyrus in imaging studies, we compared the Val^108/158Met influence with the COMT haplotypes and found the latter to be more predictive of attention. Our results confirm that important aspects of cognitive development including attention depend on the interaction of genes and early environment.     

Vascular endothelial growth factor genotypes and haplotypes are associated with pre-eclampsia but not with gestational hypertension

Vascular endothelial growth factor (VEGF) is relevant for normalpregnancy, and abnormalities in VEGF functions are associatedwith hypertensive disorders of pregnancy. Because there arefew studies on how VEGF genetic polymorphisms affect susceptibilityto pre-eclampsia (PE), and no studies on how they affect susceptibilityto gestational hypertension (GH), we compared VEGF genotypeand haplotype distributions in normotensive and hypertensivepregnancies. Genotypes and haplotypes for VEGF polymorphisms(C-2578A, G-1154A and G-634C) were determined in 303 pregnantwomen (108 healthy pregnant, HP; 101 with GH and 94 with PE).When white and non-white pregnant women were considered together,no significant differences were found in the distributions ofVEGF genotypes or haplotypes (P > 0.05) in the three groups.However, with only white subjects, significant differences werefound in genotypes distributions for two (C-2578A and G-634C)VEGF polymorphisms (both P < 0.05) between the HP and thePE groups. Importantly, the haplotype including the variantsC-2578, G-1154 and C-634, which is associated with higher VEGFgene expression, was less common in the PE group compared withthe HP group (4% versus 16%; P = 0.0047). However, we foundno significant differences in VEGF haplotypes distributionswhen the HP and GH groups were compared (P > 0.05). Thesefindings suggest a protective effect for the ‘C-2578,G-1154 and C-634’ haplotype against the development ofPE, but no major effects of VEGF gene variants on susceptibilityto GH.     

Chronic pain and use of ambulatory health care

Chronic pain status and health care utilization were assessed in a probability sample of 1016 adult HMO enrollees, and among 242 HMO enrollees seeking treatment for Temporomandibular Disorder (TMD) pain. Likelihood of health care contact for a painful symptom: Among persons reporting back pain, headache, chest pain, abdominal pain or temporomandibular pain in the prior six months, we evaluated whether (1) pain characteristics (severity, persistence, recency of onset), and (2) psychological distress were associated with the likelihood of recent use of health care for each pain symptom. Severity, persistence, and recency of onset of pain were generally associated with recent health care contact for a pain symptom. Females with a pain symptom were no more likely than males to report recent health care contact for the symptom after controlling for pain characteristics. The presence of psychological distress did not increase the likelihood of health care contact for individual pain symptoms. However, psychologically distressed persons were more likely to report pain at multiple anatomical sites and to report recent health care contact for one or more of the five pain symptoms (as a group). Chronic pain status and total use of ambulatory health care: Total number of health care visits (irrespective of reason for visit) was measured by automated data. Chronic pain status (summarized across all five anatomical sites) showed a modest correlation with the volume of health care use. Persons with recurrent pain and severe-persistent pain with no pain-related disability days used ambulatory care at rates close to population means. Persons with severe-persistent pain and seven or more pain related disability days used health care at rates substantially above population means. There was a statistically significant association between the volume of health care use and chronic pain after controlling for age, sex, self-rated health status, and psychological distress.     

Conditioned pain modulation in temporomandibular disorders (TMD) pain patients

The aims were to investigate (1) if temporomandibular disorders (TMD) patients with temporomandibular joint (TMJ) pain had different conditioned pain modulation (CPM) compared with healthy subjects and, (2) if clinical pain characteristics influenced CPM. Sixteen TMD pain patients and 16 age-matched healthy subjects were participated. A mechanical conditioning stimulus (CS) was applied to pericranial muscles provoking a pain intensity of 5/10 on a visual analogue scale. Pressure pain thresholds (PPT) and pressure pain tolerance thresholds (PPTol) were assessed at masseter, forearm and painful TMJ (only PPT) before, during, and 20 min after CS. Data were analyzed with ANOVAs. The correlations between CPM effect and ratings of TMD pain intensity on a numerical rating scale (NRS) or the pain duration were calculated (correlation coefficient; R). The relative PPT and PPTol increases (mean for the three assessment sites) during CS were significantly higher than baseline in healthy subjects (43.0 ± 3.6, 33.0 ± 4.0 %; P < 0.001, P < 0.001) but not in the TMD pain patients (4.9 ± 2.7, ?1.4 ± 4.1 %; P = 0.492, P = 1.000) with significant differences between groups (P < 0.001). In the patients, the relative PPT changes during CS were not significantly higher than baseline at TMJ (5.3 ± 3.8 %, P = 0.981) and masseter (?2.8 ± 4.8 %, P = 1.000) but significantly higher at forearm (12.3 ± 4.7 %, P = 0.039). No correlation was detected between TMD pain intensity and CPM effect (R = ?0.261; P = 0.337) or between pain duration and CPM effect (R = ?0.423; P = 0.103) at painful TMJ. These findings indicate that CPM is impaired in TMD pain patients especially at sites with chronic pain but not at pain-free sites and that the clinical pain characteristics do not influence CPM.     

DNA variability of human genes

We have investigated the level of DNA-based variation (both SNPs and haplotypes) for several thousand human genes. In addition, we have characterized how this variation is distributed in a number of biologically and clinically important ways. First, we have determined how SNPs are distributed within human genes: where they occur relative to various functional regions; levels of variability of human SNPs; pattern of the molecular sequence of SNPs; and how these compare with the corresponding sequence of a chimpanzee. Second, we have determined how these aspects of SNP distribution vary among four human population samples. All genes were sequenced on DNA obtained from 82 unrelated individuals: 20 African-Americans, 20 East Asians, 21 European-Americans, 18 Hispanic-Latinos and three Native Americans. In particular, we looked at patterns of SNP and haplotype sharing among the four larger population samples. Third, we have determined the patterns of linkage disequilibrium among SNPs, which also determines the haplotype variability of each gene. These characteristics also vary substantially among populations. A deeper understanding of these aspects of human genetic variation will be of vital importance when trying to identify the genetic contribution to complex phenotypes such as aging.     

Local adaptation and population differentiation at the interleukin 13 and interleukin 4 loci

A 25.6 kb region at chromosome 5q31, covering the entire human interleukin 13 (IL-13) and interleukin 4 (IL-4) genes, has been reported to be associated with bronchial asthma. We have examined nucleotide variations at this locus in African, European American, and Japanese populations, using 120 diallelic variants. A block of strong linkage disequilibrium (LD) (mid R:D'mid R:>0.7) spans a 10 kb region containing IL-4 in European American and Japanese populations, and is present but less clear in African samples. Two major haplotypes at IL-4 account for >80% of haplotypes in European Americans and Japanese. These haplotypes are common and quite diverged from each other and the ancestral haplotype, resulting in highly significant deviations from neutrality. F(ST) statistics show that European American and Japanese populations are unusually distinct at the IL-4 locus. The most common haplotype in the European American population is much less common in the Japanese population, and vice versa. This implies that natural selection has acted on IL-4 haplotypes differently in different populations. This selected variation at IL-4 may account for some genetic variance underlying susceptibility to asthma and other allergic diseases. The strong LD observed in the IL-4 region may allow more efficient disease-association studies using this locus.     

Exploring interactive effects of genes and environments in etiology of individual differences in reading comprehension

It is established that reading and reading-related processes are heritable; genes thus play an important role in the foundation of individual differences in reading. In this article, we focus on one facet of reading-comprehension. Comprehension is a higher order cognitive skill that requires many other cognitive processes for it to unfold completely and successfully. One such process is executive functioning, which has been associated with genetic variation in the catechol-O-methyltransferase (COMT) gene. Genotypes and haplotypes of four single nucleotide polymorphisms in COMT were investigated in 179 incarcerated adolescent delinquents. Four hierarchical logistic regression models predicting the presence/absence of comprehension difficulties were fitted to the data; genetic variation in COMT and the presence/absence of maternal rejection were investigated as main effects and as effects acting interactively. Three out of four interaction terms were found to be important predictors of individual differences in comprehension. These findings were supported by the results of the haplotype analyses, in which the four investigated polymorphisms were considered simultaneously.     

An MCMC algorithm for haplotype assembly from whole-genome sequence data

In comparison to genotypes, knowledge about haplotypes (the combination of alleles present on a single chromosome) is much more useful for whole-genome association studies and for making inferences about human evolutionary history. Haplotypes are typically inferred from population genotype data using computational methods. Whole-genome sequence data represent a promising resource for constructing haplotypes spanning hundreds of kilobases for an individual. In this article, we propose a Markov chain Monte Carlo (MCMC) algorithm, HASH (haplotype assembly for single human), for assembling haplotypes from sequenced DNA fragments that have been mapped to a reference genome assembly. The transitions of the Markov chain are generated using min-cut computations on graphs derived from the sequenced fragments. We have applied our method to infer haplotypes using whole-genome shotgun sequence data from a recently sequenced human individual. The high sequence coverage and presence of mate pairs result in fairly long haplotypes (N50 length ~ 350 kb). Based on comparison of the sequenced fragments against the individual haplotypes, we demonstrate that the haplotypes for this individual inferred using HASH are significantly more accurate than the haplotypes estimated using a previously proposed greedy heuristic and a simple MCMC method. Using haplotypes from the HapMap project, we estimate the switch error rate of the haplotypes inferred using HASH to be quite low, ~1.1%. Our Markov chain Monte Carlo algorithm represents a general framework for haplotype assembly that can be applied to sequence data generated by other sequencing technologies. The code implementing the methods and the phased individual haplotypes can be downloaded from (http://www.cse.ucsd.edu/users/vibansal/HASH/).     

B27-bearing HLA haplotypes in rheumatoid arthritis: characterization in Finnish patients

The frequency of human leukocyte antigen (HLA)-B27 has been found to be increased in rheumatoid arthritis (RA) in Finland and marginally also in some other populations. In the present study HLA-B27-bearing haplotypes in RA patients were found to carry DR1 and DR4 genes more often than do B27 haplotypes in control population. B27;DR4,DW14;DQw7 was a typical B27-DR4 haplotype whereas DR4 in the majority of other haplotypes occurs with Dw4 and DQw8 genes. The result indicates that the B27 association with RA is not independent of DR1 and DR4, but whether the B27;DR4;DQw7 haplotype subjects a person to a higher disease risk than do other DR4 haplotypes, or is associated with a more severe course of the disease, remains to be investigated.     

No association between catechol-O-methyltransferase (COMT) gene polymorphism and attention deficit hyperactivity disorder (ADHD) in an Irish sample

Pharmacological and biochemical studies have indicated that imbalances in dopaminergic transmission may contribute to the aetiology of attention deficit hyperactivity disorder (ADHD). The enzyme catechol-O-methyltransferase (COMT) plays a key role in the degradation of catecholamines such as dopamine, L-DOPA, adrenaline, and noradrenaline and therefore could be considered as a candidate locus for ADHD susceptibility. We hypothesised that a proportion of the genetic susceptibility to ADHD may be a consequence of dopamine depletion in the synapses due to high-level activity of the COMT gene (allele 1). Using the haplotype-based haplotype relative risk method and 94 affected children and their parents genotyped for COMT alleles, we found no significant differences in the frequency of the transmitted and nontransmitted alleles to ADHD cases from their parents. The absence of association between COMT alleles and ADHD indicated that this locus does not play a significant role or at least a role independent of other genes, in predisposing to ADHD in the Irish population.     

Evidence for origin, by recurrent mutation, of the phenylalanine hydroxylase R408W mutation on two haplotypes in European and Quebec populations

The R408W mutation in the phenylalanine hydroxylase gene (PAH)of phenylketonurla patients occurs on haplotypes 2.3 and 1.8in Europeans. The mutation involves a CpG dinucleotide; nonetheless,a single recombination event might also explain the two haplotypeassociations. By analysis of an STR in the PAH gene 5' to the408 codon and of the VNTR system in the 3' UTR, we identifiedunique features of the haplotype 1.8 chromosome harbouring theR408W mutation which are not accounted for by recombination.We conclude that recurrent mutation is the origin of R408W ondifferent PAH haplotypes in Europeans.     

Linkage disequilibrium and haplotype blocks in the MHC vary in an HLA haplotype specific manner assessed mainly by DRB1*03 and DRB1*04 haplotypes

First generation linkage disequilibrium (LD) and haplotype maps of the human major histocompatibility complex (MHC) have been generated in order to aid the unraveling of the numerous disease predisposing genes in this region by offering a first set of haplotype tagSNPs. Several parameters, like the population studied, the marker map used, the density of polymorphisms and the applied algorithm, are influencing the appearance of haplotype blocks and selection of tags. The MHC comprises a limited number of ancestral, conserved haplotypes. We address the impact of the underlying HLA haplotypes on the LD patterns, haplotype blocks and tag selection throughout the entire extended MHC (xMHC) by studying DR-DQ haplotypes, mainly those carrying DRB1*03 and DRB1*04 alleles. We observed significantly different degree and extent of LD calculated on different HLA backgrounds, as well as variation in the size and boundaries of the defined haplotype and tags selected. Our results demonstrate that the underlying ancestral HLA haplotypic architecture is yet another parameter to take into consideration when constructing LD maps of the xMHC. This may be essential for mapping of disease susceptibility genes since many diseases are associated with and map on particular HLA haplotypes.     

Human leukocyte antigen class I and II haplotypes and risk of cervical cancer

Human leukocyte antigen (HLA) variations may affect immune response to human papillomavirus infection and subsequent cervical neoplasia risk. We investigated the frequency and relationship between HLA-A-B and HLA-A-B-DR haplotypes among women with cervical cancer/high-grade lesions (n=365) and cytologically normal population controls (n=681) within three cervical neoplasia studies in the US and Costa Rica. Notable differences in haplotype frequencies were observed; the HLA-A*01-B*08 haplotype occurred in >5% of US Caucasians but in <1% of Costa Ricans. The most prevalent HLA-A*24-B*40-DR*04 haplotype in Costa Rica (5%) was found in <1% of US Caucasians. No HLA haplotype was significantly associated with cervical neoplasia, suggesting that individual allele associations reported to date (e.g. HLA-DR*13) are not likely explained by underlying haplotypes.     

Network analysis of human Y microsatellite haplotypes

To investigate the utility of Y chromosome microsatellites for studying human male-lineage evolution, we typed samples from three populations for five tetranucleotide repeats and an Alu insertion polymorphism. We found very high levels of haplotype diversity and evidence that most mutations involve the gain or loss of only one repeat unit, implying that any given microsatellite haplotype may have arisen independently on two or more Y-chromosome lineages. Together, these factors suggest that interpretation of small sample sizes (< 30) will be problematic. By typing a large sample of individuals (n = 174) from one population, East Anglia, we were able to construct a haplotype network. The network exhibits a well-connected core structure of commoner haplotypes. Computer simulations based on this network estimate the convergence time for African and Caucasian groups may be between 1.4 and 1.8 times as long as the convergence of the East Anglian population. Based on our comparison between large and small sample sizes, we suggest that large sample sizes are necessary in order to interpret Y-microsatellite haplotypes, and that a network analysis of the type we describe may prove informative in future studies.