Linkage disequilibrium across two different single-nucleotide polymorphism genome scans

Juan Manuel Peralta, Thomas D. Dyer, Diane M. Warren, John Blangero, Laura Almasy

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Linkage disequilibdrium (LD) content was calculated for the Genetic Analysis Workshop 14 Affymetrix and Illumina single-nucleotide polymorphism (SNP) genome scans of the Collaborative Study on the Genetics of Alcoholism samples. Pair-wise LD was measured as both D' and r2 on 505 pedigree founder individuals. The r2 estimates were then used to correct the multipoint identity by descent matrix (MIBD) calculation to account for LD and LOD scores on chromosomes 3 and 18 were calculated for COGA's ttdt3 electrophysiological trait using those MIBDs. Extensive LD was observed throughout both marker sets, and it was higher in Affymetrix's more dense SNP map. However, SNP density did not solely account for Affymetrix's higher LD. MIBD estimation procedures assume linkage equilibrium to construct genotypes of non-genotyped pedigree founder individuals, and dense SNP genotyping maps are likely to contain moderate to high LD between markers. LOD score plots calculated after correction for LD followed the same general pattern as uncorrected ones. Since in our study almost half of the pedigree founders were genotyped, it is possible that LD had a minor impact on the LOD scores. Caution should probably be taken when using high density SNP maps when many non-genotyped founders are present in the study pedigrees.

Original languageEnglish (US)
Article numberS86
JournalBMC Genetics
Volume6
Issue numberSUPPL.1
DOIs
StatePublished - Dec 30 2005
Externally publishedYes

Fingerprint

Linkage Disequilibrium
Single Nucleotide Polymorphism
Pedigree
Genome
Chromosomes, Human, Pair 18
Chromosomes, Human, Pair 3
Alcoholism
Genotype
Education

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Peralta, J. M., Dyer, T. D., Warren, D. M., Blangero, J., & Almasy, L. (2005). Linkage disequilibrium across two different single-nucleotide polymorphism genome scans. BMC Genetics, 6(SUPPL.1), [S86]. https://doi.org/10.1186/1471-2156-6-S1-S86

Linkage disequilibrium across two different single-nucleotide polymorphism genome scans. / Peralta, Juan Manuel; Dyer, Thomas D.; Warren, Diane M.; Blangero, John; Almasy, Laura.

In: BMC Genetics, Vol. 6, No. SUPPL.1, S86, 30.12.2005.

Research output: Contribution to journalArticle

Peralta, JM, Dyer, TD, Warren, DM, Blangero, J & Almasy, L 2005, 'Linkage disequilibrium across two different single-nucleotide polymorphism genome scans', BMC Genetics, vol. 6, no. SUPPL.1, S86. https://doi.org/10.1186/1471-2156-6-S1-S86
Peralta, Juan Manuel ; Dyer, Thomas D. ; Warren, Diane M. ; Blangero, John ; Almasy, Laura. / Linkage disequilibrium across two different single-nucleotide polymorphism genome scans. In: BMC Genetics. 2005 ; Vol. 6, No. SUPPL.1.
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