Are Interactions between cis-Regulatory Variants Evidence for Biological Epistasis or Statistical Artifacts?

The importance of epistasis-or statistical interactions between genetic variants-to the development of complex disease in humans has been controversial. Genome-wide association studies of statistical interactions influencing human traits have recently become computationally feasible and have identified many putative interactions. However, statistical models used to detect interactions can be confounded, which makes it difficult to be […]

Epistatic Gene-Based Interaction Analyses for Glaucoma in eMERGE and NEIGHBOR Consortium.

Primary open angle glaucoma (POAG) is a complex disease and is one of the major leading causes of blindness worldwide. Genome-wide association studies have successfully identified several common variants associated with glaucoma; however, most of these variants only explain a small proportion of the genetic risk. Apart from the standard approach to identify main effects […]

ICB Softball is Number 1!

  A successful season came to a close last night when the ICB-sponsored Away Team beat their arch nemesis Senior Tequila softball team 5-4 and 10-9 (in extra innings!) in a playoff double header.  The Cavs have nothing on us!  Go Away!!

eMERGE Phenome-Wide Association Study (PheWAS) identifies clinical associations and pleiotropy for stop-gain variants.

We explored premature stop-gain variants to test the hypothesis that variants, which are likely to have a consequence on protein structure and function, will reveal important insights with respect to the phenotypes associated with them. We performed a phenome-wide association study (PheWAS) exploring the association between a selected list of functional stop-gain genetic variants (variation […]

Pathway analysis by randomization incorporating structure-PARIS: an update.

We present an update to the pathway enrichment analysis tool ‘Pathway Analysis by Randomization Incorporating Structure (PARIS)’ that determines aggregated association signals generated from genome-wide association study results. Pathway-based analyses highlight biological pathways associated with phenotypes. PARIS uses a unique permutation strategy to evaluate the genomic structure of interrogated pathways, through permutation testing of genomic […]

Genetic variation among 82 pharmacogenes: The PGRNseq data from the eMERGE network.

Genetic variation can affect drug response in multiple ways, although it remains unclear how rare genetic variants affect drug response. The electronic Medical Records and Genomics (eMERGE) Network, collaborating with the Pharmacogenomics Research Network, began eMERGE-PGx, a targeted sequencing study to assess genetic variation in 82 pharmacogenes critical for implementation of “precision medicine.” The February […]

International Congress of Human Genetics (ICHG) 2016 in Kyoto, Japan

In a typical calendar year, my conference season tends to be concentrated to the fall semester, culminating with the Pacific Symposium on Biocomputing in the first week of January just before or as the spring semester begins.  Travel outside this schedule is generally limited to special meetings such as NIH study section, consortium meetings, etc.  […]

It’s the End of the Semester (Spring 2016)!

It’s the end of another semester, and in this case, another academic year.  This past semester, I taught EPBI 444 Communicating in Population Health Science Research and co-organized EPBI 502 Seminar in Genetic Epidemiology and Bioinformatics.  I don’t mind teaching all by myself, but it’s certainly more fun with friends! This past semester, I was […]

Population Stratification in the Context of Diverse Epidemiologic Surveys Sans Genome-Wide Data.

Population stratification or confounding by genetic ancestry is a potential cause of false associations in genetic association studies. Estimation of and adjustment for genetic ancestry has become common practice thanks in part to the availability of ancestry informative markers on genome-wide association study (GWAS) arrays. While array data is now widespread, these data are not […]

Population Stratification in the Context of Diverse Epidemiologic Surveys Sans Genome-Wide Data.

Population stratification or confounding by genetic ancestry is a potential cause of false associations in genetic association studies. Estimation of and adjustment for genetic ancestry has become common practice thanks in part to the availability of ancestry informative markers on genome-wide association study (GWAS) arrays. While array data is now widespread, these data are not […]

Population Stratification in the Context of Diverse Epidemiologic Surveys Sans Genome-Wide Data.

Population stratification or confounding by genetic ancestry is a potential cause of false associations in genetic association studies. Estimation of and adjustment for genetic ancestry has become common practice thanks in part to the availability of ancestry informative markers on genome-wide association study (GWAS) arrays. While array data is now widespread, these data are not […]