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Human Molecular Genetics, 2000, Vol. 9, No. 20 2947-2957
© 2000 Oxford University Press

Major factors influencing linkage disequilibrium by analysis of different chromosome regions in distinct populations: demography, chromosome recombination frequency and selection

Patrizia Zavattari1, Elisabetta Deidda1, Michael Whalen1, Rosanna Lampis1, Annapaola Mulargia1,2, Miriam Loddo1,2, Iain Eaves3, Giuseppe Mastio4, John A. Todd3 and Francesco Cucca1,+

1Dipartimento di Scienze Biomediche e Biotecnologie, University of Cagliari, Via Jenner, Cagliari 09121, Italy, 2Servizio di Diabetologia Pediatrica, Ospedale G. Brotzu, Via Peretti, Cagliari 09121, Italy, 3Wellcome Trust Centre for Molecular Mechanisms in Disease, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 2XY, UK and 4Ambulatorio di Medicina di base di Gavoi, ASL 3, Via Manno 2, Gavoi 08020, Italy

Linkage disequilibrium (LD) mapping of disease genes is complicated by population- and chromosome-region-specific factors. We have analysed demographic factors by contrasting intermarker LD results obtained in a large cosmopolitan population (UK), a large genetic isolate (Sardinia) and a subisolate (village of Gavoi) for two regions of the X chromosome. A dramatic increase of LD was found in the subisolate. Demographic history of populations therefore influences LD. Chromosome-region-specific effects, namely the pattern and frequency of homologous recombination, were next delineated by the analysis of chromosome 6p21, including the HLA region. Patterns of global LD in this region were very similar in the UK and Sardinian populations despite their entirely distinct demographies, and correlate well with the pattern of recombinations. Nevertheless, haplotypes extend across recombination hot spots indicative of selection of certain haplotypes. Subisolate aside, chromosome-region-specific differences in LD patterns appear to be more important than the differences in intermarker LD between distinct populations.

+ To whom correspondence should be addressed. Tel: +39 070 6095681; Fax: +39 070 6095558; Email: fcucca@mcweb.unica.it


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