Analysis of Single Nucleotide Polymorphisms in Candidate Genes Using the Pedigree Disequilibrium Test

The pedigree disequilibrium test (PDT) has been proposed recently as a test for association in general pedigrees [Martin et al., Am J Hum Genet 67:146–54, 2000]. The Genetic Analysis Workshop (GAW) 12 simulated data, with many extended pedigrees, is an example the type of data to which the PDT is ideally suited. In replicate 42 from the general population the PDT correctly identifies candidate genes 1, 2, and 6 as containing single nucleotide polymorphisms (SNPs) that arc significantly associated with the disease. We also applied the truncated product method (TPM) [Zaykin et al., Genet Epidemiol, in press] to combine p‐values in overlapping windows across the genes. Our results show that the TPM is helpful in identifying significant SNPs as well as removing spurious false positives. Our results indicate that, using the PDT, functional disease‐associated SNPs can be successfully identified with a dense map of moderately polymorphic SNPs. © 2001 Wiley‐Liss, Inc.     

Evaluation of Candidate Genes for Cholinesterase Activity in Farmworkers Exposed to Organophosphorus Pesticides: Association of Single Nucleotide Polymorphisms in BCHE

Background

Organophosphate pesticides act as cholinesterase inhibitors. For those with agricultural exposure to these chemicals, risk of potential exposure-related health effects may be modified by genetic variability in cholinesterase metabolism. Cholinesterase activity is a useful, indirect measurement of pesticide exposure, especially in high-risk individuals such as farmworkers. To understand fully the links between pesticide exposure and potential human disease, analyses must be able to consider genetic variability in pesticide metabolism.

Objectives

We studied participants in the Community Participatory Approach to Measuring Farmworker Pesticide Exposure (PACE3) study to determine whether cholinesterase levels are associated with single-nucleotide polymorphisms (SNPs) involved in pesticide metabolism.

Methods

Cholinesterase levels were measured from blood samples taken from 287 PACE3 participants at up to four time points during the 2007 growing season. We performed association tests of cholinesterase levels and 256 SNPs in 30 candidate genes potentially involved in pesticide metabolism. A false discovery rate (FDR) p-value was used to account for multiple testing.

Results

Thirty-five SNPs were associated (unadjusted p < 0.05) based on at least one of the genetic models tested (general, additive, dominant, and recessive). The strongest evidence of association with cholinesterase levels was observed with two SNPs, rs2668207 and rs2048493, in the butyrylcholinesterase (BCHE) gene (FDR adjusted p = 0.15 for both; unadjusted p = 0.00098 and 0.00068, respectively). In participants with at least one minor allele, cholinesterase levels were lower by 4.3–9.5% at all time points, consistent with an effect that is independent of pesticide exposure.

Conclusions

Common genetic variation in the BCHE gene may contribute to subtle changes in cholinesterase levels.     

Association between Single Nucleotide Polymorphisms and Weight Reduction in Behavioural Interventions—A Pooled Analysis

Knowledge of the association between single nucleotide polymorphisms (SNPs) and weight loss is limited. The aim was to analyse whether selected obesity-associated SNPs within the fat mass and obesity-associated (FTO), transmembrane protein 18 (TMEM18), melanocortin-4 receptor (MC4R), SEC16 homolog B (SEC16B), and brain-derived neurotrophic factor (BDNF) gene are associated with anthropometric changes during behavioural intervention for weight loss. genetic and anthropometric data from 576 individuals with overweight and obesity from four lifestyle interventions were obtained. A genetic predisposition score (GPS) was calculated. Our results show that study participants had a mean age of 48.2 ± 12.6 years and a mean baseline body mass index of 33.9 ± 6.4 kg/m². Mean weight reduction after 12 months was −7.7 ± 10.9 kg. After 12 months of intervention, the MC4R SNPs rs571312 and rs17782313 were significantly associated with a greater decrease in body weight and BMI (p = 0.012, p = 0.011, respectively). The investigated SNPs within the other four genetic loci showed no statistically significant association with changes in anthropometric parameters. The GPS showed no statistically significant association with weight reduction. In conclusion there was no consistent evidence for statistically significant associations of SNPs with anthropometric changes during a behavioural intervention. It seems that other factors play a more significant in weight management than the investigated SNPs.     

XPC基因启动区单核苷酸多态与肺癌易感性的相关性

[目的]研究DNA修复基因XPC启动区-371和-27位点单核苷酸多态与肺癌易感性的关系。[方法]以401例肺癌患者为病例组，同时以383名年龄性别频数相匹配的非肿瘤患者作为对照组，采用Taqman MGB探针荧光标记的聚合酶链反应方法检测XPC基因启动区G-371A和G-27C的基因型；运用Phase2．0软件构建这两个多态位点的单体型；以比值比（OR）及其95％可信区间（CI）比较不同基因型的肺癌相对危险度。[结果]病例组与对照组间，XPC G-371A等位基因型和G-27C等位基因型分布差异具有显著性（Х^2=4．33，P〈0．05；Х^2=9．84，P〈0．01）。与携带XPC-371GG基因型的个体相比较，携带XPC-371GA＋AA基因型的个体患肺癌的风险明显降低（OR校正=0．69；95％CI：0．51—0．94）；而携带XPC-27GG基因型的个体相比较，XPC-27CG＋CC基因型患肺癌的风险明显增加（OR校正=2．18；95％CI：1．23—3．85）。进一步单体型分析显示，与人群中分布最广泛的GG单体型比较，AG单体型可以降低风险（OR=0．76；95％CI：0．60。0．96；P〈0．05）；GC单体型明显增加患肺癌的风险（OR=2．06；95％CI：1．20—3．54；P〈0．05）。[结论]XPC启动区．27位点CG＋CC基因型和．371位点GA＋AA基因型与中国人群肺癌易感性有关。     

REG1a基因单核苷酸多态性与胃癌遗传易感性研究

目的寻找中国汉族人群REG1a基因单核苷酸多态性位点,探讨其基因多态性与胃癌(Gastric Cancer)的关系。方法应用PCR产物测序的方法在中国人群中检测散发性胃癌组(n=183)及对照组(n=204)REG1a基因的单核苷酸多态性(single nucleotide polymorphisms,SNPs)。结果REG1a基因第929位(T/C)、第1790位(C/G)、第2751位(A/T)发现3个新的SNP位点,其中第929位和第1790位2个位点基因型在胃癌与健康人群的差异具有统计学意义(P<0.05)。结论对特定人群进行测序可有效筛查出候选SNP位点,初步发现REG1a基因的2处单核苷酸多态性与胃癌的发生、淋巴转移和远处转移有一定关系,为后续利用单核苷酸多态性标志进行胃癌风险预测奠定了研究基础。     

Investigation of a Candidate Gene,Environment, and G×E Interaction Using Case‐Control and Case‐Parent Study Designs

We investigated the independent contributions of a candidate gene and an environmental factor, and the presence of gene×environment (G×E) interaction, in the etiology of a disease in the Genetic Analysis Workshop (GAW) 12 problem 2 simulated data using a two‐stage approach utilizing both case‐control and case‐parent study designs. Using the case‐control design, several SNPs within candidate gene 1 (CG1) and environmental factor 1 (dichotomized using the 75^th percentile as a cut‐off) (EXP) were independently associated with disease status, in models adjusted for age and sex. We found evidence of gene×environment (G×E) interaction between EXP and two single‐nucleotide polymorphisms (SNPs) within CGI using the case‐control design. Using the case‐parent study design in the same population, we detected association between SNPs within CG1 and disease, but no G×E interaction was detected. © 2001 Wiley‐Liss, Inc.     

Analysis of 60 Reported Glioma Risk SNPs Replicates Published GWAS Findings but Fails to Replicate Associations From Published Candidate‐Gene Studies

Genomewide association studies (GWAS) and candidate‐gene studies have implicated single‐nucleotide polymorphisms (SNPs) in at least 45 different genes as putative glioma risk factors. Attempts to validate these associations have yielded variable results and few genetic risk factors have been consistently replicated. We conducted a case‐control study of Caucasian glioma cases and controls from the University of California San Francisco (810 cases, 512 controls) and the Mayo Clinic (852 cases, 789 controls) in an attempt to replicate previously reported genetic risk factors for glioma. Sixty SNPs selected from the literature (eight from GWAS and 52 from candidate‐gene studies) were successfully genotyped on an Illumina custom genotyping panel. Eight SNPs in/near seven different genes (TERT, EGFR, CCDC26, CDKN2A, PHLDB1, RTEL1, TP53) were significantly associated with glioma risk in the combined dataset (P < 0.05), with all associations in the same direction as in previous reports. Several SNP associations showed considerable differences across histologic subtype. All eight successfully replicated associations were first identified by GWAS, although none of the putative risk SNPs from candidate‐gene studies was associated in the full case‐control sample (all P values > 0.05). Although several confirmed associations are located near genes long known to be involved in gliomagenesis (e.g., EGFR, CDKN2A, TP53), these associations were first discovered by the GWAS approach and are in noncoding regions. These results highlight that the deficiencies of the candidate‐gene approach lay in selecting both appropriate genes and relevant SNPs within these genes.     

Genetic Association Analysis and Meta‐Analysis of Imputed SNPs in Longitudinal Studies

In this paper we propose a new method to analyze time‐to‐event data in longitudinal genetic studies. This method address the fundamental problem of incorporating uncertainty when analyzing survival data and imputed single‐nucleotide polymorphisms (SNPs) from genome‐wide association studies (GWAS). Our method incorporates uncertainty in the likelihood function, the opposite of existing methods that incorporate the uncertainty in the design matrix. Through simulation studies and real data analyses, we show that our proposed method is unbiased and provides powerful results. We also show how combining results from different GWAS (meta‐analysis) may lead to wrong results when effects are not estimated using our approach. The model is implemented in an R package that is designed to analyze uncertainty not only arising from imputed SNPs, but also from copy number variants.     

Linkage Disequilibrium Structure and Its Impact on the Localization of a Candidate Functional Mutation

We have used the unblinded MG1/Q1 Genetic Analysis Workshop 12 simulated data as a model system for investigating the use of linkage disequilibrium structure and simple genotype‐phenotype associations to identify candidate functional mutations within a gene of interest. Analysis of the pattern of pair‐wise linkage disequilibrium indicated three groups of single‐nucleotide polymorphisms for which the linkage disequilibrium was high between sites within a group, but lower between sites of different groups. Using linear regression to predict levels of the trait Q1 showed that the known functional site, 5782, was usually not the best genetic predictor of Q1, but sites belonging to the same group as 5782 (i.e., group 2) were always included in the prediction model. In 49 out of the 50 replicates, the functional site was not the best predictor of the trait. Finally, more detailed analyses demonstrate that the relationship between the adjusted R² for the marker in the prediction model and its disequilibrium with 5782 was linear with the intercept at the origin and terminating at the R² value for the known functional mutation when the disequilibrium is maximal. These data indicate that simple association studies will not identify the functional mutation, but rather will identify candidate functional mutations that are in very tight linkage disequilibrium with the functional mutation. © 2001 Wiley‐Liss, Inc.     

Power and Sample Size Calculations for SNP Association Studies With Censored Time-to-Event Outcomes

For many clinical studies in cancer, germline DNA is prospectively collected for the purpose of discovering or validating single-nucleotide polymorphisms (SNPs) associated with clinical outcomes. The primary clinical endpoint for many of these studies are time-to-event outcomes such as time of death or disease progression which are subject to censoring mechanisms. The Cox score test can be readily employed to test the association between a SNP and the outcome of interest. In addition to the effect and sample size, and censoring distribution, the power of the test will depend on the underlying genetic risk model and the distribution of the risk allele. We propose a rigorous account for power and sample size calculations under a variety of genetic risk models without resorting to the commonly used contiguous alternative assumption. Practical advice along with an open-source software package to design SNP association studies with survival outcomes are provided.     

荧光杂交探针技术检测单核苷酸多态性

目的 建立一种基于荧光杂交探针技术快速检测单核苷酸多态性方法。方法 提取线粒体DNA，在LightCycler仪器上进行实时PCR和熔解曲线分析，测序验证。结果 熔解曲线分析获得的150个基因型分析结果与测序结果100％一致。结论 实时PCR和杂交探针技术能快速、有效的检测单核苷酸多态性。     

Black Carbon Exposures,Blood Pressure,and Interactions with Single Nucleotide Polymorphisms in MicroRNA Processing Genes

Background

Black carbon (BC) is a marker of traffic pollution that has been associated with blood pressure (BP), but findings have been inconsistent. MicroRNAs (miRNAs) are emerging as key regulators of gene expression, but whether polymorphisms in genes involved in processing of miRNAs to maturity influence susceptibility to BC has not been elucidated.

Objectives

We investigated the association between BC and BP, as well as potential effect modification by single nucleotide polymorphisms (SNPs) in miRNA processing genes.

Methods

Repeated measures analyses were performed using data from the VA Normative Aging Study. Complete covariate data were available for 789 participants with one to six study visits between 1995 and 2008. In models of systolic and diastolic BP, we examined SNP-by-BC interactions with 19 miRNA-related variants under recessive models of inheritance. Mixed-effects models were adjusted for potential confounders including clinical characteristics, lifestyle, and meteorologic factors.

Results

A 1-SD increase in BC (0.415 μg/m³) was associated with 3.04 mmHg higher systolic (95% confidence interval (CI), 2.29–3.79) and 2.28 mmHg higher diastolic BP (95% CI, 1.88–2.67). Interactions modifying BC associations were observed with SNPs in the DICER, GEMIN4, and DiGeorge critical region-8 (DGCR8) genes, and in GEMIN3 and GEMIN4, predicting diastolic and systolic BP, respectively.

Conclusions

We observed evidence of effect modification of the association between BP and 7-day BC moving averages by SNPs associated with miRNA processing. Although the mechanisms underlying these associations are not well understood, they suggest a role for miRNA genesis and processing in influencing BC effects.     

PADI4—94及104单核苷酸多态性与类风湿关节炎的相关性研究

目的研究肽酰精氨酸脱亚胺基酶（peptidylargininedeiminase,PADI）基因多态性与类风湿关节炎（rheumatoidarthritis,RA）易感性和发病机制的关系。方法采用直接测序法检测了130例RA患者和性别、年龄匹配的130名健康体检者的PADI4—94和104单核苷酸多态性（SNP）,同时对RA患者的抗环瓜氨酸肽抗体fcycliccitrullinatedpeptide,CCP）等指标进行检测。结果RA组与健康对照组的PADI4—94和104基因均检测到cc、cT和TT三种基因型,RA组PADI4—94各基因型频率（CC：26．1％,CT：50．8％,TT：23．1％）与健康对照组（CC：40．8％,CT：41．5％,TT：17．7％）比较,差异有统计学意义（x2=6．274,P=0．043）;RA组PADI4—94少见等位基因T频率（48．5％）与健康对照组（38．5％）比较,差异有统计学意义（P=0．021）。RA组PADI4—104各基因型频率（CC：33．1％,CT：48．5％,TT：18．5％）与健康对照组（CC：43．8％,CT：43．1％,TT：13．1％）比较,差异无统计学意义（X2=3．567,P=0．168）：RA组PADI4—104少见等位基因T频率（42．7％）与健康对照组（34．6％）比较差异无统计学意义（P=0．059）。就少见基因T携带者（TT和CT）频率在两组中的统计显示,RA患者PADI4—94和104基因中少见基因T携带频率显著高于健康对照组（P值分别为0．013和0．041）。按性别分组分析未发现PADI4—94和104基因型分布有性别差异。结论汉族人群PADI4—94基因与RA易感性相关,PADI4—94和PADI4—104少见基因携带者的RA患病风险较高,PADI4基因在RA发生发展中的作用机制值得进一步深入研究。     

A Robust Score Test for Linkage Disequilibrium in General Pedigrees

Many family‐based tests of linkage disequilibrium are not valid when related nuclear families from larger pedigrees are used, or when independent nuclear families with multiple cases are used. The Pedigree Disequilibrium Test (PDT) proposed by Martin et al. [Am J Hum Genet 67:146–54, 2000] avoids these problems. This paper sketches an extension of the PDT that can account for measured covariates. Where the PDT is based on allele‐counting methods, this extension is based on conditional logistic regression. Versions of these statistics were used to test for association between disease and two known functional single nucleotide polymorphisms (SNPs) on gene 1 and gene 6 and one inert SNP on gene 7 in the first 25 replicates of the simulated population‐isolate data. The new method was also used to test for linkage disequilibrium after correcting for the effect of the environmental factor E1. The PDT and the conditional logistic extension had similar power to detect the functional SNPs (100% for gene 1, approximately 50% for gene 6) and appropriate type I error rates for the inert SNP. Correcting for E1 slightly increased power to detect the association between gene 6 and disease. © 2001 Wiley‐Liss, Inc.     

G‐STRATEGY: Optimal Selection of Individuals for Sequencing in Genetic Association Studies

In a large‐scale genetic association study, the number of phenotyped individuals available for sequencing may, in some cases, be greater than the study's sequencing budget will allow. In that case, it can be important to prioritize individuals for sequencing in a way that optimizes power for association with the trait. Suppose a cohort of phenotyped individuals is available, with some subset of them possibly already sequenced, and one wants to choose an additional fixed‐size subset of individuals to sequence in such a way that the power to detect association is maximized. When the phenotyped sample includes related individuals, power for association can be gained by including partial information, such as phenotype data of ungenotyped relatives, in the analysis, and this should be taken into account when assessing whom to sequence. We propose G‐STRATEGY, which uses simulated annealing to choose a subset of individuals for sequencing that maximizes the expected power for association. In simulations, G‐STRATEGY performs extremely well for a range of complex disease models and outperforms other strategies with, in many cases, relative power increases of 20–40% over the next best strategy, while maintaining correct type 1 error. G‐STRATEGY is computationally feasible even for large datasets and complex pedigrees. We apply G‐STRATEGY to data on high‐density lipoprotein and low‐density lipoprotein from the AGES‐Reykjavik and REFINE‐Reykjavik studies, in which G‐STRATEGY is able to closely approximate the power of sequencing the full sample by selecting for sequencing a only small subset of the individuals.     

Association between Single Nucleotide Polymorphisms of SULT1A1, SULT1C4, ABCC2 and Phase II Flavanone Metabolites Excretion after Orange Juice Intake

Citrus fruits and juices are a major source of dietary flavanones, and the regular consumption of these foods is inversely associated with the development of cardiometabolic diseases. However, the biological benefits depend on the bioavailability of these compounds, and previous studies have reported a large interindividual variability in the absorption and excretion of these compounds. Different factors, such as age, gender or genetic polymorphism of genes coding enzymes involved in the metabolism and transport of the flavanones, may explain this heterogeneity. This study aimed to assess the impact of single nucleotide polymorphism of sulfotransferases SULT1A1 and SULT1C4, and ABCC2 transporter genes on excretion of phase II flavanone metabolites in volunteers after 24 h of orange juice intake. Forty-six volunteers ingested a single dose of 500 mL of orange juice and 24-h urine was collected. The hesperetin and naringenin phase II metabolites were quantified in urine, and SNPs in SULT1A1, SULT1C4 and ABCC2 genes were genotyped. A significant (p < 0.05) relationship between the SNPs in these genes and the high excretion of phase II flavanone metabolites were observed. These results identified novel polymorphisms associated with higher absorption of flavanones, which may provide bases for future personalized nutritional guidelines for consuming flavanone-rich foods rich in these nutrients for better benefit from their health properties.     

DNA修复基因XRCC1单核苷酸多态与辐射损伤易感性相关性研究

[目的]研究DNA修复基因XRCC1多态性与辐射损伤易感性的关系。[方法]采用1:1配对病例-对照设计,在对唐山市放射人员体检基础上,以113名出现染色体畸变的射线工作人员为病例组,按性别、年龄(±5岁)、民族、工种配对,选择与病例在同一工作岗位、工龄相近、累积受照剂量相同或相近且无辐射损伤的放射人员为对照组(113名)。以多聚酶链反应-限制性长度多态性分析技术(PCR-RFLP)检测XRCC1基因,比较不同基因型与辐射损伤易感性的关系。[结果]26304位点病例组和对照组同时携带CT/TT基因型的有23对,病例组携带CT/TT基因型而对照组携带CC基因型的有37对,病例组携带CC基因型而对照组携带CT/TT基因型的有20对,两组同时携带CC基因型的有33对,χ2检验显示两组间分布差异有显著性(P=0.0243),携带26304CT/TT基因型的射线暴露者发生染色体损伤的风险是携带其他基因型个体的1.85倍(95%CI1.08~3.16)。XRCC1 G27466A位点和G28152A位点的各基因型频率在两组中的分布差异无显著性(P>0.05)。XRCC1 26304T等位基因频率病例组(35.84%)高于对照组(22.57%),差异有显著性(P=0.002);XRCC1 G27466A位点和G28152A位点的各等位基因频率在两组间的分布差异均无显著性(P>0.05)。[结论]XRCC1 C26304T基因多态性与辐射致染色体畸变有关联。未发现XRCC1 G27466A和G28152A基因多态性与辐射致染色体畸变有关。     

宫颈癌相关基因单核苷酸多态性研究进展

宫颈癌是妇科常见的恶性肿瘤之一.与机体遗传背景相关的基因多态性,被认为是决定人乳头瘤病毒(human papilloma virus, HPV)感染后宫颈癌发病与否及预后的重要因素.单核苷酸多态性(single nucleotide polymorphisms, SNPs)是指某基因中人群发生率超过1%的单碱基替换或缺失现象.本文就近年来与宫颈癌相关的单核苷酸多态性的研究进展综述如下.     

Tag SNP selection for association studies

This report describes current methods for selection of informative single nucleotide polymorphisms (SNPs) using data from a dense network of SNPs that have been genotyped in a relatively small panel of subjects. We discuss the following issues: (1) Optimal selection of SNPs based upon maximizing either the predictability of unmeasured SNPs or the predictability of SNP haplotypes as selection criteria. (2) The dependence of the performance of tag SNP selection methods upon the density of SNP markers genotyped for the purpose of haplotype discovery and tag SNP selection. (3) The likely power of case-control studies to detect the influence upon disease risk of common disease-causing variants in candidate genes in a haplotype-based analysis. We propose a quasi-empirical approach towards evaluating the power of large studies with this calculation based upon the SNP genotype and haplotype frequencies estimated in a haplotype discovery panel. In this calculation, each common SNP in turn is treated as a potential unmeasured causal variant and subjected to a correlation analysis using the remaining SNPs. We use a small portion of the HapMap ENCODE data (488 common SNPs genotyped over approximately a 500 kb region of chromosome 2) as an illustrative example of this approach towards power evaluation.     

The Single‐Nucleotide Polymorphism Lottery: How Useful are a Few Common SNPs in Identifying Disease‐Associated Alleles?

It has been proposed that using association analysis of single nucleotide polymorphism (SNP) markers in candidate genes may be more successful in identifying disease susceptibility genes for complex diseases. Finding all the SNPs within a candidate gene and genotyping a large case‐control cohort is a resource‐intensive process. As linkage disequilibrium extends across small regions of the genome, the expectation is that a few common anonymous SNPs will be sufficient to detect functional disease‐associated alleles. The aim of this investigation was to compare the ability of a number of family‐ and population‐based association methods to identify known susceptibility loci using the Genetic Analysis Workshop 12 simulated data set. As expected, case‐control methods were more likely to detect association with individual SNPs but family‐based haplotyping methods appeared better able to localize the position of functional polymorphism. © 2001 Wiley‐Liss, Inc.