Join us for the next instalment of the STAGE International Speaker Seminar Series (ISSS) with
Dr. Heather J. Cordell
Professor of Statistical Genetics
Population Health Sciences Institute
Faculty of Medical Sciences
Newcastle University
United Kingdom
Talk Title
A Bayesian network approach incorporating imputation of missing data enables exploratory analysis of complex causal biological relationships
Abstract
Bayesian networks can be used to identify possible causal relationships between variables based on their conditional dependencies and independencies, which can be particularly useful in complex biological scenarios with many measured variables. When there is missing data, the standard approach is to remove every individual with any missing data before performing analysis. This can be wasteful and undesirable when there are many individuals with missing data, perhaps with only one or a few variables missing. This motivates the use of imputation. We present a new imputation method designed to increase the power to detect causal relationships, where the data may include a mixture of both discrete and continuous variables. Our method uses a version of nearest neighbour imputation, whereby missing data from one individual is replaced with data from another individual, their nearest neighbour. For each individual with missing data, the subsets of variables to be used to select the nearest neighbour are chosen by sampling without replacement the complete data and estimating a best fit Bayesian network. We show that this approach leads to marked improvements in the recall and precision of directed edges in the final network identified. We illustrate the approach through application to data from a recent study investigating the causal relationship between methylation and gene expression in early inflammatory arthritis patients.
Speaker Profile
Heather Cordell is Professor of Statistical Genetics in the Population Health Sciences Institute at Newcastle University, UK. Heather obtained a BA in Mathematics in 1990 from Cambridge University, followed by an MSc in Applied Statistics and DPhil (PhD) in Mathematical Genetics from Oxford University. She then spent three postdoctoral years at Case Western Reserve University in Cleveland, Ohio, USA. After returning to the UK, Heather held a Wellcome Trust/JDRF Career Development Fellowship, followed by a Wellcome Senior Fellowship, at the Department of Medical Genetics at Cambridge University. In 2006 Heather moved to Newcastle University to take up the newly-established Chair of Statistical Genetics.
In addition to being involved in a number of applied studies, Heather’s research interests include the development of methods for detecting linkage/association (including maternal and parent-of-origin effects) using family-based data; modelling effects at multiple disease loci (including interaction effects) simultaneously; and using approaches based on causal inference to elucidate the causal pathways between genotype and phenotype.
Heather was previously (2006-2012) a member of the Board of Directors of the International Genetic Epidemiology Society (IGES) and she acted as IGES President in 2010. For the past five years (2016-2021) she has held the post of IGES Secretary.
Sponsors
CANSSI Ontario STAGE (STAGE) is a training program in genetic epidemiology and statistical genetics housed at the University of Toronto Dalla Lana School of Public Health. It operates with financial and in-kind support from CANSSI Ontario, an extra-departmental unit in the Faculty of Arts & Science at U of T.
STAGE would like to thank our generous seminar sponsors!
For a complete list of sponsors, please see here.
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