varLD: a program for quantifying variation in linkage disequilibrium patterns between populations - PubMed (original) (raw)
varLD: a program for quantifying variation in linkage disequilibrium patterns between populations
Rick Twee-Hee Ong et al. Bioinformatics. 2010.
Abstract
Motivation: Linkage disequilibrium (LD) differences between populations can potentially result in failure to replicate primary signals of trait association in independent genome-wide association studies (GWAS). However, such inter-population LD differences can be leveraged to narrow the search for common causal variants responsible for the association signals observed. The ability to assess and quantify LD variations among populations is thus expected to contribute to both replication and fine-mapping stages of GWAS.
Availability: The program varLD is available for download from http://www.nus-cme.org.sg/software/varld.html.
Similar articles
- A method for identifying haplotypes carrying the causative allele in positive natural selection and genome-wide association studies.
Ong RT, Liu X, Poh WT, Sim X, Chia KS, Teo YY. Ong RT, et al. Bioinformatics. 2011 Mar 15;27(6):822-8. doi: 10.1093/bioinformatics/btr007. Epub 2011 Jan 6. Bioinformatics. 2011. PMID: 21216773 - snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package.
Luna A, Nicodemus KK. Luna A, et al. Bioinformatics. 2007 Mar 15;23(6):774-6. doi: 10.1093/bioinformatics/btl657. Epub 2007 Jan 18. Bioinformatics. 2007. PMID: 17234637 - Building chromosome-wide LD maps.
Abad-Grau MM, Montes R, Sebastiani P. Abad-Grau MM, et al. Bioinformatics. 2006 Aug 15;22(16):1933-4. doi: 10.1093/bioinformatics/btl288. Epub 2006 Jun 16. Bioinformatics. 2006. PMID: 16782726 Free PMC article. - Patterns of linkage disequilibrium in the human genome.
Ardlie KG, Kruglyak L, Seielstad M. Ardlie KG, et al. Nat Rev Genet. 2002 Apr;3(4):299-309. doi: 10.1038/nrg777. Nat Rev Genet. 2002. PMID: 11967554 Review.
Cited by
- Analyzing the Korean reference genome with meta-imputation increased the imputation accuracy and spectrum of rare variants in the Korean population.
Hwang MY, Choi NH, Won HH, Kim BJ, Kim YJ. Hwang MY, et al. Front Genet. 2022 Nov 24;13:1008646. doi: 10.3389/fgene.2022.1008646. eCollection 2022. Front Genet. 2022. PMID: 36506321 Free PMC article. - Within- and between-Breed Selection Signatures in the Original and Improved Valachian Sheep.
Mészárosová M, Mészáros G, Moravčíková N, Pavlík I, Margetín M, Kasarda R. Mészárosová M, et al. Animals (Basel). 2022 May 25;12(11):1346. doi: 10.3390/ani12111346. Animals (Basel). 2022. PMID: 35681809 Free PMC article. - Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.
Balagué-Dobón L, Cáceres A, González JR. Balagué-Dobón L, et al. Brief Bioinform. 2022 Mar 10;23(2):bbac043. doi: 10.1093/bib/bbac043. Brief Bioinform. 2022. PMID: 35211719 Free PMC article. - Genetic Risk Prediction of COVID-19 Susceptibility and Severity in the Indian Population.
Prakrithi P, Lakra P, Sundar D, Kapoor M, Mukerji M, Gupta I, The Indian Genome Variation Consortium. Prakrithi P, et al. Front Genet. 2021 Oct 11;12:714185. doi: 10.3389/fgene.2021.714185. eCollection 2021. Front Genet. 2021. PMID: 34707636 Free PMC article. - Selection for environmental variance of litter size in rabbits involves genes in pathways controlling animal resilience.
Casto-Rebollo C, Argente MJ, García ML, Blasco A, Ibáñez-Escriche N. Casto-Rebollo C, et al. Genet Sel Evol. 2021 Jul 13;53(1):59. doi: 10.1186/s12711-021-00653-y. Genet Sel Evol. 2021. PMID: 34256696 Free PMC article.
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Research Materials