Improving Pedigree-based Linkage Analysis by Estimating Coancestry Among Families
-
Chris Glazner
We present a method for improving the power of linkage analysis by detecting chromosome segments shared identical by descent (IBD) by individuals not known to be related. Existing Markov chain Monte Carlo methods sample descent patterns on pedigrees conditional on observed marker data. These patterns can be stored as IBD graphs, which express shared ancestry only, rather than specific family relationships. A model for IBD between unrelated individuals allows the estimation of coancestry between individuals in different pedigrees. IBD graphs on separate pedigrees can then be combined using these estimates. We report results from analyses of three sets of simulated marker data on two different pedigrees. We show that when families share a gene for a trait due to shared ancestry on the order of tens of generations, our method can detect a linkage signal when independent analyses of the families do not.
©2012 Walter de Gruyter GmbH & Co. KG, Berlin/Boston
Articles in the same Issue
- Editorial Introduction
- Special Issue on Computational Statistical Methods for Genomics and Systems Biology
- Article
- A Generalized Hidden Markov Model for Determining Sequence-based Predictors of Nucleosome Positioning
- Gene Filtering in the Analysis of Illumina Microarray Experiments
- Principal Components of Heritability for High Dimension Quantitative Traits and General Pedigrees
- Bayesian Sparsity-Path-Analysis of Genetic Association Signal using Generalized t Priors
- A Family-Based Probabilistic Method for Capturing De Novo Mutations from High-Throughput Short-Read Sequencing Data
- Adjusting for Spurious Gene-by-Environment Interaction Using Case-Parent Triads
- Querying Genomic Databases: Refining the Connectivity Map
- A Model-Based Analysis to Infer the Functional Content of a Gene List
- Candidate Pathway Based Analysis for Cleft Lip with or without Cleft Palate
- Improving Pedigree-based Linkage Analysis by Estimating Coancestry Among Families
Articles in the same Issue
- Editorial Introduction
- Special Issue on Computational Statistical Methods for Genomics and Systems Biology
- Article
- A Generalized Hidden Markov Model for Determining Sequence-based Predictors of Nucleosome Positioning
- Gene Filtering in the Analysis of Illumina Microarray Experiments
- Principal Components of Heritability for High Dimension Quantitative Traits and General Pedigrees
- Bayesian Sparsity-Path-Analysis of Genetic Association Signal using Generalized t Priors
- A Family-Based Probabilistic Method for Capturing De Novo Mutations from High-Throughput Short-Read Sequencing Data
- Adjusting for Spurious Gene-by-Environment Interaction Using Case-Parent Triads
- Querying Genomic Databases: Refining the Connectivity Map
- A Model-Based Analysis to Infer the Functional Content of a Gene List
- Candidate Pathway Based Analysis for Cleft Lip with or without Cleft Palate
- Improving Pedigree-based Linkage Analysis by Estimating Coancestry Among Families
