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1.  An aggregating U-Test for a genetic association study of quantitative traits 
BMC Proceedings  2011;5(Suppl 9):S23.
We propose a novel aggregating U-test for gene-based association analysis. The method considers both rare and common variants. It adaptively searches for potential disease-susceptibility rare variants and collapses them into a single “supervariant.” A forward U-test is then used to assess the joint association of the supervariant and other common variants with quantitative traits. Using 200 simulated replicates from the Genetic Analysis Workshop 17 mini-exome data, we compare the performance of the proposed method with that of a commonly used approach, QuTie. We find that our method has an equivalent or greater power than QuTie to detect nine genes that influence the quantitative trait Q1. This new approach provides a powerful tool for detecting both common and rare variants associated with quantitative traits.
doi:10.1186/1753-6561-5-S9-S23
PMCID: PMC3287858  PMID: 22373246
2.  Collapsing ROC approach for risk prediction research on both common and rare variants 
BMC Proceedings  2011;5(Suppl 9):S42.
Risk prediction that capitalizes on emerging genetic findings holds great promise for improving public health and clinical care. However, recent risk prediction research has shown that predictive tests formed on existing common genetic loci, including those from genome-wide association studies, have lacked sufficient accuracy for clinical use. Because most rare variants on the genome have not yet been studied for their role in risk prediction, future disease prediction discoveries should shift toward a more comprehensive risk prediction strategy that takes into account both common and rare variants. We are proposing a collapsing receiver operating characteristic (CROC) approach for risk prediction research on both common and rare variants. The new approach is an extension of a previously developed forward ROC (FROC) approach, with additional procedures for handling rare variants. The approach was evaluated through the use of 533 single-nucleotide polymorphisms (SNPs) in 37 candidate genes from the Genetic Analysis Workshop 17 mini-exome data set. We found that a prediction model built on all SNPs gained more accuracy (AUC = 0.605) than one built on common variants alone (AUC = 0.585). We further evaluated the performance of two approaches by gradually reducing the number of common variants in the analysis. We found that the CROC method attained more accuracy than the FROC method when the number of common variants in the data decreased. In an extreme scenario, when there are only rare variants in the data, the CROC reached an AUC value of 0.603, whereas the FROC had an AUC value of 0.524.
doi:10.1186/1753-6561-5-S9-S42
PMCID: PMC3287879  PMID: 22373267
3.  The effect of multiple genetic variants in predicting the risk of type 2 diabetes 
BMC Proceedings  2009;3(Suppl 7):S49.
While recently performed genome-wide association studies have advanced the identification of genetic variants predisposing to type 2 diabetes (T2D), the potential application of these novel findings for disease prediction and prevention has not been well studied. Diabetes prediction and prevention have become urgent issues owing to the rapidly increasing prevalence of diabetes and its associated mortality, morbidity, and health care cost. New prediction approaches using genetic markers could facilitate early identification of high risk sub-groups of the population so that appropriate prevention methods could be effectively applied to delay, or even prevent, disease onset.
This paper assessed 18 recently identified T2D loci for their potential role in diabetes prediction. We built a new predictive genetic test for T2D using the Framingham Heart Study dataset. Using logistic regression and 15 additional loci, the new test was slightly improved over the existing test using just three loci. A formal comparison between the two tests suggests no significant improvement. We further formed a predictive genetic test for identifying early onset T2D and found higher classification accuracy for this test, not only indicating that these 18 loci have great potential for predicting early onset T2D, but also suggesting that they may play important roles in causing early-onset T2D.
To further improve the test's accuracy, we applied a newly developed nonparametric method capable of capturing high order interactions to the data, but it did not outperform a logistic regression that only considers single-locus effects. This could be explained by the absence of gene-gene interactions among the 18 loci.
PMCID: PMC2795948  PMID: 20018041
4.  Linkage studies of catechol-O-methyltransferase (COMT) and dopamine-beta-hydroxylase (DBH) cDNA expression levels 
BMC Proceedings  2007;1(Suppl 1):S95.
The COMT and DBH genes are physically located at chromosomes 22q11 and 9q34, respectively, and both COMT and DBH are involved in catecholamine metabolism and are strong candidates for certain psychiatric and neurological disorders. Although the genetic determinants for both enzymes' activities have been widely studied, their genetic involvement on gene mRNA expression levels remains unclear. In this study we performed quantitative linkage analysis of COMT and DBH cDNA expression levels, identifying transcriptional regulatory regions for both genes. Multiple Haseman-Elston regression was used to detect both additive and interactive effects between two loci. We found that the master transcriptional regulatory region 20q13 had an additive effect on the COMT expression level. We also found that chromosome 19p13 showed both additive and interactive effects with 9q34 on DBH expression level. Furthermore, a potential interaction between COMT and DBH was indicated.
PMCID: PMC2367604  PMID: 18466599
5.  Genome-wide association studies using an adaptive two-stage analysis for a case-control design 
BMC Proceedings  2007;1(Suppl 1):S147.
A new type of test is presented for genome-wide association studies using a case-control design. It is referred to as the adaptive two-stage (ATS) analysis, being based on both the Hardy-Weinberg disequilibrium trend test (HWDTT) and the Cochran-Armitage trend test (CATT). The procedure for the ATS is to screen single-nucleotide polymorphisms (SNPs) using the HWDTT in a first stage, and then test a reduced number of SNPs that pass the screening step in a second stage using the CATT. In the Genetic Analysis Workshop 15 simulated data set, this ATS analysis captured, after Bonferroni correction, the region from 32447.149 kb to 32859.819 kb and the region around 37363.880 kb that are close to the actual trait loci on chromosome 6. We compared the ATS with other ways of combining the p-values of the HWDTT and the CATT, the classical form of Fisher's test and a weighted form of Fisher's test. Results showed that the proposed ATS has good performance and could detect the regions containing a susceptibility locus.
PMCID: PMC2367582  PMID: 18466491
6.  Two-stage analysis strategy for identifying the IgM quantitative trait locus 
BMC Proceedings  2007;1(Suppl 1):S139.
Genetic association studies offer an opportunity to find genetic variants underlying complex human diseases. Various tests have been developed to improve their power. However, none of these tests is uniformly best and it is usually unclear at the outset what test is best for a specific dataset. For example, Hotelling's T2 test is best for normally distributed data, but it can lose considerable power when normality is not met. To achieve satisfactory power in most cases, without compromising the overall significance level, we propose to adopt a two-stage adaptive analysis strategy – several statistics are compared on a portion of the samples at the first stage and the most powerful statistic is then used for the remaining samples. We evaluated this procedure by mapping the quantitative trait locus of IgM with the simulated data in Genetic Analysis Workshop 15 Problem 3. The results show that the gain in power of the two-stage adaptive analysis procedure could be considerable when the initial choice of test statistic is wrong, whereas the loss is relatively small in the case that the optimal test chosen initially is correct.
PMCID: PMC2367539  PMID: 18466482
7.  A logistic mixture model for a family-based association study 
BMC Proceedings  2007;1(Suppl 1):S44.
A family-based association study design is not only able to localize causative genes more precisely than linkage analysis, but it also helps explain the genetic mechanism underlying the trait under study. Therefore, it can be used to follow up an initial linkage scan. For an association study of binary traits in general pedigrees, we propose a logistic mixture model that regresses the trait value on the genotypic values of markers under investigation and other covariates such as environmental factors. We first tested both the validity and power of the new model by simulating nuclear families inheriting a simple Mendelian trait. It is powerful when the correct disease model is specified and shows much loss of power when the dominance of a model is inversely specified, i.e., a dominant model is wrongly specified as recessive or vice versa. We then applied the new model to the Genetic Analysis Workshop (GAW) 15 simulation data to test the performance of the model when adjusting for covariates in the case of complex traits. Adjusting for the covariate that interacts with disease loci improves the power to detect association. The simplest version of the model only takes monogenic inheritance into account, but analysis of the GAW simulation data shows that even this simple model can be powerful for complex traits.
PMCID: PMC2359869  PMID: 18466543

Results 1-7 (7)