Epistasis Blog

From the Computational Genetics Laboratory at Dartmouth Medical School (www.epistasis.org)

Tuesday, October 23, 2007

ASHG

I will be at the American Society of Human Genetics (ASHG) annual meeting in San Diego on Thursday to present our poster on Multifactor Dimensionality Reduction 1.0. I will be presenting in Poster Session II from 4:30-6:30. I will also be at the University of Michigan party Thursday night at 8:00. Stop by and say hello!

Saturday, October 06, 2007

Methodological issues in detecting gene-gene interactions

I highly recommend the following paper by Briollais et al. in BMC Medicine that explores the use of multiple different methods, including MDR, for detecting gene-gene interactions. This paper represents one of the more thoughtful analyses I have seen. I particularly like their attempts to interpret interactions results. I also like their conclusion that multiple methods should be used. I agree that no one method will be ideal.

Briollais L, Wang Y, Rajendram I, Onay V, Shi E, Knight J, Ozcelik H. Methodological issues in detecting gene-gene interactions in breast cancer susceptibility: a population-based study in Ontario. BMC Med. 2007 Aug 7;5:22. [PubMed] [PDF]

BACKGROUND: There is growing evidence that gene-gene interactions are ubiquitous in determining the susceptibility to common human diseases. The investigation of such gene-gene interactions presents new statistical challenges for studies with relatively small sample sizes as the number of potential interactions in the genome can be large. Breast cancer provides a useful paradigm to study genetically complex diseases because commonly occurring single nucleotide polymorphisms (SNPs) may additively or synergistically disturb the system-wide communication of the cellular processes leading to cancer development. METHODS: In this study, we systematically studied SNP-SNP interactions among 19 SNPs from 18 key genes involved in major cancer pathways in a sample of 398 breast cancer cases and 372 controls from Ontario. We discuss the methodological issues associated with the detection of SNP-SNP interactions in this dataset by applying and comparing three commonly used methods: the logistic regression model, classification and regression trees (CART), and the multifactor dimensionality reduction (MDR) method. RESULTS: Our analyses show evidence for several simple (two-way) and complex (multi-way) SNP-SNP interactions associated with breast cancer. For example, all three methods identified XPD-[Lys751Gln]*IL10-[G(-1082)A] as the most significant two-way interaction. CART and MDR identified the same critical SNPs participating in complex interactions. Our results suggest that the use of multiple statistical approaches (or an integrated approach) rather than a single methodology could be the best strategy to elucidate complex gene interactions that have generally very different patterns. CONCLUSION: The strategy used here has the potential to identify complex biological relationships among breast cancer genes and processes. This will lead to the discovery of novel biological information, which will improve breast cancer risk management.

Thursday, October 04, 2007

PSB 2008

I have made plans to be at the Pacific Symposium on Biocomputing (PSB) Jan. 4-8, 2008. This is one of my favorite conferences. They are accepting abstracts for posters until Nov. 9th. Hope to see you there!

Wednesday, October 03, 2007

EvoBIO 2008

This is a bioinformatics conference that I help organize every year. This is an appropriate venue for theoretical and applied work in genetics and genetic epidemiology. Let me know if you are interested in submitting a paper and have questions. I hope to see you in Napoli!

**** EVOBIO 2008 ****

Sixth European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics

26-28 March 2008, Napoli, Italy

http://www.cs.vu.nl/~elena/evobio08.html

EvoBIO covers research in all aspects of Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics.

The goal of the conference is to not only present recent research resultsand to identify and explore directions of future research, but also stimulate synergy and cross fertilization among Evolutionary Computation, Machine Learning and Data Mining for Bioinformatics.

The emphasis is on novel advanced techniques addressing important problems in molecular biology, proteomics, genomics and genetics, that have been implemented and tested in simulations and on real-life datasets.

Topics of interest include but are not limited to:
* biomarker discovery
* cell simulation and modelling
* ecological modelling* fluxomics
* gene networks
* high-throughput biotechnology
* metabolomics
* microarray analysis
* phylogeny
* protein interaction
* proteomics
* sequence analysis and alignment
* biological networks analysis
* systems biology

EvoBIO started in 2002 as workshop organized by the EvoNet (European Network of Excellence in Evolutionary Computation) working group on bioinformatics, and was held annually since then.

The conference will be held in conjunction with the EuroGP (11th European Conference on Genetic Programming), EvoCOP 2008 (8th European Conference on Evolutionary Computation in Combinatorial Optimization) and EvoWorkshops 2008, the specialist workshops on a range of evolutionary computation topics and applications.

__Submissions__

Submit your manuscript, at most 12 A4 pages long, in Springer LNCS format (instructions are downloadable here) using the online submission service no later than November 1,2007. The papers will be peer reviewed by at least two members of theprogram committee. Authors will be notified via email on the results of the review by December 15, 2007.

The authors of accepted papers will have to improve their paper on thebasis of the reviewers' comments and will be asked to send a cameraready version of their manuscripts, along with text sources and pictures, by January 8, 2008.

The accepted papers will appear in theconference proceedings, published in Springer LNCS Series, which will beavailable at the conference. The accepted papers of the previous editions of EvoBIO were published in the Springer Verlag LNCS 2611, 3005, 3449, 3449, 3449, 3907, 4447, respectively.

Each accepted paper will be presented orally or as a poster at the conference.

The authors of papers which receive the best reviews will be nominated for the 'Best paper Award'.

__Important dates__

* Submission deadline: 1 November 2007
* Notification of acceptance: 15 December 2007
* Camera ready papers due: 8 January 2008
* Conference: 26-28 March 2008