2001 SSC Annual Meeting

2001 Annual Meeting of the SSC in Burnaby

Inferences from Genetic Data on Pedigrees

Burnaby, British Columbia


Leader: E. A. Thompson, University of Washington

This Short Course will be based on material in the CBMS Monograph `Statistical Inferences from Genetic Data on Pedigrees' by Elizabeth A. Thompson, University of Washington; NSF-CBMS Regional Conference Series in Probability and Statistics. Volume 6. Published by IMS, Beachwood, Ohio ISBN 0-940600-49-8.

The course develops probability models and analysis methods for genetic data on related individuals. The focus is on simple Mendelian traits, such as DNA markers, but on joint models for data at multiple genetic loci, such as arise in modern genome scan studies. The statistical approach is that of likelihood, maximum likelihood estimation, and methods for the analysis of latent-variable and hidden-Markov models including the EM algorithm, the Baum algorithm, and Monte Carlo imputation methods.

The first part of the course develops the basic concepts and approaches, focusing on the ideas of gene identity by descent and the tracing of gene descent in pedigrees. Knowledge of discrete probability and mathematical statistics (likelihood inference) are assumed. No genetic knowledge is presupposed, although some familiarity with basic terminology will be helpful.

Building on these foundations, the second half of the course develops Markov chain Monte Carlo (MCMC) and Monte Carlo likelihood methods for the analysis of data on individuals in a known pedigree structure. Some familiarity with hidden Markov models and/or MCMC methods will be helpful. The objective is Monte Carlo estimation of likelihood surfaces and conditional probabilities, rather than of Bayesian posterior distributions. Finally the methods are illustrated through two examples, using recently implemented MCMC samplers and likelihood estimation procedures.

About the Leader
Dr. Elizabeth Thompson is Professor of Statistics and Biostatistics and Adjunct Professor of Genetics, University of Washington, Seattle, and Adjunct Professor of Statistics, University of North Carolina. She received her Ph.D. in Statistics in 1974 from Cambridge University, UK, and from 1976-1985 was a University Lecturer in the Department of Pure Mathematics and Mathematical Statistics, University of Cambridge. From 1975-81 she was a Fellow of King's College, Cambridge, and from 1981-85 was Fellow and Director of Studies in Mathematics at Newnham College. She joined the faculty of the University of Washington in December 1985, and served as Chair of the Department of Statistics from 1989-94.

Dr. Thompson's research interest is in the development of methods for inference from genetic data, and particularly from data observed on large and complex pedigree structures. Questions of interest range from analyses of long-term gene frequency differentiation in widely dispersed populations, to short-term extinction of genes in the small population of a highly endangered species; from inference of genealogical relationships among individuals to inference of the genetic basis of traits from data observed on members of a known pedigree; and from analyses of patterns of genome sharing in plants to modern methods for human linkage analysis. In recent years, many of these questions have been addressed using Monte Carlo likelihood.

Dr. Thompson is a member of the International Biometric Society, the Royal Statistical Society, and the International Statistical Institute. She was awarded an Sc.D. degree by the University of Cambridge in 1988, and in 1998 was elected a Fellow of the American Academy of Arts and Sciences.