原创力文档assignment of chromosomal locations for unassigned snpsscaffolds based on pair-wise linkage disequilibrium estimates作业的染色体位置未赋值的snpsscaffolds基于成对连锁不平衡的估计.pdfVIP
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assignment of chromosomal locations for unassigned snpsscaffolds based on pair-wise linkage disequilibrium estimates作业的染色体位置未赋值的snpsscaffolds基于成对连锁不平衡的估计
Khatkar et al. BMC Bioinformatics 2010, 11:171
/1471-2105/11/171
METHODOLOGY ARTICLE Open Access
Assignment of chromosomal locations for
unassigned SNPs/scaffolds based on pair-wise
linkage disequilibrium estimates
1* 1 2 2 1
Mehar S Khatkar , Matthew Hobbs , Markus Neuditschko , Johann Sölkner , Frank W Nicholas ,
Herman W Raadsma1
Abstract
Background: Recent developments of high-density SNP chips across a number of species require accurate genetic
maps. Despite rapid advances in genome sequence assembly and availability of a number of tools for creating
genetic maps, the exact genome location for a number of SNPs from these SNP chips still remains unknown. We
have developed a locus ordering procedure based on linkage disequilibrium (LODE) which provides estimation of
the chromosomal positions of unaligned SNPs and scaffolds. It also provides an alternative means for verification of
genetic maps. We exemplified LODE in cattle.
Results: The utility of the LODE procedure was demonstrated using data from 1,943 bulls genotyped for 73,569
SNPs across three different SNP chips. First, the utility of the procedure was tested by analysing the masked
positions of 1,500 randomly-chosen SNPs with known locations (50 from each chromosome), representing three
classes of minor allele frequencies (MAF), namely 0.05, 0.01MAF ≤ 0.05 and 0.001MAF ≤ 0.01. The efficiency
(percentage of masked SNPs that could be assigned a location) was 96.7%, 30.6% and 2.0%; with an accuracy (the
percentage of SNPs assigned correctly) of 99.9%, 98.9% and 33.3% in the three classes of MAF, respectively. The
average precision for placement of the SNPs was 914, 3,137 and 6,853 kb, respectively. Secondly, 4,688 of 5,314
SNPs unpositioned in the Btau4.0
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