Transmission Based Conditional Logistic Model for Testing Main and Interaction Effects

Transmission disequilibrium test (TDT) is a popular family based genetic association method. Under multiplicative assumption, a conditional logistic regression for matched pair, affected offspring with allele transmitted from parents and pseudo-offspring (control) with allele non-transmitted from parents, was built to detect the main effects of genes and gene-covariate interactions. When there exist genotype uncertainties, expectation-maximization (EM) algorithm was adopted to estimate the coefficients. The transmission model was applied to detect the association between M235T polymorphism in AGT gene and essential hypertension (ESH). Most of parents are not available in the 126 families from HongKong Chinese population. The results showed M235T is associated with hypertension and there is interaction between M235T and the case’s sex. The allele T is higher risk for male than female.

Transmission of NOTCH4 and GRIK2 in a population of Han Chinese with schizophrenia and affective disorder

BACKGROUND： Increasing evidence suggests overlapped genetic susceptibility across traditional classification systems that divided psychotic disorders into schizophrenia or affective disorder. OBJECTIVE： This study aimed to explore whether schizophrenia and affective disorder share genetic susceptibility in NOTCH4 and GRIK2 loci in a population of Han Chinese. DESIGN： Repetitive measurements. SETTING： The experiment was carried out at Shanghai Mental Health Center and Hongkou Mental Health Center of Shanghai between January 2001 and June 2004. PARTICIPANTS： Sixty-five mixed pedigrees （suffering from various diseases, in combination with schizophrenia and affective disorder）, composed of 45 completed trios and 20 single-parent families, were selected from Shanghai Mental Health Center and Hongkou Mental Health Center of Shanghai between January 2001 and June 2004. Probands received clinical diagnosis according to ICD-10; an independent clinician used identical criteria to review all diagnoses. All subjects were Han Chinese in origin and provided informed consent. There were 65 probands and 110 parents among the subjects. The probands comprised 30 males and 35 females： 33 with schizophrenia, 32 with affective disorder, mean age of （30.9 ± 9.8） years, mean age of onset （24.3 ± 8.8） years, mean duration （6.6 ± 7.0） years, and mean age of parents （58.8 ±10.9） years. METHODS： DNA samples from probands and their biological parents were extracted from peripheral blood according to standard methods. Four polymorphisms, -1725T/G and -25T/C in NOTCH4, rs6922753T/C and rs2227283G/A in GRIK2, were amplified and genotyped with PCR-RFLP techniques. MAIN OUTCOME MEASURES： Association between NOTCH4, GRIK2 polymorphism, and schizophrenia was analyzed by transmission disequilibrium test （TDT）. RESULTS： Sixty-five probands and 110 parents were included in the result analysis, with no dropouts. The results showed that the -25T/C polymorphism of NOTCH4 associated significantly with affective disorder and -1725G/-25T haplotype with schizophrenia. SNP rs6922753 of GRIK2 did not associate with the two diseases; SNP rs2227283 and haplotypes, TG and CA, were significantly associated with both diseases. CONCLUSION： Schizophrenia and affective disorder might share genetic susceptibility among mixed pedigrees of the Han Chinese population. NOTCH4 and GRIK2 might be two of the most common susceptibility genes for these psychoses.

Case-control study and transmission/disequilibrium tests of the genes encoding GABRA5 and GABRB3 in a Chinese population affected by childhood absence epilepsy

Background Childhood absence epilepsy (CAE) is one of the most frequently recognized syndromes among the idiopathic generalized epilepsies (IGEs). CAE is considered to be a genetic disease, with a possible polygenic inheritance pattern. The genes responsible for CAE have not been identified yet. The object of this study was to investigate whether or not CAE is associated with the gene encoding the gamma-aminobutyric acid (GABA) type-A receptor subunits α5 (GABRA5) and β3 (GABRB3) in a Chinese population. Methods Five microsatellite DNA repeats, 69CA, 85CA, 155CA1, 155CA2, and A55CA1, adjoining chromosome 15q11-q13, were used as genetic markers. Both case-control study and transmission/disequilibrium tests (TDTs), as well as fluorescence-based semi-automated genotyping techniques, were used in 90 CAE patient-mother-father trios and 100 normal controls of Han ethnicity to conduct association analysis. Results The frequencies of allele 5 of 69CA, alleles 2 and 8 of 85CA, alleles 6 and 7 of 155CA1, allele 2 of 155CA2, and alleles 1 and 11 of A55CA1 were significantly higher in CAE patients than in normal controls. To prevent spurious associations arising from population admixture, we further conducted TDT tests in the 90 CAE trios. The results of TDT analysis further suggested that microsatellite DNA repeats 85CA, 155CA1, and 155CA2 were associated with CAE.Conclusions GABA type-A receptor subunit genes GABRA5 and GABRB3 may be either directly involved in the etiology of CAE in the Chinese population or in linkage disequilibrium with disease-predisposing sites.

ROR2 gene is associated with risk of non-syndromic cleft palate in an Asian population

Background The receptor tyrosine kinase-like orphan receptor 2 （ROR2） gene has been recently shown to play important roles in palatal development in animal models and resides in the chromosomal region linked to non syndromic cleft lip with or without cleft palate in humans.The aim of this study was to investigate the possible association between ROR2 gene and non-syndromic oral clefts.Methods Here we tested 38 eligible single-nucleotide polymorphisms （SNPs） in ROR2 gene in 297 non-syndromic cleft lip with or without cleft palate and in 82 non-syndromic cleft palate case parent trios recruited from Asia and Maryland.Family Based Association Test was used to test for deviation from Mendelian inheritance.Plink software was used to test potential parent of origin effect.Possible maternally mediated in utero effects were assessed using the TRlad Multi-Marker approach under an assumption of mating symmetry in the population.Results Significant evidence of linkage and association was shown for 3 SNPs （rs7858435,rs10820914 and rs3905385） among 57 Asian non-syndromic cleft palate trios in Family Based Association Tests.P values for these 3 SNPs equaled to 0.000068,0.000115 and 0.000464 respectively which were all less than the significance level （0.05/38=0.0013） adjusted by strict Bonferroni correction.Relevant odds ratios for the risk allele were 3.42 （1.80-6.50）,3.45 （1.75-6.67） and 2.94 （1.56-5.56）,respectively.Statistical evidence of linkage and association was not shown for study groups other than non-syndromic cleft palate.Neither evidence for parent-of-origin nor maternal genotypic effect was shown for any of the ROR2 markers in our analysis for all study groups.Conclusion Our results provided evidence of linkage and association between the ROR2 gene and a gene controlling risk to non-syndromic cleft palate.

Association between Tourette Syndrome and the Dopamine D3 Receptor Gene Rs6280

Background：Tourette syndrome （TS） is a complex,heterozygous genetic disorder.The number of molecular genetic studies have investigated several candidate genes,particularly those implicated in the dopamine system.The dopamine D3 receptor （DRD3） gene has been considered as a candidate gene in TS.There was not any report about the association study of TS and DRD3 gene in Han Chinese population.We combined a case-control genetic association analysis and nuclear pedigrees transmission disequilibrium test （TDT） analysis to investigate the association between DRD3 gene rs6280 single nucleotide polymorphisms （SNPs） and TS in a Han Chinese population.Methods：A total of 160 TS patients was diagnosed by the diagnostic criteria of the Diagnostic and Statistical Manual of Mental Disorders,Fourth Edition.The DRD3 gene rs6280 SNPs were genotyped by TaqMan SNP genotyping assay technique in all subjects.We used a case-control genetic association analysis to compare the difference in genotype and allele frequencies between 160 TS patients and 90 healthy controls.At the same time,we used TDT analysis to identify the DRD3 gene rs6280 transmission disequilibrium among 10l nuclear pedigrees.Results：The genotype and allele frequency of DRD3 gene rs6280 SNPs had no statistical difference between control group （90） and TS group （160） （χ^2 =3.647,P =0.161; χ^2 =0.643,P =0.423） using Chi-squared test.At the basis of the 101 nuclear pedigrees,TDT analysis showed no transmission disequilibrium ofDRD3 gene rs6280 SNPs （χ^2 =0; P =1）.Conclusions：Our findings provide no evidence for an association between DRD3 gene rs6280 and TS in the Han Chinese population.

Association of the GLI gene with ventricular septal defect after the susceptibility gene being narrowed to 3.56 cM in 12q13

Background Our previous research has suggested that genes around D12S1056 in 12q13 may confer susceptibility to ventricular septal defect （VSD） in humans. The present study was to define the chromosome region assignment by transmission disequilibrium test （TDT）, and to identify the important candidate gene by family-based association study and haplotype analysis. Methods Surrounding D12S1056, ten microsatellite markers including D12S329, D12S305, D12S1662, D12S1056, D12S1293, D12S334, D12S102, D12S83, D12S1655 and D12S1691 were chosen, and TDT was performed in 62 nuclear family trios each consisting of an affected child and two healty parents. Subsequently, the GLI gene, a positional candidate gene that maps to the target region, was selected for further analysis. Three single nucleotide polymorphisms （SNPs）, G11888C, G11388A, and G11625T, were selected for family-based association study and haplotype analysis. Results VSD was significantly associated with all selected markers except D12S1691 [72.2 centi morgen （cM）] and D12S1700 （75.76 cM）. VSD was also significantly associated with G11888C （X^2 = 5.918, P = 0.015）, G11388A （X^2 = 8.067, P = 0.005）, and G11625T （X^2 = 11.842, P = 0.001）. Haplotype analysis showed a strong linkage disequilibrium between G11888C and G11388A （D＇=0.999）, but in significant （X^2 = 1.035, df = 2, P 〉 0.05）. Conclusions The susceptibility gene of VSD was mapped to 3.56 cM in 12q13 by TDT, and the GLI gene, an important candidate in the target region, was associated with VSD.