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Linkage disequilibrium between microsatellite markers in the Swedish Sami relative to a worldwide selection of populations

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Abstract

The pattern of linkage disequilibrium (LD) is affected by a number of factors, including population demography. High LD is seen in populations with a relatively limited and constant size, presumably because of genetic drift. We have examined the extent of LD among over 300 genome-wide pattern microsatellite loci in 29 populations from around the world. The pattern of LD varied between populations, with a larger extent of LD in populations with limited size relative to larger populations. In addition, the LD between 88 less well-spaced microsatellite markers from 10 different genomic regions was examined in the Sami compared with the general Swedish population. For these markers, increased LD extending up to 5 Mb was detected in the Sami. The amount of LD also differed between the chromosomal regions. The amount of LD in the Sami makes this population suitable for the mapping of complex genetic traits.

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References

  • Abecasis GR, Noguchi E, Heinzmann A, Traherne JA, Bhattacharyya S, Leaves NI, Anderson GG, Zhang Y, Lench NJ, Carey A, Cardon LR, Moffatt MF, Cookson WO (2001) Extent and distribution of linkage disequilibrium in three genomic regions. Am J Hum Genet 68:191–197

    Article  CAS  PubMed  Google Scholar 

  • Ardlie KG, Kruglyak L, Seielstad M (2002) Patterns of linkage disequilibrium in the human genome. Nat Rev Genet 3:299–309

    Article  CAS  PubMed  Google Scholar 

  • Beckman L (1996) Samerna en genetiskt unik urbefolkning. Solfjädern Offset, Umeå

    Google Scholar 

  • Cann HM, de Toma C, Cazes L, Legrand MF, Morel V, Piouffre L, Bodmer J, Bodmer WF, Bonne-Tamir B, Cambon-Thomsen A, Chen Z, Chu J, Carcassi C, Contu L, Du R, Excoffier L, Ferrara GB, Friedlaender JS, Groot H, Gurwitz D, Jenkins T, Herrera RJ, Huang X, Kidd J, Kidd KK, Langaney A, Lin AA, Mehdi SQ, Parham P, Piazza A, Pistillo MP, Qian Y, Shu Q, Xu J, Zhu S, Weber JL, Greely HT, Feldman MW, Thomas G, Dausset J, Cavalli-Sforza LL (2002) A human genome diversity cell line panel. Science 296:261–262

    Google Scholar 

  • Cavalli-Sforza LL, Wilson AC, Cantor CR, Cook-Deegan RM, King MC (1991) Call for a worldwide survey of human genetic diversity: a vanishing opportunity for the Human Genome Project. Genomics 11:490–491

    CAS  PubMed  Google Scholar 

  • Chakraborty R, Weiss KM (1988) Admixture as a tool for finding linked genes and detecting that difference from allelic association between loci. Proc Natl Acad Sci USA 85:9119–9123

    CAS  PubMed  Google Scholar 

  • Chapman NH, Wijsman EM (1998) Genome screens using linkage disequilibrium tests: optimal marker characteristics and feasibility. Am J Hum Genet 63:1872–1885

    Article  CAS  PubMed  Google Scholar 

  • Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S, Beare DM, Pabial J, Dibling T, Tinsley E, Kirby S, Carter D, Papaspyridonos M, Livingstone S, Ganske R, Lohmussaar E, Zernant J, Tonisson N, Remm M, Magi R, Puurand T, Vilo J, Kurg A, Rice K, Deloukas P, Mott R, Metspalu A, Bentley DR, Cardon LR, Dunham I (2002) A first-generation linkage disequilibrium map of human chromosome 22. Nature 418:544–548

    Article  CAS  PubMed  Google Scholar 

  • Dunning AM, Durocher F, Healey CS, Teare MD, McBride SE, Carlomagno F, Xu CF, Dawson E, Rhodes S, Ueda S, Lai E, Luben RN, Van Rensburg EJ, Mannermaa A, Kataja V, Rennart G, Dunham I, Purvis I, Easton D, Ponder BA (2000) The extent of linkage disequilibrium in four populations with distinct demographic histories. Am J Hum Genet 67:1544–1554

    Article  CAS  PubMed  Google Scholar 

  • Hassler S, Sjolander P, Barnekow-Bergkvist M, Kadesjo A (2001) Cancer risk in the reindeer breeding Saami population of Sweden, 1961–1997. Eur J Epidemiol 17:969–976

    Article  PubMed  Google Scholar 

  • Hassler S, Sjölander P, Ericsson AJ (2003) Construction of a database on health and living conditions of the Swedish Sami population. In: Lantto P, Sköld P (eds) Befolkning och bosättning i norr - etnicitet, identitet och gränser i historiens sken. Centre for Sami Research, Umeå University, Umeå, pp 107–124

    Google Scholar 

  • Hill W, Robertson A (1968) Linkage disequilibrium in finite populations. Theor Appl Genet 38:226–231

    Google Scholar 

  • Hudson RR (1990) Gene geneologies and the coalescent process. Oxf Surv Evol Biol 7:1–44

    Google Scholar 

  • Johansson Å, Karlsson P, Gyllensten U (2003) A novel method for automatic genotyping of microsatellite markers based on parametric pattern recognition. Hum Genet 113:316–324

    Article  CAS  PubMed  Google Scholar 

  • Kaessmann H, Zollner S, Gustafsson AC, Wiebe V, Laan M, Lundeberg J, Uhlen M, Paabo S (2002) Extensive linkage disequilibrium in small human populations in Eurasia. Am J Hum Genet 70:673–685

    Article  CAS  PubMed  Google Scholar 

  • Kauppi L, Sajantila A, Jeffreys AJ (2003) Recombination hotspots rather than population history dominate linkage disequilibrium in the MHC class II region. Hum Mol Genet 12:33–40

    Article  CAS  PubMed  Google Scholar 

  • Laan M, Paabo S (1997) Demographic history and linkage disequilibrium in human populations. Nat Genet 17:435–438

    Article  CAS  PubMed  Google Scholar 

  • Larsen LA, Vuust J, Nystad M, Evseeva I, Van Ghelue M, Tranebjaerg L (2001) Analysis of FMR1 (CGG)(n) alleles and DXS548-FRAXAC1 haplotypes in three European circumpolar populations: traces of genetic relationship with Asia. Eur J Hum Genet 9:724–727

    Article  CAS  PubMed  Google Scholar 

  • Lewontin RC, Kojima K (1960) The evolutionary dynamics of complex polymorphisms. Evolution 14:458–472

    Google Scholar 

  • Lindqvist AK, Magnusson PK, Balciuniene J, Wadelius C, Lindholm E, Alarcon-Riquelme ME, Gyllensten UB (1996) Chromosome-specific panels of tri- and tetranucleotide microsatellite markers for multiplex fluorescent detection and automated genotyping: evaluation of their utility in pathology and forensics. Genome Res 6:1170–1176

    CAS  PubMed  Google Scholar 

  • Pritchard JK, Przeworski M (2001) Linkage disequilibrium in humans: models and data. Am J Hum Genet 69:1–14

    Article  CAS  PubMed  Google Scholar 

  • Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249

    Google Scholar 

  • Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ, Lavery T, Kouyoumjian R, Farhadian SF, Ward R, Lander ES (2001) Linkage disequilibrium in the human genome. Nature 411:199–204

    Article  CAS  PubMed  Google Scholar 

  • Sajantila A, Lahermo P, Anttinen T, Lukka M, Sistonen P, Savontaus ML, Aula P, Beckman L, Tranebjaerg L, Gedde-Dahl T, Issel-Tarver L, DiRienzo A, Paabo S (1995) Genes and languages in Europe: an analysis of mitochondrial lineages. Genome Res 5:42–52

    CAS  PubMed  Google Scholar 

  • Sheffield VC, Stone EM, Carmi R (1998) Use of isolated inbred human populations for identification of disease genes. Trends Genet 14:391–396

    Article  CAS  PubMed  Google Scholar 

  • Shifman S, Darvasi A (2001) The value of isolated populations. Nat Genet 28:309–310

    Article  CAS  PubMed  Google Scholar 

  • Slatkin M (1994) Linkage disequilibrium in growing and stable populations. Genetics 137:331–336

    PubMed  Google Scholar 

  • Smith MW, Lautenberger JA, Shin HD, Chretien JP, Shrestha S, Gilbert DA, O’Brien SJ (2001) Markers for mapping by admixture linkage disequilibrium in African American and Hispanic populations. Am J Hum Genet 69:1080–1094

    Article  CAS  PubMed  Google Scholar 

  • Soininen L, Jarvinen S, Pukkala E (2002) Cancer incidence among Sami in Northern Finland, 1979–1998. Int J Cancer 100:342–346

    Article  CAS  PubMed  Google Scholar 

  • Tambets K, Rootsi S, Kivisild T, Help H, Serk P, Loogvali EL, Tolk HV, Reidla M, Metspalu E, Pliss L, Balanovsky O, Pshenichnov A, Balanovska E, Gubina M, Zhadanov S, Osipova L, Damba L, Voevoda M, Kutuev I, Bermisheva M, Khusnutdinova E, Gusar V, Grechanina E, Parik J, Pennarun E, Richard C, Chaventre A, Moisan JP, Barac L, Pericic M, Rudan P, Terzic R, Mikerezi I, Krumina A, Baumanis V, Koziel S, Rickards O, De Stefano GF, Anagnou N, Pappa KI, Michalodimitrakis E, Ferak V, Furedi S, Komel R, Beckman L, Villems R (2004) The western and eastern roots of the Saami–the story of genetic “outliers” told by mitochondrial DNA and Y chromosomes. Am J Hum Genet 74:661–682

    Article  CAS  PubMed  Google Scholar 

  • Tenesa A, Wright AF, Knott SA, Carothers AD, Hayward C, Angius A, Persico I, Maestrale G, Hastie ND, Pirastu M, Visscher PM (2004) Extent of linkage disequilibrium in a Sardinian sub-isolate: sampling and methodological considerations. Hum Mol Genet 13:25–33

    Article  CAS  PubMed  Google Scholar 

  • Terwilliger JD, Zollner S, Laan M, Paabo S (1998) Mapping genes through the use of linkage disequilibrium generated by genetic drift: “drift mapping” in small populations with no demographic expansion. Hum Hered 48:138–154

    Article  CAS  PubMed  Google Scholar 

  • Varilo T, Laan M, Hovatta I, Wiebe V, Terwilliger JD, Peltonen L (2000) Linkage disequilibrium in isolated populations: Finland and a young sub-population of Kuusamo. Eur J Hum Genet 8:604–612

    Article  CAS  PubMed  Google Scholar 

  • Varilo T, Paunio T, Parker A, Perola M, Meyer J, Terwilliger JD, Peltonen L (2003) The interval of linkage disequilibrium (LD) detected with microsatellite and SNP markers in chromosomes of Finnish populations with different histories. Hum Mol Genet 12:51–59

    Article  CAS  PubMed  Google Scholar 

  • Wiklund K, Holm LE, Eklund G (1990) Cancer risks in Swedish Lapps who breed reindeer. Am J Epidemiol 132:1078–1082

    CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank the members of the Sami communities for their participation. We are also grateful for the contribution of Laila Daerga and the Southern Lapland Research Department at Vilhelmina and Inger Jonasson, Jenny Jonsson and Per-Ivan Wyöni at the SSF National Genotyping Center, Department of Genetics and Pathology, Rudbeck laboratory, Uppsala University, Uppsala, Sweden. Åsa Johansson is affiliated to The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden. This study was supported by grants from the Swedish Foundation for Strategic Research, the National Swedish Research Council, the Knut and Alice Wallenberg Foundation and Mål 1 Sápmi (dnr. SN 1.42–11/00).

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Authors and Affiliations

  1. Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 571 85, Uppsala, Sweden

    Åsa Johansson, Veronika Vavruch-Nilsson & Ulf Gyllensten

  2. Southern Lapland Research Department, Postgatan 7, 91232, Vilhelmina, Sweden

    Anette Edin-Liljegren & Per Sjölander

  3. Centre for Musculoskeletal Research, University of Gävle, Umea, Sweden

    Anette Edin-Liljegren & Per Sjölander

Authors
  1. Åsa Johansson
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  2. Veronika Vavruch-Nilsson
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  3. Anette Edin-Liljegren
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  4. Per Sjölander
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  5. Ulf Gyllensten
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Correspondence to Ulf Gyllensten.

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Åsa Johansson, Veronika Vavruch-Nilsson contributed equally to the report

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Johansson, Å., Vavruch-Nilsson, V., Edin-Liljegren, A. et al. Linkage disequilibrium between microsatellite markers in the Swedish Sami relative to a worldwide selection of populations. Hum Genet 116, 105–113 (2005). https://doi.org/10.1007/s00439-004-1213-8

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