Please use this identifier to cite or link to this item: https://hdl.handle.net/1959.11/7184
Title: Recursive Long Range Phasing and Long Haplotype Library Imputation: Building a Global Haplotype Library for Holstein cattle
Contributor(s): Hickey, John (author); Kinghorn, Brian  (author); Cleveland, MA (author); Tier, Bruce  (author); Van Der Werf, Julius H  (author)orcid 
Publication Date: 2010
Handle Link: https://hdl.handle.net/1959.11/7184
Abstract: Long range phasing (LRP) is a fast and accurate rule based method which uses information from both related and unrelated individuals by invoking the concepts of surrogate parents and Erdös numbers (Kong et al., 2008). Recursive long range phasing and long haplotype imputation (RLRPLHI; Hickey et al., 2009) is an extended LRP algorithm with increased robustness partially due to the extra long haplotype imputation step (LHI) which is based on a the construction of a library of long haplotypes (e.g. 10cM) for a dataset. The LHI part of the algorithm is computationally much less intensive and less error prone compared to the LRP part, and it can easily incorporate prior information from other phasing methods, both laboratory and in silico. After building the initial haplotype library it may be possible to phase other genotyped individuals from the same population simply via the LHI step. The application of such an approach may be useful where small numbers of extra individuals are regularly added to a data set of previously phased individuals, especially where very many animals are genotyped making even a fast phasing method feasible for only small subsets of the data. It may also be useful through incorporation into the LRP part of RLRPLHI in order to improve the accuracy and speed of RLRPLHI. Another application of a long haplotype library could be to use it in combination with segregation analysis (Kerr and Kinghorn, 1996) to impute dense genotype or sequence data in ungenotyped individuals in a sparsely genotyped pedigree. The objectives of this research were to evaluate LHI for phasing genotyped individuals, and segregation analysis and long haplotype imputation (SALHI) for imputing genotypes in ungenotyped individuals, using simulated genotypic data in a national and global Holstein pedigree.
Publication Type: Conference Publication
Conference Name: 9th World Congress on Genetics Applied to Livestock Production (WCGALP), Leipzig, Germany, 1-6 August, 2010
Conference Details: 9th World Congress on Genetics Applied to Livestock Production (WCGALP), Leipzig, Germany, 1-6 August, 2010
Source of Publication: Proceedings of the 9th World Congress on Genetics Applied to Livestock Production
Publisher: German Society for Animal Science
Place of Publication: Germany
Field of Research (FOR): 070201 Animal Breeding
Peer Reviewed: Yes
HERDC Category Description: E1 Refereed Scholarly Conference Publication
Other Links: http://www.kongressband.de/wcgalp2010/assets/html/0934.htm
http://www.wcgalp2010.org/
Statistics to Oct 2018: Visitors: 203
Views: 203
Downloads: 0
Appears in Collections:Animal Genetics and Breeding Unit (AGBU)
Conference Publication

Files in This Item:
3 files
File Description SizeFormat 
Show full item record

Page view(s)

140
checked on May 3, 2019
Google Media

Google ScholarTM

Check


Items in Research UNE are protected by copyright, with all rights reserved, unless otherwise indicated.