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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Research Project #426953

Research Project: Improvement of Algorithms and Software to Process Very Large Genomic Datasets

Location: Animal Genomics and Improvement Laboratory

Project Number: 8042-31000-002-04-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Aug 1, 2014
End Date: Jul 31, 2019

To 1) develop DNA sequence analysis methods to estimate effects of sequence variants that impact economically important traits in the US dairy industry; 2) refine imputation methods to efficiently and accurately combine genotypes from a variety of input data with differing densities or coverage; and 3) test for parent of origin effects to determine if genes are expressed differently when inherited from the sire or from the dam.

Hundreds or thousands of animals may have full DNA sequence data in the near future. Efficient computer methods to process such data will be developed and tested on simulated data before the actual sequences become available. Many more animals already have medium or high density genotypes and can be used to estimate the effects of new sequence variants if these can be accurately imputed. Fast algorithms have been derived and will be updated and refined to impute genotype probabilities and to estimate genetic effects from larger datasets. These imputation methods can determine which allele was inherited from the sire or the dam. Effects of parent of origin (imprinting) will be estimated for several traits using software (MMAP) already developed by the Cooperator.