DTL Focus meeting: ‘Genome Imputation’

6 June 2014, Radix building, Wageningen University
13:00 – 17:00

Genome wide imputation of untyped variants within the genome has been one of the biggest drives behind the recent “gold rush” of identifying genes for various complex traits in human, animal and plant genetics. One major advantage of imputation is making (human) GWAS studies comparable even though different genotyping procedures have been applied, and the imputed variants enhance the genomic scans as the extra information provides a much clearer picture of the possible associations. Imputation has become standard practice, and genotypes of imputed variants are considered to be valid measures. In agricultural species, imputation plays a critical role in cost-saving genotyping strategies in genomic prediction of large pools of selection candidates.

However, behind the advantages of imputation lies a complex field of rapid developing methods and decisions, which may affect the outcome of association studies. Progress in quality of the imputation as well as improving the calculation speed of imputing millions of variants are basically made monthly by statisticians, bio-technicians and geneticists. However, the numbers of variants, subjects in the datasets and reference sets are increasing with the same speed. It leads to a demanding field, where researchers continuously have to keep updated with developments.This meeting will focus on recent developments in genome imputation and give participants the opportunity to share experiences in dealing with issues of imputation, such as platforms, data size, used methods and quality control.

Programme

13:00 – 13:20 welcome with coffee and tea
13:20 – 13:55 Marco Bink – Challenges and some experiences on genotype
imputation in plants
13:55 – 14:30 Mario Calus – Genotype imputation in livestock
14:30 – 14:45 tea break
14:45 – 15:20 Stefan Boehringer – Technical aspects of implementing
reproducible imputation pipelines
15:20 – 15:55 Jouke Jan Hottenga – Progress and possible pitfalls in human
genome imputations
15:55 – 16:30 discussion
16:30 – 17:00 drinks

 

Contact person: David van Enckevort, UMC Groningen

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