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COMPLEX TRAIT PREDICTION WORKING GROUP (CTPWG)

The Complex Trait Prediction Working Group (CTPWG) meets on the third Thursday of each month from 12-1 pm. The purpose of the CTPWG is to stay abreast of current research in statistical genetics, explore issues related to prediction from large genomic data sets, and to start new collaborations, generate ideas, and get help on analytical techniques from colleagues. We have an open format that has included presentation and discussion of published papers, presentation of original research, and discussion of particular topics. Some topics of interest include but are not limited to: genetic association studies (GWAS, candidate gene, etc.), prediction (machine learning methods, Bayesian Networks, genome-wide selection, etc.), epigenetics, gene expression/regulation, classification (disease subtypes, personalized medicine), and comparative genomics, evolution, and population genetics. All are welcome to participate!

Upcoming Meetings

Location: School of Health Profession Bldg. Room 226
Time: 12-1 pm

Date Topic Presenter/Speaker Detail
17-November-11 Proposed simulation study to compare power between mean and factor scores to test SNP-phenotype associations Lekki Frazier-Wood In genetic psychiatry, the situation often arises in which several measurements have been collected on the same trait. For example, you may have several measures of reaction time data. Where an investigator wishes to test SNP associations with the underlying trait, i.e. reaction time, not the individual measures, aggregating across measures is suggested to increase the power for these associations, through a reduction in measure-specific error. There are several possible ways exist to perform the association. These include taking the mean of the observed traits, using a factor score, and other approaches. Lekki wishes to perform a simulation study in which she evaluates the power of competing approaches as a function of the correlation structure among observed traits, genetic effect size, genetic correlation between traits etc. and is looking for a collaborator to help with this study. She will apply these approaches to a real analysis in the GOLDN study, on lipid traits.


CTPWG meetings are organized by Christine W. Duarte.
 

Topics Discussed in Previous Meetings

  • 2011
  • 2010
Date Topic Presenter/Speaker Detail
20-Oct-11 No meeting
15-Sep-11 No meeting
18-Aug-11 No meeting
21-July-11 No meeting
16-June-11 Haplotype methods for rare variant detection Wan-Yu Lin  
19-May-11 Methods to elucidate potential environmental contributions to complex diseases Julia Gohlke, Assistant Professor of Environmental Health Sciences  
21-Apr-11 New methods for genomic association with rare variants Degui Zhi, Nengjun Yi, and Wan-Yu Lin Discussion of recent statistical methods for handling rare variants in large genomic studies
17-Mar-11 No meeting
17-Feb-11 Meet with Dr. Almeida Jonas Alemeida (Division of Informatics, UAB) Discussion of new issues, and opportunities, in informatics raised by GWASs: recent work with Glioblastoma performed at MD Anderson
20-Jan-11 Meet with SSG seminar speaker Dr. Scheet Paul Scheet (MD Anderson) Discussion of new applications for imputation and other issues
Date Topic Presenter/Speaker Detail
16-Dec-10 Meet with SSG seminar speaker Dr. Schork Nicholas Schork (Scripps Institute) Discussion of new sequencing methods and other issues
18-Nov-10 Thousand Genomes project Guo-Bo Chen Discussion of "A map of human genome variation from population-scale sequencing" by the 1000 Genomes Project Consortium in Nature 467:1061.
21-Oct-10 No meeting
16-Sep-10 Prediction from GWAS continued Christine Duarte Continued discussion of two papers "Estimation of effect size distribution from genome-wide association studies and implications for future discoveries" by Park et al., 2010, Nature Genetics 42:570 and "Common SNPs explain a large proportion of the heritability for human height" by Yang et al., 2010 Nature Genetics 42:565.
19-Aug-10 No meeting in August because of SSG retreat
15-Jul-10 Prediction from GWAS Christine Duarte Discussion of two papers "Estimation of effect size distribution from genome-wide association studies and implications for future discoveries" by Park et al., 2010, Nature Genetics 42:570 and "Common SNPs explain a large proportion of the heritability for human height" by Yang et al., 2010 Nature Genetics 42:565.
16-Jun-10 Predictive modeling with epistasis with QTLBIM Nengjun Yi Prediction of lung cancer with inclusion of epistatic interactions using QTLBIM
19-May-10 Prediction of BMI/Mortality from Framingham Gustavo de los Campos Prediction from BMI/mortality data from the Framingham study
15-Apr-10 Missing heritability in GWAS Alexis Wood Discussion of "Finding the missing heritability of complex diseases" by Manolio, et al., 2009, Nature 461(8):747.
18-Mar-10 Introductory meeting Christine Duarte Introduction, discussion of purpose/format of group