Haplotype structure, LD blocks, and uneven recombination within the LRPS gene

Twells, Rebecca C. J., Mein, Charles A., Philips, Michael S., Hess, J. Fred, Veijola, Riitta, Gilbey, Matthew, Bright, Matthew, Metzker, Michael, Lie, Benedicte A., Kingsnorth, Amanda, Gregory, Edward, Nakagawa, Yusuke, Snook, Hywel, Wang, William Y. S., Masters, Jennifer, Johnson, Gillian, Eaves, Iain, Howson, Joanna M. M., Clayton, David, Cordell, Heather J., Nutland, Sarah, Rance, Helen, Carr, Philippa and Todd, John A. (2003) Haplotype structure, LD blocks, and uneven recombination within the LRPS gene. Genome Research, 13 5: 845-855. doi:10.1101/gr.563703

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Author Twells, Rebecca C. J.
Mein, Charles A.
Philips, Michael S.
Hess, J. Fred
Veijola, Riitta
Gilbey, Matthew
Bright, Matthew
Metzker, Michael
Lie, Benedicte A.
Kingsnorth, Amanda
Gregory, Edward
Nakagawa, Yusuke
Snook, Hywel
Wang, William Y. S.
Masters, Jennifer
Johnson, Gillian
Eaves, Iain
Howson, Joanna M. M.
Clayton, David
Cordell, Heather J.
Nutland, Sarah
Rance, Helen
Carr, Philippa
Todd, John A.
Title Haplotype structure, LD blocks, and uneven recombination within the LRPS gene
Journal name Genome Research   Check publisher's open access policy
ISSN 1088-9051
1549-5469
Publication date 2003-05
Sub-type Article (original research)
DOI 10.1101/gr.563703
Open Access Status File (Publisher version)
Volume 13
Issue 5
Start page 845
End page 855
Total pages 11
Place of publication Cold Spring Harbor, NY, United States
Publisher Cold Spring Harbor Laboratory Press
Language eng
Formatted abstract
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 bothLRP5 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. ForLRP5, 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.
Keyword Single-nucleotide polymorphisms
Lipoprotein-lipase gene
Human genome
Linkage disequilibrium
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: School of Medicine Publications
Centre for Advanced Imaging Publications
 
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