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1.  Pathway-based joint effects analysis of rare genetic variants using Genetic Analysis Workshop 17 exon sequence data 
BMC Proceedings  2011;5(Suppl 9):S45.
Pathway-based analysis has been recently used in joint tests of association between disease and a group of common genetic variants. Here we explore this idea for the joint effects analysis of rare genetic variants and their association with quantitative traits and disease. We accumulate multiple rare minor alleles in a genetic risk score for each individual in a given pathway; this score is then used to assess association with quantitative phenotypes and disease. We demonstrate that this approach may be better than studying single rare variants or a gene risk score for identifying individuals with significantly greater risk.
doi:10.1186/1753-6561-5-S9-S45
PMCID: PMC3287882  PMID: 22373371
2.  Transmission-ratio distortion in the Framingham Heart Study 
BMC Proceedings  2009;3(Suppl 7):S51.
Transmission-ratio distortion (TRD) is a phenomenon in which the segregation of alleles does not obey Mendel's laws. As a simple example, a recessive locus that results in fetal lethality will result in live-born individuals sharing more alleles at this locus than expected under Mendel's laws. This could result in apparent linkage of the phenotype of 'being alive' to such a chromosomal regions. Further, this could result in false-positive linkage when 'affected-only' parametric or non-parametric linkage analysis is performed. Similarly, loci demonstrating TRD may be detectable in family-based association tests as deviant transmission of alleles. Therefore, TRD could result in confounding of family-based association studies of diseases. The Framingham Heart Study data available for Genetic Analysis Workshop 16 is a suitable dataset to determine whether there are loci in the genome that reveal TRD because of the large number of individuals from families, the high-resolution genotyping, and the population-based nature of the study. We have used both genome-wide linkage and family-based association methods to determine whether there are loci that demonstrate TRD in the Framingham Heart Study. Family-based association analysis identified thousands of loci with apparent TRD. However, the vast majority of these are likely the result of genotyping errors with application of strict quality control criteria to the genotype data, and automated inspection of the intensity plots, we identify a small number of loci that may show true TRD, including rs1000548 in intron 6 of S-antigen (arrestin, SAG) on chromosome 2 (p = 7 × 10-10).
PMCID: PMC2795951  PMID: 20018044
3.  Using a latent growth curve model for an integrative assessment of the effects of genetic and environmental factors on multiple phenotypes 
BMC Proceedings  2009;3(Suppl 7):S44.
We propose the use of latent growth curve model to assess the influence of genetic, environmental, demographic, and lifestyle factors on multiple phenotypes related to coronary heart disease. We model four quantitative traits (systolic blood pressure, high-density lipoprotein, low-density lipoprotein, and triglycerides) simultaneously in a multivariate framework that allows us to study their change over time, assess individual variation, and investigate cross-phenotype relationships. Environmental, demographic, and lifestyle covariates are included at different levels of the model as time-varying or time-invariant, as appropriate. To investigate the change over time attributed to genetic factors, we use candidate markers that have previously been shown to be associated with the quantitative traits. We illustrate our approach using independent observations from the offspring cohort of the Framingham Heart Study data.
PMCID: PMC2795943  PMID: 20018036
4.  Pathway-based analysis of a genome-wide case-control association study of rheumatoid arthritis 
BMC Proceedings  2009;3(Suppl 7):S128.
Evaluation of the association between single-nucleotide polymorphisms (SNPs) and disease outcomes is widely used to identify genetic risk factors for complex diseases. Although this analysis paradigm has made significant progress in many genetic studies, many challenges remain, such as the requirement of a large sample size to achieve adequate power. Here we use rheumatoid arthritis (RA) as an example and explore a new analysis strategy: pathway-based analysis to search for related genes and SNPs contributing to the disease.
We first propose the application of measure of explained variation to quantify the predictive ability of a given SNP. We then use gene set enrichment analysis to evaluate enrichment of specific pathways, where pathways, are considered enriched if they consist of genes that are associated with the phenotype of interest above and beyond is expected by chance. The results are also compared with score tests for association analysis by adjusting for population stratification.
Our study identified some significantly enriched pathways, such as "cell adhesion molecules," which are known to play a key role in RA. Our results showed that pathway-based analysis may identify other biologically interesting loci (e.g., rs1018361) related to RA: the gene (CTLA4) closest to this marker has previously been shown to be associated with RA and the gene is in the significant pathways we identified, even though the marker has not reached genome-wide significance in univariate single-marker analysis.
PMCID: PMC2795901  PMID: 20017994
5.  Genome-wide association analysis of cardiovascular-related quantitative traits in the Framingham Heart Study 
BMC Proceedings  2009;3(Suppl 7):S117.
Multivariate linear growth curves were used to model high-density lipoprotein (HDL), low-density lipoprotein (LDL), triglycerides (TG), and systolic blood pressure (SBP) measured during four exams from 1659 independent individuals from the Framingham Heart Study. The slopes and intercepts from each of two phenotype models were tested for association with 348,053 autosomal single-nucleotide polymorphisms from the Affymetrix Gene Chip 500 k set. Three regions were associated with LDL intercept, TG slope, and SBP intercept (p < 1.44 × 10-7). We observed results consistent with previously reported associations between rs599839, on chromosome 1p13, and LDL. We note that the association is significant with LDL intercept but not slope. Markers on chromosome 17q25 were associated with TG slope, and a single-nucleotide polymorphism on chromosome 7p11 was associated with SBP intercept. Growth curve models can be used to gain more insight on the relationships between SNPs and traits than traditional association analysis when longitudinal data has been collected. The power to detect association with changes over time may be limited if the subjects are not followed over a long enough time period.
PMCID: PMC2795889  PMID: 20017982
6.  The multiplicity problem in linkage analysis of gene expression data – the power of differentiating cis- and trans-acting regulators 
BMC Proceedings  2007;1(Suppl 1):S142.
In this report, we focused on the multiplicity issue in Problem 1 of Genetic Analysis Workshop 15. We investigated and compared the performance of the stratified false-discovery rate control method with the traditional aggregated approach, in an application to genome-wide linkage analyses of single-nucleotide polymorphism-to-gene expression data. We showed the importance of utilizing the available map information and demonstrated the power gained by conducting false-discovery rate control separately for cis and trans regulators under three different frameworks: fixed rejection region, fixed false-discovery rate, and fixed number of rejections.
PMCID: PMC2367579  PMID: 18466486
7.  Sex, age and generation effects on genome-wide linkage analysis of gene expression in transformed lymphoblasts 
BMC Proceedings  2007;1(Suppl 1):S92.
Background
Many traits differ by age and sex in humans, but genetic analysis of gene expression has typically not included them in the analysis.
Methods
We used Genetic Analysis Workshop 15 Problem 1 data to determine whether gene expression in lymphoblasts showed differences by age and/or sex using generalized estimating equations (GEE). We performed quantitative trait linkage analysis of these genes including age and sex as covariates to determine whether the linkage results changed when they were included as covariates. Because the families included in the study all contain three generations, we also determined what effect inclusion of generation in the model had on the age effects.
Results
When controlling the false-discovery rate at 1%, using GEE we identified 30 transcripts that showed significant differences in expression by sex, while 1950 transcripts showed differences in expression associated with age. When subjected to linkage analysis, there were 37 linkages that disappeared, while 17 appeared when sex was included as a covariate. All these genes were, as expected, on the sex chromosomes. In contrast, when age was included in the linkage analysis, 462 linkage signals were no longer significant, while 223 became significant. When generation was included in the model with age, all but 6 of the GEE age effects were no longer significant. However, there were minimal changes in the linkage results.
Conclusion
The effect of age on linkage analyses was apparent for the expression of many genes, which appear to be mostly due to differences between the generations.
PMCID: PMC2367486  PMID: 18466596

Results 1-7 (7)