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Gilbert E, Zurel H, MacMillan ME, Demiriz S, Mirhendi S, Merrigan M, O'Reilly S, Molloy AM, Brody LC, Bodmer W, Leach RA, Scott REM, Mugford G, Randhawa R, Stephens JC, Symington AL, Cavalleri GL, Phillips MS. The Newfoundland and Labrador mosaic founder population descends from an Irish and British diaspora from 300 years ago. Commun Biol 2023; 6:469. [PMID: 37117635 PMCID: PMC10147672 DOI: 10.1038/s42003-023-04844-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 03/28/2023] [Indexed: 04/30/2023] Open
Abstract
The founder population of Newfoundland and Labrador (NL) is a unique genetic resource, in part due to its geographic and cultural isolation, where historical records describe a migration of European settlers, primarily from Ireland and England, to NL in the 18th and 19th centuries. Whilst its historical isolation, and increased prevalence of certain monogenic disorders are well appreciated, details of the fine-scale genetic structure and ancestry of the population are lacking. Understanding the genetic origins and background of functional, disease causing, genetic variants would aid genetic mapping efforts in the Province. Here, we leverage dense genome-wide SNP data on 1,807 NL individuals to reveal fine-scale genetic structure in NL that is clustered around coastal communities and correlated with Christian denomination. We show that the majority of NL European ancestry can be traced back to the south-east and south-west of Ireland and England, respectively. We date a substantial population size bottleneck approximately 10-15 generations ago in NL, associated with increased haplotype sharing and autozygosity. Our results reveal insights into the population history of NL and demonstrate evidence of a population conducive to further genetic studies and biomarker discovery.
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Affiliation(s)
- Edmund Gilbert
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland.
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland.
| | - Heather Zurel
- Sequence Bioinformatics, Inc., St. John's, Newfoundland and Labrador, Canada
| | | | - Sedat Demiriz
- Sequence Bioinformatics, Inc., St. John's, Newfoundland and Labrador, Canada
| | - Sadra Mirhendi
- Sequence Bioinformatics, Inc., St. John's, Newfoundland and Labrador, Canada
| | | | | | - Anne M Molloy
- School of Medicine, Trinity College, Dublin, Ireland
| | - Lawrence C Brody
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Walter Bodmer
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Richard A Leach
- Sequence Bioinformatics, Inc., St. John's, Newfoundland and Labrador, Canada
| | - Roderick E M Scott
- Sequence Bioinformatics, Inc., St. John's, Newfoundland and Labrador, Canada
| | - Gerald Mugford
- Sequence Bioinformatics, Inc., St. John's, Newfoundland and Labrador, Canada
| | - Ranjit Randhawa
- Sequence Bioinformatics, Inc., St. John's, Newfoundland and Labrador, Canada
| | | | - Alison L Symington
- Sequence Bioinformatics, Inc., St. John's, Newfoundland and Labrador, Canada
| | - Gianpiero L Cavalleri
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Michael S Phillips
- Sequence Bioinformatics, Inc., St. John's, Newfoundland and Labrador, Canada
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Surnames in south-eastern France: structure of the rural population during the 19th century through isonymy. J Biosoc Sci 2023; 55:174-189. [PMID: 34907866 DOI: 10.1017/s0021932021000699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
An analysis of the distribution of surnames through time and space allows us to understand the structure of human groups, their exchanges or even their possible isolation. The French population has already been studied through surnames and it has been shown that the Sud-Provence-Alpes-Côte d'Azur region differed from the rest of France in both the 20th and 21st centuries (Mourrieras et al., ; Scapoli et al., ). The objective of this study was to understand the population evolution and particularities of the Sud-Provence-Alpes-Côte d'Azur region through an analysis of the distribution of surnames over an earlier period: the 19th century. For this work, 806,069 birth records from 521 communes between 1810 and 1890 were recorded and a total of 23,340 surnames were collected. The estimation of various isonymic parameters has allowed a description of this corpus never exploited before. In order to appreciate the population evolution, the data set was divided into three periods of 25 years. The canton was the geographical unit of this study, and similarities and differences between each of them were evaluated using Lasker distances, which allow the construction of dendrograms. A positive and significant correlation (p<0.0001) was found between Lasker distances and geographical distances using the Mantel test. The lowest inbreeding estimates were found in the Durance Valley. Migration, estimated from the v-index of Karlin and McGregor (), showed higher values in the south-western quarter of the region. The decrease in Rst values across the three periods is consistent with a homogenization of the patronymic between the cantons. This three-period approach showed a population evolution influenced by linguistic, cultural, historical and migratory phenomena since the Middle Ages, disrupted by the socioeconomic changes of the 19th century.
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Huszar TI, Bodmer WF, Hutnik K, Wetton JH, Jobling MA. Sequencing of autosomal, mitochondrial and Y-chromosomal forensic markers in the People of the British Isles cohort detects population structure dominated by patrilineages. Forensic Sci Int Genet 2022; 59:102725. [DOI: 10.1016/j.fsigen.2022.102725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/08/2022] [Accepted: 05/13/2022] [Indexed: 11/27/2022]
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British surname origins, population structure and health outcomes-an observational study of hospital admissions. Sci Rep 2022; 12:2156. [PMID: 35140220 PMCID: PMC8828752 DOI: 10.1038/s41598-022-05651-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 01/14/2022] [Indexed: 11/23/2022] Open
Abstract
Population structure is a confounder on pathways linking genotypes to health outcomes. This study examines whether the historical, geographical origins of British surnames are associated with health outcomes today. We coded hospital admissions of over 30 million patients in England between 1999 and 2013 to their British surname origin and divided their diagnoses into 125 major disease categories (of which 94 were complete-case). A base population was constructed with patients’ first admission of any kind. Age- and sex-standardised odds ratios were calculated with logistic regression using patients with ubiquitous English surnames such as “Smith” as reference (alpha = .05; Benjamini–Hochberg false discovery rate (FDR) = .05). The results were scanned for “signals”, where a branch of related surname origins all had significantly higher or lower risk. Age- and sex-standardised admission (alpha = .05) was calculated for each signal across area deprivation and surname origin density quintiles. Signals included three branches of English surnames (disorders of teeth and jaw, fractures, upper gastrointestinal disorders). Although the signal with fractures was considered unusual overall, 2 out of the 9 origins in the branch would only be significant at a FDR > .05: OR 0.92 (95% confidence interval 0.86–0.98) and 0.70 (0.55–0.90). The risk was only different in the quintile with the highest density of that group. Differential risk remained when studied across quintiles of area deprivation. The study shows that surname origins are associated with diverse health outcomes and thus act as markers of population structure over and above area deprivation.
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Phylogeographic review of Y chromosome haplogroups in Europe. Int J Legal Med 2021; 135:1675-1684. [PMID: 34216266 DOI: 10.1007/s00414-021-02644-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/16/2021] [Indexed: 10/20/2022]
Abstract
The Y chromosome has been widely explored for the study of human migrations. Due to its paternal inheritance, the Y chromosome polymorphisms are helpful tools for understanding the geographical distribution of populations all over the world and for inferring their origin, which is really useful in forensics. The remarkable historical context of Europe, with numerous migrations and invasions, has turned this continent into a melting pot. For this reason, it is interesting to study the Y chromosome variability and how it has contributed to improving our knowledge of the distribution and development of European male genetic pool as it is today. The analysis of Y lineages in Europe shows the predominance of four haplogroups, R1b-M269, I1-M253, I2-M438 and R1a-M420. However, other haplogroups have been identified which, although less frequent, provide significant evidence about the paternal origin of the populations. In addition, the study of the Y chromosome in Europe is a valuable tool for revealing the genetic trace of the different European colonizations, mainly in several American countries, where the European ancestry is mostly detected by the presence of the R1b-M269 haplogroup. Therefore, the objective of this review is to compile the studies of the Y chromosome haplogroups in current European populations, in order to provide an outline of these haplogroups which facilitate their use in forensic studies.
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Y chromosome analysis for common surnames in the Japanese male population. J Hum Genet 2021; 66:731-738. [PMID: 33526818 DOI: 10.1038/s10038-020-00884-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/06/2020] [Accepted: 11/23/2020] [Indexed: 11/08/2022]
Abstract
For many years of Japan's long history, Japanese surnames have been handed down patrilineally. This study investigated relations between major surnames and Y chromosomal polymorphism among the Japanese male population. To analyze genetic phylogeny in namesakes, the Y-single nucleotide polymorphism (SNP) plus Y-short tandem repeat (STR) approach was employed. A haplogroup based on SNPs and haplotypes at 17 STR loci were typed in 567 unrelated volunteers recruited in Kanagawa, Japan. Samples covered 27 common surnames such as Satoh and Suzuki, each name having 10-55 bearers. Significant difference was found for SNP haplogroup compositions and a multidimensional scaling plot using STR haplotypes in several surname groups. By contrast, these common surnames displayed wide diversity with phylogenetic networks, suggesting that no genetic drift event has occurred in their history. In all, 22 descent clusters were found, as judgcriteria ed by ad hoc of groups within five mutational steps in the 15 STR loci with the same haplogroup. The times of the most recent common ancestor ranged from 279 to over 2577 years. According to the approximate millennium span of Japanese surname history, descent criteria are expected to be reasonable for grouping within four step-neighbors. High heterogeneity of common surnames resembles that observed for England and Spain, but not for Ireland. Our results highlight that common Japanese surnames consist of descent clusters and many singletons, reflecting a mixture of long-term bearers and short-term bearers among the population. The genetic study of this population revealed characteristic features of Japanese surnames.
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Bro N, Mendoza M. Surname affinity in Santiago, Chile: A network-based approach that uncovers urban segregation. PLoS One 2021; 16:e0244372. [PMID: 33406147 PMCID: PMC7787389 DOI: 10.1371/journal.pone.0244372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/09/2020] [Indexed: 11/18/2022] Open
Abstract
Based on a geocoded registry of more than four million residents of Santiago, Chile, we build two surname-based networks that reveal the city’s population structure. The first network is formed from paternal and maternal surname pairs. The second network is formed from the isonymic distances between the city’s neighborhoods. These networks uncover the city’s main ethnic groups and their spatial distribution. We match the networks to a socioeconomic index, and find that surnames of high socioeconomic status tend to cluster, be more diverse, and occupy a well-defined quarter of the city. The results are suggestive of a high degree of urban segregation in Santiago.
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Affiliation(s)
- Naim Bro
- Millennium Institute of Foundational Research on Data, Santiago, Chile
| | - Marcelo Mendoza
- Millennium Institute of Foundational Research on Data, Santiago, Chile
- Department of Informatics, Universidad Técnica Federico Santa María, Santiago, Chile
- * E-mail:
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Abstract
It has been suggested that Dupuytren's disease has an origin in Norse countries. We harnessed data from a genome-wide association study of Dupuytren's disease and the People of the British Isles study to determine evidence for a Norse origin of Dupuytren's disease. We computed Wright's Fixation Index between Orkney (Norse ancestry), Wales (ancient British) and South East England (Anglo-Saxons); compared mean Wright's Fixation Index in cases versus controls; used permutation to determine any excess of Norse inheritance in disease associated variants; constructed a genetic risk score for Dupuytren's disease and applied this to the People of the British Isles dataset to look for systematic differences between counties with known high and low levels of Norse ancestry. Finally, chromosome painting was used to see whether Dupuytren's disease-associated single nucleotide polymorphisms are geographically structured. In all analyses, no evidence was found for an excess of Norse ancestry in Dupuytren's disease. We conclude that there is no genetic evidence for a 'Viking origin of Dupuytren's disease'.
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Affiliation(s)
- Michael Ng
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford, Oxford, UK
| | - Daniel J Lawson
- Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Bruce Winney
- Department of Oncology, University of Oxford, Oxford, UK
| | - Dominic Furniss
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford, Oxford, UK.,NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
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Anderson K, Cañadas-Garre M, Chambers R, Maxwell AP, McKnight AJ. The Challenges of Chromosome Y Analysis and the Implications for Chronic Kidney Disease. Front Genet 2019; 10:781. [PMID: 31552093 PMCID: PMC6737325 DOI: 10.3389/fgene.2019.00781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/24/2019] [Indexed: 12/17/2022] Open
Abstract
The role of chromosome Y in chronic kidney disease (CKD) remains unknown, as chromosome Y is typically excluded from genetic analysis in CKD. The complex, sex-specific presentation of CKD could be influenced by chromosome Y genetic variation, but there is limited published research available to confirm or reject this hypothesis. Although traditionally thought to be associated with male-specific disease, evidence linking chromosome Y genetic variation to common complex disorders highlights a potential gap in CKD research. Chromosome Y variation has been associated with cardiovascular disease, a condition closely linked to CKD and one with a very similar sexual dimorphism. Relatively few sources of genetic variation in chromosome Y have been examined in CKD. The association between chromosome Y aneuploidy and CKD has never been explored comprehensively, while analyses of microdeletions, copy number variation, and single-nucleotide polymorphisms in CKD have been largely limited to the autosomes or chromosome X. In many studies, it is unclear whether the analyses excluded chromosome Y or simply did not report negative results. Lack of imputation, poor cross-study comparability, and requirement for separate or additional analyses in comparison with autosomal chromosomes means that chromosome Y is under-investigated in the context of CKD. Limitations in genotyping arrays could be overcome through use of whole-chromosome sequencing of chromosome Y that may allow analysis of many different types of genetic variation across the chromosome to determine if chromosome Y genetic variation is associated with CKD.
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Affiliation(s)
- Kerry Anderson
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, c/o Regional Genetics Centre, Belfast City Hospital, Belfast, United Kingdom
| | - Marisa Cañadas-Garre
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, c/o Regional Genetics Centre, Belfast City Hospital, Belfast, United Kingdom
| | - Robyn Chambers
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, c/o Regional Genetics Centre, Belfast City Hospital, Belfast, United Kingdom
| | - Alexander Peter Maxwell
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, c/o Regional Genetics Centre, Belfast City Hospital, Belfast, United Kingdom.,Regional Nephrology Unit, Belfast City Hospital, Belfast, United Kingdom
| | - Amy Jayne McKnight
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, c/o Regional Genetics Centre, Belfast City Hospital, Belfast, United Kingdom
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Orrù A, De Iasio S, Frederic P, Girotti M, Boano R, Sanna E. Spatial diffusion of surnames by long transhumance routes between highland and lowland: A study in Sardinia. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2018; 69:127-138. [PMID: 30017379 DOI: 10.1016/j.jchb.2018.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 06/26/2018] [Indexed: 11/24/2022]
Abstract
RIASSUNTO.
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Affiliation(s)
- A Orrù
- Department of Life Sciences and Systems Biology, University of Turin, Italy.
| | - S De Iasio
- Department of Biosciences, University of Parma, Italy
| | - P Frederic
- Department of Economics "Marco Biagi", RECent (Center for Economic Research), University of Modena, Italy
| | - M Girotti
- Department of Life Sciences and Systems Biology, University of Turin, Italy
| | - R Boano
- Department of Life Sciences and Systems Biology, University of Turin, Italy
| | - E Sanna
- Department of Environmental and Life Sciences, University of Cagliari, Italy
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11
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Shi CM, Li C, Ma L, Chi L, Zhao J, Yuan W, Zhou Z, Yan JW, Chen H. Inferring Chinese surnames with Y-STR profiles. Forensic Sci Int Genet 2018; 33:66-71. [DOI: 10.1016/j.fsigen.2017.11.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 11/21/2017] [Accepted: 11/23/2017] [Indexed: 10/18/2022]
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12
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Crouch DJM, Winney B, Koppen WP, Christmas WJ, Hutnik K, Day T, Meena D, Boumertit A, Hysi P, Nessa A, Spector TD, Kittler J, Bodmer WF. Genetics of the human face: Identification of large-effect single gene variants. Proc Natl Acad Sci U S A 2018; 115:E676-E685. [PMID: 29301965 PMCID: PMC5789906 DOI: 10.1073/pnas.1708207114] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To discover specific variants with relatively large effects on the human face, we have devised an approach to identifying facial features with high heritability. This is based on using twin data to estimate the additive genetic value of each point on a face, as provided by a 3D camera system. In addition, we have used the ethnic difference between East Asian and European faces as a further source of face genetic variation. We use principal components (PCs) analysis to provide a fine definition of the surface features of human faces around the eyes and of the profile, and chose upper and lower 10% extremes of the most heritable PCs for looking for genetic associations. Using this strategy for the analysis of 3D images of 1,832 unique volunteers from the well-characterized People of the British Isles study and 1,567 unique twin images from the TwinsUK cohort, together with genetic data for 500,000 SNPs, we have identified three specific genetic variants with notable effects on facial profiles and eyes.
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Affiliation(s)
- Daniel J M Crouch
- Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Bruce Winney
- Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Willem P Koppen
- Centre for Vision, Speech and Signal Processing, Department of Electronic Engineering, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - William J Christmas
- Centre for Vision, Speech and Signal Processing, Department of Electronic Engineering, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - Katarzyna Hutnik
- Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Tammy Day
- Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Devendra Meena
- Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Abdelhamid Boumertit
- Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Pirro Hysi
- TwinsUK, St. Thomas' Hospital, King's College London, London SE1 7EH, United Kingdom
| | - Ayrun Nessa
- TwinsUK, St. Thomas' Hospital, King's College London, London SE1 7EH, United Kingdom
| | - Tim D Spector
- TwinsUK, St. Thomas' Hospital, King's College London, London SE1 7EH, United Kingdom
| | - Josef Kittler
- Centre for Vision, Speech and Signal Processing, Department of Electronic Engineering, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - Walter F Bodmer
- Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom;
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
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The Irish DNA Atlas: Revealing Fine-Scale Population Structure and History within Ireland. Sci Rep 2017; 7:17199. [PMID: 29222464 PMCID: PMC5722868 DOI: 10.1038/s41598-017-17124-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 11/21/2017] [Indexed: 01/31/2023] Open
Abstract
The extent of population structure within Ireland is largely unknown, as is the impact of historical migrations. Here we illustrate fine-scale genetic structure across Ireland that follows geographic boundaries and present evidence of admixture events into Ireland. Utilising the 'Irish DNA Atlas', a cohort (n = 194) of Irish individuals with four generations of ancestry linked to specific regions in Ireland, in combination with 2,039 individuals from the Peoples of the British Isles dataset, we show that the Irish population can be divided in 10 distinct geographically stratified genetic clusters; seven of 'Gaelic' Irish ancestry, and three of shared Irish-British ancestry. In addition we observe a major genetic barrier to the north of Ireland in Ulster. Using a reference of 6,760 European individuals and two ancient Irish genomes, we demonstrate high levels of North-West French-like and West Norwegian-like ancestry within Ireland. We show that that our 'Gaelic' Irish clusters present homogenous levels of ancient Irish ancestries. We additionally detect admixture events that provide evidence of Norse-Viking gene flow into Ireland, and reflect the Ulster Plantations. Our work informs both on Irish history, as well as the study of Mendelian and complex disease genetics involving populations of Irish ancestry.
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Kirijas M, Genadieva Stavrik S, Senev A, Efinska Mladenovska O, Petlichkovski A. HLA-A, -B, -C and -DRB1 allele and haplotype frequencies in the Macedonian population based on a family study. Hum Immunol 2017; 79:145-153. [PMID: 29225116 DOI: 10.1016/j.humimm.2017.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/07/2017] [Accepted: 12/02/2017] [Indexed: 11/29/2022]
Abstract
AIM The aim of this study was to determine HLA allele and 2-, 3- and 4-loci haplotype frequencies in a sample from Macedonian population with defined haplotypes based on family history. MATERIAL AND METHODS We analysed 286 unrelated individuals with Macedonian origin, parents of patients who needed stem cell transplantation, in the period of 01.01.2003 till 31.12.2016. Allele and haplotype frequencies, as well as Hardy-Weinberg equilibrium were calculated using the Arlequin3.5 software. Population comparison was calculated using the PHYLIP software. RESULTS We identified 18 HLA-A, 26 HLA-B, 13 HLA-C and 13 HLA-DRB1 allele group families. The most frequent allele groups in our population were HLA-A*02 (29.0%), HLA-A*24 (13.8%), HLA-B*35 (16.1%), HLA-B*51 (14.7%), HLA-B*18 (14.7%), HLA-C*07 (27.9%), HLA-DRB1*11 (25.5%) and HLA-DRB1*16 (14.8%). The most frequent four loci haplotype was HLA-A*01-B*08-C*07-DRB1*03 (2.7%). Our comparison showed that the Macedonian population is closely related to the neighbouring countries in the Balkan Peninsula. CONCLUSION This study provides data about the HLA diversity in the Macedonian population, which can be very important in the process of unrelated donor search, and in addition yields control group for future disease association studies in our population.
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Affiliation(s)
- Meri Kirijas
- Institute for Immunobiology and Human Genetics, Medical Faculty, Skopje, Macedonia.
| | - Sonja Genadieva Stavrik
- Bone Marrow Transplantation Unit, University Hematology Clinic, Medical Faculty, Skopje, Macedonia
| | - Aleksandar Senev
- Institute for Immunobiology and Human Genetics, Medical Faculty, Skopje, Macedonia
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15
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Abstract
Coupling dense genotype data with new computational methods offers unprecedented opportunities for individual-level ancestry estimation once geographically precisely defined reference data sets become available. We study such a reference data set for Finland containing 2376 such individuals from the FINRISK Study survey of 1997 both of whose parents were born close to each other. This sampling strategy focuses on the population structure present in Finland before the 1950s. By using the recent haplotype-based methods ChromoPainter (CP) and FineSTRUCTURE (FS) we reveal a highly geographically clustered genetic structure in Finland and report its connections to the settlement history as well as to the current dialectal regions of the Finnish language. The main genetic division within Finland shows striking concordance with the 1323 borderline of the treaty of Nöteborg. In general, we detect genetic substructure throughout the country, which reflects stronger regional genetic differences in Finland compared to, for example, the UK, which in a similar analysis was dominated by a single unstructured population. We expect that similar population genetic reference data sets will become available for many more populations in the near future with important applications, for example, in forensic genetics and in genetic association studies. With this in mind, we report those extensions of the CP + FS approach that we found most useful in our analyses of the Finnish data.
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16
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Population resequencing of European mitochondrial genomes highlights sex-bias in Bronze Age demographic expansions. Sci Rep 2017; 7:12086. [PMID: 28935946 PMCID: PMC5608872 DOI: 10.1038/s41598-017-11307-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 08/22/2017] [Indexed: 11/17/2022] Open
Abstract
Interpretations of genetic data concerning the prehistory of Europe have long been a subject of great debate, but increasing amounts of ancient and modern DNA data are now providing new and more informative evidence. Y-chromosome resequencing studies in Europe have highlighted the prevalence of recent expansions of male lineages, and focused interest on the Bronze Age as a period of cultural and demographic change. These findings contrast with phylogeographic studies based on mitochondrial DNA (mtDNA), which have been interpreted as supporting expansions from glacial refugia. Here we have undertaken a population-based resequencing of complete mitochondrial genomes in Europe and the Middle East, in 340 samples from 17 populations for which Y-chromosome sequence data are also available. Demographic reconstructions show no signal of Bronze Age expansion, but evidence of Paleolithic expansions in all populations except the Saami, and with an absence of detectable geographical pattern. In agreement with previous inference from modern and ancient DNA data, the unbiased comparison between the mtDNA and Y-chromosome population datasets emphasizes the sex-biased nature of recent demographic transitions in Europe.
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17
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Affiliation(s)
- Georgios Athanasiadis
- a Bioinformatics Research Centre, C.F. Møllers Allé, Building 1110, Aarhus University , 8000, Aarhus C , Denmark
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Genomic insights into the population structure and history of the Irish Travellers. Sci Rep 2017; 7:42187. [PMID: 28181990 PMCID: PMC5299991 DOI: 10.1038/srep42187] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/04/2017] [Indexed: 01/17/2023] Open
Abstract
The Irish Travellers are a population with a history of nomadism; consanguineous unions are common and they are socially isolated from the surrounding, ‘settled’ Irish people. Low-resolution genetic analysis suggests a common Irish origin between the settled and the Traveller populations. What is not known, however, is the extent of population structure within the Irish Travellers, the time of divergence from the general Irish population, or the extent of autozygosity. Using a sample of 50 Irish Travellers, 143 European Roma, 2232 settled Irish, 2039 British and 6255 European or world-wide individuals, we demonstrate evidence for population substructure within the Irish Traveller population, and estimate a time of divergence before the Great Famine of 1845–1852. We quantify the high levels of autozygosity, which are comparable to levels previously described in Orcadian 1st/2nd cousin offspring, and finally show the Irish Traveller population has no particular genetic links to the European Roma. The levels of autozygosity and distinct Irish origins have implications for disease mapping within Ireland, while the population structure and divergence inform on social history.
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Kandt J, Cheshire JA, Longley PA. Regional surnames and genetic structure in Great Britain. TRANSACTIONS (INSTITUTE OF BRITISH GEOGRAPHERS : 1965) 2016; 41:554-569. [PMID: 27708455 PMCID: PMC5032893 DOI: 10.1111/tran.12131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Indexed: 06/06/2023]
Abstract
Following the increasing availability of DNA-sequenced data, the genetic structure of populations can now be inferred and studied in unprecedented detail. Across social science, this innovation is shaping new bio-social research agendas, attracting substantial investment in the collection of genetic, biological and social data for large population samples. Yet genetic samples are special because the precise populations that they represent are uncertain and ill-defined. Unlike most social surveys, a genetic sample's representativeness of the population cannot be established by conventional procedures of statistical inference, and the implications for population-wide generalisations about bio-social phenomena are little understood. In this paper, we seek to address these problems by linking surname data to a censored and geographically uneven sample of DNA scans, collected for the People of the British Isles study. Based on a combination of global and local spatial correspondence measures, we identify eight regions in Great Britain that are most likely to represent the geography of genetic structure of Great Britain's long-settled population. We discuss the implications of this regionalisation for bio-social investigations. We conclude that, as the often highly selective collection of DNA and biomarkers becomes a more common practice, geography is crucial to understanding variation in genetic information within diverse populations.
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Affiliation(s)
- Jens Kandt
- Department of GeographyUniversity College LondonLondonWC1E 6BT
| | | | - Paul A Longley
- Department of GeographyUniversity College LondonLondonWC1E 6BT
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Rampling R, Peoples S, Mulholland PJ, James A, Al-Salihi O, Twelves CJ, McBain C, Jefferies S, Jackson A, Stewart W, Lindner J, Kutscher S, Hilf N, McGuigan L, Peters J, Hill K, Schoor O, Singh-Jasuja H, Halford SE, Ritchie JWA. A Cancer Research UK First Time in Human Phase I Trial of IMA950 (Novel Multipeptide Therapeutic Vaccine) in Patients with Newly Diagnosed Glioblastoma. Clin Cancer Res 2016; 22:4776-4785. [PMID: 27225692 PMCID: PMC5026298 DOI: 10.1158/1078-0432.ccr-16-0506] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/11/2016] [Indexed: 12/31/2022]
Abstract
PURPOSE To perform a two-cohort, phase I safety and immunogenicity study of IMA950 in addition to standard chemoradiotherapy and adjuvant temozolomide in patients with newly diagnosed glioblastoma. IMA950 is a novel glioblastoma-specific therapeutic vaccine containing 11 tumor-associated peptides (TUMAP), identified on human leukocyte antigen (HLA) surface receptors in primary human glioblastoma tissue. EXPERIMENTAL DESIGN Patients were HLA-A*02-positive and had undergone tumor resection. Vaccination comprised 11 intradermal injections with IMA950 plus granulocyte macrophage colony-stimulating factor (GM-CSF) over a 24-week period, beginning 7 to 14 days prior to initiation of chemoradiotherapy (Cohort 1) or 7 days after chemoradiotherapy (Cohort 2). Safety was assessed according to NCI CTCAE Version 4.0 and TUMAP-specific T-cell immune responses determined. Secondary observations included progression-free survival (PFS), pretreatment regulatory T cell (Treg) levels, and the effect of steroids on T-cell responses. RESULTS Forty-five patients were recruited. Related adverse events included minor injection site reactions, rash, pruritus, fatigue, neutropenia and single cases of allergic reaction, anemia and anaphylaxis. Two patients experienced grade 3 dose-limiting toxicity of fatigue and anaphylaxis. Of 40 evaluable patients, 36 were TUMAP responders and 20 were multi-TUMAP responders, with no important differences between cohorts. No effect of pretreatment Treg levels on IMA950 immunogenicity was observed, and steroids did not affect TUMAP responses. PFS rates were 74% at 6 months and 31% at 9 months. CONCLUSIONS IMA950 plus GM-CSF was well-tolerated with the primary immunogenicity endpoint of observing multi-TUMAP responses in at least 30% of patients exceeded. Further development of IMA950 is encouraged. Clin Cancer Res; 22(19); 4776-85. ©2016 AACRSee related commentary by Lowenstein and Castro, p. 4760.
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Affiliation(s)
- Roy Rampling
- University of Glasgow, Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Sharon Peoples
- Edinburgh Centre for Neuro-Oncology, Western General Hospital, Edinburgh, United Kingdom
| | - Paul J Mulholland
- Department of Oncology, University College London Hospitals, London, United Kingdom
| | - Allan James
- University of Glasgow, Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Omar Al-Salihi
- Adult Neuro-Oncology, Southampton University Hospitals NHS Trust, Southampton, United Kingdom
| | - Christopher J Twelves
- Cancer Research UK Clinical Centre, St James's University Hospital, Leeds, United Kingdom
| | - Catherine McBain
- The Christie NHS Foundation Trust, Withington, Manchester, United Kingdom
| | - Sarah Jefferies
- Cambridge Cancer Trials Centre, Oncology Clinical Trials, Addensbrooke's Hospital, Cambridge, United Kingdom
| | - Alan Jackson
- Wolfson Molecular Imaging Centre, University of Manchester, Manchester, United Kingdom
| | - Willie Stewart
- Department of Neuropathology, The Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Juha Lindner
- Immatics Biotechnologies GmbH, Tübingen, Germany
| | | | - Norbert Hilf
- Immatics Biotechnologies GmbH, Tübingen, Germany
| | - Lesley McGuigan
- Cancer Research UK Centre for Drug Development, London, United Kingdom
| | - Jane Peters
- Cancer Research UK Centre for Drug Development, London, United Kingdom
| | - Karen Hill
- Cancer Research UK Centre for Drug Development, London, United Kingdom
| | | | | | - Sarah E Halford
- Cancer Research UK Centre for Drug Development, London, United Kingdom
| | - James W A Ritchie
- Cancer Research UK Centre for Drug Development, London, United Kingdom.
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21
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Athanasiadis G, Jørgensen FG, Cheng JY, Kjærgaard PC, Schierup MH, Mailund T. Spitting for Science: Danish High School Students Commit to a Large-Scale Self-Reported Genetic Study. PLoS One 2016; 11:e0161822. [PMID: 27571202 PMCID: PMC5003382 DOI: 10.1371/journal.pone.0161822] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 08/14/2016] [Indexed: 11/18/2022] Open
Abstract
Scientific outreach delivers science to the people. But it can also deliver people to the science. In this work, we report our experience from a large-scale public engagement project promoting genomic literacy among Danish high school students with the additional benefit of collecting data for studying the genetic makeup of the Danish population. Not only did we confirm that students have a great interest in their genetic past, but we were also gratified to see that, with the right motivation, adolescents can provide high-quality data for genetic studies.
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Affiliation(s)
- Georgios Athanasiadis
- Bioinformatics Research Centre, Aarhus University, 8000, Aarhus, Denmark
- Centre for Biocultural History, Aarhus University, 8000, Aarhus, Denmark
- * E-mail:
| | | | - Jade Y. Cheng
- Bioinformatics Research Centre, Aarhus University, 8000, Aarhus, Denmark
| | - Peter C. Kjærgaard
- Centre for Biocultural History, Aarhus University, 8000, Aarhus, Denmark
- Department of Culture and Society, Aarhus University, 8000, Aarhus, Denmark
- The Natural History Museum of Denmark, University of Copenhagen, 1471, Copenhagen, Denmark
| | - Mikkel H. Schierup
- Bioinformatics Research Centre, Aarhus University, 8000, Aarhus, Denmark
- Centre for Biocultural History, Aarhus University, 8000, Aarhus, Denmark
- Department of Bioscience, Aarhus University, 8000, Aarhus, Denmark
| | - Thomas Mailund
- Bioinformatics Research Centre, Aarhus University, 8000, Aarhus, Denmark
- Centre for Biocultural History, Aarhus University, 8000, Aarhus, Denmark
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22
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Vahia MN, Ladiwala U, Mahathe P, Mathur D. Population Dynamics of Early Human Migration in Britain. PLoS One 2016; 11:e0154641. [PMID: 27148959 PMCID: PMC4858239 DOI: 10.1371/journal.pone.0154641] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/15/2016] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Early human migration is largely determined by geography and human needs. These are both deterministic parameters when small populations move into unoccupied areas where conflicts and large group dynamics are not important. The early period of human migration into the British Isles provides such a laboratory which, because of its relative geographical isolation, may allow some insights into the complex dynamics of early human migration and interaction. METHOD AND RESULTS We developed a simulation code based on human affinity to habitable land, as defined by availability of water sources, altitude, and flatness of land, in choosing the path of migration. Movement of people on the British island over the prehistoric period from their initial entry points was simulated on the basis of data from the megalithic period. Topographical and hydro-shed data from satellite databases was used to define habitability, based on distance from water bodies, flatness of the terrain, and altitude above sea level. We simulated population movement based on assumptions of affinity for more habitable places, with the rate of movement tempered by existing populations. We compared results of our computer simulations with genetic data and show that our simulation can predict fairly accurately the points of contacts between different migratory paths. Such comparison also provides more detailed information about the path of peoples' movement over ~2000 years before the present era. CONCLUSIONS We demonstrate an accurate method to simulate prehistoric movements of people based upon current topographical satellite data. Our findings are validated by recently-available genetic data. Our method may prove useful in determining early human population dynamics even when no genetic information is available.
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Affiliation(s)
- Mayank N. Vahia
- Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
| | - Uma Ladiwala
- UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Kalina, Mumbai 400098, India
| | - Pavan Mahathe
- Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
| | - Deepak Mathur
- Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
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Traylor M, Adib‐Samii P, Harold D, Dichgans M, Williams J, Lewis CM, Markus HS. Shared genetic contribution to Ischaemic Stroke and Alzheimer's Disease. Ann Neurol 2016; 79:739-747. [PMID: 26913989 PMCID: PMC4864940 DOI: 10.1002/ana.24621] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 02/17/2016] [Accepted: 02/18/2016] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Increasing evidence suggests epidemiological and pathological links between Alzheimer's disease (AD) and Ischaemic Stroke (IS). We investigated the evidence that shared genetic factors underpin the two diseases. METHODS Using genome wide association study (GWAS) data from METASTROKE+ (15,916 IS cases and 68,826 controls) and IGAP (17,008 AD cases and 37,154 controls), we evaluated known associations with AD and IS. On the subset of data for which we could obtain compatible genotype-level data (4,610 IS cases, 1,281 AD cases and 14,320 controls), we estimated the genome-wide genetic correlation (rG) between AD and IS, and the three subtypes (cardioembolic, small vessel, large vessel), using genome-wide SNP data. We then performed a meta-analysis and pathway analysis in the combined AD and small vessel stroke datasets to identify the SNPs and molecular pathways through which disease risk may be conferred. RESULTS We found evidence of a shared genetic contribution between AD and small vessel stroke (rG(SE)=0.37(0.17); p=0.011). Conversely, there was no evidence to support shared genetic factors in AD and IS overall, or with the other stroke subtypes. Of the known GWAS associations with IS or AD, none reached significance for association with the other trait (or stroke subtypes). A meta-analysis of AD IGAP and METASTROKE+ small vessel stroke GWAS data highlighted a region (ATP5H/KCTD2/ICT1), associated with both diseases (p=1.8x10-8 ). A pathway analysis identified four associated pathways, involving cholesterol transport and immune response. INTERPRETATION Our findings indicate shared genetic susceptibility to AD and small vessel stroke and highlight potential causal pathways and loci. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Matthew Traylor
- Stroke Research Group, Department of Clinical NeurosciencesUniversity of CambridgeCambridgeUnited Kingdom
- Department of Medical & Molecular GeneticsKing's College LondonLondonUnited Kingdom
| | - Poneh Adib‐Samii
- Stroke and Dementia Research CenterSt George's University of LondonLondonUnited Kingdom
| | - Denise Harold
- School of BiotechnologyDublin City UniversityDublinIreland
| | | | - Martin Dichgans
- Institute for Stroke and Dementia ResearchKlinikum der Universität München, Ludwig‐Maximilians‐UniversitätMunichGermany
- Munich Cluster for Systems Neurology (SyNergy)MunichGermany
| | - Julie Williams
- Medical Research Council (MRC) Center for Neuropsychiatric Genetics and Genomics, Department of Psychological Medicine and Neurology, School of MedicineCardiff UniversityCardiffUnited Kingdom
| | - Cathryn M. Lewis
- Department of Medical & Molecular GeneticsKing's College LondonLondonUnited Kingdom
- Social, Genetic and Developmental Psychiatry Center, Institute of PsychiatryKing's College LondonLondonUnited Kingdom
| | - Hugh S. Markus
- Stroke Research Group, Department of Clinical NeurosciencesUniversity of CambridgeCambridgeUnited Kingdom
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24
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Schiffels S, Haak W, Paajanen P, Llamas B, Popescu E, Loe L, Clarke R, Lyons A, Mortimer R, Sayer D, Tyler-Smith C, Cooper A, Durbin R. Iron Age and Anglo-Saxon genomes from East England reveal British migration history. Nat Commun 2016; 7:10408. [PMID: 26783965 PMCID: PMC4735688 DOI: 10.1038/ncomms10408] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 12/09/2015] [Indexed: 12/14/2022] Open
Abstract
British population history has been shaped by a series of immigrations, including the early Anglo-Saxon migrations after 400 CE. It remains an open question how these events affected the genetic composition of the current British population. Here, we present whole-genome sequences from 10 individuals excavated close to Cambridge in the East of England, ranging from the late Iron Age to the middle Anglo-Saxon period. By analysing shared rare variants with hundreds of modern samples from Britain and Europe, we estimate that on average the contemporary East English population derives 38% of its ancestry from Anglo-Saxon migrations. We gain further insight with a new method, rarecoal, which infers population history and identifies fine-scale genetic ancestry from rare variants. Using rarecoal we find that the Anglo-Saxon samples are closely related to modern Dutch and Danish populations, while the Iron Age samples share ancestors with multiple Northern European populations including Britain.
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Affiliation(s)
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Pirita Paajanen
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Elizabeth Popescu
- Oxford Archaeology East, 15 Trafalgar Way, Bar Hill, Cambridge CB23 8SQ, UK
| | - Louise Loe
- Oxford Archaeology South, Janus House, Osney Mead, Oxford OX2 0ES, UK
| | - Rachel Clarke
- Oxford Archaeology East, 15 Trafalgar Way, Bar Hill, Cambridge CB23 8SQ, UK
| | - Alice Lyons
- Oxford Archaeology East, 15 Trafalgar Way, Bar Hill, Cambridge CB23 8SQ, UK
| | - Richard Mortimer
- Oxford Archaeology East, 15 Trafalgar Way, Bar Hill, Cambridge CB23 8SQ, UK
| | - Duncan Sayer
- School of Forensic and Applied Sciences, University of Central Lancashire, Preston PR1 2HE, UK
| | | | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
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25
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Tell-Martí G, Puig-Butille JA, Potrony M, Badenas C, Milà M, Malvehy J, Martí MJ, Ezquerra M, Fernández-Santiago R, Puig S. Reply. Ann Neurol 2015; 79:161-3. [PMID: 26389780 DOI: 10.1002/ana.24526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Gemma Tell-Martí
- Dermatology Department, Melanoma Unit, Hospital Clinic and August Pi i Sunyer Biomedical Research Institute.,Center for Networked Biomedical Research on Rare Diseases, Carlos III Health Institute
| | - Joan Anton Puig-Butille
- Center for Networked Biomedical Research on Rare Diseases, Carlos III Health Institute.,Biochemical and Molecular Genetics Service, Hospital Clinic and August Pi i Sunyer Biomedical Research Institute
| | - Miriam Potrony
- Dermatology Department, Melanoma Unit, Hospital Clinic and August Pi i Sunyer Biomedical Research Institute
| | - Celia Badenas
- Center for Networked Biomedical Research on Rare Diseases, Carlos III Health Institute.,Biochemical and Molecular Genetics Service, Hospital Clinic and August Pi i Sunyer Biomedical Research Institute
| | - Montserrat Milà
- Center for Networked Biomedical Research on Rare Diseases, Carlos III Health Institute.,Biochemical and Molecular Genetics Service, Hospital Clinic and August Pi i Sunyer Biomedical Research Institute
| | - Josep Malvehy
- Dermatology Department, Melanoma Unit, Hospital Clinic and August Pi i Sunyer Biomedical Research Institute.,Center for Networked Biomedical Research on Rare Diseases, Carlos III Health Institute
| | - María José Martí
- Laboratory of Neurodegenerative Disorders, Department of Clinical and Experimental Neurology, August Pi i Sunyer Biomedical Research Institute, Hospital Clinic of Barcelona, Center for Networked Biomedical Research in Neurodegenerative Diseases
| | - Mario Ezquerra
- Laboratory of Neurodegenerative Disorders, Department of Clinical and Experimental Neurology, August Pi i Sunyer Biomedical Research Institute, Hospital Clinic of Barcelona, Center for Networked Biomedical Research in Neurodegenerative Diseases
| | - Rubén Fernández-Santiago
- Laboratory of Neurodegenerative Disorders, Department of Clinical and Experimental Neurology, August Pi i Sunyer Biomedical Research Institute, Hospital Clinic of Barcelona, Center for Networked Biomedical Research in Neurodegenerative Diseases
| | - Susana Puig
- Dermatology Department, Melanoma Unit, Hospital Clinic and August Pi i Sunyer Biomedical Research Institute.,Center for Networked Biomedical Research on Rare Diseases, Carlos III Health Institute.,Medicine Department, University of Barcelona, Barcelona, Spain
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26
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Abstract
In this overview of my research, I have aimed to give the background as to how I came to be involved in my various areas of interest, with an emphasis on the early phases of my career, which largely determined my future directions. I had the enormous good fortune to have worked under two of the most outstanding scientists of the twentieth century, R.A. Fisher and Joshua Lederberg. From mathematics and statistics, I went to population genetics and the early use of computers for modeling and simulation. Molecular biology took me into the laboratory and eventually to somatic cell genetics and human gene mapping. One chance encounter led me into the HLA field and another led me into research on cancer, especially colorectal cancer. On the way, I became a champion of the Human Genome Project and of the need for scientists to help promote the public understanding of science.
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Affiliation(s)
- Walter Bodmer
- Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, United Kingdom
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27
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Mackie SL, Taylor JC, Haroon-Rashid L, Martin S, Dasgupta B, Gough A, Green M, Hordon L, Jarrett S, Pease CT, Barrett JH, Watts R, Morgan AW. Association of HLA-DRB1 amino acid residues with giant cell arteritis: genetic association study, meta-analysis and geo-epidemiological investigation. Arthritis Res Ther 2015; 17:195. [PMID: 26223536 PMCID: PMC4520081 DOI: 10.1186/s13075-015-0692-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 06/18/2015] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION Giant cell arteritis (GCA) is an autoimmune disease commonest in Northern Europe and Scandinavia. Previous studies report various associations with HLA-DRB1*04 and HLA-DRB1*01; HLA-DRB1 alleles show a gradient in population prevalence within Europe. Our aims were (1) to determine which amino acid residues within HLA-DRB1 best explained HLA-DRB1 allele susceptibility and protective effects in GCA, seen in UK data combined in meta-analysis with previously published data, and (2) to determine whether the incidence of GCA in different countries is associated with the population prevalence of the HLA-DRB1 alleles that we identified in our meta-analysis. METHODS GCA patients from the UK GCA Consortium were genotyped by using single-strand oligonucleotide polymerization, allele-specific polymerase chain reaction, and direct sequencing. Meta-analysis was used to compare and combine our results with published data, and public databases were used to identify amino acid residues that may explain observed susceptibility/protective effects. Finally, we determined the relationship of HLA-DRB1*04 population carrier frequency and latitude to GCA incidence reported in different countries. RESULTS In our UK data (225 cases and 1378 controls), HLA-DRB1*04 carriage was associated with GCA susceptibility (odds ratio (OR) = 2.69, P = 1.5×10(-11)), but HLA-DRB1*01 was protective (adjusted OR = 0.55, P = 0.0046). In meta-analysis combined with 14 published studies (an additional 691 cases and 4038 controls), protective effects were seen from HLA-DR2, which comprises HLA-DRB1*15 and HLA-DRB1*16 (OR = 0.65, P = 8.2×10(-6)) and possibly from HLA-DRB1*01 (OR = 0.73, P = 0.037). GCA incidence (n = 17 countries) was associated with population HLA-DRB1*04 allele frequency (P = 0.008; adjusted R(2) = 0.51 on univariable analysis, adjusted R(2) = 0.62 after also including latitude); latitude also made an independent contribution. CONCLUSIONS We confirm that HLA-DRB1*04 is a GCA susceptibility allele. The susceptibility data are best explained by amino acid risk residues V, H, and H at positions 11, 13, and 33, contrary to previous suggestions of amino acids in the second hypervariable region. Worldwide, GCA incidence was independently associated both with population frequency of HLA-DRB1*04 and with latitude itself. We conclude that variation in population HLA-DRB1*04 frequency may partly explain variations in GCA incidence and that HLA-DRB1*04 may warrant investigation as a potential prognostic or predictive biomarker.
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Affiliation(s)
- Sarah Louise Mackie
- School of Medicine and NIHR-Leeds Biomedical Research Unit, Chapel Allerton Hospital, Leeds, LS7 4SA, West Yorkshire, UK.
| | - John C Taylor
- School of Medicine and NIHR-Leeds Biomedical Research Unit, Chapel Allerton Hospital, Leeds, LS7 4SA, West Yorkshire, UK.
| | - Lubna Haroon-Rashid
- School of Medicine and NIHR-Leeds Biomedical Research Unit, Chapel Allerton Hospital, Leeds, LS7 4SA, West Yorkshire, UK.
| | - Stephen Martin
- School of Medicine and NIHR-Leeds Biomedical Research Unit, Chapel Allerton Hospital, Leeds, LS7 4SA, West Yorkshire, UK.
| | - Bhaskar Dasgupta
- Department of Rheumatology, Southend University Hospital, Prittlewell Chase, Southend, SS0 0RY, Essex, UK.
| | - Andrew Gough
- Department of Rheumatology, Harrogate and District Foundation NHS Trust, Lancaster Park Road, Harrogate, HG2 7SX, North Yorkshire, UK.
| | - Michael Green
- Department of Rheumatology, York Teaching Hospital NHS Foundation Trust, Wigginton Road, York, YO31 8HE, North Yorkshire, UK.
| | - Lesley Hordon
- Department of Rheumatology, Dewsbury and District Hospital, Halifax Road, Dewsbury, WF13 4HS, West Yorkshire, UK.
| | - Stephen Jarrett
- Department of Rheumatology, Pinderfields General Hospital, Aberford Road, Wakefield, WF1 4DG, West Yorkshire, UK.
| | - Colin T Pease
- Department of Rheumatology, Chapel Allerton Hospital, Leeds, Leeds, LS7 4SA, West Yorkshire, UK.
| | - Jennifer H Barrett
- School of Medicine and NIHR-Leeds Biomedical Research Unit, Chapel Allerton Hospital, Leeds, LS7 4SA, West Yorkshire, UK.
| | - Richard Watts
- Department of Rheumatology, Ipswich Hospital NHS Trust, Heath Road, Ipswich, IP4 5PD, Suffolk, UK.
| | - Ann W Morgan
- School of Medicine and NIHR-Leeds Biomedical Research Unit, Chapel Allerton Hospital, Leeds, LS7 4SA, West Yorkshire, UK.
- Wellcome Trust Brenner Building, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, West Yorkshire, UK.
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Marcovecchio ML, Capanna R, D'Adamo E, Mammarella S, De Lellis L, Chiarelli F, Cama A, Mohn A. Association between rs12970134 Near MC4R and adiposity indexes in a homogenous population of Caucasian schoolchildren. Horm Res Paediatr 2015; 82:187-93. [PMID: 25115458 DOI: 10.1159/000365103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 06/03/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND To assess whether previously identified obesity-susceptibility loci were associated with overweight/obesity risk in a homogeneous population of Caucasian schoolchildren and whether these associations varied with age. METHODS Seven hundred and forty-five schoolchildren (353 boys, mean age: 8.3 ± 1.4 years) underwent anthropometric assessments. A saliva sample was collected for DNA extraction and assessment of 19 single-nucleotide polymorphisms previously associated with obesity. RESULTS Only the rs12970134 in the MC4R gene was significantly associated with overweight/obesity risk, with a higher frequency of the AA risk genotype in children with a BMI >85th (8.3%) than in those with a BMI <85th percentile (3.0%), p = 0.001; odds ratio (95% CI) of 1.544 (1.192-1.998), p = 0.001, after adjusting for age, sex and pubertal stage. BMI standard deviation scores (SDS) and waist-to-height ratio (W/Hr) progressively increased across the rs12970134 genotypes (GG vs. AG vs. AA): BMI SDS, p = 0.004; W/Hr, p = 0.009. When dividing the study population into two groups based on the median age of participants (8.3 years), the differences in BMI SDS and W/Hr across the MC4R genotypes persisted only in children older than 8.3 years. CONCLUSIONS In a population of Caucasian schoolchildren, the rs12970134 MC4R variant was significantly associated with excess body weight, particularly in children older than 8 years of age.
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Large-scale recent expansion of European patrilineages shown by population resequencing. Nat Commun 2015; 6:7152. [PMID: 25988751 PMCID: PMC4441248 DOI: 10.1038/ncomms8152] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 04/13/2015] [Indexed: 12/12/2022] Open
Abstract
The proportion of Europeans descending from Neolithic farmers ∼ 10 thousand years ago (KYA) or Palaeolithic hunter-gatherers has been much debated. The male-specific region of the Y chromosome (MSY) has been widely applied to this question, but unbiased estimates of diversity and time depth have been lacking. Here we show that European patrilineages underwent a recent continent-wide expansion. Resequencing of 3.7 Mb of MSY DNA in 334 males, comprising 17 European and Middle Eastern populations, defines a phylogeny containing 5,996 single-nucleotide polymorphisms. Dating indicates that three major lineages (I1, R1a and R1b), accounting for 64% of our sample, have very recent coalescent times, ranging between 3.5 and 7.3 KYA. A continuous swathe of 13/17 populations share similar histories featuring a demographic expansion starting ∼ 2.1-4.2 KYA. Our results are compatible with ancient MSY DNA data, and contrast with data on mitochondrial DNA, indicating a widespread male-specific phenomenon that focuses interest on the social structure of Bronze Age Europe.
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30
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Martinez-Cadenas C, Blanco-Verea A, Hernando B, Busby GBJ, Brion M, Carracedo A, Salas A, Capelli C. The relationship between surname frequency and Y chromosome variation in Spain. Eur J Hum Genet 2015; 24:120-8. [PMID: 25898922 DOI: 10.1038/ejhg.2015.75] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 02/28/2015] [Accepted: 03/17/2015] [Indexed: 11/09/2022] Open
Abstract
In most societies, surnames are passed down from fathers to sons, just like the Y chromosome. It follows that, theoretically, men sharing the same surnames would also be expected to share related Y chromosomes. Previous investigations have explored such relationships, but so far, the only detailed studies that have been conducted are on samples from the British Isles. In order to provide additional insights into the correlation between surnames and Y chromosomes, we focused on the Spanish population by analysing Y chromosomes from 2121 male volunteers representing 37 surnames. The results suggest that the degree of coancestry within Spanish surnames is highly dependent on surname frequency, in overall agreement with British but not Irish surname studies. Furthermore, a reanalysis of comparative data for all three populations showed that Irish surnames have much greater and older surname descent clusters than Spanish and British ones, suggesting that Irish surnames may have considerably earlier origins than Spanish or British ones. Overall, despite closer geographical ties between Ireland and Britain, our analysis points to substantial similarities in surname origin and development between Britain and Spain, while possibly hinting at unique demographic or social events shaping Irish surname foundation and development.
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Affiliation(s)
- Conrado Martinez-Cadenas
- Department of Medicine, Jaume I University of Castellon, Castellon, Spain.,Human Evolutionary Genetics Group, Department of Zoology, University of Oxford, Oxford, UK
| | - Alejandro Blanco-Verea
- Instituto de Investigación Sanitaria de Santiago de Compostela, Grupo de Medicina Xenómica, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Barbara Hernando
- Department of Medicine, Jaume I University of Castellon, Castellon, Spain
| | - George B J Busby
- Human Evolutionary Genetics Group, Department of Zoology, University of Oxford, Oxford, UK.,Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, UK
| | - Maria Brion
- Instituto de Investigación Sanitaria de Santiago de Compostela, Grupo de Medicina Xenómica, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Angel Carracedo
- Instituto de Investigación Sanitaria de Santiago de Compostela, Grupo de Medicina Xenómica, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.,Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Cristian Capelli
- Human Evolutionary Genetics Group, Department of Zoology, University of Oxford, Oxford, UK
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31
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Larmuseau MHD, Boon N, Vanderheyden N, Van Geystelen A, Larmuseau HFM, Matthys K, De Clercq W, Decorte R. High Y-chromosomal diversity and low relatedness between paternal lineages on a communal scale in the Western European Low Countries during the surname establishment. Heredity (Edinb) 2015; 115:3-12. [PMID: 25873146 DOI: 10.1038/hdy.2015.5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 11/20/2014] [Accepted: 12/23/2014] [Indexed: 01/02/2023] Open
Abstract
There is limited knowledge on the biological relatedness between citizens and on the demographical dynamics within villages, towns and cities in pre-17th century Western Europe. By combining Y-chromosomal genotypes, in-depth genealogies and surname data in a strict genetic genealogical approach, it is possible to provide insights into the genetic diversity and the relatedness between indigenous paternal lineages within a particular community at the time of the surname adoption. To obtain these insights, six Flemish communities were selected in this study based on the differences in geography and historical development. After rigorous selection of appropriate DNA donors, low relatedness between Y chromosomes of different surnames was found within each community, although there is co-occurrence of these surnames in each community since the start of the surname adoption between the 14th and 15th century. Next, the high communal diversity in Y-chromosomal lineages was comparable with the regional diversity across Flanders at that time. Moreover, clinal distributions of particular Y-chromosomal lineages between the communities were observed according to the clinal distributions earlier observed across the Flemish regions and Western Europe. No significant indication for genetic differences between communities with distinct historical development was found in the analysis. These genetic results provide relevant information for studies in historical sciences, archaeology, forensic genetics and genealogy.
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Affiliation(s)
- M H D Larmuseau
- 1] Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium [2] Department of Imaging and Pathology, Forensic Biomedical Sciences, KU Leuven, Leuven, Belgium [3] Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - N Boon
- 1] Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Leuven, Belgium [2] Institute of Tropical Medicine, Antwerp, Belgium
| | - N Vanderheyden
- Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium
| | - A Van Geystelen
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - H F M Larmuseau
- Faculty of Social Sciences, Department of Social Sciences,Centre of Sociological Research (CESO), KU Leuven, Leuven, Belgium
| | - K Matthys
- Faculty of Social Sciences, Department of Social Sciences,Centre of Sociological Research (CESO), KU Leuven, Leuven, Belgium
| | - W De Clercq
- Faculty of Arts and Philosophy, Department of Archaeology, Ghent University, Ghent, Belgium
| | - R Decorte
- 1] Laboratory of Forensic Genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium [2] Department of Imaging and Pathology, Forensic Biomedical Sciences, KU Leuven, Leuven, Belgium
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32
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Calderón R, Hernández CL, Cuesta P, Dugoujon JM. Surnames and Y-chromosomal markers reveal low relationships in Southern Spain. PLoS One 2015; 10:e0123098. [PMID: 25860017 PMCID: PMC4393112 DOI: 10.1371/journal.pone.0123098] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/27/2015] [Indexed: 11/21/2022] Open
Abstract
A sample of 416 males from western and eastern Andalusia has been jointly analyzed for surnames and Y-chromosome haplogroups and haplotypes. The observed number of different surnames was 222 (353 when the second surname of the Spanish system of naming is considered). The great majority of recorded surnames have a Castilian-Leonese origin, while Catalan or Basque surnames have not been found. A few Arab-related surnames appear but none discernible of Sephardic-Jewish descent. Low correlation among surnames with different population frequencies and Y-chromosome markers, at different levels of genetic resolution, has been observed in Andalusia. This finding could be explained mainly by the very low rate of monophyletic surnames because of the historical process of surname ascription and the resulting high frequencies of the most common Spanish surnames. The introduction of surnames in Spain during the Middle Ages coincided with Reconquest of the territories under Islamic rule, and Muslims and Jews progressively adopted the present male line surname system. Sampled surnames and Y-chromosome lineages fit well a power-law distribution and observed isonymy is very close to that of the general population. Besides, our data and results show that the reliability of the isonymy method should be questioned because of the high rate of polyphyletic surnames, even in small geographic regions and autochthonous populations. Random isonymy would be consistently dependent of the most common surname frequencies in the population.
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Affiliation(s)
- Rosario Calderón
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Madrid, Spain
- * E-mail:
| | - Candela L. Hernández
- Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad Complutense, Madrid, Spain
| | - Pedro Cuesta
- Centro de Proceso de Datos, Universidad Complutense, Madrid, Spain
| | - Jean Michel Dugoujon
- CNRS UMR 5288 Laboratoire d’Anthropologie Moléculaire et d’Imagerie de Synthèse (AMIS), Université Paul Sabatier Toulouse III, Toulouse, France
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Leslie S, Winney B, Hellenthal G, Davison D, Boumertit A, Day T, Hutnik K, Royrvik EC, Cunliffe B, Lawson DJ, Falush D, Freeman C, Pirinen M, Myers S, Robinson M, Donnelly P, Bodmer W. The fine-scale genetic structure of the British population. Nature 2015; 519:309-314. [PMID: 25788095 PMCID: PMC4632200 DOI: 10.1038/nature14230] [Citation(s) in RCA: 232] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Accepted: 01/13/2015] [Indexed: 12/22/2022]
Abstract
Fine-scale genetic variation between human populations is interesting as a signature of historical demographic events and because of its potential for confounding disease studies. We use haplotype-based statistical methods to analyse genome-wide single nucleotide polymorphism (SNP) data from a carefully chosen geographically diverse sample of 2,039 individuals from the United Kingdom. This reveals a rich and detailed pattern of genetic differentiation with remarkable concordance between genetic clusters and geography. The regional genetic differentiation and differing patterns of shared ancestry with 6,209 individuals from across Europe carry clear signals of historical demographic events. We estimate the genetic contribution to southeastern England from Anglo-Saxon migrations to be under half, and identify the regions not carrying genetic material from these migrations. We suggest significant pre-Roman but post-Mesolithic movement into southeastern England from continental Europe, and show that in non-Saxon parts of the United Kingdom, there exist genetically differentiated subgroups rather than a general 'Celtic' population.
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Affiliation(s)
- Stephen Leslie
- Murdoch Childrens Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia
- University of Melbourne, Department of Mathematics and Statistics, Parkville, Victoria 3010, Australia
| | - Bruce Winney
- University of Oxford, Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Garrett Hellenthal
- University College London Genetics Institute, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Dan Davison
- Counsyl, Inc. 180 Kimball Way, South San Francisco, CA 94080, USA
| | - Abdelhamid Boumertit
- University of Oxford, Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Tammy Day
- University of Oxford, Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Katarzyna Hutnik
- University of Oxford, Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Ellen C Royrvik
- University of Oxford, Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Barry Cunliffe
- University of Oxford, Institute of Archaeology, 36 Beaumont Street, Oxford, OX1 2PG, UK
| | - Daniel J Lawson
- University of Bristol, Department of Mathematics, University Walk, Bristol, BS8 1TW, UK
| | - Daniel Falush
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Colin Freeman
- The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Matti Pirinen
- University of Helsinki, P.O. Box 20, Helsinki, FI-00014, Finland
| | - Simon Myers
- University of Oxford, Department of Statistics, 1 South Parks Road, Oxford, OX1 3TG, UK
| | - Mark Robinson
- University of Oxford, University Museum of Natural History, Parks Road, Oxford, OX1 3PW, UK
| | - Peter Donnelly
- The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
- University of Oxford, Department of Statistics, 1 South Parks Road, Oxford, OX1 3TG, UK
| | - Walter Bodmer
- University of Oxford, Department of Oncology, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
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34
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Abdellaoui A, Hottenga JJ, Willemsen G, Bartels M, van Beijsterveldt T, Ehli EA, Davies GE, Brooks A, Sullivan PF, Penninx BWJH, de Geus EJ, Boomsma DI. Educational attainment influences levels of homozygosity through migration and assortative mating. PLoS One 2015; 10:e0118935. [PMID: 25734509 PMCID: PMC4347978 DOI: 10.1371/journal.pone.0118935] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 01/07/2015] [Indexed: 12/02/2022] Open
Abstract
Individuals with a higher education are more likely to migrate, increasing the chance of meeting a spouse with a different ancestral background. In this context, the presence of strong educational assortment can result in greater ancestry differences within more educated spouse pairs, while less educated individuals are more likely to mate with someone with whom they share more ancestry. We examined the association between educational attainment and Froh (= the proportion of the genome consisting of runs of homozygosity [ROHs]) in ~2,000 subjects of Dutch ancestry. The subjects’ own educational attainment showed a nominally significant negative association with Froh (p = .045), while the contribution of parental education to offspring Froh was highly significant (father: p < 10-5; mother: p = 9×10-5), with more educated parents having offspring with fewer ROHs. This association was significantly and fully mediated by the physical distance between parental birthplaces (paternal education: pmediation = 2.4 × 10-4; maternal education: pmediation = 2.3 × 10-4), which itself was also significantly associated with Froh (p = 9 × 10-5). Ancestry-informative principal components from the offspring showed a significantly decreasing association with geography as parental education increased, consistent with the significantly higher migration rates among more educated parents. Parental education also showed a high spouse correlation (Spearman’s ρ = .66, p = 3 × 10-262). We show that less educated parents are less likely to mate with the more mobile parents with a higher education, creating systematic differences in homozygosity due to ancestry differences not directly captured by ancestry-informative principal components (PCs). Understanding how behaviors influence the genomic structure of a population is highly valuable for studies on the genetic etiology of behavioral, cognitive, and social traits.
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Affiliation(s)
- Abdel Abdellaoui
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
- Neuroscience Campus Amsterdam, Amsterdam, The Netherlands
- * E-mail:
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
- EMGO+ Institute for Health and Care Research, Amsterdam, The Netherlands
| | - Meike Bartels
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
- Neuroscience Campus Amsterdam, Amsterdam, The Netherlands
- EMGO+ Institute for Health and Care Research, Amsterdam, The Netherlands
| | - Toos van Beijsterveldt
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Erik A. Ehli
- Avera Institute for Human Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, South Dakota, United States of America
| | - Gareth E. Davies
- Avera Institute for Human Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, South Dakota, United States of America
| | - Andrew Brooks
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
| | - Patrick F. Sullivan
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Brenda W. J. H. Penninx
- Neuroscience Campus Amsterdam, Amsterdam, The Netherlands
- EMGO+ Institute for Health and Care Research, Amsterdam, The Netherlands
- Department of Psychiatry, VU University Medical Center, Amsterdam, Netherlands
| | - Eco J. de Geus
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
- Neuroscience Campus Amsterdam, Amsterdam, The Netherlands
- EMGO+ Institute for Health and Care Research, Amsterdam, The Netherlands
| | - Dorret I. Boomsma
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
- Neuroscience Campus Amsterdam, Amsterdam, The Netherlands
- EMGO+ Institute for Health and Care Research, Amsterdam, The Netherlands
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35
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Bodmer W. Genetic characterization of human populations: from ABO to a genetic map of the British people. Genetics 2015; 199:267-79. [PMID: 25657345 PMCID: PMC4317642 DOI: 10.1534/genetics.114.173062] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
From 1900, when Landsteiner first described the ABO blood groups, to the present, the methods used to characterize the genetics of human populations have undergone a remarkable development. Concomitantly, our understanding of the history and spread of human populations across the earth has become much more detailed. As has often been said, a better understanding of the genetic relationships among the peoples of the world is one of the best antidotes to racial prejudices. Such an understanding provides us with a fascinating, improved insight into our origins as well as with valuable information about population differences that are of medical relevance. The study of genetic polymorphisms has been essential to the analysis of the relationships between human populations. The evolution of methods used to study human polymorphisms and the resulting contributions to our understanding of human health and history is the subject of this Perspectives.
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Affiliation(s)
- Walter Bodmer
- Weatherall Institute of Molecular Medicine and Department of Oncology, University of Oxford, Oxford, United Kingdom OX3 9DS
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36
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Fine-scale human genetic structure in Western France. Eur J Hum Genet 2014; 23:831-6. [PMID: 25182131 DOI: 10.1038/ejhg.2014.175] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 07/21/2014] [Accepted: 07/30/2014] [Indexed: 11/08/2022] Open
Abstract
The difficulties arising from association analysis with rare variants underline the importance of suitable reference population cohorts, which integrate detailed spatial information. We analyzed a sample of 1684 individuals from Western France, who were genotyped at genome-wide level, from two cohorts D.E.S.I.R and CavsGen. We found that fine-scale population structure occurs at the scale of Western France, with distinct admixture proportions for individuals originating from the Brittany Region and the Vendée Department. Genetic differentiation increases with distance at a high rate in these two parts of Northwestern France and linkage disequilibrium is higher in Brittany suggesting a lower effective population size. When looking for genomic regions informative about Breton origin, we found two prominent associated regions that include the lactase region and the HLA complex. For both the lactase and the HLA regions, there is a low differentiation between Bretons and Irish, and this is also found at the genome-wide level. At a more refined scale, and within the Pays de la Loire Region, we also found evidence of fine-scale population structure, although principal component analysis showed that individuals from different departments cannot be confidently discriminated. Because of the evidence for fine-scale genetic structure in Western France, we anticipate that rare and geographically localized variants will be identified in future full-sequence analyses.
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37
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Morris DW, Pearson RD, Cormican P, Kenny EM, O'Dushlaine CT, Perreault LPL, Giannoulatou E, Tropea D, Maher BS, Wormley B, Kelleher E, Fahey C, Molinos I, Bellini S, Pirinen M, Strange A, Freeman C, Thiselton DL, Elves RL, Regan R, Ennis S, Dinan TG, McDonald C, Murphy KC, O'Callaghan E, Waddington JL, Walsh D, O'Donovan M, Grozeva D, Craddock N, Stone J, Scolnick E, Purcell S, Sklar P, Coe B, Eichler EE, Ophoff R, Buizer J, Szatkiewicz J, Hultman C, Sullivan P, Gurling H, Mcquillin A, St Clair D, Rees E, Kirov G, Walters J, Blackwood D, Johnstone M, Donohoe G, O'Neill FA, Kendler KS, Gill M, Riley BP, Spencer CCA, Corvin A. An inherited duplication at the gene p21 Protein-Activated Kinase 7 (PAK7) is a risk factor for psychosis. Hum Mol Genet 2014; 23:3316-26. [PMID: 24474471 PMCID: PMC4030770 DOI: 10.1093/hmg/ddu025] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 12/24/2013] [Accepted: 01/20/2014] [Indexed: 12/14/2022] Open
Abstract
Identifying rare, highly penetrant risk mutations may be an important step in dissecting the molecular etiology of schizophrenia. We conducted a gene-based analysis of large (>100 kb), rare copy-number variants (CNVs) in the Wellcome Trust Case Control Consortium 2 (WTCCC2) schizophrenia sample of 1564 cases and 1748 controls all from Ireland, and further extended the analysis to include an additional 5196 UK controls. We found association with duplications at chr20p12.2 (P = 0.007) and evidence of replication in large independent European schizophrenia (P = 0.052) and UK bipolar disorder case-control cohorts (P = 0.047). A combined analysis of Irish/UK subjects including additional psychosis cases (schizophrenia and bipolar disorder) identified 22 carriers in 11 707 cases and 10 carriers in 21 204 controls [meta-analysis Cochran-Mantel-Haenszel P-value = 2 × 10(-4); odds ratio (OR) = 11.3, 95% CI = 3.7, ∞]. Nineteen of the 22 cases and 8 of the 10 controls carried duplications starting at 9.68 Mb with similar breakpoints across samples. By haplotype analysis and sequencing, we identified a tandem ~149 kb duplication overlapping the gene p21 Protein-Activated Kinase 7 (PAK7, also called PAK5) which was in linkage disequilibrium with local haplotypes (P = 2.5 × 10(-21)), indicative of a single ancestral duplication event. We confirmed the breakpoints in 8/8 carriers tested and found co-segregation of the duplication with illness in two additional family members of one of the affected probands. We demonstrate that PAK7 is developmentally co-expressed with another known psychosis risk gene (DISC1) suggesting a potential molecular mechanism involving aberrant synapse development and plasticity.
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Affiliation(s)
- Derek W Morris
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Richard D Pearson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Paul Cormican
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Elaine M Kenny
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Colm T O'Dushlaine
- Broad Institute and Center for Human Genetics Research of Massachusetts General Hospital, Boston, MA 02142, USA
| | - Louis-Philippe Lemieux Perreault
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Montreal Heart Institute, Université de Montréal, Montréal, Québec H1T 1C8, Canada
| | - Eleni Giannoulatou
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Daniela Tropea
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Brion S Maher
- Departments of Psychiatry and Human Genetics, Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Brandon Wormley
- Departments of Psychiatry and Human Genetics, Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Eric Kelleher
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Ciara Fahey
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Ines Molinos
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Stefania Bellini
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Matti Pirinen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Amy Strange
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Colin Freeman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Dawn L Thiselton
- Departments of Psychiatry and Human Genetics, Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Rachel L Elves
- Departments of Psychiatry and Human Genetics, Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Regina Regan
- School of Medicine and Medical Science, University College Dublin, Ireland
| | - Sean Ennis
- School of Medicine and Medical Science, University College Dublin, Ireland
| | - Timothy G Dinan
- Department of Psychiatry, University College Cork, Cork, Ireland
| | - Colm McDonald
- Department of Psychiatry, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Kieran C Murphy
- Department of Psychiatry, RCSI Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland
| | - Eadbhard O'Callaghan
- DETECT Early Intervention in Psychosis Services, Dun Laoghaire, Co. Dublin, Ireland
| | - John L Waddington
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Dermot Walsh
- Health Research Board, 73 Lower Baggot St, Dublin 2, Ireland
| | - Michael O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, and Neuroscience and Mental Health Research Institute, Cardiff University, Heath Park, Cardiff CF4 4XN, UK
| | - Detelina Grozeva
- MRC Centre for Neuropsychiatric Genetics and Genomics, and Neuroscience and Mental Health Research Institute, Cardiff University, Heath Park, Cardiff CF4 4XN, UK
| | - Nick Craddock
- MRC Centre for Neuropsychiatric Genetics and Genomics, and Neuroscience and Mental Health Research Institute, Cardiff University, Heath Park, Cardiff CF4 4XN, UK
| | - Jennifer Stone
- Broad Institute and Center for Human Genetics Research of Massachusetts General Hospital, Boston, MA 02142, USA
| | - Ed Scolnick
- Broad Institute and Center for Human Genetics Research of Massachusetts General Hospital, Boston, MA 02142, USA
| | - Shaun Purcell
- Broad Institute and Center for Human Genetics Research of Massachusetts General Hospital, Boston, MA 02142, USA The Mount Sinai Hospital, New York, NY 10029, USA
| | - Pamela Sklar
- Broad Institute and Center for Human Genetics Research of Massachusetts General Hospital, Boston, MA 02142, USA The Mount Sinai Hospital, New York, NY 10029, USA
| | - Bradley Coe
- University of Washington School of Medicine, Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Evan E Eichler
- University of Washington School of Medicine, Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Roel Ophoff
- Department of Human Genetics, UCLA School of Medicine, Los Angeles, CA 90095, USA
| | - Jacobine Buizer
- Rudolf Magnus Institute, University of Utrecht, 3584 CG Utrecht, Netherlands
| | - Jin Szatkiewicz
- University of North Carolina, Chapel Hill, NC 27599-7264, USA
| | - Christina Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | | | - Hugh Gurling
- Molecular Psychiatry Laboratory, Mental Health Sciences Unit, University College London, London WC1E 6BT, UK
| | - Andrew Mcquillin
- Molecular Psychiatry Laboratory, Mental Health Sciences Unit, University College London, London WC1E 6BT, UK
| | - David St Clair
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Elliott Rees
- MRC Centre for Neuropsychiatric Genetics and Genomics, and Neuroscience and Mental Health Research Institute, Cardiff University, Heath Park, Cardiff CF4 4XN, UK
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, and Neuroscience and Mental Health Research Institute, Cardiff University, Heath Park, Cardiff CF4 4XN, UK
| | - James Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, and Neuroscience and Mental Health Research Institute, Cardiff University, Heath Park, Cardiff CF4 4XN, UK
| | - Douglas Blackwood
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh EH10 5HF, UK and
| | - Mandy Johnstone
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh EH10 5HF, UK and
| | - Gary Donohoe
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Francis A O'Neill
- Department of Psychiatry, Queen's University, Belfast BT7 1NN, Northern Ireland
| | - Kenneth S Kendler
- Departments of Psychiatry and Human Genetics, Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Michael Gill
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Brien P Riley
- Departments of Psychiatry and Human Genetics, Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Chris C A Spencer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Aiden Corvin
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland
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Nudel R, Simpson NH, Baird G, O'Hare A, Conti-Ramsden G, Bolton PF, Hennessy ER, Monaco AP, Knight JC, Winney B, Fisher SE, Newbury DF. Associations of HLA alleles with specific language impairment. J Neurodev Disord 2014; 6:1. [PMID: 24433325 PMCID: PMC3906746 DOI: 10.1186/1866-1955-6-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 01/02/2014] [Indexed: 01/28/2023] Open
Abstract
Background Human leukocyte antigen (HLA) loci have been implicated in several neurodevelopmental disorders in which language is affected. However, to date, no studies have investigated the possible involvement of HLA loci in specific language impairment (SLI), a disorder that is defined primarily upon unexpected language impairment. We report association analyses of single-nucleotide polymorphisms (SNPs) and HLA types in a cohort of individuals affected by language impairment. Methods We perform quantitative association analyses of three linguistic measures and case-control association analyses using both SNP data and imputed HLA types. Results Quantitative association analyses of imputed HLA types suggested a role for the HLA-A locus in susceptibility to SLI. HLA-A A1 was associated with a measure of short-term memory (P = 0.004) and A3 with expressive language ability (P = 0.006). Parent-of-origin effects were found between HLA-B B8 and HLA-DQA1*0501 and receptive language. These alleles have a negative correlation with receptive language ability when inherited from the mother (P = 0.021, P = 0.034, respectively) but are positively correlated with the same trait when paternally inherited (P = 0.013, P = 0.029, respectively). Finally, case control analyses using imputed HLA types indicated that the DR10 allele of HLA-DRB1 was more frequent in individuals with SLI than population controls (P = 0.004, relative risk = 2.575), as has been reported for individuals with attention deficit hyperactivity disorder (ADHD). Conclusion These preliminary data provide an intriguing link to those described by previous studies of other neurodevelopmental disorders and suggest a possible role for HLA loci in language disorders.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Dianne F Newbury
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
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Huang Y, Hidalgo-Bravo A, Zhang E, Cotton VE, Mendez-Bermudez A, Wig G, Medina-Calzada Z, Neumann R, Jeffreys AJ, Winney B, Wilson JF, Clark DA, Dyer MJ, Royle NJ. Human telomeres that carry an integrated copy of human herpesvirus 6 are often short and unstable, facilitating release of the viral genome from the chromosome. Nucleic Acids Res 2013; 42:315-27. [PMID: 24057213 PMCID: PMC3874159 DOI: 10.1093/nar/gkt840] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Linear chromosomes are stabilized by telomeres, but the presence of short dysfunctional telomeres triggers cellular senescence in human somatic tissues, thus contributing to ageing. Approximately 1% of the population inherits a chromosomally integrated copy of human herpesvirus 6 (CI-HHV-6), but the consequences of integration for the virus and for the telomere with the insertion are unknown. Here we show that the telomere on the distal end of the integrated virus is frequently the shortest measured in somatic cells but not the germline. The telomere carrying the CI-HHV-6 is also prone to truncations that result in the formation of a short telomere at a novel location within the viral genome. We detected extra-chromosomal circular HHV-6 molecules, some surprisingly comprising the entire viral genome with a single fully reconstituted direct repeat region (DR) with both terminal cleavage and packaging elements (PAC1 and PAC2). Truncated CI-HHV-6 and extra-chromosomal circular molecules are likely reciprocal products that arise through excision of a telomere-loop (t-loop) formed within the CI-HHV-6 genome. In summary, we show that the CI-HHV-6 genome disrupts stability of the associated telomere and this facilitates the release of viral sequences as circular molecules, some of which have the potential to become fully functioning viruses.
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Affiliation(s)
- Yan Huang
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK, Department of Oncology, ORCRB, University of Oxford, Old Road Campus, Headington, Oxford, OX3 7DQ, UK, Centre for Population Health Sciences, College of Medicine and Veterinary Medicine, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland, Department of Virology, Barts Health NHS Trust, Pathology and Pharmacy Building, 80 Newark St, London E1 2ES, UK and Department of Cancer Studies and Molecular Medicine, University of Leicester, University Road, Leicester, LE1 7RH, UK
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40
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Boattini A, Pettener D. What can we do with surnames today? An anthropologist point of view: comment on "Surname distribution in population genetics and in statistical physics" by Paolo Rossi. Phys Life Rev 2013; 10:418-9; discussion 426-7. [PMID: 23948141 DOI: 10.1016/j.plrev.2013.07.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 07/25/2013] [Indexed: 11/26/2022]
Affiliation(s)
- Alessio Boattini
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), Università di Bologna, Via Selmi 3, 40126, Bologna, Italy.
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41
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Ralph P, Coop G. The geography of recent genetic ancestry across Europe. PLoS Biol 2013; 11:e1001555. [PMID: 23667324 PMCID: PMC3646727 DOI: 10.1371/journal.pbio.1001555] [Citation(s) in RCA: 192] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 03/27/2013] [Indexed: 01/11/2023] Open
Abstract
A genomic survey of recent genealogical relatedness reveals the close ties of kinship and the impact of events across the past 3,000 years of European history. The recent genealogical history of human populations is a complex mosaic formed by individual migration, large-scale population movements, and other demographic events. Population genomics datasets can provide a window into this recent history, as rare traces of recent shared genetic ancestry are detectable due to long segments of shared genomic material. We make use of genomic data for 2,257 Europeans (in the Population Reference Sample [POPRES] dataset) to conduct one of the first surveys of recent genealogical ancestry over the past 3,000 years at a continental scale. We detected 1.9 million shared long genomic segments, and used the lengths of these to infer the distribution of shared ancestors across time and geography. We find that a pair of modern Europeans living in neighboring populations share around 2–12 genetic common ancestors from the last 1,500 years, and upwards of 100 genetic ancestors from the previous 1,000 years. These numbers drop off exponentially with geographic distance, but since these genetic ancestors are a tiny fraction of common genealogical ancestors, individuals from opposite ends of Europe are still expected to share millions of common genealogical ancestors over the last 1,000 years. There is also substantial regional variation in the number of shared genetic ancestors. For example, there are especially high numbers of common ancestors shared between many eastern populations that date roughly to the migration period (which includes the Slavic and Hunnic expansions into that region). Some of the lowest levels of common ancestry are seen in the Italian and Iberian peninsulas, which may indicate different effects of historical population expansions in these areas and/or more stably structured populations. Population genomic datasets have considerable power to uncover recent demographic history, and will allow a much fuller picture of the close genealogical kinship of individuals across the world. Few of us know our family histories more than a few generations back. It is therefore easy to overlook the fact that we are all distant cousins, related to one another via a vast network of relationships. Here we use genome-wide data from European individuals to investigate these relationships over the past 3,000 years, by looking for long stretches of genome that are shared between pairs of individuals through their inheritance from common genetic ancestors. We quantify this ubiquitous recent common ancestry, showing for instance that even pairs of individuals from opposite ends of Europe share hundreds of genetic common ancestors over this time period. Despite this degree of commonality, there are also striking regional differences. Southeastern Europeans, for example, share large numbers of common ancestors that date roughly to the era of the Slavic and Hunnic expansions around 1,500 years ago, while most common ancestors that Italians share with other populations lived longer than 2,500 years ago. The study of long stretches of shared genetic material promises to uncover rich information about many aspects of recent population history.
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Affiliation(s)
- Peter Ralph
- Department of Evolution and Ecology & Center for Population Biology, University of California, Davis, California, United States of America
- * E-mail: (PR); (GC)
| | - Graham Coop
- Department of Evolution and Ecology & Center for Population Biology, University of California, Davis, California, United States of America
- * E-mail: (PR); (GC)
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42
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Boattini A, Lisa A, Fiorani O, Zei G, Pettener D, Manni F. General method to unravel ancient population structures through surnames, final validation on Italian data. Hum Biol 2013; 84:235-70. [PMID: 23020096 DOI: 10.3378/027.084.0302] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We analyze the geographic location of 77,451 different Italian surnames (17,579,891 individuals) obtained from the lists of telephone subscribers of the year 1993. By using a specific neural network analysis (Self-Organizing Maps, SOMs), we automatically identify the geographic origin of 49,117 different surnames. To validate the methodology, we compare the results to a study, previously conducted, on the same database, with accurate supervised methods. By comparing the results, we find an overlap of 97%, meaning that the SOMs methodology is highly reliable and well traces back the geographic origin of surnames at the time of their introduction (Late Middle Ages/Renaissance in Italy). SOMs results enables one to distinguish monophyletic surnames from polyphyletic ones, that is surnames having had a single geographic and historic origin from those that started to be in use, with an identical spelling, in different locations (respectively, 76.06% and 21.05% of the total). As we are interested in geographic origins, polyphyletic surnames are excluded from further analyses. By comparing the present location of each monophyletic surname to its inferred geographic origin in late Middle Ages/Renaissance, we measure the extent of the migrations having occurred in Italy since that time. We find that the percentage of individuals presently living in the very area where their surname started to be in use centuries ago is extremely variable (ranging from 22.77% to 77.86% according to the province), thus meaning that self-assessed regional identities seldom correspond to the "autochthony" they imply. For example the upper part of the Thyrennian coast (Northern Latium, Tuscany) has a strong identity but few "autochthonous" inhabitants (∼28%) having been a passageway from the North to the South of Italy.
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43
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Larmuseau MHD, Van Geystelen A, van Oven M, Decorte R. Genetic genealogy comes of age: perspectives on the use of deep-rooted pedigrees in human population genetics. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 150:505-11. [PMID: 23440589 DOI: 10.1002/ajpa.22233] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 12/21/2012] [Accepted: 01/03/2013] [Indexed: 11/06/2022]
Abstract
In this article, we promote the implementation of extensive genealogical data in population genetic studies. Genealogical records can provide valuable information on the origin of DNA donors in a population genetic study, going beyond the commonly collected data such as residence, birthplace, language, and self-reported ethnicity. Recent studies demonstrated that extended genealogical data added to surname analysis can be crucial to detect signals of (past) population stratification and to interpret the population structure in a more objective manner. Moreover, when in-depth pedigree data are combined with haploid markers, it is even possible to disentangle signals of temporal differentiation within a population genetic structure during the last centuries. Obtaining genealogical data for all DNA donors in a population genetic study is a labor-intensive task but the vastly growing (genetic) genealogical databases, due to the broad interest of the public, are making this job more time-efficient if there is a guarantee for sufficient data quality. At the end, we discuss the advantages and pitfalls of using genealogy within sampling campaigns and we provide guidelines for future population genetic studies.
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Affiliation(s)
- M H D Larmuseau
- UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium.
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44
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Genetic ancestry inference using support vector machines, and the active emergence of a unique American population. Eur J Hum Genet 2012; 21:554-62. [PMID: 23211701 DOI: 10.1038/ejhg.2012.258] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We use genotype data from the Marshfield Clinical Research Foundation Personalized Medicine Research Project to investigate genetic similarity and divergence between Europeans and the sampled population of European Americans in Central Wisconsin, USA. To infer recent genetic ancestry of the sampled Wisconsinites, we train support vector machines (SVMs) on the positions of Europeans along top principal components (PCs). Our SVM models partition continent-wide European genetic variance into eight regional classes, which is an improvement over the geographically broader categories of recent ancestry reported by personal genomics companies. After correcting for misclassification error associated with the SVMs (<10%, in all cases), we observe a >14% discrepancy between insular ancestries reported by Wisconsinites and those inferred by SVM. Values of FST as well as Mantel tests for correlation between genetic and European geographic distances indicate minimal divergence between Europe and the local Wisconsin population. However, we find that individuals from the Wisconsin sample show greater dispersion along higher-order PCs than individuals from Europe. Hypothesizing that this pattern is characteristic of nascent divergence, we run computer simulations that mimic the recent peopling of Wisconsin. Simulations corroborate the pattern in higher-order PCs, demonstrate its transient nature, and show that admixture accelerates the rate of divergence between the admixed population and its parental sources relative to drift alone. Together, empirical and simulation results suggest that genetic divergence between European source populations and European Americans in Central Wisconsin is subtle but already under way.
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45
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Novotný J, Cheshire JA. The surname space of the Czech Republic: examining population structure by network analysis of spatial co-occurrence of surnames. PLoS One 2012; 7:e48568. [PMID: 23119060 PMCID: PMC3485322 DOI: 10.1371/journal.pone.0048568] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 09/26/2012] [Indexed: 11/21/2022] Open
Abstract
In the majority of countries, surnames represent a ubiquitous cultural attribute inherited from an individual's ancestors and predominantly only altered through marriage. This paper utilises an innovative method, taken from economics, to offer unprecedented insights into the “surname space” of the Czech Republic. We construct this space as a network based on the pairwise probabilities of co-occurrence of surnames and find that the network representation has clear parallels with various ethno-cultural boundaries in the country. Our inductive approach therefore formalizes a simple assumption that the more frequently the bearers of two surnames concentrate in the same locations the higher the probability that these two surnames can be related (considering ethno-cultural relatedness, common co-ancestry or genetic relatedness, or some other type of relatedness). Using the Czech Republic as a case study this paper offers a fresh perspective on surnames as a quantitative data source and provides a methodology that can be easily incorporated within wider cultural, ethnic, geographic and population genetics studies already utilizing surnames.
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Affiliation(s)
- Josef Novotný
- Department of Social Geography and Regional Development, Faculty of Science, Charles University in Prague, Czech Republic.
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46
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Darlu P, Bloothooft G, Boattini A, Brouwer L, Brouwer M, Brunet G, Chareille P, Cheshire J, Coates R, Dräger K, Desjardins B, Hanks P, Longley P, Mandemakers K, Mateos P, Pettener D, Useli A, Manni F. The family name as socio-cultural feature and genetic metaphor: from concepts to methods. Hum Biol 2012; 84:169-214. [PMID: 22708820 DOI: 10.3378/027.084.0205] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A recent workshop entitled "The Family Name as Socio-Cultural Feature and Genetic Metaphor: From Concepts to Methods" was held in Paris in December 2010, sponsored by the French National Centre for Scientific Research (CNRS) and by the journal Human Biology. This workshop was intended to foster a debate on questions related to the family names and to compare different multidisciplinary approaches involving geneticists, historians, geographers, sociologists and social anthropologists. This collective paper presents a collection of selected communications.
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Affiliation(s)
- Pierre Darlu
- UMR7206, CNRS, Muséum National d'Histoire Naturelle, Université Paris 7 Paris, France.
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Su Z, Gay LJ, Strange A, Palles C, Band G, Whiteman DC, Lescai F, Langford C, Nanji M, Edkins S, van der Winkel A, Levine D, Sasieni P, Bellenguez C, Howarth K, Freeman C, Trudgill N, Tucker AT, Pirinen M, Peppelenbosch MP, van der Laan LJW, Kuipers EJ, Drenth JPH, Peters WH, Reynolds JV, Kelleher DP, McManus R, Grabsch H, Prenen H, Bisschops R, Krishnadath K, Siersema PD, van Baal JWPM, Middleton M, Petty R, Gillies R, Burch N, Bhandari P, Paterson S, Edwards C, Penman I, Vaidya K, Ang Y, Murray I, Patel P, Ye W, Mullins P, Wu AH, Bird NC, Dallal H, Shaheen NJ, Murray LJ, Koss K, Bernstein L, Romero Y, Hardie LJ, Zhang R, Winter H, Corley DA, Panter S, Risch HA, Reid BJ, Sargeant I, Gammon MD, Smart H, Dhar A, McMurtry H, Ali H, Liu G, Casson AG, Chow WH, Rutter M, Tawil A, Morris D, Nwokolo C, Isaacs P, Rodgers C, Ragunath K, MacDonald C, Haigh C, Monk D, Davies G, Wajed S, Johnston D, Gibbons M, Cullen S, Church N, Langley R, Griffin M, Alderson D, Deloukas P, Hunt SE, Gray E, Dronov S, Potter SC, Tashakkori-Ghanbaria A, Anderson M, Brooks C, Blackwell JM, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Markus HS, Mathew CG, Palmer CNA, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood N, Trynka G, Wijmenga C, Cazier JB, Atherfold P, Nicholson AM, Gellatly NL, Glancy D, Cooper SC, Cunningham D, Lind T, Hapeshi J, Ferry D, Rathbone B, Brown J, Love S, Attwood S, MacGregor S, Watson P, Sanders S, Ek W, Harrison RF, Moayyedi P, de Caestecker J, Barr H, Stupka E, Vaughan TL, Peltonen L, Spencer CCA, Tomlinson I, Donnelly P, Jankowski JAZ. Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett's esophagus. Nat Genet 2012; 44:1131-6. [PMID: 22961001 PMCID: PMC3459818 DOI: 10.1038/ng.2408] [Citation(s) in RCA: 146] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/15/2012] [Indexed: 02/07/2023]
Abstract
Barrett's esophagus is an increasingly common disease that is strongly associated with reflux of stomach acid and usually a hiatus hernia, and it strongly predisposes to esophageal adenocarcinoma (EAC), a tumor with a very poor prognosis. We report the first genome-wide association study on Barrett's esophagus, comprising 1,852 UK cases and 5,172 UK controls in the discovery stage and 5,986 cases and 12,825 controls in the replication stage. Variants at two loci were associated with disease risk: chromosome 6p21, rs9257809 (Pcombined=4.09×10(-9); odds ratio (OR)=1.21, 95% confidence interval (CI)=1.13-1.28), within the major histocompatibility complex locus, and chromosome 16q24, rs9936833 (Pcombined=2.74×10(-10); OR=1.14, 95% CI=1.10-1.19), for which the closest protein-coding gene is FOXF1, which is implicated in esophageal development and structure. We found evidence that many common variants of small effect contribute to genetic susceptibility to Barrett's esophagus and that SNP alleles predisposing to obesity also increase risk for Barrett's esophagus.
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Affiliation(s)
- Zhan Su
- Wellcome Trust Centre for Human Genetics, Oxford, UK
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An overview of the genetic structure within the Italian population from genome-wide data. PLoS One 2012; 7:e43759. [PMID: 22984441 PMCID: PMC3440425 DOI: 10.1371/journal.pone.0043759] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 07/24/2012] [Indexed: 12/21/2022] Open
Abstract
In spite of the common belief of Europe as reasonably homogeneous at genetic level, advances in high-throughput genotyping technology have resolved several gradients which define different geographical areas with good precision. When Northern and Southern European groups were considered separately, there were clear genetic distinctions. Intra-country genetic differences were also evident, especially in Finland and, to a lesser extent, within other European populations. Here, we present the first analysis using the 125,799 genome-wide Single Nucleotide Polymorphisms (SNPs) data of 1,014 Italians with wide geographical coverage. We showed by using Principal Component analysis and model-based individual ancestry analysis, that the current population of Sardinia can be clearly differentiated genetically from mainland Italy and Sicily, and that a certain degree of genetic differentiation is detectable within the current Italian peninsula population. Pair-wise F(ST) statistics Northern and Southern Italy amounts approximately to 0.001 between, and around 0.002 between Northern Italy and Utah residents with Northern and Western European ancestry (CEU). The Italian population also revealed a fine genetic substructure underscoring by the genomic inflation (Sardinia vs. Northern Italy = 3.040 and Northern Italy vs. CEU = 1.427), warning against confounding effects of hidden relatedness and population substructure in association studies.
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Role of rare variants in undetermined multiple adenomatous polyposis and early-onset colorectal cancer. J Hum Genet 2012; 57:709-716. [PMID: 22875147 DOI: 10.1038/jhg.2012.99] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Some 15-20% of multiple adenomatous polyposis have no genetic explanation and 20-30% of colorectal cancer (CRC) cases are thought to be due to inherited multifactorial causes. Accumulation of deleterious effects of low-frequency dominant and independently acting variants may be a partial explanation for such patients. The aim of this study was to type a selection of rare and low-frequency variants (<5%) to elucidate their role in CRC susceptibility. A total of 1181 subjects were included (866 controls; 315 cases). Cases comprised UK (n=184) and French (n=131) patients with MAP (n=187) or early-onset CRC (n=128). Seventy variants in 17 genes were examined in cases and controls. The effect of the variant effect on protein function was investigated in silico. Out of the 70 variants typed, 36 (51%) were tested for association. Twenty-one variants were rare (minor allele frequency (MAF) <1%). Four rare variants were found to have a significantly higher MAF in cases (EXO1-12, MLH1-1, CTNNB1-1 and BRCA2-37, P<0.05) than in controls. Pooling all rare variants with a MAF <0.5% showed an excess risk in cases (odds ratio=3.2; 95% confidence interval=1.1-9.5; P=0.04). Rare variants are important risk factors in CRC and, as such, should be systematically assayed alongside common variation in the search for the genetic basis of complex diseases.
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Larmuseau MHD, Vanoverbeke J, Gielis G, Vanderheyden N, Larmuseau HFM, Decorte R. In the name of the migrant father--analysis of surname origins identifies genetic admixture events undetectable from genealogical records. Heredity (Edinb) 2012; 109:90-5. [PMID: 22511074 PMCID: PMC3400745 DOI: 10.1038/hdy.2012.17] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 03/01/2012] [Accepted: 03/09/2012] [Indexed: 11/08/2022] Open
Abstract
Patrilineal heritable surnames are widely used to select autochthonous participants for studies on small-scale population genetic patterns owing to the unique link between the surname and a genetic marker, the Y-chromosome (Y-chr). Today, the question arises as to whether the surname origin will be informative on top of in-depth genealogical pedigrees. Admixture events that happened in the period after giving heritable surnames but before the start of genealogical records may be informative about the additional value of the surname origin. In this context, an interesting historical event is the demic migration from French-speaking regions in Northern France to the depopulated and Dutch-speaking region Flanders at the end of the sixteenth century. Y-chr subhaplogroups of individuals with a French/Roman surname that could be associated with this migration event were compared with those of a group with autochthonous Flemish surnames. Although these groups could not be differentiated based on in-depth genealogical data, they were significantly genetically different from each other. Moreover, the observed genetic divergence was related to the differences in the distributions of main Y-subhaplogroups between contemporary populations from Northern France and Flanders. Therefore, these results indicate that the surname origin can be an important feature on top of in-depth genealogical results to select autochthonous participants for a regional population genetic study based on Y-chromosomes.
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Affiliation(s)
- M H D Larmuseau
- UZ Leuven, Department of Forensic Medicine, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium.
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