Linkage Disequilibrium and Haplotype Homozygosity in Population Samples Genotyped at a High Marker Density

ABSTRACT: Objective: Analyze the information contained in homozygous haplotypes detected with high density genotyping. Methods: We analyze the genotypes of ∼2,500 markers on chr 22 in 12 population samples, each including 200 individuals. We develop a measure of disequilibrium based on haplotype homozygosity and an algorithm to identify genomic segments characterized by non-random homozygosity (NRH), taking into account allele frequencies, missing data, genotyping error, and linkage disequilibrium. Results: We show how our measure of linkage disequilibrium based on homozygosity leads to results comparable to those of R2, as well as the importance of correcting for small sample variation when evaluating D′. We observe that the regions that harbor NRH segments tend to be consistent across populations, are gene rich, and are characterized by lower recombination. Conclusions: It is crucial to take into account LD patterns when interpreting long stretches of homozygous markers.

• Autores: Bedoya Berrío, Gabriel de Jesús; Lin, Chia-Ho; Service, Susan; Chen, Yuguo; Freimer, Nelson; Sabatti, Chiara; Wang, Hui; Ospina Duque, Jorge
• Tipo de recurso: Article of investigation
• Fecha de publicación: 2006
• Institución: Universidad de Antioquia
• Repositorio: Repositorio UdeA
• Idioma: eng
• OAI Identifier: oai:bibliotecadigital.udea.edu.co:10495/41530
• Acceso en línea: https://hdl.handle.net/10495/41530
• Palabra clave: Consanguinidad; Consanguinity; Cromosomas Humanos Par 22; Chromosomes, Human, Pair 22; Frecuencia de los Genes; Gene Frequency; Marcadores Genéticos; Genetic Markers; Cadenas de Markov; Markov Chains; Homocigoto; Homozygote; https://id.nlm.nih.gov/mesh/D003241; https://id.nlm.nih.gov/mesh/D002892; https://id.nlm.nih.gov/mesh/D005787; https://id.nlm.nih.gov/mesh/D005819; https://id.nlm.nih.gov/mesh/D008390; https://id.nlm.nih.gov/mesh/D006720
• Rights: openAccess
• License: https://creativecommons.org/licenses/by-nc/4.0/