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Patterns of linkage disequilibrium (LD) in the human genome are beginning to be characterized, with a paucity of haplotype diversity in "LD blocks," interspersed by apparent "hot spots" of recombination. Previously, we cloned and physically characterized the low-density lipoprotein-receptor-related protein 5 (LRP5) gene. Here, we have extensively analysed both LRP5 and its flanking three genes, spanning 269 kb, for single nucleotide polymorphisms (SNPs), and we present a comprehensive SNP map comprising 95 polymorphisms. Analysis revealed high levels of recombination across LRP5, including a hot-spot region from intron 1 to intron 7 of LRP5, where there are 109 recombinants/Mb (4882 meioses), in contrast to flanking regions of 14.6 recombinants/Mb. This region of high recombination could be delineated into three to four hot spots, one within a 601-bp interval. For LRP5, three haplotype blocks were identified, flanked by the hot spots. Each LD block comprised over 80% common haplotypes, concurring with a previous study of 14 genes that showed that common haplotypes account for at least 80% of all haplotypes. The identification of hot spots in between these LD blocks provides additional evidence that LD blocks are separated by areas of higher recombination.

Original publication

DOI

10.1101/gr.563703

Type

Journal article

Journal

Genome Res

Publication Date

05/2003

Volume

13

Pages

845 - 855

Keywords

3’ Flanking Region, 5’ Flanking Region, Alleles, Chromosome Mapping, Chromosomes, Human, Pair 11, Diabetes Mellitus, Type 1, Gene Frequency, Genetic Markers, Genetics, Population, Genotype, Haplotypes, Humans, Introns, LDL-Receptor Related Proteins, Linkage Disequilibrium, Low Density Lipoprotein Receptor-Related Protein-5, Microsatellite Repeats, Nuclear Family, Polymorphism, Single Nucleotide, Receptors, LDL, Recombination, Genetic