Accurate power approximations for χ2-tests in case-control association studies of complex disease genes

A popular method for the analysis of case-control association studies is to compare the frequencies of the alleles between cases and controls by means of Pearson's χ²-statistic. Here, an approach for computing the power of this test is presented, which by computer simulation is shown to be more reliable than a previously published power approximation. Since the test based on Pearson's χ²-statistic can be anti-conservative if there is an excess of homozygotes for the susceptibility allele in the general population, it has been proposed to analyze case-control association studies by means of a trend test based on genotypes instead of alleles. We present an accurate power approximation for the trend test. The power approximations are implemented in an available computer program 'GenOdyPower', which in addition has an option to determine the empirical power of these tests by simulations.     

The power of genome-wide association studies of complex disease genes: statistical limitations of indirect approaches using SNP markers

Genome-wide association studies using a dense map of single nucleotide polymorphism (SNP) markers seem to enable us to detect a number of complex disease genes. In such indirect association studies, whether susceptibility genes can be detected is dependent not only on the degree of linkage disequilibrium between the disease variant and the SNP marker but also on the difference in their allele frequencies. These factors, as well as penetrance of the disease variant, influence the statistical power of such approaches. However, the power of indirect association studies is not well understood. We calculated the number of individuals necessary for the detection of the disease variant in both direct and indirect association studies with a case-control design. The result shows that a remarkable reduction in the statistical power of indirect studies, compared with that of direct ones, is unavoidable in the genome-wide screening of complex disease genes. If there is a large difference in allele frequency between the disease variant and the marker, the disease variant cannot be detected. Because the frequency of the disease variant is unknown, SNP markers with various allele frequencies, or a large number of SNP markers, must be used in indirect association studies. However, if the number of SNP markers is increased, the obtained P value may not reach the significance level due to the Bonferroni adjustment. Thus, to test a possible association between functional variants and a complex disease directly, we should identify such SNPs in as many genes as possible for use in genome-wide association studies. Reveived: March 27, 2001 / Accepted: April 21, 2001     

Association studies between the plasmin genes and late-onset Alzheimer's disease

The plasmin system is involved in the degradation of Abeta peptides, the accumulation of which in brain is a hallmark of Alzheimer's disease (AD). In a North European case-control AD dataset we studied 14 common variations in the PLG, PAI-1, PLAT and PLI genes encoding components of the plasmin system. Among the four polymorphisms in the PLAT, PAI-1 and PLI genes showing nominally significant evidence for an association with AD (allele p-value=0.01-0.00003) the strongest association was detected for the deletion allele in the Alu-repeat region of the PLAT gene. However, none of these positive results were confirmed in follow-up studies using an independent Canadian case-control cohort and two familial AD datasets of North European and Caribbean Hispanic origin. Thus, the current survey does not support the notion that common polymorphisms in the plasmin genes influence the development of AD.     

The power of statistical studies in consultation-liaison psychiatry.

Several authors recently have proclaimed the need for empirically based research articles in consultation-liaison psychiatry. The authors report that although the proportion of empirically based studies published in Psychosomatics increased 148% from 1979 to 1989, the power of statistical analyses and the deleterious effect of multiple tests were often neglected. A power analysis of empirical studies published in the 1989 volume year of Psychosomatics is reported, showing statistical power to be low for all but the most robust of effect sizes.     

Overdispersion of allele frequency differences between populations: implications for meta-analyses of genotypic disease associations

Methods correcting case-control studies of genetic polymorphisms for unmeasured genetic population substructure by modelling the variation at a number of variant loci provide no standard and easily implemented approach to meta-analysis, which is a key to understanding the effects of minor genotypic risks on complex diseases. A correction of the odds ratio estimate and its confidence interval is shown to be easy to implement using a mixed effects logistic regression. The method is shown to substantially reduce bias and to give accurate coverage even when there is substantial overdispersion of allele frequency differences between populations. Major sequence classes of single-nucleotide polymorphism (SNP) are likely to act as valid controls for each other, since CpG SNPs did not differ in the extent of population structure from other SNPs. Agreement among investigators and journals to provide these straightforward statistics in publications of polymorphism studies will enhance the ability of future investigators to perform meta-analyses of weak genetic effects across accumulated studies that allow for population structure.     

Association between Parkinson's disease and polymorphisms in the nNOS and iNOS genes in a community-based case-control study

Excess of nitric oxide (NO) has been shown to exert neurotoxic impacts in the brain. Moreover, inhibition of two NO-synthesizing enzymes, neuronal NOS (nNOS) and inducible NOS (iNOS), displays neuroprotective effects in the MPTP model of Parkinson's disease (PD). These data suggest a possible involvement of NOS as factors controlling the resistance of the nigral dopaminergic neurons to environmental insults. Therefore, we investigated whether polymorphisms present in these genes could contribute to the risk of developing PD. We carried out a community-based case-control study among subjects enrolled in the Mutualité Sociale Agricole, the French health insurance organization for workers connected to agriculture. Two-hundred and nine PD patients and 488 controls of European (mostly French) ancestry and matched for age, sex and region of residency were included in this study. Associations were observed with polymorphisms present in exon 22 of iNOS (OR for AA carriers=0.50, 95% CI=0.29-0.86, P=0.01) and in exon 29 of nNOS (OR for carriers of the T allele=1.53, 95% CI=1.08-2.16, P=0.02); no association was observed with a polymorphism in exon 18 of nNOS (OR for carriers of the T allele=1.20, 95% CI=0.85-1.69, P=0.30). Moreover, a significant interaction of the nNOS polymorphisms with current and ever cigarette smoking was found (nNOS 18, P=0.05; nNOS 29, P=0.04). All together, these data favour an involvement of these two genes as new modifier genes in PD.     

Sample-size properties of a case-control association analysis of multistage SNP studies for identifying disease susceptibility genes

A two-stage association study is the most commonly used method to efficiently identify disease susceptibility genes. However, some recent single nucleotide polymorphism (SNP) studies recently utilized three-stage designs. The purpose of this study was to investigate the practical properties of statistical powers and positive predictive values (PPVs) of replication-based analysis (RBA) and the joint analysis (JA) in multistage designs. For this purpose, a program for multistage designs was developed to calculate these performance indicators under various conditions of the number of samples, alleles of candidates, alleles remaining in the final stage, and genotypings. The results showed that the powers and PPVs of RBA and JA in three-stage designs were higher than those in two-stage designs in the range of a smaller proportion of sample size than 0.5 at the first stage. This tendency was more remarkable in JA. In conclusion, researchers who perform SNP studies for identifying disease susceptibility genes need to take account of three-stage case-control association studies, corresponding to study conditions such as the total numbers of samples, alleles, and genotypings. Furthermore, the program developed in this study is useful for estimating powers and PPVs in planning multistage association studies.     

Correlations between TLR polymorphisms and inflammatory bowel disease: a meta-analysis of 49 case-control studies

Immunologic Research - Recently, the roles of toll-like receptor (TLR) polymorphisms in inflammatory bowel disease (IBD) were intensively explored, with conflicting results. Therefore, we performed...     

Inference from the relationships between linkage disequilibrium and allele frequency distributions of 240 candidate SNPs in 109 drug-related genes in four Asian populations

The extensive nucleotide diversity in drug-related genes predisposes individuals to different drug responses and is a major problem in current clinical practice and drug development. Striking allelic frequency differences exist in these genes between populations. In this study, we genotyped 240 sites known to be polymorphic in the Japanese population in each of 270 unrelated healthy individuals comprising 90 each of Malaysian Malays, Indians, and Chinese. These sites are distributed in 109 genes that are drug related, such as genes encoding drug-metabolizing enzymes and drug transporters. Allele frequency and linkage disequilibrium distributions of these sites were determined and compared. They were also compared with similar data of 752 Japanese. Extensive similarities in allele frequency and linkage disequilibrium distributions were observed among Japanese, Malaysian Chinese, and Malays. However, significant differences were observed between Japanese and Malaysian Chinese with Malaysian Indians. These four populations were grouped into two genetic clusters of different ancestries. However, a higher correlation was found between Malaysian Malays and Indians, indicating the existence of extensive admixture between them. The results also imply the possible and rational use of existing single nucleotide polymorphism databases as references to assist future pharmacogenetic studies involving populations of similar ancestry.     

The relative power of family-based and case-control designs for linkage disequilibrium studies of complex human diseases. II. Individual genotyping

In this paper we consider test statistics based on individual genotyping. For sibships without parents, but with unaffected as well as affected sibs, we introduce a new test statistic (referred to as TDS), which contrasts the allele frequency in affected sibs versus that estimated for the parents from the entire sibship. For sibships without parents, this test is analogous to the TDT and is completely robust to nonrandom mating patterns. The efficiency of the TDS test is comparable to that of the THS test (which compares affected vs. unaffected sibs and was based on DNA pooling), for sibships with one affected child. However, as the number of affected sibs in the sibship grows, the relative efficiency of the TDS test versus the THS test also increases. For example, for sibships with three affected, one-third fewer families are required; for families with four affected, nearly half as many are required. Thus, when sibships contain multiple affected individuals, the TDS test provides both an increase in power and robustness to nonrandom mating.     

Comparison of differentially expressed genes in T lymphocytes between human autoimmune disease and murine models of autoimmune disease

A general view is that critical genes involved in biological pathways are highly conserved among species. To understand human autoimmune diseases, a great deal of effort has been devoted to the study of murine models that mirror many pathologic properties observed in the human disease. We have found that lymphocytes from humans with different autoimmune disease all carry a common conserved gene expression profile. Therefore, we wanted to determine if lymphocytes from common murine models of autoimmune disease carried a gene expression profile similar to the human profile and if both mouse models carried a shared gene expression profile. We identified numerous differentially expressed genes (DEGs) in the autoimmune strains compared to non-autoimmune strains. However, we found very little overlap in the gene expression profile between human autoimmune disease and murine models of autoimmune disease and between different murine autoimmune models. Our research further confirms that murine models of autoimmunity do not perfectly match human autoimmune diseases.     

Comparison of simple and modified Bernstein's methods in estimation of recessive allele frequency in the HLA system

Bias and inefficiency of Bernstein's estimator of the recessive allele frequency in generalized ABO-like systems are important for situations where the frequency is small and the number of codominant alleles is large. A modified Bernstein's estimator of the recessive (Smith, 1967) has much smaller bias and higher efficiency than Bernstein's for large samples. Analogous findings are generally observed for small and moderate samples by Monte Carlo experiments. The modified method is preferred for the recessive frequency in the HLA system. The results are illustrated by numerical examples.     

No evidence of association between the alpha-2 macroglobulin gene and Parkinson's disease in a case-control sample

Alpha-2 macroglobulin (A2M) is a component of Lewy bodies, a hallmark of Parkinson's disease (PD). In 159 PD patients and 190 normal controls, we studied two A2M polymorphisms by the polymerase chain reaction-restriction fragment length polymorphism method: a five-nucleotide deletion at the 5' splice site of exon 18; and a valine to isoleucine exchange in amino acid position 1000 near the thiolester active site. No significant differences in allelic and genotypic distribution were found between cases and controls or between early and late-onset PD patients. The present data suggest that these polymorphisms do not represent a risk factor for PD and do not modulate the age at onset of PD.     

Comparison between maximal power in the power-endurance relationship and maximal instantaneous power

The purpose of this study was to analyze the relevance of introducing the maximal power ( P _m) into a critical-power model. The aims were to compare the P _m with the instantaneous maximal power ( P _max) and to determine how the P _m affected other model parameters: the critical power ( P _c) and a constant amount of work performed over P _c ( W ). Twelve subjects [22.9 (1.6) years, 179 (7) cm, 74.1 (8.9) kg, 49.4 (3.6) ml/min/kg] completed one 15 W/min ramp test to assess their ventilatory threshold (VT), five or six constant-power to exhaustion tests with one to measure the maximal accumulated oxygen deficit (MAOD), and six 5-s all-out friction-loaded tests to measure P _max at 75 rpm, which was the pedaling frequency during tests. The power and time to exhaustion values were fitted to a 2-parameter hyperbolic model (NLin-2), a 3-parameter hyperbolic model (NLin-3) and a 3-parameter exponential model (EXP). The P _m values from NLin-3 [760 (702) W] and EXP [431 (106) W] were not significantly correlated with the P _max at 75 rpm [876 (82) W]. The P _c value estimated from NLin-3 [186 (47) W] was not significantly correlated with the power at VT [225 (32) W], contrary to other models ( P <0.001). The W from NLin-2 [25.7 (5.7) kJ] was greater than the MAOD [14.3 (2.7) kJ, P <0.001] with a significant correlation between them ( R =0.76, P <0.01). For NLin-3, computation of W _{P >P c}, the amount of work done over P _C, yielded results similar to the W value from NLin-2: 27.8 (7.4) kJ, which correlated significantly with the MAOD ( R =0.72, P <0.01). In conclusion, the P _m was not related to the maximal instantaneous power and did not improve the correlations between other model parameters and physiological variables.     

Leprosy epidemics during history increased protective allele frequency of PARK2/PACRG genes in the population of the Mljet Island, Croatia

Introduction

Two regulatory polymorphisms (rs1040079 and rs9356058) shared by PARK2 and PACRG genes were identified as major risk variants for leprosy susceptibility. The aim of this study was to investigate if allele frequencies of these polymorphisms in the isolated population of the island of Mljet, which served as a quarantine for leprosy patients during past centuries, were different to allele frequencies in two control populations with no history of leprosy.

Subjects and methods

This study included 88 unrelated Caucasian individuals from the island of Mljet while two control groups included 93 individuals from the island of Rab and 160 individuals from the region of Split. Genotyping for rs1040079 and rs9356058 was performed by “real-time” PCR analysis. We also compared the allele frequency of the rs9356058 polymorphism from the population of Mljet with allele frequencies derived from the existing genome wide association scans in two additional island populations, Vis (924 subjects) and Korcula (909 subjects).

Results

We found a significant increase in the frequency of rs9356058 allele C in the population of Mljet when compared to both control groups. We also observed a significant increase in the frequency of rs1040079 allele A in the population of Mljet when compared with the population of Rab, however this increase was not significant when compared with the population of Split. Allele frequencies of both examined polymorphisms did not differ between the two control populations. Protective haplotype rs9356058-rs1040079 CA was also more frequent in the population of Mljet compared with the Rab and Split populations. In addition, an increase of frequency of rs9356058 allele C was also observed in the population of Mljet when compared with the frequency in the Korcula population.

Conclusion

The results of our study show the association of polymorphisms rs9356058 and rs1040079 in gene PARK2/PACRG with leprosy. The results of our study indicate that exposure to leprosy and mortality in the population caused by leprosy on Mljet resulted in the selection of rs9356058 “protective” C allele in the PARK2 gene, while this was not observed in the two control groups. This is the first study to assess the genetic susceptibility to leprosy in a European population.     

High frequency of mitochondrial complex I mutations in Parkinson's disease and aging

Idiopathic Parkinson’s disease (PD) involves a systemic loss of activity of complex I of the mitochondrial electron transport chain. This biochemical lesion plays a key pathogenic role. Transfer of PD mitochondrial DNA recapitulates this loss of activity and several other pathogenic features of PD suggesting that this lesion may arise, at least in part, from mitochondrial DNA. We investigated this possibility by an extensive clonal sequencing of the seven mitochondrial genes encoding complex I subunits in PD and age-matched control frontal cortex. Each gene was completely sequenced an average of 94.4 times for each subject. Aminoacid-changing mutations were found at the frequency of 59.3 per million bases in both PD and controls, corresponding to approximately 32% of the mitochondrial genomes in the average sample having at least one mutation in a complex I gene. Individual low frequency mutations had an abundance of 1–10%. Significant interindividual variation in mutation frequency was observed. Several aminoacid-changing mutations were identified and multiple PD brains but not in controls. Genetic algorithm analysis detected areas in ND genes with a higher mutation frequency in PD that allowed differentiation of PD from controls. Total mutational burden due to low-abundance heteroplasmy is high and may play a role in human disease.     

Increased frequency of apolipoprotein ε2 allele in non-insulin dependent diabetic (NIDDM) patients with nephropathy

The genetic polymorphism of apolipoprotein E (ε2, ε3 and ε4) is associated with lipid abnormalities. It has been suggested that lipid abnormalities may contribute to the development and progression of kidney diseases, including diabetic nephropathy. Thus, in this study we compared the apo E allele frequencies among 146 non-insulin-dependent diabetic (NIDDM) patients with nephropathy, 135 NIDDM patients without nephropathy and 576 of the general Japanese population. The ε2 allele frequency was significantly higher in diabetic patients with nephropathy (7.2%) and with renal failure (9.7%) than in diabetic patients without nephropathy (2.6%) and in the general Japanese population (3.7%). It is concluded that there is a possibility that the ε2 allele is associated with nephropathy in NIDDM.     

脂肪细胞因子基因单核苷酸多态性与2型糖尿病关联性研究进展

脂肪细胞因子影响机体对胰岛素的敏感性,导致胰岛素抵抗.其中,肿瘤坏死因子和脂联素两基因多态性与2型糖尿病关联性受到广泛关注.此文对近年来国内外相关研究进行了系统性回顾,发现其多态性与2型糖尿病的关联性在不同人群和种族中存在明显差异.