Title |
A scalable, knowledge-based analysis framework for genetic association studies
|
---|---|
Published in |
BMC Bioinformatics, October 2013
|
DOI | 10.1186/1471-2105-14-312 |
Pubmed ID | |
Authors |
James W Baurley, David V Conti |
Abstract |
Testing for marginal associations between numerous genetic variants and disease may miss complex relationships among variables (e.g., gene-gene interactions). Bayesian approaches can model multiple variables together and offer advantages over conventional model building strategies, including using existing biological evidence as modeling priors and acknowledging that many models may fit the data well. With many candidate variables, Bayesian approaches to variable selection rely on algorithms to approximate the posterior distribution of models, such as Markov-Chain Monte Carlo (MCMC). Unfortunately, MCMC is difficult to parallelize and requires many iterations to adequately sample the posterior. We introduce a scalable algorithm called PEAK that improves the efficiency of MCMC by dividing a large set of variables into related groups using a rooted graph that resembles a mountain peak. Our algorithm takes advantage of parallel computing and existing biological databases when available. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 1 | 17% |
Germany | 1 | 17% |
Unknown | 4 | 67% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Practitioners (doctors, other healthcare professionals) | 2 | 33% |
Scientists | 2 | 33% |
Members of the public | 2 | 33% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Spain | 2 | 3% |
United States | 2 | 3% |
United Kingdom | 1 | 2% |
Netherlands | 1 | 2% |
Unknown | 53 | 90% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 20 | 34% |
Student > Ph. D. Student | 11 | 19% |
Student > Master | 9 | 15% |
Professor > Associate Professor | 4 | 7% |
Student > Doctoral Student | 3 | 5% |
Other | 3 | 5% |
Unknown | 9 | 15% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 23 | 39% |
Computer Science | 7 | 12% |
Biochemistry, Genetics and Molecular Biology | 4 | 7% |
Medicine and Dentistry | 4 | 7% |
Environmental Science | 3 | 5% |
Other | 6 | 10% |
Unknown | 12 | 20% |