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      Recent genomic heritage in Scotland.

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          Abstract

          The Generation Scotland Scottish Family Health Study (GS:SFHS) includes 23,960 participants from across Scotland with records for many health-related traits and environmental covariates. Genotypes at ~700 K SNPs are currently available for 10,000 participants. The cohort was designed as a resource for genetic and health related research and the study of complex traits. In this study we developed a suite of analyses to disentangle the genomic differentiation within GS:SFHS individuals to describe and optimise the sample and methods for future analyses.

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          Assessing the impact of population stratification on genetic association studies.

          Matthew Freedman, David Reich, Kathryn Penney … (2004)
          Population stratification refers to differences in allele frequencies between cases and controls due to systematic differences in ancestry rather than association of genes with disease. It has been proposed that false positive associations due to stratification can be controlled by genotyping a few dozen unlinked genetic markers. To assess stratification empirically, we analyzed data from 11 case-control and case-cohort association studies. We did not detect statistically significant evidence for stratification but did observe that assessments based on a few dozen markers lack power to rule out moderate levels of stratification that could cause false positive associations in studies designed to detect modest genetic risk factors. After increasing the number of markers and samples in a case-cohort study (the design most immune to stratification), we found that stratification was in fact present. Our results suggest that modest amounts of stratification can exist even in well designed studies.
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            Genomic Runs of Homozygosity Record Population History and Consanguinity

            Mirna Kirin, Ruth McQuillan, Christopher S. Franklin … (2010)
            The human genome is characterised by many runs of homozygous genotypes, where identical haplotypes were inherited from each parent. The length of each run is determined partly by the number of generations since the common ancestor: offspring of cousin marriages have long runs of homozygosity (ROH), while the numerous shorter tracts relate to shared ancestry tens and hundreds of generations ago. Human populations have experienced a wide range of demographic histories and hold diverse cultural attitudes to consanguinity. In a global population dataset, genome-wide analysis of long and shorter ROH allows categorisation of the mainly indigenous populations sampled here into four major groups in which the majority of the population are inferred to have: (a) recent parental relatedness (south and west Asians); (b) shared parental ancestry arising hundreds to thousands of years ago through long term isolation and restricted effective population size (Ne), but little recent inbreeding (Oceanians); (c) both ancient and recent parental relatedness (Native Americans); and (d) only the background level of shared ancestry relating to continental Ne (predominantly urban Europeans and East Asians; lowest of all in sub-Saharan African agriculturalists), and the occasional cryptically inbred individual. Moreover, individuals can be positioned along axes representing this demographic historic space. Long runs of homozygosity are therefore a globally widespread and under-appreciated characteristic of our genomes, which record past consanguinity and population isolation and provide a distinctive record of the demographic history of an individual's ancestors. Individual ROH measures will also allow quantification of the disease risk arising from polygenic recessive effects.
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              Haplotype blocks and linkage disequilibrium in the human genome.

              Judy Wall, Jonathan Pritchard (2003)
              There is great interest in the patterns and extent of linkage disequilibrium (LD) in humans and other species. Characterizing LD is of central importance for gene-mapping studies and can provide insights into the biology of recombination and human demographic history. Here, we review recent developments in this field, including the recently proposed 'haplotype-block' model of LD. We describe some of the recent data in detail and compare the observed patterns to those seen in simulations.
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                Author and article information

                Journal
                Journal ID (iso-abbrev): BMC Genomics
                Title: BMC genomics
                Publisher: Springer Science and Business Media LLC
                ISSN (Electronic): 1471-2164
                ISSN (Print): 1471-2164
                Publication date (Electronic): Jun 06 2015
                Volume: 16
                Affiliations
                [1 ] MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK. Carmen.Amador@igmm.ed.ac.uk.
                [2 ] MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK. Jennifer.Huffman@igmm.ed.ac.uk.
                [3 ] MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK. HTrochet@gmail.com.
                [4 ] MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK. Archie.Campbell@igmm.ed.ac.uk.
                [5 ] MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK. David.Porteous@igmm.ed.ac.uk.
                [6 ] Centre for Population Health Sciences, University of Edinburgh, Edinburgh, EH8 9AG, UK. Jim.Wilson@ed.ac.uk.
                [7 ] MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK. Nick.Hastie@igmm.ed.ac.uk.
                [8 ] MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK. Veronique.Vitart@igmm.ed.ac.uk.
                [9 ] MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK. Caroline.Hayward@igmm.ed.ac.uk.
                [10 ] MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK. Pau.Navarro@ed.ac.uk.
                [11 ] MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK. Chris.Haley@roslin.ed.ac.uk.
                [12 ] Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK. Chris.Haley@roslin.ed.ac.uk.
                Article
                Publisher Item ID: 10.1186/s12864-015-1605-2
                DOI: 10.1186/s12864-015-1605-2
                PMC ID: 4458001
                PubMed ID: 26048416
                SO-VID: b357c4c7-e916-4f4b-9aa7-3a2fd4e88015
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