Population-genetic comparison of the Sorbian isolate population in Germany with the German KORA population using genome-wide SNP arrays

Persistent Link:
http://hdl.handle.net/10150/610390
Title:
Population-genetic comparison of the Sorbian isolate population in Germany with the German KORA population using genome-wide SNP arrays
Author:
Gross, Arnd; Tonjes, Anke; Kovacs, Peter; Veeramah, Krishna; Ahnert, Peter; Roshyara, Nab; Gieger, Christian; Rueckert, Ina-Maria; Loeffler, Markus; Stoneking, Mark; Wichmann, Heinz-Erich; Novembre, John; Stumvoll, Michael; Scholz, Markus
Affiliation:
Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, 04107 Leipzig, Germany; LIFE Center (Leipzig Interdisciplinary Research Cluster of Genetic Factors, Phenotypes and Environment), University of Leipzig, Philipp-Rosenthal Strasse 27, 04103 Leipzig, Germany; Department of Medicine, University of Leipzig, Liebigstrasse 18, 04103 Leipzig, Germany; IFB Adiposity Diseases, University of Leipzig, Stephanstrasse 9c, 04103 Leipzig, Germany; Interdisciplinary Center for Clinical Research, University of Leipzig, Liebigstrasse 21, 04103 Leipzig, Germany; Dept Eco & Evo Biol, Interdepartmental Program in Bioinformatics, University of California, 621 Charles E. Young Dr South, Box 951606, Los Angeles, Los Angeles, CA 90095-1606 USA; Center for Society and Genetics. University of California, 1323 Rolfe Hall, Box 957221, Los Angeles, Los Angeles, CA 90095-7221, USA; Dept of History, University of California, 6265 Bunche Hall, Box 951473, Los Angeles, Los Angeles, CA 90095-1473, USA; Helmholtz Centre Munich, German Research Center for Environmental Health, Institute of Epidemiology, Ingolstaedter Landstraße 1, 85764 Neuherberg, Germany; Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology, Ludwig-Maximilians-University, Marchioninistraße 15, 81377 Munich, Germany; Klinikum Grosshadern, Ludwig Maximilians University, Marchioninistraße 15, 81377 Munich, Germany
Issue Date:
2011
Publisher:
BioMed Central
Citation:
Gross et al. BMC Genetics 2011, 12:67 http://www.biomedcentral.com/1471-2156/12/67
Journal:
BMC Genetics
Rights:
© 2011 Gross et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND:The Sorbs are an ethnic minority in Germany with putative genetic isolation, making the population interesting for disease mapping. A sample of N = 977 Sorbs is currently analysed in several genome-wide meta-analyses. Since genetic differences between populations are a major confounding factor in genetic meta-analyses, we compare the Sorbs with the German outbred population of the KORA F3 study (N = 1644) and other publically available European HapMap populations by population genetic means. We also aim to separate effects of over-sampling of families in the Sorbs sample from effects of genetic isolation and compare the power of genetic association studies between the samples.RESULTS:The degree of relatedness was significantly higher in the Sorbs. Principal components analysis revealed a west to east clustering of KORA individuals born in Germany, KORA individuals born in Poland or Czech Republic, Half-Sorbs (less than four Sorbian grandparents) and Full-Sorbs. The Sorbs cluster is nearest to the cluster of KORA individuals born in Poland. The number of rare SNPs is significantly higher in the Sorbs sample. FST between KORA and Sorbs is an order of magnitude higher than between different regions in Germany. Compared to the other populations, Sorbs show a higher proportion of individuals with runs of homozygosity between 2.5 Mb and 5 Mb. Linkage disequilibrium (LD) at longer range is also slightly increased but this has no effect on the power of association studies.Oversampling of families in the Sorbs sample causes detectable bias regarding higher FST values and higher LD but the effect is an order of magnitude smaller than the observed differences between KORA and Sorbs. Relatedness in the Sorbs also influenced the power of uncorrected association analyses.CONCLUSIONS:Sorbs show signs of genetic isolation which cannot be explained by over-sampling of relatives, but the effects are moderate in size. The Slavonic origin of the Sorbs is still genetically detectable.Regarding LD structure, a clear advantage for genome-wide association studies cannot be deduced. The significant amount of cryptic relatedness in the Sorbs sample results in inflated variances of Beta-estimators which should be considered in genetic association analyses.
EISSN:
1471-2156
DOI:
10.1186/1471-2156-12-67
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2156/12/67

Full metadata record

DC FieldValue Language
dc.contributor.authorGross, Arnden
dc.contributor.authorTonjes, Ankeen
dc.contributor.authorKovacs, Peteren
dc.contributor.authorVeeramah, Krishnaen
dc.contributor.authorAhnert, Peteren
dc.contributor.authorRoshyara, Naben
dc.contributor.authorGieger, Christianen
dc.contributor.authorRueckert, Ina-Mariaen
dc.contributor.authorLoeffler, Markusen
dc.contributor.authorStoneking, Marken
dc.contributor.authorWichmann, Heinz-Erichen
dc.contributor.authorNovembre, Johnen
dc.contributor.authorStumvoll, Michaelen
dc.contributor.authorScholz, Markusen
dc.date.accessioned2016-05-20T09:05:44Z-
dc.date.available2016-05-20T09:05:44Z-
dc.date.issued2011en
dc.identifier.citationGross et al. BMC Genetics 2011, 12:67 http://www.biomedcentral.com/1471-2156/12/67en
dc.identifier.doi10.1186/1471-2156-12-67en
dc.identifier.urihttp://hdl.handle.net/10150/610390-
dc.description.abstractBACKGROUND:The Sorbs are an ethnic minority in Germany with putative genetic isolation, making the population interesting for disease mapping. A sample of N = 977 Sorbs is currently analysed in several genome-wide meta-analyses. Since genetic differences between populations are a major confounding factor in genetic meta-analyses, we compare the Sorbs with the German outbred population of the KORA F3 study (N = 1644) and other publically available European HapMap populations by population genetic means. We also aim to separate effects of over-sampling of families in the Sorbs sample from effects of genetic isolation and compare the power of genetic association studies between the samples.RESULTS:The degree of relatedness was significantly higher in the Sorbs. Principal components analysis revealed a west to east clustering of KORA individuals born in Germany, KORA individuals born in Poland or Czech Republic, Half-Sorbs (less than four Sorbian grandparents) and Full-Sorbs. The Sorbs cluster is nearest to the cluster of KORA individuals born in Poland. The number of rare SNPs is significantly higher in the Sorbs sample. FST between KORA and Sorbs is an order of magnitude higher than between different regions in Germany. Compared to the other populations, Sorbs show a higher proportion of individuals with runs of homozygosity between 2.5 Mb and 5 Mb. Linkage disequilibrium (LD) at longer range is also slightly increased but this has no effect on the power of association studies.Oversampling of families in the Sorbs sample causes detectable bias regarding higher FST values and higher LD but the effect is an order of magnitude smaller than the observed differences between KORA and Sorbs. Relatedness in the Sorbs also influenced the power of uncorrected association analyses.CONCLUSIONS:Sorbs show signs of genetic isolation which cannot be explained by over-sampling of relatives, but the effects are moderate in size. The Slavonic origin of the Sorbs is still genetically detectable.Regarding LD structure, a clear advantage for genome-wide association studies cannot be deduced. The significant amount of cryptic relatedness in the Sorbs sample results in inflated variances of Beta-estimators which should be considered in genetic association analyses.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2156/12/67en
dc.rights© 2011 Gross et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.titlePopulation-genetic comparison of the Sorbian isolate population in Germany with the German KORA population using genome-wide SNP arraysen
dc.typeArticleen
dc.identifier.eissn1471-2156en
dc.contributor.departmentInstitute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, 04107 Leipzig, Germanyen
dc.contributor.departmentLIFE Center (Leipzig Interdisciplinary Research Cluster of Genetic Factors, Phenotypes and Environment), University of Leipzig, Philipp-Rosenthal Strasse 27, 04103 Leipzig, Germanyen
dc.contributor.departmentDepartment of Medicine, University of Leipzig, Liebigstrasse 18, 04103 Leipzig, Germanyen
dc.contributor.departmentIFB Adiposity Diseases, University of Leipzig, Stephanstrasse 9c, 04103 Leipzig, Germanyen
dc.contributor.departmentInterdisciplinary Center for Clinical Research, University of Leipzig, Liebigstrasse 21, 04103 Leipzig, Germanyen
dc.contributor.departmentDept Eco & Evo Biol, Interdepartmental Program in Bioinformatics, University of California, 621 Charles E. Young Dr South, Box 951606, Los Angeles, Los Angeles, CA 90095-1606 USAen
dc.contributor.departmentCenter for Society and Genetics. University of California, 1323 Rolfe Hall, Box 957221, Los Angeles, Los Angeles, CA 90095-7221, USAen
dc.contributor.departmentDept of History, University of California, 6265 Bunche Hall, Box 951473, Los Angeles, Los Angeles, CA 90095-1473, USAen
dc.contributor.departmentHelmholtz Centre Munich, German Research Center for Environmental Health, Institute of Epidemiology, Ingolstaedter Landstraße 1, 85764 Neuherberg, Germanyen
dc.contributor.departmentMax Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germanyen
dc.contributor.departmentInstitute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology, Ludwig-Maximilians-University, Marchioninistraße 15, 81377 Munich, Germanyen
dc.contributor.departmentKlinikum Grosshadern, Ludwig Maximilians University, Marchioninistraße 15, 81377 Munich, Germanyen
dc.identifier.journalBMC Geneticsen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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