Population-specific patterns of linkage disequilibrium in the human 5q31 region

ABSTRACT Linkage disequilibrium across the human genome is generally lower in West Africans than Europeans. However in the 5q31 region, which is rich in immune genes, we find significantly

more examples of apparent nonrecombination between distant marker pairs in West Africans. Much of this effect is due to SNPs that are absent in Europeans, possibly reflecting recent positive

selection in the West African population. Access through your institution Buy or subscribe This is a preview of subscription content, access via your institution ACCESS OPTIONS Access

through your institution Subscribe to this journal Receive 6 digital issues and online access to articles $119.00 per year only $19.83 per issue Learn more Buy this article * Purchase on

SpringerLink * Instant access to full article PDF Buy now Prices may be subject to local taxes which are calculated during checkout ADDITIONAL ACCESS OPTIONS: * Log in * Learn about

institutional subscriptions * Read our FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS AN ENHANCED FRAMEWORK FOR LOCAL GENETIC CORRELATION ANALYSIS Article 10 March

2025 EXTREMELY SPARSE MODELS OF LINKAGE DISEQUILIBRIUM IN ANCESTRALLY DIVERSE ASSOCIATION STUDIES Article 28 August 2023 SCALABLE BIAS-CORRECTED LINKAGE DISEQUILIBRIUM ESTIMATION UNDER

GENOTYPE UNCERTAINTY Article 09 August 2021 REFERENCES * Hinds DA, Stuve LL, Nilsen GB et al. Whole-genome patterns of common DNA variation in three human populations. _Science_ 2005; 307:

1072–1079. Article  CAS  Google Scholar  * Ahmadi KR, Weale ME, Xue ZY et al. A single-nucleotide polymorphism tagging set for human drug metabolism and transport. _Nat Genet_ 2005; 37:

84–89. Article  CAS  Google Scholar  * Daly MJ, Rioux JD, Schaffner SF et al. High-resolution haplotype structure in the human genome. _Nat Genet_ 2001; 29: 229–232. Article  CAS  Google

Scholar  * Rihet P, Traore Y, Abel L et al. Malaria in humans: _Plasmodium falciparum_ blood infection levels are linked to chromosome 5q31–q33. _Am J Hum Genet_ 1998; 63: 498–505. Article 

CAS  Google Scholar  * Marquet S, Abel L, Hillaire D et al. Genetic localization of a locus controlling the intensity of infection by _Schistosoma mansoni_ on chromosome 5q31–q33. _Nat

Genet_ 1996; 14: 181–184. Article  CAS  Google Scholar  * Ansel KM, Lee DU, Rao A . An epigenetic view of helper T cell differentiation. _Nat Immunol_ 2003; 4: 616–623. Article  CAS  Google

Scholar  * Lee GR, Fields PE, Griffin TJ et al. Regulation of the Th2 cytokine locus by a locus control region. _Immunity_ 2003; 19: 145–153. Article  CAS  Google Scholar  * Ardlie KG,

Kruglyak L, Seielstad M . Patterns of linkage disequilibrium in the human genome. _Nat Rev Genet_ 2002; 3: 299–309. Article  CAS  Google Scholar  * Bamshad M, Wooding SP . Signatures of

natural selection in the human genome. _Nat Rev Genet_ 2003; 4: 99–111. Article  CAS  Google Scholar  * Sabeti PC, Reich DE, Higgins JM et al. Detecting recent positive selection in the

human genome from haplotype structure. _Nature_ 2002; 419: 832–837. Article  CAS  Google Scholar  * Luoni G, Verra F, Arca B et al. Antimalarial antibody levels and IL4 polymorphism in the

Fulani of West Africa. _Genes Immun_ 2001; 2: 411–414. Article  CAS  Google Scholar  * Zhang K, Jin L . HaploBlockFinder: haplotype block analyses. _Bioinformatics_ 2003; 19: 1300–1301.

Article  CAS  Google Scholar  * Rioux JD, Daly MJ, Silverberg MS et al. Genetic variation in the 5q31 cytokine gene cluster confers susceptibility to Crohn disease. _Nat Genet_ 2001; 29:

223–228. Article  CAS  Google Scholar  * Noguchi E, Nukaga-Nishio Y, Jian Z et al. Haplotypes of the 5′ region of the IL-4 gene and SNPs in the intergene sequence between the IL-4 and IL-13

genes are associated with atopic asthma. _Hum Immunol_ 2001; 62: 1251–1257. Article  CAS  Google Scholar  * Howard TD, Whittaker PA, Zaiman AL et al. Identification and association of

polymorphisms in the interleukin-13 gene with asthma and atopy in a Dutch population. _Am J Resp Cell Mol Biol_ 2001; 25: 377–384. Article  CAS  Google Scholar  * Stephens M, Smith NJ,

Donnelly P . A new statistical method for haplotype reconstruction from population data. _Am J Hum Genet_ 2001; 68: 978–989. Article  CAS  Google Scholar  * Ackerman H, Usen S, Mott R et al.

Haplotypic analysis of the TNF locus by association efficiency and entropy. _Genome Biol_ 2003; 4: R24. Article  Google Scholar  * Mott R . Marker selection by maximum entropy.

http://www.well.ox.ac.uk/~rmott/SNPS/2003. * Gabriel SB, Schaffner SF, Nguyen H et al. The structure of haplotype blocks in the human genome. _Science_ 2002; 296: 2225–2229. Article  CAS 

Google Scholar  Download references ACKNOWLEDGEMENTS This work was funded by a Marie Curie fellowship (GL), a Wellcome Trust research training fellowship (JF) and the Medical Research

Council. AUTHOR INFORMATION Author notes * G Luoni: Deceased * M Jallow and E Sadighi Akha: These authors made an equal contribution. AUTHORS AND AFFILIATIONS * Wellcome Trust Centre for

Human Genetics, Oxford, UK G Luoni, J Forton, E Sadighi Akha, N Hanchard, M Kimber, R Mott, K Rockett & D Kwiatkowski * University Department of Paediatrics, Oxford, UK J Forton, N

Hanchard, M Herbert, J Hull & D Kwiatkowski * MRC Laboratories, Fajara, The Gambia M Jallow, F Sisay-Joof & M Pinder Authors * G Luoni View author publications You can also search

for this author inPubMed Google Scholar * J Forton View author publications You can also search for this author inPubMed Google Scholar * M Jallow View author publications You can also

search for this author inPubMed Google Scholar * E Sadighi Akha View author publications You can also search for this author inPubMed Google Scholar * F Sisay-Joof View author publications

You can also search for this author inPubMed Google Scholar * M Pinder View author publications You can also search for this author inPubMed Google Scholar * N Hanchard View author

publications You can also search for this author inPubMed Google Scholar * M Herbert View author publications You can also search for this author inPubMed Google Scholar * M Kimber View

author publications You can also search for this author inPubMed Google Scholar * R Mott View author publications You can also search for this author inPubMed Google Scholar * J Hull View

author publications You can also search for this author inPubMed Google Scholar * K Rockett View author publications You can also search for this author inPubMed Google Scholar * D

Kwiatkowski View author publications You can also search for this author inPubMed Google Scholar CORRESPONDING AUTHOR Correspondence to D Kwiatkowski. ADDITIONAL INFORMATION Supplementary

information accompanies the paper on Genes and Immunity website (http://www.nature.com/gene). SUPPLEMENTARY INFORMATION SUPPLEMENTARY TABLE A (PDF 56 KB) SUPPLEMENTARY FIGURE A (TIF 969 KB)

RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Luoni, G., Forton, J., Jallow, M. _et al._ Population-specific patterns of linkage disequilibrium in the

human 5q31 region. _Genes Immun_ 6, 723–727 (2005). https://doi.org/10.1038/sj.gene.6364250 Download citation * Received: 09 May 2005 * Revised: 08 June 2005 * Accepted: 08 June 2005 *

Published: 28 July 2005 * Issue Date: 01 December 2005 * DOI: https://doi.org/10.1038/sj.gene.6364250 SHARE THIS ARTICLE Anyone you share the following link with will be able to read this

content: Get shareable link Sorry, a shareable link is not currently available for this article. Copy to clipboard Provided by the Springer Nature SharedIt content-sharing initiative