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PubMed2005

Identification of functional candidate genes for body composition by expression analyses and evidencing impact by association analysis and mapping.

This study aims to identify hepatic genes affecting traits related to muscularity and obesity by combining expression analyses, association studies, and gene mapping. Functional candidate genes with trait-associated expression were obtained by hybridising custom made application-specific cDNA microarrays with targets of discordant sib pairs of a porcine experimental population. Out of 238 genes addressed, nine genes were regulated by the factor>or=2 between the sib pairs. Differential gene expression was independently confirmed for selected genes by real time RT-PCR. Transcript levels of four genes (APOH, PEDF, SLCO1B3, TBG) were significantly different between the phenotype groups. Screening for trait associated markers within TBG and APOH by comparative sequencing of discordant sib pairs revealed a SNP at position nt 778 (A>C) (N229H) of TBG. No polymorphism in APOH was detected. Association analysis confirmed effects of TBG on carcass traits statistically. Allocating TBG to a QTL region on chromosome X revealed genetic evidence for the effect. Moreover, our results indicate that there are probably two polymorphisms segregating-one (N229H) altering binding capability of TBG and another still to be detected altering the transcription rate of TBG.

Analysis of Variance↗

PubMed2005

PBAT: a comprehensive software package for genome-wide association analysis of complex family-based studies.

The PBAT software package (v2.5) provides a unique set of tools for complex family-based association analysis at a genome-wide level. PBAT can handle nuclear families with missing parental genotypes, extended pedigrees with missing genotypic information, analysis of single nucleotide polymorphisms (SNPs), haplotype analysis, quantitative traits, multivariate/longitudinal data and time to onset phenotypes. The data analysis can be adjusted for covariates and gene/environment interactions. Haplotype-based features include sliding windows and the reconstruction of the haplotypes of the probands. PBAT's screening tools allow the user successfully to handle the multiple comparisons problem at a genome-wide level, even for 100,000 SNPs and more. Moreover, PBAT is computationally fast. A genome scan of 300,000 SNPs in 2,000 trios takes 4 central processing unit (CPU)-days. PBAT is available for Linux, Sun Solaris and Windows XP.

Family↗

PubMed2006

Family-based association analysis validates chromosome 3p21 as a putative nasopharyngeal carcinoma susceptibility locus.

PURPOSE: Nasopharyngeal carcinoma (NPC) poses one of the serious health problems in southern Chinese, with an incidence rate ranging from 15 to 50/100,000. In our previously linkage analysis, a locus on 3p21 was identified to link to NPC. In this study, family-based association analysis was performed to test the transmission disequilibrium of chromosome 3p in 18 high-risk nasopharyngeal carcinoma families of Hunan province in southern China. METHODS: Single locus and multi-point of transmission disequilibrium test was performed by Genehunter program package with 15 microsatellite markers on chromosome 3p in 18 nasopharyngeal carcinoma pedigrees. RESULTS: A major transmission disequilibrium peak was observed near D3S1568, which possessed 20 alleles or haplotypes of 6 loci, spanning a 12.4 cM region from D3S1298 to D3S1289 on chromosome 3p21.31-3p21.2, and 3 alleles or haplotypes reached high significantly difference (P < 0.01). CONCLUSION: These results reflected a link disequilibrium between this chromosome region and a nasopharyngeal carcinoma susceptibility locus, and provided further evidence that a novel nasopharyngeal carcinoma susceptibility gene may be located in this chromosome region. These alleles or haplotypes transmitting disequilibrium in nasopharyngeal carcinoma pedigrees may act as the highly risk molecular markers after verified in large population.

Alleles↗

PubMed2006

A technique for identifying three diagnostic findings using association analysis.

In diagnosing diseases in clinical practice, a combination of three clinical findings is often used to represent each disease. This is largely because it is often difficult or impractical to assess for all possible combinations of symptoms and abnormal exam findings that occur in any particular disease. For most diseases, diagnostic triads are based on empirical observations. In this study, we determined diagnostic triads for chronic diseases using data mining procedures. We also verified the combinations' validity as well as our procedure for determining them. We used symptoms and examination findings from 477 patients with chronic diseases, collected as part of a 35-year longitudinal study begun in 1968. For each patient there were 295 items from examinations in internal medicine, dermatology, ophthalmology, dentistry and blood tests. We judged each item to be either normal or abnormal, and restricted the analysis to the abnormal findings. To analyze such an exhaustive assortment, we used the data mining technique of association analysis. The analysis generated three clinical findings for each disease. Diseases were defined based on blood tests. Searching through all 295 items to find the three most useful clinical findings would be impractical on a commodity PC. However, by excluding normal items, we were able to sufficiently reduce the total number of combinations so as to make combinatorial analysis on a PC feasible. In addition to more accurate diagnoses, we believe our technique can identify those diagnostic data that are more cost effective in terms of time and other resources required for their collection.

Data Collection↗

PubMed1999

Gene mapping by linkage and association analysis.

Genetic analysis is used to map genes, including disease loci, to positions within the human genome. Linkage analysis depends on the co-segregation of a gene (locus) and a phenotype through a pedigree, while association analysis, or linkage disequilibrium mapping, depends on measuring deviation from the random occurrence of alleles in a haplotype in unrelated individuals or nuclear families. Complex computer programs may be used in both forms of analysis. In recent years most interest has focused on identifying genes involved in common, multifactorial diseases. Here I review some current and developing techniques of genetic analysis and give references to where further information can be obtained.

Animals↗

PubMed2000

Power of linkage versus association analysis of quantitative traits, by use of variance-components models, for sibship data.

Optimal design of quantitative-trait loci (QTL) mapping studies requires a precise understanding of the power of QTL linkage versus QTL association analysis, under a range of different conditions. In this article, we investigate the power of QTL linkage and association analyses for simple random sibship samples, under the variance-components model proposed by Fulker et al. After a brief description of an extension of this variance-components model, we show that the powers of both linkage and association analyses are crucially dependent on the proportion of phenotypic variance attributable to the QTL. The main difference between the two tests is that, whereas the power of association is directly related to the QTL heritability, the power of linkage is related more closely to the square of the QTL heritability. We also describe both how the power of linkage is attenuated by incomplete linkage and incomplete marker information and how the power of association is attenuated by incomplete linkage disequilibrium.

Chi-Square Distribution↗

PubMed1999

Genetic association analysis of serotonin system genes in bipolar affective disorder.

OBJECTIVE: This study examined the putative role of serotonin genes in the etiology of bipolar affective disorder. METHOD: Genetic association analysis was performed for individuals with bipolar affective disorder and unaffected subjects closely matched in age, sex, and ethnic background (N=103 in each group). The allele and genotype frequencies of polymorphisms at the genes for serotonin receptors HTR1A, HTR1Dalpha, HTR1Dbeta, HTR2A, HTR2C, HTR7, tryptophan hydroxylase (TPH), and the serotonin transporter (hSERT) were compared in the two groups of subjects. RESULTS: Statistically significant positive associations were found for HTR2A and hSERT polymorphisms. However, results from an independent replication group of over 100 patients with bipolar affective disorder and their matched comparison subjects failed to confirm these associations. CONCLUSIONS: These results suggest that the serotonin genes studied are not associated with bipolar affective disorder, although transmission disequilibrium studies are required in order to confirm this conclusion.

Adult↗

PubMed2002

[Association analysis of childhood absence epilepsy by microsatellite DNA].

OBJECTIVE: To investigate whether or not the gamma-aminobutyric acid GABA receptor subtype Alpha genes GABRA5 and GABRB3 are associated with childhood absence epilepsy CAE . METHODS: Five microsatellite DNA 69CA 85CA 155CA1 155CA2 and A55CA1 adjacent to chromosome 15q11-15q13 were used as genetic markers. Fluorescence-based semi-automated genotyping technique was used in 90 CAE patients and 100 normal controls to conduct genotyping. Case-control study was used to do association analysis. RESULTS: In Chinese normal population the allele frequencies of the five microsatellite DNAs were in good agreement with Hardy- Weinberg equilibrium. The polymorphism information content PIC of the five microsatellite DNA were 0.47 0.82 0.66 0.86, and 0.86 respectively. The frequencies of some alleles of the 5 microsatellite DNAs in CAE patients were significantly higher than those in normal controls. CONCLUSION: Four of the five microsatellite DNAs are good genetic markers. GABA subtype Alpha genes GABRA5 and GABRB3 may be associated with the pathogenic mechanism of CAE.

Adolescent↗

PubMed2006

Association analysis of delta-opioid receptor gene polymorphisms in methamphetamine dependence/psychosis.

The role of the delta-opioid receptor (OPRD1) in methamphetamine (MAP) addiction was investigated using association analysis between OPRD1 gene polymorphisms and MAP dependence/psychosis. DNA samples from Japanese patients with MAP dependence/psychosis were analyzed to find polymorphisms in OPRD1 gene exons and exon-intron boundaries. One novel single nucleotide polymorphism (SNP) in intron 1 and two SNPs in exon 3 were identified. The two SNPs in exon 3 were in linkage disequilibrium. No significant difference was observed in either genotypic or allelic frequencies of these SNPs between controls (n = 260) and MAP dependent/psychotic patients (n = 170). Global analyses using the three SNPs and subcategory analyses on clinical parameters also showed no significant differences. These results suggest that the OPRD1 gene variants may not be a factor in vulnerability to MAP dependence/psychosis.

Adult↗

PubMed2004

Association analysis of SLC22A4, SLC22A5 and DLG5 in Japanese patients with Crohn disease.

Crohn disease (CD) is an inflammatory bowel disease characterized by chronic transmural, segmental, and typically granulomatous inflammation of the gut. Recently, two novel candidate gene loci associated with CD, SLC22A4 and SLC22A5 on chromosome 5 known as IBD5 and DLG5 on chromosome 10, were identified through association analysis of Caucasian CD patients. We validated these candidate genes in Japanese patients with CD and found a weak but possible association with both SLC22A4 (P=0.028) and DLG5 (P=0.023). However, the reported genetic variants that were indicated to be causative in the Caucasian population were completely absent in or were not associated with Japanese CD patients. These findings imply significant differences in genetic background with CD susceptibility among different ethnic groups and further indicate some difficulty of population-based studies.

Case-Control Studies↗

PubMedDate not supplied

Genetic association analysis of the adiponectin polymorphisms in type 1 diabetes with and without diabetic nephropathy.

OBJECTIVE: Adiponectin [adipocyte C1q and collagen domain containing (ACDC)] is the most abundant adipose-specific protein. It is beneficial in that it improves insulin sensitivity and mitigates vascular damage, in addition to the possibility of it having anti-inflammatory properties. Clinical evidences demonstrate that serum adiponectin concentrations are increased in patients with type 1 diabetes (T1D) as well as in patients with microvascular complications. However, the genetic influence of the ACDC gene in T1D and diabetic microvascular complications is still unclear. The present study aims to evaluate the association of the ACDC genetic variation in T1D and diabetic nephropathy (DN). MATERIALS AND METHODS: Ten single nucleotide polymorphisms (SNPs) of the ACDC gene were genotyped in 432 T1D patients (of which, 196 had DN) and 187 nondiabetic control subjects, who were all Swedish Caucasians, by using dynamic allele specific hybridization. RESULTS: Single-marker association analysis demonstrated that SNPs +45G15G(T/G) and +276(G/T) were strongly associated with T1D [P=.002, OR=1.855 (1.266-2.717) and P=.001, OR=1.694 (1.337-2.147)]. Further analysis for haplotypes of these two SNPs indicated that one of the common haplotype (T_G) was strongly associated with T1D [P<.001, OR=1.769 (1.430-2.188)]. However, there was no significant difference in the allele frequencies of these two SNPs between the groups of T1D patients with nephropathy and the patients without nephropathy. CONCLUSIONS: The present study thus suggests that SNPs +45G15G(T/G) and +276(G/T) in the ACDC gene are associated with T1D but not with DN among Swedish Caucasians.

Adiponectin↗

PubMed2002

Association analysis between Alzheimer's disease and the Nicastrin gene polymorphisms.

The biological study of the Nicastrin protein shows its crucial role in the pathogenesis of Alzheimer's disease (AD). We tested the hypothesis that the Nicastrin (NCSTN) gene might be genetically associated with AD. The association analysis of two single nucleotide polymorphisms (SNPs) in the coding region (cSNPs) of NCSTN were performed in an Italian population. No evidence of association was obtained between the two SNPs investigated in sporadic and familial AD cases under the stratification of currently known genetic risk factors including the apolipoprotein E (APOE), the presenilins and the beta-amyloid precursor protein. The result suggests no apparent synergic interaction between the NCSTN and APOE epsilon 4 in the risk to develop the late onset sporadic form of AD. But considering its biological effects, the result can not exclude the NCSTN as candidate for genetic factor in AD. Further genetic study of the NCSTN would be necessary to evaluate the potential genetic involvement in AD.

Aged↗

PubMed1994

Association analysis of the dopamine D2 receptor gene in Tourette's syndrome using the haplotype relative risk method.

Comings et al. [1991: JAMA 266: 1793-1800] have recently reported a highly significant association between Tourette's syndrome (TS) and a restriction fragment length polymorphism (RFLP) of the dopamine D2 receptor gene (DRD2) locus. The A1 allele of the DRD2 Taq I RFLP was present in 45% of the Tourette patients compared with 25% of controls. We tried to replicate this finding by using the haplotype relative risk (HRR) method for association analysis. This method overcomes a major problem of conventional case-control studies, where undetected ethnic differences between patients and controls may result in a false-positive finding, by using parental alleles not inherited to the proband as control alleles. Sixty-one nuclear families encompassing an affected child and parents were typed for the DRD2 Taq I polymorphism. No significant differences in DRD2 A1 allele frequency were observed between TS probands, subpopulations of probands classified according to tic severity, or parental control alleles. Our data do not support the hypothesis that the DRD2 locus may act as a modifying gene in the expression of the disorder in TS probands.

Adolescent↗

PubMed1999

Association analysis using refined microsatellite markers localizes a susceptibility locus for psoriasis vulgaris within a 111 kb segment telomeric to the HLA-C gene.

The HLA-Cw6 antigen has been associated with psoriasis vulgaris despite racial and ethnic differences. However, it remains unclear whether it is the HLA-Cw6 antigen itself or a closely linked, hitherto unidentified, locus that predisposes to the disease. Here, in order to map the susceptibility locus for psoriasis vulgaris precisely within the HLA class I region, 11 polymorphic microsatellite markers distributed throughout a 1060 kb segment surrounding the HLA-C locus were subjected to association analysis in Japanese psoriasis vulgaris patients. Statistical analyses of the distribution and deviation from Hardy-Weinberg equilibrium of the allelic frequency at each micro-satellite locus revealed that the pathogenic gene for psoriasis vulgaris is located within a reduced interval of 111 kb spanning 89-200 kb telomeric of the HLA-C gene. In addition to three known genes, POU5F1, TCF19 and S, this 111 kb fragment contains four new, expressed genes identified in the course of our genomic sequencing of the entire HLA class I region. Therefore, these seven genes are the potential candidates for susceptibility to psoriasis vulgaris.

Adult↗

PubMed2005

No association of serotonin transporter gene (SLC6A4) with schizophrenia and bipolar disorder in Japanese patients: association analysis based on linkage disequilibrium.

Serotonin transporter gene (SLC6A4) is one of the most promising candidate genes for psychiatric disorders such as schizophrenia (SCZ) and bipolar disorder (BP). Two functional polymorphisms, 5HTTLPR and 5HTTVNTR, have been a focus for genetic association analyses; however, no conclusive results have been obtained. We conducted, 1) a mutation search of SLC6A4, 2) LD mapping to select 'tagging' markers (10 SNPs and 5HTTVNTR, while 5HTTLPR was treated as an independent marker because of its allelic form), and 3) association analysis of these 'tagging' markers and independent markers (5HTTLPR and Asn605Lys) with SCZ and BP in Japanese patients. In this mutation search, a nonsynonymous SNP, Asn605Lys, was detected. No associations of 'tagging' markers and independent markers with such conditions were found. These results indicate that SLC6A4 might not play a major role in SCZ and BP in Japanese patients, a finding that agrees with both the common disease-common variant hypothesis and common disease-rare variant hypothesis.

Adult↗

PubMed2004

Association analysis of cystatin A and zinc finger protein 148, two genes located at the psoriasis susceptibility locus PSORS5.

Psoriasis is a multifactorial hereditary skin disease. The searches for causative DNA variations have generated several susceptibility loci, but at present, the gene(s) involved has not been identified. In this article, we investigated whether cystatin A, an upregulated gene in psoriatic plaques and located at chromosome 3q21, is the disease-causing gene at the psoriasis susceptibility locus PSORS5. We also investigated association to a second gene located in this region, zinc finger protein 148. The two genes have been sequenced in a small case/control set in search for SNP markers, followed by family-based association analysis using the transmission disequilibrium test. We did not detect association with either of the genes.

Chromosomes, Human, Pair 3↗

PubMed2005

A genome-wide tree- and forest-based association analysis of comorbidity of alcoholism and smoking.

Genetic mechanisms underlying alcoholism are complex. Understanding the etiology of alcohol dependence and its comorbid conditions such as smoking is important because of the significant health concerns. In this report, we describe a method based on classification trees and deterministic forests for association studies to perform a genome-wide joint association analysis of alcoholism and smoking. This approach is used to analyze the single-nucleotide polymorphism data from the Collaborative Study on the Genetics of Alcoholism in the Genetic Analysis Workshop 14. Our analysis reaffirmed the importance of sex difference in alcoholism. Our analysis also identified genes that were reported in other studies of alcoholism and identified new genes or single-nucleotide polymorphisms that can be useful candidates for future studies.

Alcoholism↗

PubMed2003

Linkage and association analysis of nevus density and the region containing the melanoma gene CDKN2A in UK twins.

Rare mutations in the CDKN2A gene are highly penetrant for melanoma. Density of nevi is under strong genetic control and high density is a potent risk factor for melanoma. We used linkage and association analysis in adolescent twins from the UK to examine the hypothesis that the region containing the CDKN2A gene also contains a quantitative trait locus influencing normal nevus development. Five markers in the CDKN2A region were genotyped in 115 dizygotic twin pairs, and one marker (D9S942) was genotyped in 103 monozygotic twin pairs, all of whom had been phenotyped for nevus density. Linkage analysis showed no evidence of a quantitative trait locus influencing nevus density in this chromosomal region. A model partitioning the variation in phenotype into within- and between-twin pair components showed weak evidence of association between higher nevus density and longer mean length of the two D9S942 alleles (P=0.01). This relation, which was also observed in an earlier Australian twin study, could be because of the linkage disequilibrium between D9S942 and a neighbouring functional locus. Further investigation of this region is warranted in large-scale linkage or association studies.

Adolescent↗