Minor differences in haplotype frequency estimates can produce very large differences in heterogeneity test statistics

Common variants in SLC1A2 and schizophrenia: Association and cognitive function in patients with schizophrenia and healthy individuals

SLC1A2 is reported to be responsible for the majority of glutamate uptake, which has a crucial role in neural development and synaptic plasticity, and a disturbance in glutamatergic transmission has been suggested to be involved in the pathophysiology of schizophrenia (SCZ) and cognition. To evaluate the relationship of common variants within SLC1A2 with SCZ and cognition in Han Chinese, 28 tag SNPs were genotyped in the discovery stage, which included 1117 cases and 2289 controls; significantly associated markers were genotyped in the replication stage with 2128 cases and 3865 controls. The rs4354668 SNP was identified to be significantly associated with SCZ in both datasets, and a similar pattern was also observed in the two-stage study on conducting imputation and haplotype association analyses. In addition, significant associations between the rs4354668 SNP and cognition were observed when processing the perseverative error of the Wisconsin Card Sorting Test in patients and controls. Our results provide supportive evidence for an effect of SLC1A2 on the etiology of SCZ, suggesting that genetic variation (rs4354668 and its haplotypes) in SLC1A2 may be involved in impaired executive function, which adds to the current body of knowledge regarding the risk of SCZ and the impairment of cognitive performance.

Evaluation of genetic susceptibility of common variants in CACNA1D with schizophrenia in Han Chinese

The heritability of schizophrenia (SCZ) has been estimated to be as high as 80%, suggesting that genetic factors may play an important role in the etiology of SCZ. Cav1.2 encoded by CACNA1C and Cav1.3 encoded by CACNA1D are dominant calcium channel-forming subunits of L-type Voltage-dependent Ca²⁺ channels, expressed in many types of neurons. The CACNA1C has been consistently found to be a risk gene for SCZ, but it is unknown for CACNA1D. To investigate the association of CACNA1D with SCZ, we designed a two-stage case-control study, including a testing set with 1117 cases and 1815 controls and a validation set with 1430 cases and 4295 controls in Han Chinese. A total of selected 97 tag single nucleotide polymorphisms (SNPs) in CACNA1D were genotyped, and single-SNP association, imputation analysis and gender-specific association analyses were performed in the two independent datasets. None was found to associate with SCZ. Further genotype and haplotype association analyses indicated a similar pattern in the two-stage study. Our findings suggested CACNA1D might not be a risk gene for SCZ in Han Chinese population, which add to the current state of knowledge regarding the susceptibility of CACNA1D to SCZ.

A population-based association study of 2q32.3 and 8q21.3 loci with schizophrenia in Han Chinese

It has been reported that two new schizophrenia susceptibility loci (2q32.3 and 8q21.3) containing two single-nucleotide polymorphisms (SNPs; rs17662626 and rs7004633) have been identified in Europeans by a genome-wide association study. To determine if the two regions are associated with schizophrenia in Han Chinese, which are distinct from Europeans, we analyzed 9 SNPs, including rs17662626 and rs7004633, within 2 regions involving 1430 cases and 1570 controls from the Han population. Single SNP association, haplotype association, and gender-specific association analyses were performed. Single SNP analyses revealed that there was no association with schizophrenia in the region of 2q32.3, but rs7004633 mapping to the region of 8q21.3 was significantly associated with schizophrenia (p = 5.1 × 10(-5); OR = 1.274; 95% CI, 1.134-1.429). Further genotype and haplotype association analyses for the region of 8q21.3 suggested a similar pattern. Additionally, analyses by haplotypes indicated that a haplotype block in the region of 8q21.3 highly associated with schizophrenia and one haplotype in this haploblock had a 1.5-fold increase in the cases. Our results provide further evidence regarding the association of the region of 8q21.3 with schizophrenia in Han Chinese, as well as Europeans, which confirmed the previous report that 8q21.3 may play important roles in the etiology of schizophrenia.

Association study of a new schizophrenia susceptibility locus of 10q24.32-33 in a Han Chinese population

Recently, a new schizophrenia susceptibility locus 10q24.32-q24.33, containing two single-nucleotide polymorphisms (SNPs: rs7914558 and rs11191580), was identified in a genome-wide association study. To examine if this locus is associated with schizophrenia in the Han Chinese population, we analyzed six SNPs, including two SNPs within the region of interest. The sample consisted of 1430 schizophrenia cases and 1570 controls from genetically independent members of the Han population. Single-SNP association, haplotype association and sex-specific association analyses were performed. Three SNPs, rs7914558 (p=1.41×10(-4); OR=1.11; 95% CI 1.05-1.17), rs12220375 (p=1.18×10(-4); OR=1.06; 95% CI 1.03-1.09) and rs11191580 (p=3.03×10(-4); OR=1.05; 95% CI 1.02-1.10), mapped to the locus and were significantly associated in our sample set. Further genotype and haplotype association analyses suggested a similar pattern. Similar to results from European populations, our results provide further evidence that this region associated with schizophrenia in Han Chinese. Results also confirm previous reports suggesting that 10q24.32-q24.33 offers an intriguing new insight into the pathogenesis of schizophrenia and may play an important role in its etiology.

Association of PDE4B polymorphisms and schizophrenia in Northwestern Han Chinese

The phosphodiesterase 4B (PDE4B) is a candidate susceptibility gene for schizophrenia (SCZ), interacting with DISC1, a known genetic risk factor for SCZ. To examine if variants within PDE4B gene are associated with SCZ in Northwestern Han Chinese, and if these effects vary in gender-specific subgroup, we analyzed 20 SNPs, selected from previous studies and preliminary HapMap data analyses with minor allele frequency (MAF) ≥ 20%, in a cohort of 428 cases and 572 controls from genetically independent Northwestern Han Chinese. Single SNP association, haplotype association and sex-specific association analysis were performed. We found that rs472952 is significantly associated with SCZ and rs7537440 is associated with SCZ in females. Further analysis indicated that a haplotype block spanning PDE4B2 splice site is highly associated with SCZ and several haplotypes in this block have about twofold to threefold increase in cases. Our results provide further evidence that PDE4B may play important roles in the etiology of SCZ.

Genetic variation in neuregulin1 is associated with differences in prefrontal engagement in children

The majority of psychopathology is rooted early in life and first emerges during childhood and adolescence. However, little is known about how risk genes affect brain function to increase biological vulnerability to psychopathology in childhood, because most imaging genetic studies published so far have been conducted on adult participants. We examined the impact of neuregulin1 (NRG1), a probable susceptibility gene for schizophrenia and bipolar disorder, on brain function in a sample of 102 ten- to twelve-year-old children. Each participant performed a Go/Nogo task, whereas brain responses were measured using functional magnetic resonance imaging. Statistical parametric mapping was used to estimate the impact of genetic variation in NRG1 on brain activation. Response accuracy and reaction times did not differ as a function of NRG1 genotype. However, individuals with the high-risk variant expressed greater brain activation for both Go and Nogo stimuli in the right posterior orbital gyrus, where NRG1 genotype accounted for 11% of interindividual variance. There were no regions showing a significant interaction between NRG1 genotype and stimulus type even at trend level, suggesting that the impact of NRG1 on brain activation was not specific to either response inhibition or motor execution. These results suggest that that genetic variation in NRG1 is associated with different levels of prefrontal engagement in children as young as 10-12 years of age. Our investigation provides support to the idea that genetic factors may affect brain function to moderate vulnerability to psychopathology from childhood.

Genetic polymorphisms and human sensitivity to opioid analgesics

Opioid analgesics are commonly used for the treatment of acute as well as chronic, moderate to severe pain. Well-known, however, is the wide interindividual variability in sensitivity to opioids that exists, which has often been a critical problem in pain treatment. To date, only a limited number of studies have addressed the relationship between human genetic variations and sensitivity to opioids, and such studies are still in their early stages. Therefore, revealing the relationship between genetic variations in many candidate genes and individual differences in sensitivity to opioids will provide valuable information for appropriate individualization of opioid doses required for adequate pain control. Although the methodologies for such association studies can be diverse, here we summarize protocols for investigating the association between genetic polymorphisms and sensitivity to opioids in human volunteers and patients undergoing painful surgery.

The effects of neuregulin1 on brain function in controls and patients with schizophrenia and bipolar disorder

Recent studies have identified neuregulin1 as a probable susceptibility gene for schizophrenia and bipolar disorder. However, little is known about how this gene may affect brain function to increase vulnerability to these disorders. The present investigation examined the impact of neuregulin1 genotype on brain function in patients with schizophrenia, patients with bipolar I disorder and healthy volunteers. We used functional magnetic resonance imaging to measure brain responses during a verbal fluency task in a total of 115 subjects comprising 41 patients with schizophrenia, 29 patients with bipolar disorder and 45 healthy volunteers. We then used statistical parametric mapping to estimate the main effects of diagnostic group, the main effect of genotype and their interaction. We tested the hypothesis that the high-risk variant of neuregulin1 would be associated with altered prefrontal function. In all three diagnostic groups, the high-risk variant of neuregulin1 was associated with greater deactivation in the left precuneus. In addition, there was an interaction between diagnosis and genotype in two regions of the prefrontal cortex. The right inferior frontal gyrus expressed increased activation in individuals with the high-risk variant, but only in patients with schizophrenia. Conversely, the right posterior orbital gyrus expressed increased activation in individuals with the high-risk variant, but only in patients with bipolar disorder. Our results suggest that genetic variation in neuregulin1 has a measurable impact on brain function and provide preliminary evidence for a disease-specific pattern of gene action in different regions of the prefrontal cortex.

Investigation into the ability of SNP chipsets and microsatellites to detect association with a disease locus

We wished to investigate the ability of different SNP chipsets to detect association with a disease and to investigate the linkage disequilibrium (LD) relationships between microsatellites and nearby SNPs in order to assess their potential usefulness to detect association.

SNP genotypes were obtained from HapMap and microsatellite genotypes from CEPH. 5000 SNPs were simulated as disease genes which increased penetrance from 0.01 to 0.02 in a sample of 400 cases and 400 controls. The power of flanking SNPs to detect association was tested using sets of 1, 2, 3 or 4 markers analysed with haplotype analysis or logistic regression and using either all HapMap markers or those from the Affymetrix 500K, Illumina 300K or Illumina 550K chipsets. Additionally, LD relationships between 10 microsatellites and SNPs within 2Mb of each other were studied.

The power for one of the markers to detect association at p = 0.001 was around 0.4. Power was slightly better for logistic regression than haplotype analysis and for two-marker as opposed to single marker analysis but analysing with larger numbers markers had little benefit. The Illumina 550K marker set was better able to detect association than the other two and was almost as powerful as using all HapMap markers. Microsatellites had detectable LD with only a small number of nearby SNPs and the pattern of LD was very variable.

Available chipsets have quite good ability to detect association although obviously results will be critically dependent on the nature of the genetic effect on risk, sample size and the actual LD relationships of the susceptibility polymorphisms involved. Microsatellites seem ill-suited for systematic studies to detect association.