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Herzig AF, Velo-Suárez L, Dina C, Redon R, Deleuze JF, Génin E. How local reference panels improve imputation in French populations. Sci Rep 2024; 14:370. [PMID: 38172507 PMCID: PMC10764714 DOI: 10.1038/s41598-023-49931-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
Imputation servers offer the exclusive possibility to harness the largest public reference panels which have been shown to deliver very high precision in the imputation of European genomes. Many studies have nonetheless stressed the importance of 'study specific panels' (SSPs) as an alternative and have shown the benefits of combining public reference panels with SSPs. But such combined approaches are not attainable when using external imputation servers. To investigate how to confront this challenge, we imputed 550 French individuals using either the University of Michigan imputation server with the Haplotype Reference Consortium (HRC) panel or an in-house SSP of 850 whole-genome sequenced French individuals. With approximate geo-localization of both our target and SSP individuals we are able to pinpoint different scenarios where SSP-based imputation would be preferred over server-based imputation or vice-versa. This is achieved by showing to a high degree of resolution the importance of the proximity of the reference panel to target individuals; with a focus on the clear added value of SSPs for estimating haplotype phase and for the imputation of rare variants (minor allele-frequency below 0.01). Such benefits were most evident for individuals from the same geographical regions in France as the SSP individuals. Overall, only 42.3% of all 125,442 variants evaluated were better imputed with an SSP from France compared to an external reference panel, however this rises to 58.1% for individuals from geographic regions well covered by the SSP. By investigating haplotype sharing and population fine-structure in France, we show the importance of including SSP haplotypes for imputation but also that they should ideally be combined with large public panels. In the absence of the unattainable results from a combined panel of the HRC and our French SSP, we put forward a pragmatic solution where server-based and SSP-based imputation outcomes can be combined based on comparing posterior genotype probabilities. We show that such an approach can give a level of imputation accuracy in excess of what could be achieved with either strategy alone. The results presented provide detailed insights into the accuracy of imputation that should be expected from different strategies for European populations.
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Affiliation(s)
| | - Lourdes Velo-Suárez
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
- CHRU Brest, Brest, France
| | - Christian Dina
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Richard Redon
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, CEA, Evry, France
- Fondation Jean Dausset - Centre d'Etude du Polymorphisme Humain (CEPH), Paris, France
| | - Emmanuelle Génin
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
- CHRU Brest, Brest, France
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2
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Ma J, Tang L, Peng P, Wang T, Gui H, Ren X. Shifting as an executive function separate from updating and inhibition in old age: Behavioral and genetic evidence. Behav Brain Res 2023; 452:114604. [PMID: 37516210 DOI: 10.1016/j.bbr.2023.114604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/09/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
This study aimed to examine the organization of executive functions (EFs), specifically working memory updating, prepotent response inhibition, and mental-set shifting in old age, with a particular focus on determining whether the shifting function was behaviorally and genetically separated from the other functions. A total of 248 healthy older Chinese individuals participated, and multiple measures of executive functions were collected. Additionally, measures of fluid intelligence were included to explore the varying relationships between the three executive functions and this higher-order cognitive ability. Furthermore, genetic data were gathered and analyzed to investigate the associations between EFs and six candidate single-nucleotide polymorphisms (SNPs) mapped to dopaminergic, serotonergic, or glutamatergic genes. The results indicated that both the three-factor model and the two-factor model, which combined updating and inhibition, demonstrated a good fit. Furthermore, shifting was found to be behaviorally separated from the other two functions, and the correlation between shifting and fluid intelligence was smaller compared to the correlations between updating and inhibition with fluid intelligence. Moreover, the DRD2 SNPs showed significant associations with shifting, rather than with updating and inhibition. These findings provide evidence that shifting is distinct and separate from updating and inhibition, highlighting the diversity of EFs among older adults.
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Affiliation(s)
- Juanjuan Ma
- School of Education, Huazhong University of Science & Technology, Wuhan, China
| | - Lixu Tang
- School of Wushu, Wuhan Sports University, Wuhan 430079, China
| | - Peng Peng
- Department of Special Education, University of Texas at Austin, Austin, USA
| | - Tengfei Wang
- Department of Psychology, Zhejiang University, Hangzhou, China
| | - Hongsheng Gui
- Behavioral Health Services and Psychiatry Research, Henry Ford Health, USA; Department of Psychiatry, Michigan State University, USA
| | - Xuezhu Ren
- School of Education, Huazhong University of Science & Technology, Wuhan, China.
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3
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Choi J, Kim S, Kim J, Son HY, Yoo SK, Kim CU, Park YJ, Moon S, Cha B, Jeon MC, Park K, Yun JM, Cho B, Kim N, Kim C, Kwon NJ, Park YJ, Matsuda F, Momozawa Y, Kubo M, Kim HJ, Park JH, Seo JS, Kim JI, Im SW. A whole-genome reference panel of 14,393 individuals for East Asian populations accelerates discovery of rare functional variants. SCIENCE ADVANCES 2023; 9:eadg6319. [PMID: 37556544 PMCID: PMC10411914 DOI: 10.1126/sciadv.adg6319] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/06/2023] [Indexed: 08/11/2023]
Abstract
Underrepresentation of non-European (EUR) populations hinders growth of global precision medicine. Resources such as imputation reference panels that match the study population are necessary to find low-frequency variants with substantial effects. We created a reference panel consisting of 14,393 whole-genome sequences including more than 11,000 Asian individuals. Genome-wide association studies were conducted using the reference panel and a population-specific genotype array of 72,298 subjects for eight phenotypes. This panel yields improved imputation accuracy of rare and low-frequency variants within East Asian populations compared with the largest reference panel. Thirty-nine previously unidentified associations were found, and more than half of the variants were East Asian specific. We discovered genes with rare protein-altering variants, including LTBP1 for height and GPR75 for body mass index, as well as putative regulatory mechanisms for rare noncoding variants with cell type-specific effects. We suggest that this dataset will add to the potential value of Asian precision medicine.
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Affiliation(s)
- Jaeyong Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | | | - Juhyun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ho-Young Son
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Seong-Keun Yoo
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Young Jun Park
- Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sungji Moon
- Interdisciplinary Program in Cancer Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Bukyoung Cha
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Min Chul Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyunghyuk Park
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Jae Moon Yun
- Department of Family Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Belong Cho
- Department of Family Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Family Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | | | | | | | - Young Joo Park
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | | | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Hyun-Jin Kim
- National Cancer Control Institute, National Cancer Center, Goyang, Republic of Korea
| | - Jin-Ho Park
- Department of Family Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Family Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jeong-Sun Seo
- Macrogen Inc., Seoul, Republic of Korea
- Asian Genome Center, Seoul National University Bundang Hospital, Gyeonggi, Republic of Korea
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sun-Wha Im
- Department of Biochemistry and Molecular Biology, Kangwon National University School of Medicine, Gangwon, Republic of Korea
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4
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Dekeyser T, Génin E, Herzig AF. Opening the Black Box of Imputation Software to Study the Impact of Reference Panel Composition on Performance. Genes (Basel) 2023; 14:410. [PMID: 36833337 PMCID: PMC9956390 DOI: 10.3390/genes14020410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/22/2023] [Accepted: 01/30/2023] [Indexed: 02/09/2023] Open
Abstract
Genotype imputation is widely used to enrich genetic datasets. The operation relies on panels of known reference haplotypes, typically with whole-genome sequencing data. How to choose a reference panel has been widely studied and it is essential to have a panel that is well matched to the individuals who require missing genotype imputation. However, it is broadly accepted that such an imputation panel will have an enhanced performance with the inclusion of diversity (haplotypes from many different populations). We investigate this observation by examining, in fine detail, exactly which reference haplotypes are contributing at different regions of the genome. This is achieved using a novel method of inserting synthetic genetic variation into the reference panel in order to track the performance of leading imputation algorithms. We show that while diversity may globally improve imputation accuracy, there can be occasions where incorrect genotypes are imputed following the inclusion of more diverse haplotypes in the reference panel. We, however, demonstrate a technique for retaining and benefitting from the diversity in the reference panel whilst avoiding the occasional adverse effects on imputation accuracy. What is more, our results more clearly elucidate the role of diversity in a reference panel than has been shown in previous studies.
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Affiliation(s)
- Thibault Dekeyser
- Inserm, Université de Brest, EFS, UMR 1078, GGB, F-29200 Brest, France
- CHRU Brest, F-29200 Brest, France
| | - Emmanuelle Génin
- Inserm, Université de Brest, EFS, UMR 1078, GGB, F-29200 Brest, France
- CHRU Brest, F-29200 Brest, France
| | - Anthony F. Herzig
- Inserm, Université de Brest, EFS, UMR 1078, GGB, F-29200 Brest, France
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5
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Ruotsalainen SE, Partanen JJ, Cichonska A, Lin J, Benner C, Surakka I, Reeve MP, Palta P, Salmi M, Jalkanen S, Ahola-Olli A, Palotie A, Salomaa V, Daly MJ, Pirinen M, Ripatti S, Koskela J. An expanded analysis framework for multivariate GWAS connects inflammatory biomarkers to functional variants and disease. Eur J Hum Genet 2021; 29:309-324. [PMID: 33110245 PMCID: PMC7868371 DOI: 10.1038/s41431-020-00730-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 08/02/2020] [Accepted: 09/04/2020] [Indexed: 12/19/2022] Open
Abstract
Multivariate methods are known to increase the statistical power to detect associations in the case of shared genetic basis between phenotypes. They have, however, lacked essential analytic tools to follow-up and understand the biology underlying these associations. We developed a novel computational workflow for multivariate GWAS follow-up analyses, including fine-mapping and identification of the subset of traits driving associations (driver traits). Many follow-up tools require univariate regression coefficients which are lacking from multivariate results. Our method overcomes this problem by using Canonical Correlation Analysis to turn each multivariate association into its optimal univariate Linear Combination Phenotype (LCP). This enables an LCP-GWAS, which in turn generates the statistics required for follow-up analyses. We implemented our method on 12 highly correlated inflammatory biomarkers in a Finnish population-based study. Altogether, we identified 11 associations, four of which (F5, ABO, C1orf140 and PDGFRB) were not detected by biomarker-specific analyses. Fine-mapping identified 19 signals within the 11 loci and driver trait analysis determined the traits contributing to the associations. A phenome-wide association study on the 19 representative variants from the signals in 176,899 individuals from the FinnGen study revealed 53 disease associations (p < 1 × 10-4). Several reported pQTLs in the 11 loci provided orthogonal evidence for the biologically relevant functions of the representative variants. Our novel multivariate analysis workflow provides a powerful addition to standard univariate GWAS analyses by enabling multivariate GWAS follow-up and thus promoting the advancement of powerful multivariate methods in genomics.
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Affiliation(s)
- Sanni E Ruotsalainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Juulia J Partanen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Anna Cichonska
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Computer Science, Helsinki Institute for Information Technology HIIT, Aalto University, Espoo, Finland
- Department of Future Technologies, University of Turku, Turku, Finland
| | - Jake Lin
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Christian Benner
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ida Surakka
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Mary Pat Reeve
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Priit Palta
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Marko Salmi
- MediCity Research Laboratory, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Sirpa Jalkanen
- MediCity Research Laboratory, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Ari Ahola-Olli
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Mark J Daly
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Public Health, Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - Jukka Koskela
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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6
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Hassan S, Surakka I, Taskinen MR, Salomaa V, Palotie A, Wessman M, Tukiainen T, Pirinen M, Palta P, Ripatti S. High-resolution population-specific recombination rates and their effect on phasing and genotype imputation. Eur J Hum Genet 2020; 29:615-624. [PMID: 33249422 PMCID: PMC8114909 DOI: 10.1038/s41431-020-00768-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/01/2020] [Accepted: 10/20/2020] [Indexed: 11/24/2022] Open
Abstract
Previous research has shown that using population-specific reference panels has a significant effect on downstream population genomic analyses like haplotype phasing, genotype imputation, and association, especially in the context of population isolates. Here, we developed a high-resolution recombination rate mapping at 10 and 50 kb scale using high-coverage (20–30×) whole-genome sequenced data of 55 family trios from Finland and compared it to recombination rates of non-Finnish Europeans (NFE). We tested the downstream effects of the population-specific recombination rates in statistical phasing and genotype imputation in Finns as compared to the same analyses performed by using the NFE-based recombination rates. We found that Finnish recombination rates have a moderately high correlation (Spearman’s ρ = 0.67–0.79) with NFE, although on average (across all autosomal chromosomes), Finnish rates (2.268 ± 0.4209 cM/Mb) are 12–14% lower than NFE (2.641 ± 0.5032 cM/Mb). Finnish recombination map was found to have no significant effect in haplotype phasing accuracy (switch error rates ~2%) and average imputation concordance rates (97–98% for common, 92–96% for low frequency and 78–90% for rare variants). Our results suggest that haplotype phasing and genotype imputation mostly depend on population-specific contexts like appropriate reference panels and their sample size, but not on population-specific recombination maps. Even though recombination rate estimates had some differences between the Finnish and NFE populations, haplotyping and imputation had not been noticeably affected by the recombination map used. Therefore, the currently available HapMap recombination maps seem robust for population-specific phasing and imputation pipelines, even in the context of relatively isolated populations like Finland.
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Affiliation(s)
- Shabbeer Hassan
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ida Surakka
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Marja-Riitta Taskinen
- Clinical and molecular metabolism, Research program unit, University of Helsinki, Helsinki, Finland
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland.,Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA.,Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Maija Wessman
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Taru Tukiainen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Matti Pirinen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland.,Department of Public Health, Faculty of Medicine, Clinicum, University of Helsinki, Helsinki, Finland.,Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Priit Palta
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland.,Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, Finland. .,Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA. .,Department of Public Health, Faculty of Medicine, Clinicum, University of Helsinki, Helsinki, Finland.
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7
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Svensson D, Rentoft M, Dahlin AM, Lundholm E, Olason PI, Sjödin A, Nylander C, Melin BS, Trygg J, Johansson E. A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences. PLoS One 2020; 15:e0237721. [PMID: 32915809 PMCID: PMC7485808 DOI: 10.1371/journal.pone.0237721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/31/2020] [Indexed: 12/30/2022] Open
Abstract
The number of national reference populations that are whole-genome sequenced are rapidly increasing. Partly driving this development is the fact that genetic disease studies benefit from knowing the genetic variation typical for the geographical area of interest. A whole-genome sequenced Swedish national reference population (n = 1000) has been recently published but with few samples from northern Sweden. In the present study we have whole-genome sequenced a control population (n = 300) (ACpop) from Västerbotten County, a sparsely populated region in northern Sweden previously shown to be genetically different from southern Sweden. The aggregated variant frequencies within ACpop are publicly available (DOI 10.17044/NBIS/G000005) to function as a basic resource in clinical genetics and for genetic studies. Our analysis of ACpop, representing approximately 0.11% of the population in Västerbotten, indicates the presence of a genetic substructure within the county. Furthermore, a demographic analysis showed that the population from which samples were drawn was to a large extent geographically stationary, a finding that was corroborated in the genetic analysis down to the level of municipalities. Including ACpop in the reference population when imputing unknown variants in a Västerbotten cohort resulted in a strong increase in the number of high-confidence imputed variants (up to 81% for variants with minor allele frequency < 5%). ACpop was initially designed for cancer disease studies, but the genetic structure within the cohort will be of general interest for all genetic disease studies in northern Sweden.
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Affiliation(s)
- Daniel Svensson
- Department of Chemistry, Computational Life Science Cluster, Umeå University, Umeå, Sweden
| | - Matilda Rentoft
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Anna M. Dahlin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Emma Lundholm
- Centre for Demography and Ageing, Umeå University, Umeå, Sweden
| | - Pall I. Olason
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Andreas Sjödin
- Department of Chemistry, Computational Life Science Cluster, Umeå University, Umeå, Sweden
- Division of CBRN Security and Defence, FOI–Swedish Defence Research Agency, Umeå, Sweden
| | - Carin Nylander
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Beatrice S. Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Johan Trygg
- Department of Chemistry, Computational Life Science Cluster, Umeå University, Umeå, Sweden
| | - Erik Johansson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- * E-mail:
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8
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Im SW, Chae J, Son HY, Cho B, Kim JI, Park JH. A population-specific low-frequency variant of SLC22A12 (p.W258*) explains nearby genome-wide association signals for serum uric acid concentrations among Koreans. PLoS One 2020; 15:e0231336. [PMID: 32271837 PMCID: PMC7145145 DOI: 10.1371/journal.pone.0231336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/20/2020] [Indexed: 11/30/2022] Open
Abstract
Prolonged hyperuricemia is a cause of gout and an independent risk factor for chronic health conditions including diabetes and chronic kidney diseases. Genome-wide association studies (GWASs) for serum uric acid (SUA) concentrations have repeatedly confirmed genetic loci including those encoding uric acid transporters such as ABCG2 and SLC9A2. However, many single nucleotide polymorphisms (SNPs) found in GWASs have been common variants with small effects and unknown functions. In addition, there is still much heritability to be explained. To identify the causative genetic variants for SUA concentrations in Korean subjects, we conducted a GWAS (1902 males) and validation study (2912 males and females) and found four genetic loci reaching genome-wide significance on chromosomes 4 (ABCG2) and 11 (FRMD8, EIF1AD and SLC22A12-NRXN2). Three loci on chromosome 11 were distributed within a distance of 1.3 megabases and they were in weak or moderate linkage disequilibrium (LD) states (r2 = 0.02–0.68). In a subsequent association analysis on the GWAS loci of chromosome 11 using closely positioned markers derived from whole genome sequencing data, the most significant variant to be linked with the nearby GWAS signal was rs121907892 (c.774G>A, p.W258*) of the SLC22A12 gene. This variant, and each of the three GWAS SNPs, were in LD (r2 = 0.06–0.32). The strength of association of SNPs with SUA concentration (negative logarithm of P-values) and the genetic distance (r2 of LD) between rs121907892 and the surrounding SNPs showed a quantitative correlation. This variant has been found only in Korean and Japanese subjects and is known to lower the SUA concentration in the general population. Thus, this low-frequency variant, rs121907892, known to regulate SUA concentrations in previous studies, is responsible for the nearby GWAS signals.
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Affiliation(s)
- Sun-Wha Im
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Jeesoo Chae
- Department of Biomedical Science, Seoul National University Graduate School, Seoul, Republic of Korea
| | - Ho-Young Son
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Belong Cho
- Departments of Family Medicine, Seoul National University College of Medicine and Seoul National University Hospital, Seoul, Republic of Korea
| | - Jong-Il Kim
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University Graduate School, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
- * E-mail: (JK); (JP)
| | - Jin-Ho Park
- Departments of Family Medicine, Seoul National University College of Medicine and Seoul National University Hospital, Seoul, Republic of Korea
- * E-mail: (JK); (JP)
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9
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Nutile T, Ruggiero D, Herzig AF, Tirozzi A, Nappo S, Sorice R, Marangio F, Bellenguez C, Leutenegger AL, Ciullo M. Whole-Exome Sequencing in the Isolated Populations of Cilento from South Italy. Sci Rep 2019; 9:4059. [PMID: 30858532 PMCID: PMC6411969 DOI: 10.1038/s41598-019-41022-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 02/22/2019] [Indexed: 12/21/2022] Open
Abstract
The present study describes the genetic architecture of the isolated populations of Cilento, through the analysis of exome sequence data of 245 representative individuals of these populations. By annotating the exome variants and cataloguing them according to their frequency and functional effects, we identified 347,684 variants, 67.4% of which are rare and low frequency variants, and 1% of them (corresponding to 319 variants per person) are classified as high functional impact variants; also, 39,946 (11.5% of the total) are novel variants, for which we determined a significant enrichment for deleterious effects. By comparing the allele frequencies in Cilento with those from the Tuscan population from the 1000 Genomes Project Phase 3, we highlighted an increase in allele frequency in Cilento especially for variants which map to genes involved in extracellular matrix formation and organization. Furthermore, among the variants showing increased frequency we identified several known rare disease-causing variants. By different population genetics analyses, we corroborated the status of the Cilento populations as genetic isolates. Finally, we showed that exome data of Cilento represents a useful local reference panel capable of improving the accuracy of genetic imputation, thus adding power to genetic studies of human traits in these populations.
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Affiliation(s)
- T Nutile
- Institute of Genetics and Biophysics A. Buzzati-Traverso-CNR, Naples, Italy
| | - D Ruggiero
- Institute of Genetics and Biophysics A. Buzzati-Traverso-CNR, Naples, Italy.,IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - A F Herzig
- Inserm, UMR 946, Genetic variation and Human diseases, F-75010, Paris, France.,Université Paris-Diderot, Sorbonne Paris Cité, UMR946, F-75010, Paris, France
| | - A Tirozzi
- IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - S Nappo
- AORN Santobono-Pausilipon Hospital, Naples, Italy
| | - R Sorice
- Institute of Genetics and Biophysics A. Buzzati-Traverso-CNR, Naples, Italy
| | - F Marangio
- Institute of Genetics and Biophysics A. Buzzati-Traverso-CNR, Naples, Italy
| | - C Bellenguez
- Inserm, U1167, RID-AGE-Risk factors and molecular determinants of aging-related diseases, F-59000, Lille, France.,Institut Pasteur de Lille, F-59000, Lille, France.,Univ. Lille, U1167-Excellence Laboratory LabEx DISTALZ, F-59000, Lille, France
| | - A L Leutenegger
- Inserm, UMR 946, Genetic variation and Human diseases, F-75010, Paris, France.,Université Paris-Diderot, Sorbonne Paris Cité, UMR946, F-75010, Paris, France
| | - M Ciullo
- Institute of Genetics and Biophysics A. Buzzati-Traverso-CNR, Naples, Italy. .,IRCCS Neuromed, Pozzilli, Isernia, Italy.
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10
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Hua F, Guo Y, Sun Q, Yang L, Gao F. HapMap-based study: CYP2A13 may be a potential key metabolic enzyme gene in the carcinogenesis of lung cancer in non-smokers. Thorac Cancer 2019; 10:601-606. [PMID: 30807688 PMCID: PMC6449263 DOI: 10.1111/1759-7714.12954] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/03/2018] [Accepted: 12/03/2018] [Indexed: 12/30/2022] Open
Abstract
Background The aim of this study was to evaluate the association between CYP2A13 polymorphisms and lung cancer susceptibility using the HapMap database. Methods A case‐control analysis of 532 subjects with lung cancer and 614 controls with no personal history of the disease was performed. The tag SNPs rs1645690 and rs8192789 for CYP2A13 were selected, and the genetic polymorphisms were confirmed experimentally through real‐time PCR, cloning, and sequencing assay. Results SNP frequency in this study was consistent with the HapMap Project database of Han‐Chinese and lung cancer risk was associated with CYP2A13 polymorphisms in non‐smokers. CYP2A13 shares a 93.5% identity with CYP2A6 in the amino acid sequence and the homologous sequences may interfere with the study of SNPs of CYP2A13. Conclusions CYP2A13 may be a potential key metabolic enzyme gene in the carcinogenesis of lung cancer in non‐smokers. The common polymorphisms of CYP2A13 may be candidate biomarkers for lung cancer susceptibility in Han‐Chinese.
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Affiliation(s)
- Feng Hua
- Department of Thoracic Surgery, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, China
| | - Yonglu Guo
- Department of Respiratory, Jiuquan City People's Hospital, Jiuquan, China
| | - Qiang Sun
- Department of Infection, Jiuquan City People's Hospital, Jiuquan, China
| | - Leizhou Yang
- Department of Internal Medicine, Jining City Yanzhou District Railway Hospital, Jining, China
| | - Fang Gao
- Department of Thoracic Surgery, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, China
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11
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Jousilahti P, Laatikainen T, Salomaa V, Pietilä A, Vartiainen E, Puska P. 40-Year CHD Mortality Trends and the Role of Risk Factors in Mortality Decline: The North Karelia Project Experience. Glob Heart 2018; 11:207-12. [PMID: 27242088 DOI: 10.1016/j.gheart.2016.04.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 04/25/2016] [Indexed: 11/29/2022] Open
Abstract
In the 1960s and early 1970s, coronary heart disease (CHD) mortality in Finland was the highest in the world, and within Finland, mortality was particularly high in the eastern part of the country. The North Karelia Project, the first large community-based cardiovascular diseases prevention program was established in 1972 to reduce the extremely high CHD mortality through behavioral change and reduction of the main cardiovascular disease risk factors among the whole population of North Karelia, the easternmost province of Finland. During the 40-year period from 1972 to 2012, smoking prevalence, serum total cholesterol, and systolic blood pressure declined markedly, except a small increase in serum cholesterol levels between 2007 and 2012. From the early 1970s to 2012, CHD mortality decreased by 82% (from 643 to 118 per 100,000) among working-age (35 to 64 years) men. Among working-age women, the decline was 84% (from 114 to 17 per 100,000). During the first 10 years, changes in these 3 target risk factors explained nearly all of the observed mortality reduction. Since the mid-1980s, the observed reduction in mortality has been larger than the predicted reduction. In the early 1970s, premature CHD mortality (35 to 74 years) was about 37% higher among Eastern Finnish men and 23% higher among Eastern Finnish women, compared with men and women in Southwestern Finland. During the last 40 years, premature CHD mortality declined markedly in both areas, but the decline was larger in Eastern Finland and the mortality gap between the two areas nearly disappeared.
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Affiliation(s)
- Pekka Jousilahti
- National Institute for Health and Welfare, Department of Health, Helsinki, Finland.
| | | | - Veikko Salomaa
- National Institute for Health and Welfare, Department of Health, Helsinki, Finland
| | - Arto Pietilä
- National Institute for Health and Welfare, Department of Health, Helsinki, Finland
| | - Erkki Vartiainen
- National Institute for Health and Welfare, Department of Health, Helsinki, Finland
| | - Pekka Puska
- National Institute for Health and Welfare, Department of Health, Helsinki, Finland
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12
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Herzig AF, Nutile T, Babron MC, Ciullo M, Bellenguez C, Leutenegger AL. Strategies for phasing and imputation in a population isolate. Genet Epidemiol 2018; 42:201-213. [PMID: 29319195 DOI: 10.1002/gepi.22109] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 11/16/2017] [Accepted: 11/16/2017] [Indexed: 11/05/2022]
Abstract
In the search for genetic associations with complex traits, population isolates offer the advantage of reduced genetic and environmental heterogeneity. In addition, cost-efficient next-generation association approaches have been proposed in these populations where only a subsample of representative individuals is sequenced and then genotypes are imputed into the rest of the population. Gene mapping in such populations thus requires high-quality genetic imputation and preliminary phasing. To identify an effective study design, we compare by simulation a range of phasing and imputation software and strategies. We simulated 1,115,604 variants on chromosome 10 for 477 members of the large complex pedigree of Campora, a village within the established isolate of Cilento in southern Italy. We assessed the phasing performance of identical by descent based software ALPHAPHASE and SLRP, LD-based software SHAPEIT2, SHAPEIT3, and BEAGLE, and new software EAGLE that combines both methodologies. For imputation we compared IMPUTE2, IMPUTE4, MINIMAC3, BEAGLE, and new software PBWT. Genotyping errors and missing genotypes were simulated to observe their effects on the performance of each software. Highly accurate phased data were achieved by all software with SHAPEIT2, SHAPEIT3, and EAGLE2 providing the most accurate results. MINIMAC3, IMPUTE4, and IMPUTE2 all performed strongly as imputation software and our study highlights the considerable gain in imputation accuracy provided by a genome sequenced reference panel specific to the population isolate.
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Affiliation(s)
- Anthony Francis Herzig
- Université Paris-Diderot, Sorbonne Paris Cité, U946, Paris, France.,Inserm, U946, Genetic Variation and Human Diseases, Paris, France
| | - Teresa Nutile
- Institute of Genetics and Biophysics A. Buzzati-Traverso-CNR, Naples, Italy
| | - Marie-Claude Babron
- Université Paris-Diderot, Sorbonne Paris Cité, U946, Paris, France.,Inserm, U946, Genetic Variation and Human Diseases, Paris, France
| | - Marina Ciullo
- Institute of Genetics and Biophysics A. Buzzati-Traverso-CNR, Naples, Italy.,IRCCS Neuromed, Pozzilli, Isernia, Italy
| | - Céline Bellenguez
- Inserm, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France.,Institut Pasteur de Lille, Lille, France.,Université de Lille, U1167-Excellence Laboratory LabEx DISTALZ, Lille, France
| | - Anne-Louise Leutenegger
- Université Paris-Diderot, Sorbonne Paris Cité, U946, Paris, France.,Inserm, U946, Genetic Variation and Human Diseases, Paris, France
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13
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Genetics in an isolated population like Finland: a different basis for genomic medicine? J Community Genet 2017; 8:319-326. [PMID: 28730583 PMCID: PMC5614886 DOI: 10.1007/s12687-017-0318-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/29/2017] [Indexed: 11/24/2022] Open
Abstract
A unique genetic background in an isolated population like that of Finland offers special opportunities for genetic research as well as for applying the genetic developments to the health care. On the other hand, the different genetic background may require local attempts to develop diagnostics and treatment as the selection of diseases and mutations differs from that in the other populations. In this review, we describe the experiences of research and health care in this genetic isolate starting from the identification of specific monogenic diseases enriched in the Finnish population all the way to implementing the knowledge of the unique genetic background to genomic medicine at population level.
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14
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Byars SG, Huang QQ, Gray LA, Bakshi A, Ripatti S, Abraham G, Stearns SC, Inouye M. Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy. PLoS Genet 2017; 13:e1006328. [PMID: 28640878 PMCID: PMC5480811 DOI: 10.1371/journal.pgen.1006328] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 05/02/2017] [Indexed: 12/18/2022] Open
Abstract
Traditional genome-wide scans for positive selection have mainly uncovered selective sweeps associated with monogenic traits. While selection on quantitative traits is much more common, very few signals have been detected because of their polygenic nature. We searched for positive selection signals underlying coronary artery disease (CAD) in worldwide populations, using novel approaches to quantify relationships between polygenic selection signals and CAD genetic risk. We identified new candidate adaptive loci that appear to have been directly modified by disease pressures given their significant associations with CAD genetic risk. These candidates were all uniquely and consistently associated with many different male and female reproductive traits suggesting selection may have also targeted these because of their direct effects on fitness. We found that CAD loci are significantly enriched for lifetime reproductive success relative to the rest of the human genome, with evidence that the relationship between CAD and lifetime reproductive success is antagonistic. This supports the presence of antagonistic-pleiotropic tradeoffs on CAD loci and provides a novel explanation for the maintenance and high prevalence of CAD in modern humans. Lastly, we found that positive selection more often targeted CAD gene regulatory variants using HapMap3 lymphoblastoid cell lines, which further highlights the unique biological significance of candidate adaptive loci underlying CAD. Our study provides a novel approach for detecting selection on polygenic traits and evidence that modern human genomes have evolved in response to CAD-induced selection pressures and other early-life traits sharing pleiotropic links with CAD.
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Affiliation(s)
- Sean G. Byars
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Qin Qin Huang
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Lesley-Ann Gray
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Andrew Bakshi
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Samuli Ripatti
- Institute of Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Gad Abraham
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Stephen C. Stearns
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America
| | - Michael Inouye
- Centre for Systems Genomics, School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
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15
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Abstract
Despite thousands of genetic loci identified to date, a large proportion of genetic variation predisposing to complex disease and traits remains unaccounted for. Advances in sequencing technology enable focused explorations on the contribution of low-frequency and rare variants to human traits. Here we review experimental approaches and current knowledge on the contribution of these genetic variants in complex disease and discuss challenges and opportunities for personalised medicine.
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Affiliation(s)
- Lorenzo Bomba
- Human Genetics, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, CB10 1HH, UK
| | - Klaudia Walter
- Human Genetics, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, CB10 1HH, UK
| | - Nicole Soranzo
- Human Genetics, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, CB10 1HH, UK. .,Department of Haematology, University of Cambridge, Hills Rd, Cambridge, CB2 0AH, UK. .,The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK.
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16
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Lemmelä S, Solovieva S, Shiri R, Benner C, Heliövaara M, Kettunen J, Anttila V, Ripatti S, Perola M, Seppälä I, Juonala M, Kähönen M, Salomaa V, Viikari J, Raitakari OT, Lehtimäki T, Palotie A, Viikari-Juntura E, Husgafvel-Pursiainen K. Genome-Wide Meta-Analysis of Sciatica in Finnish Population. PLoS One 2016; 11:e0163877. [PMID: 27764105 PMCID: PMC5072673 DOI: 10.1371/journal.pone.0163877] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 09/15/2016] [Indexed: 12/14/2022] Open
Abstract
Sciatica or the sciatic syndrome is a common and often disabling low back disorder in the working-age population. It has a relatively high heritability but poorly understood molecular mechanisms. The Finnish population is a genetic isolate where small founder population and bottleneck events have led to enrichment of certain rare and low frequency variants. We performed here the first genome-wide association (GWAS) and meta-analysis of sciatica. The meta-analysis was conducted across two GWAS covering 291 Finnish sciatica cases and 3671 controls genotyped and imputed at 7.7 million autosomal variants. The most promising loci (p<1x10-6) were replicated in 776 Finnish sciatica patients and 18,489 controls. We identified five intragenic variants, with relatively low frequencies, at two novel loci associated with sciatica at genome-wide significance. These included chr9:14344410:I (rs71321981) at 9p22.3 (NFIB gene; p = 1.30x10-8, MAF = 0.08) and four variants at 15q21.2: rs145901849, rs80035109, rs190200374 and rs117458827 (MYO5A; p = 1.34x10-8, MAF = 0.06; p = 2.32x10-8, MAF = 0.07; p = 3.85x10-8, MAF = 0.06; p = 4.78x10-8, MAF = 0.07, respectively). The most significant association in the meta-analysis, a single base insertion rs71321981 within the regulatory region of the transcription factor NFIB, replicated in an independent Finnish population sample (p = 0.04). Despite identifying 15q21.2 as a promising locus, we were not able to replicate it. It was differentiated; the lead variants within 15q21.2 were more frequent in Finland (6–7%) than in other European populations (1–2%). Imputation accuracies of the three significantly associated variants (chr9:14344410:I, rs190200374, and rs80035109) were validated by genotyping. In summary, our results suggest a novel locus, 9p22.3 (NFIB), which may be involved in susceptibility to sciatica. In addition, another locus, 15q21.2, emerged as a promising one, but failed to replicate.
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Affiliation(s)
- Susanna Lemmelä
- Health and Work Ability, Finnish Institute of Occupational Health, 00250 Helsinki, Finland
| | - Svetlana Solovieva
- Health and Work Ability, Finnish Institute of Occupational Health, 00250 Helsinki, Finland
| | - Rahman Shiri
- Health and Work Ability, Finnish Institute of Occupational Health, 00250 Helsinki, Finland
| | - Christian Benner
- Institute for Molecular Medicine Finland (FIMM), 00014 University of Helsinki, Helsinki, Finland
- Department of Public Health, 00014 University of Helsinki, Helsinki, Finland
| | - Markku Heliövaara
- Population Health Unit, National Institute for Health and Welfare, 00251 Helsinki, Finland
| | - Johannes Kettunen
- Faculty of Medicine, Institute of Health Sciences, University of Oulu, 90220 Oulu, Finland
- NMR Metabolomics Laboratory, University of Eastern Finland, Kuopio, Finland
- National Institute for Health and Welfare, Helsinki, Finland
| | - Verneri Anttila
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States of America
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), 00014 University of Helsinki, Helsinki, Finland
- Department of Public Health, 00014 University of Helsinki, Helsinki, Finland
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, United Kingdom
| | - Markus Perola
- Institute for Molecular Medicine Finland (FIMM), 00014 University of Helsinki, Helsinki, Finland
- Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, 00271 Helsinki, Finland
- The Estonian Genome Center, University of Tartu, 51010 Tartu, Estonia
| | - Ilkka Seppälä
- Department of Clinical Chemistry, Fimlab Laboratories, University of Tampere School of Medicine, 33520 Tampere, Finland
| | - Markus Juonala
- Division of Medicine, Turku University Hospital, 20521 Turku, Finland
- Department of Medicine, University of Turku, 20521 Turku, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, 33521 Tampere, Finland
| | - Veikko Salomaa
- Department of Health, National Institute for Health and Welfare, 00251 Helsinki, Finland
| | - Jorma Viikari
- Division of Medicine, Turku University Hospital, 20521 Turku, Finland
- Department of Medicine, University of Turku, 20521 Turku, Finland
| | - Olli T. Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, 20520 Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, 20521 Turku, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, University of Tampere School of Medicine, 33520 Tampere, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), 00014 University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States of America
- Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts 02114, United States of America
| | - Eira Viikari-Juntura
- Disability Prevention Centre, Finnish Institute of Occupational Health, 00250 Helsinki, Finland
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17
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Mohandesan E, Speller CF, Peters J, Uerpmann HP, Uerpmann M, De Cupere B, Hofreiter M, Burger PA. Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel. Mol Ecol Resour 2016; 17:300-313. [PMID: 27289015 PMCID: PMC5324683 DOI: 10.1111/1755-0998.12551] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/28/2016] [Accepted: 05/06/2016] [Indexed: 12/29/2022]
Abstract
The performance of hybridization capture combined with next‐generation sequencing (NGS) has seen limited investigation with samples from hot and arid regions until now. We applied hybridization capture and shotgun sequencing to recover DNA sequences from bone specimens of ancient‐domestic dromedary (Camelus dromedarius) and its extinct ancestor, the wild dromedary from Jordan, Syria, Turkey and the Arabian Peninsula, respectively. Our results show that hybridization capture increased the percentage of mitochondrial DNA (mtDNA) recovery by an average 187‐fold and in some cases yielded virtually complete mitochondrial (mt) genomes at multifold coverage in a single capture experiment. Furthermore, we tested the effect of hybridization temperature and time by using a touchdown approach on a limited number of samples. We observed no significant difference in the number of unique dromedary mtDNA reads retrieved with the standard capture compared to the touchdown method. In total, we obtained 14 partial mitochondrial genomes from ancient‐domestic dromedaries with 17–95% length coverage and 1.27–47.1‐fold read depths for the covered regions. Using whole‐genome shotgun sequencing, we successfully recovered endogenous dromedary nuclear DNA (nuDNA) from domestic and wild dromedary specimens with 1–1.06‐fold read depths for covered regions. Our results highlight that despite recent methodological advances, obtaining ancient DNA (aDNA) from specimens recovered from hot, arid environments is still problematic. Hybridization protocols require specific optimization, and samples at the limit of DNA preservation need multiple replications of DNA extraction and hybridization capture as has been shown previously for Middle Pleistocene specimens.
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Affiliation(s)
- Elmira Mohandesan
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße 1, 1160, Vienna, Austria.,Institute of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Camilla F Speller
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Joris Peters
- Department of Veterinary Sciences, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität München (LMU Munich), 80539, Munich, Germany.,Staatliche Naturwissenschaftliche Sammlungen Bayerns, Bavarian State Collection of Anthropology and Palaeoanatomy, 80333, Munich, Germany
| | - Hans-Peter Uerpmann
- Abteilung Archäozoologie, Institut für Naturwissenschaftliche Archäologie, Eberhard-Karls-Universität Tübingen, Rümelinstrasse 23, 7207, Tübingen, Germany
| | - Margarethe Uerpmann
- Staatliche Naturwissenschaftliche Sammlungen Bayerns, Bavarian State Collection of Anthropology and Palaeoanatomy, 80333, Munich, Germany
| | - Bea De Cupere
- Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000, Brussels, Belgium
| | - Michael Hofreiter
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York, YO10 5DD, UK.,Evolutionary and Adaptive Genomics, Department of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Street 24-25, Potsdam, 14476, Germany
| | - Pamela A Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße 1, 1160, Vienna, Austria
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18
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Genetic and Environmental Contributions to Cardiovascular Risk: Lessons
From North Karelia and FINRISK. Glob Heart 2016; 11:229-33. [DOI: 10.1016/j.gheart.2016.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/26/2016] [Indexed: 11/23/2022] Open
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19
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Flegontov P, Changmai P, Zidkova A, Logacheva MD, Altınışık NE, Flegontova O, Gelfand MS, Gerasimov ES, Khrameeva EE, Konovalova OP, Neretina T, Nikolsky YV, Starostin G, Stepanova VV, Travinsky IV, Tříska M, Tříska P, Tatarinova TV. Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry. Sci Rep 2016; 6:20768. [PMID: 26865217 PMCID: PMC4750364 DOI: 10.1038/srep20768] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/07/2016] [Indexed: 01/11/2023] Open
Abstract
The Kets, an ethnic group in the Yenisei River basin, Russia, are considered the last nomadic hunter-gatherers of Siberia, and Ket language has no transparent affiliation with any language family. We investigated connections between the Kets and Siberian and North American populations, with emphasis on the Mal'ta and Paleo-Eskimo ancient genomes, using original data from 46 unrelated samples of Kets and 42 samples of their neighboring ethnic groups (Uralic-speaking Nganasans, Enets, and Selkups). We genotyped over 130,000 autosomal SNPs, identified mitochondrial and Y-chromosomal haplogroups, and performed high-coverage genome sequencing of two Ket individuals. We established that Nganasans, Kets, Selkups, and Yukaghirs form a cluster of populations most closely related to Paleo-Eskimos in Siberia (not considering indigenous populations of Chukotka and Kamchatka). Kets are closely related to modern Selkups and to some Bronze and Iron Age populations of the Altai region, with all these groups sharing a high degree of Mal'ta ancestry. Implications of these findings for the linguistic hypothesis uniting Ket and Na-Dene languages into a language macrofamily are discussed.
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Affiliation(s)
- Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budĕjovice, Czech Republic
| | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Anastassiya Zidkova
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Maria D. Logacheva
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - N. Ezgi Altınışık
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Olga Flegontova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budĕjovice, Czech Republic
| | - Mikhail S. Gelfand
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Evgeny S. Gerasimov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina E. Khrameeva
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Olga P. Konovalova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana Neretina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yuri V. Nikolsky
- Biomedical Cluster, Skolkovo Foundation, Skolkovo, Russia
- George Mason University, Fairfax, VA, USA
| | - George Starostin
- Russian State University for the Humanities, Moscow, Russia
- Russian Presidential Academy (RANEPA), Moscow, Russia
| | - Vita V. Stepanova
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | | | - Martin Tříska
- Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Petr Tříska
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Instituto de Ciências Biomédicas da Universidade do Porto (ICBAS), Porto, Portugal
| | - Tatiana V. Tatarinova
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Children’s Hospital Los Angeles, Los Angeles, CA, USA
- Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
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20
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Xavier A, Muir WM, Rainey KM. Impact of imputation methods on the amount of genetic variation captured by a single-nucleotide polymorphism panel in soybeans. BMC Bioinformatics 2016; 17:55. [PMID: 26830693 PMCID: PMC4736474 DOI: 10.1186/s12859-016-0899-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 01/19/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Success in genome-wide association studies and marker-assisted selection depends on good phenotypic and genotypic data. The more complete this data is, the more powerful will be the results of analysis. Nevertheless, there are next-generation technologies that seek to provide genotypic information in spite of great proportions of missing data. The procedures these technologies use to impute genetic data, therefore, greatly affect downstream analyses. This study aims to (1) compare the genetic variance in a single-nucleotide polymorphism panel of soybean with missing data imputed using various methods, (2) evaluate the imputation accuracy and post-imputation quality associated with these methods, and (3) evaluate the impact of imputation method on heritability and the accuracy of genome-wide prediction of soybean traits. The imputation methods we evaluated were as follows: multivariate mixed model, hidden Markov model, logical algorithm, k-nearest neighbor, single value decomposition, and random forest. We used raw genotypes from the SoyNAM project and the following phenotypes: plant height, days to maturity, grain yield, and seed protein composition. RESULTS We propose an imputation method based on multivariate mixed models using pedigree information. Our methods comparison indicate that heritability of traits can be affected by the imputation method. Genotypes with missing values imputed with methods that make use of genealogic information can favor genetic analysis of highly polygenic traits, but not genome-wide prediction accuracy. The genotypic matrix captured the highest amount of genetic variance when missing loci were imputed by the method proposed in this paper. CONCLUSIONS We concluded that hidden Markov models and random forest imputation are more suitable to studies that aim analyses of highly heritable traits while pedigree-based methods can be used to best analyze traits with low heritability. Despite the notable contribution to heritability, advantages in genomic prediction were not observed by changing the imputation method. We identified significant differences across imputation methods in a dataset missing 20 % of the genotypic values. It means that genotypic data from genotyping technologies that provide a high proportion of missing values, such as GBS, should be handled carefully because the imputation method will impact downstream analysis.
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Affiliation(s)
- A Xavier
- Department of Agronomy, Purdue University, Lilly Hall of Life Sciences, 915 W. State St., West Lafayette, Indiana, 47907, USA.
| | - William M Muir
- Department of Animal Science, Purdue University, Lilly Hall of Life Sciences, 915 W. State St., West Lafayette, Indiana, 47907, USA.
| | - Katy M Rainey
- Department of Agronomy, Purdue University, Lilly Hall of Life Sciences, 915 W. State St., West Lafayette, Indiana, 47907, USA.
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21
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Choosing Subsamples for Sequencing Studies by Minimizing the Average Distance to the Closest Leaf. Genetics 2015; 201:499-511. [PMID: 26307072 PMCID: PMC4596665 DOI: 10.1534/genetics.115.176909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 08/14/2015] [Indexed: 12/29/2022] Open
Abstract
Imputation of genotypes in a study sample can make use of sequenced or densely genotyped external reference panels consisting of individuals that are not from the study sample. It also can employ internal reference panels, incorporating a subset of individuals from the study sample itself. Internal panels offer an advantage over external panels because they can reduce imputation errors arising from genetic dissimilarity between a population of interest and a second, distinct population from which the external reference panel has been constructed. As the cost of next-generation sequencing decreases, internal reference panel selection is becoming increasingly feasible. However, it is not clear how best to select individuals to include in such panels. We introduce a new method for selecting an internal reference panel—minimizing the average distance to the closest leaf (ADCL)—and compare its performance relative to an earlier algorithm: maximizing phylogenetic diversity (PD). Employing both simulated data and sequences from the 1000 Genomes Project, we show that ADCL provides a significant improvement in imputation accuracy, especially for imputation of sites with low-frequency alleles. This improvement in imputation accuracy is robust to changes in reference panel size, marker density, and length of the imputation target region.
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22
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Lappalainen I, Almeida-King J, Kumanduri V, Senf A, Spalding JD, Ur-Rehman S, Saunders G, Kandasamy J, Caccamo M, Leinonen R, Vaughan B, Laurent T, Rowland F, Marin-Garcia P, Barker J, Jokinen P, Torres AC, de Argila JR, Llobet OM, Medina I, Puy MS, Alberich M, de la Torre S, Navarro A, Paschall J, Flicek P. The European Genome-phenome Archive of human data consented for biomedical research. Nat Genet 2015; 47:692-5. [PMID: 26111507 PMCID: PMC5426533 DOI: 10.1038/ng.3312] [Citation(s) in RCA: 240] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The European Genome-phenome Archive (EGA) is a permanent archive that promotes distribution and sharing of genetic and phenotype data consented for specific approved uses, but not fully open public distribution. The EGA follows strict protocols for information management, data storage, security and dissemination. Authorized access to the data is managed in partnership with the data providing organizations. The EGA includes major reference data collections for human genetics research.
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Affiliation(s)
- Ilkka Lappalainen
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Jeff Almeida-King
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Vasudev Kumanduri
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Alexander Senf
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - John Dylan Spalding
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Saif Ur-Rehman
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Gary Saunders
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Jag Kandasamy
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Mario Caccamo
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Rasko Leinonen
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Brendan Vaughan
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Thomas Laurent
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Francis Rowland
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Pablo Marin-Garcia
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Jonathan Barker
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Petteri Jokinen
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | | | | | | | - Ignacio Medina
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | | | | | | | - Arcadi Navarro
- 1] Centre for Genomic Regulation, Barcelona, Spain. [2] Institute of Evolutionary Biology, Universitat Pompeu Fabra-Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain. [3] Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Justin Paschall
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
| | - Paul Flicek
- European Molecular Biology Laboratory-European Bioinformatics Institute, Hinxton, UK
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23
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Peil B, Kabisch M, Fischer C, Hamann U, Bermejo JL. Tailored selection of study individuals to be sequenced in order to improve the accuracy of genotype imputation. Genet Epidemiol 2014; 39:114-21. [PMID: 25537753 DOI: 10.1002/gepi.21873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 08/28/2014] [Accepted: 11/05/2014] [Indexed: 01/21/2023]
Abstract
The addition of sequence data from own-study individuals to genotypes from external data repositories, for example, the HapMap, has been shown to improve the accuracy of imputed genotypes. Early approaches for reference panel selection favored individuals who best reflect recombination patterns in the study population. By contrast, a maximization of genetic diversity in the reference panel has been recently proposed. We investigate here a novel strategy to select individuals for sequencing that relies on the characterization of the ancestral kernel of the study population. The simulated study scenarios consisted of several combinations of subpopulations from HapMap. HapMap individuals who did not belong to the study population constituted an external reference panel which was complemented with the sequences of study individuals selected according to different strategies. In addition to a random choice, individuals with the largest statistical depth according to the first genetic principal components were selected. In all simulated scenarios the integration of sequences from own-study individuals increased imputation accuracy. The selection of individuals based on the statistical depth resulted in the highest imputation accuracy for European and Asian study scenarios, whereas random selection performed best for an African-study scenario. Present findings indicate that there is no universal 'best strategy' to select individuals for sequencing. We propose to use the methodology described in the manuscript to assess the advantage of focusing on the ancestral kernel under own study characteristics (study size, genetic diversity, availability and properties of external reference panels, frequency of imputed variants…).
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Affiliation(s)
- Barbara Peil
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
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24
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Loukola A, Wedenoja J, Keskitalo-Vuokko K, Broms U, Korhonen T, Ripatti S, Sarin AP, Pitkäniemi J, He L, Häppölä A, Heikkilä K, Chou YL, Pergadia ML, Heath AC, Montgomery GW, Martin NG, Madden PAF, Kaprio J. Genome-wide association study on detailed profiles of smoking behavior and nicotine dependence in a twin sample. Mol Psychiatry 2014; 19:615-24. [PMID: 23752247 PMCID: PMC3883996 DOI: 10.1038/mp.2013.72] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 03/28/2013] [Accepted: 04/29/2013] [Indexed: 01/11/2023]
Abstract
Smoking is a major risk factor for several somatic diseases and is also emerging as a causal factor for neuropsychiatric disorders. Genome-wide association (GWA) and candidate gene studies for smoking behavior and nicotine dependence (ND) have disclosed too few predisposing variants to account for the high estimated heritability. Previous large-scale GWA studies have had very limited phenotypic definitions of relevance to smoking-related behavior, which has likely impeded the discovery of genetic effects. We performed GWA analyses on 1114 adult twins ascertained for ever smoking from the population-based Finnish Twin Cohort study. The availability of 17 smoking-related phenotypes allowed us to comprehensively portray the dimensions of smoking behavior, clustered into the domains of smoking initiation, amount smoked and ND. Our results highlight a locus on 16p12.3, with several single-nucleotide polymorphisms (SNPs) in the vicinity of CLEC19A showing association (P<1 × 10(-6)) with smoking quantity. Interestingly, CLEC19A is located close to a previously reported attention-deficit hyperactivity disorder (ADHD) linkage locus and an evident link between ADHD and smoking has been established. Intriguing preliminary association (P<1 × 10(-5)) was detected between DSM-IV (Diagnostic and Statistical Manual of Mental Disorders, 4th edition) ND diagnosis and several SNPs in ERBB4, coding for a Neuregulin receptor, on 2q33. The association between ERBB4 and DSM-IV ND diagnosis was replicated in an independent Australian sample. Recently, a significant increase in ErbB4 and Neuregulin 3 (Nrg3) expression was revealed following chronic nicotine exposure and withdrawal in mice and an association between NRG3 SNPs and smoking cessation success was detected in a clinical trial. ERBB4 has previously been associated with schizophrenia; further, it is located within an established schizophrenia linkage locus and within a linkage locus for a smoker phenotype identified in this sample. In conclusion, we disclose novel tentative evidence for the involvement of ERBB4 in ND, suggesting the involvement of the Neuregulin/ErbB signalling pathway in addictions and providing a plausible link between the high co-morbidity of schizophrenia and ND.
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Affiliation(s)
- Anu Loukola
- Department of Public Health, Hjelt Institute, University of
Helsinki, Finland
| | - Juho Wedenoja
- Department of Public Health, Hjelt Institute, University of
Helsinki, Finland
| | | | - Ulla Broms
- Department of Public Health, Hjelt Institute, University of
Helsinki, Finland
- National Institute for Health and Welfare, Helsinki,
Finland
| | - Tellervo Korhonen
- Department of Public Health, Hjelt Institute, University of
Helsinki, Finland
- National Institute for Health and Welfare, Helsinki,
Finland
| | - Samuli Ripatti
- National Institute for Health and Welfare, Helsinki,
Finland
- Institute for Molecular Medicine Finland FIMM, University
of Helsinki, Finland
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Antti-Pekka Sarin
- National Institute for Health and Welfare, Helsinki,
Finland
- Institute for Molecular Medicine Finland FIMM, University
of Helsinki, Finland
| | - Janne Pitkäniemi
- Department of Public Health, Hjelt Institute, University of
Helsinki, Finland
| | - Liang He
- Department of Public Health, Hjelt Institute, University of
Helsinki, Finland
| | - Anja Häppölä
- Department of Public Health, Hjelt Institute, University of
Helsinki, Finland
| | - Kauko Heikkilä
- Department of Public Health, Hjelt Institute, University of
Helsinki, Finland
| | - Yi-Ling Chou
- Washington University School of Medicine, Saint Louis,
USA
| | | | - Andrew C Heath
- Washington University School of Medicine, Saint Louis,
USA
| | | | | | | | - Jaakko Kaprio
- Department of Public Health, Hjelt Institute, University of
Helsinki, Finland
- National Institute for Health and Welfare, Helsinki,
Finland
- Institute for Molecular Medicine Finland FIMM, University
of Helsinki, Finland
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25
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Skoglund P, Malmström H, Omrak A, Raghavan M, Valdiosera C, Günther T, Hall P, Tambets K, Parik J, Sjögren KG, Apel J, Willerslev E, Storå J, Götherström A, Jakobsson M. Genomic diversity and admixture differs for Stone-Age Scandinavian foragers and farmers. Science 2014; 344:747-50. [PMID: 24762536 DOI: 10.1126/science.1253448] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Prehistoric population structure associated with the transition to an agricultural lifestyle in Europe remains a contentious idea. Population-genomic data from 11 Scandinavian Stone Age human remains suggest that hunter-gatherers had lower genetic diversity than that of farmers. Despite their close geographical proximity, the genetic differentiation between the two Stone Age groups was greater than that observed among extant European populations. Additionally, the Scandinavian Neolithic farmers exhibited a greater degree of hunter-gatherer-related admixture than that of the Tyrolean Iceman, who also originated from a farming context. In contrast, Scandinavian hunter-gatherers displayed no significant evidence of introgression from farmers. Our findings suggest that Stone Age foraging groups were historically in low numbers, likely owing to oscillating living conditions or restricted carrying capacity, and that they were partially incorporated into expanding farming groups.
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Affiliation(s)
- Pontus Skoglund
- Department of Evolutionary Biology, Uppsala University, Uppsala 752 36, Sweden
| | - Helena Malmström
- Department of Evolutionary Biology, Uppsala University, Uppsala 752 36, Sweden
| | - Ayça Omrak
- Department of Archaeology and Classical studies, Stockholm University, Stockholm 106 91, Sweden
| | - Maanasa Raghavan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - Cristina Valdiosera
- Department of Archaeology, Environment and Community Planning, La Trobe University, Melbourne VIC 3086, Australia
| | - Torsten Günther
- Department of Evolutionary Biology, Uppsala University, Uppsala 752 36, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Kristiina Tambets
- Evolutionary Biology Group, Estonian Biocentre and University of Tartu, Tartu 51010, Estonia
| | - Jüri Parik
- Evolutionary Biology Group, Estonian Biocentre and University of Tartu, Tartu 51010, Estonia
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, Gothenburg, 405 30, Sweden
| | - Jan Apel
- Department of Archaeology and Ancient History, Lund University, Lund, 221 00, Sweden
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - Jan Storå
- Department of Archaeology and Classical studies, Stockholm University, Stockholm 106 91, Sweden
| | - Anders Götherström
- Department of Archaeology and Classical studies, Stockholm University, Stockholm 106 91, Sweden.
| | - Mattias Jakobsson
- Department of Evolutionary Biology, Uppsala University, Uppsala 752 36, Sweden. Science for Life Laboratory, Uppsala University, Uppsala 752 36, Sweden.
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26
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Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. Nature 2014; 507:225-8. [PMID: 24463515 DOI: 10.1038/nature12960] [Citation(s) in RCA: 209] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 12/17/2013] [Indexed: 12/19/2022]
Abstract
Ancient genomic sequences have started to reveal the origin and the demographic impact of farmers from the Neolithic period spreading into Europe. The adoption of farming, stock breeding and sedentary societies during the Neolithic may have resulted in adaptive changes in genes associated with immunity and diet. However, the limited data available from earlier hunter-gatherers preclude an understanding of the selective processes associated with this crucial transition to agriculture in recent human evolution. Here we sequence an approximately 7,000-year-old Mesolithic skeleton discovered at the La Braña-Arintero site in León, Spain, to retrieve a complete pre-agricultural European human genome. Analysis of this genome in the context of other ancient samples suggests the existence of a common ancient genomic signature across western and central Eurasia from the Upper Paleolithic to the Mesolithic. The La Braña individual carries ancestral alleles in several skin pigmentation genes, suggesting that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times. Moreover, we provide evidence that a significant number of derived, putatively adaptive variants associated with pathogen resistance in modern Europeans were already present in this hunter-gatherer.
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27
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Raghavan M, Skoglund P, Graf KE, Metspalu M, Albrechtsen A, Moltke I, Rasmussen S, Stafford TW, Orlando L, Metspalu E, Karmin M, Tambets K, Rootsi S, Mägi R, Campos PF, Balanovska E, Balanovsky O, Khusnutdinova E, Litvinov S, Osipova LP, Fedorova SA, Voevoda MI, DeGiorgio M, Sicheritz-Ponten T, Brunak S, Demeshchenko S, Kivisild T, Villems R, Nielsen R, Jakobsson M, Willerslev E. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 2013; 505:87-91. [PMID: 24256729 DOI: 10.1038/nature12736] [Citation(s) in RCA: 438] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 10/04/2013] [Indexed: 12/19/2022]
Abstract
The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians, there is no consensus with regard to which specific Old World populations they are closest to. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal'ta in south-central Siberia, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date. The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages. Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians. Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans.
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Affiliation(s)
- Maanasa Raghavan
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark [2]
| | - Pontus Skoglund
- 1] Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, Uppsala 752 36, Sweden [2]
| | - Kelly E Graf
- Center for the Study of the First Americans, Texas A&M University, TAMU-4352, College Station, Texas 77845-4352, USA
| | - Mait Metspalu
- 1] Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia [2] Department of Integrative Biology, University of California, Berkeley, California 94720, USA [3] Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen 2200, Denmark
| | - Ida Moltke
- 1] The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen 2200, Denmark [2] Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Thomas W Stafford
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark [2] AMS 14C Dating Centre, Department of Physics and Astronomy, University of Aarhus, Ny Munkegade 120, Aarhus DK-8000, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Ene Metspalu
- Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Monika Karmin
- 1] Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia [2] Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia
| | - Kristiina Tambets
- Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia
| | - Siiri Rootsi
- Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Paula F Campos
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Elena Balanovska
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moskvorechie Street 1, Moscow 115479, Russia
| | - Oleg Balanovsky
- 1] Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moskvorechie Street 1, Moscow 115479, Russia [2] Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina Street 3, Moscow 119991, Russia
| | - Elza Khusnutdinova
- 1] Institute of Biochemistry and Genetics, Ufa Scientific Centre, Russian Academy of Sciences, Ufa, Bashkorostan 450054, Russia [2] Biology Department, Bashkir State University, Ufa, Bashkorostan 450074, Russia
| | - Sergey Litvinov
- 1] Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia [2] Institute of Biochemistry and Genetics, Ufa Scientific Centre, Russian Academy of Sciences, Ufa, Bashkorostan 450054, Russia
| | - Ludmila P Osipova
- The Institute of Cytology and Genetics, Center for Brain Neurobiology and Neurogenetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyeva Avenue, Novosibirsk 630090, Russia
| | - Sardana A Fedorova
- Department of Molecular Genetics, Yakut Research Center of Complex Medical Problems, Russian Academy of Medical Sciences and North-Eastern Federal University, Yakutsk, Sakha (Yakutia) 677010, Russia
| | - Mikhail I Voevoda
- 1] The Institute of Cytology and Genetics, Center for Brain Neurobiology and Neurogenetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyeva Avenue, Novosibirsk 630090, Russia [2] Institute of Internal Medicine, Siberian Branch of the Russian Academy of Medical Sciences, Borisa Bogatkova 175/1, Novosibirsk 630089, Russia
| | - Michael DeGiorgio
- Department of Integrative Biology, University of California, Berkeley, California 94720, USA
| | - Thomas Sicheritz-Ponten
- 1] Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby 2800, Denmark [2] Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Søren Brunak
- 1] Center for Biological Sequence Analysis, Technical University of Denmark, Kongens Lyngby 2800, Denmark [2] Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | | | - Toomas Kivisild
- 1] Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia [2] Department of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
| | - Richard Villems
- 1] Estonian Biocentre, Evolutionary Biology group, Tartu 51010, Estonia [2] Department of Evolutionary Biology, University of Tartu, Tartu 51010, Estonia [3] Estonian Academy of Sciences, Tallinn 10130, Estonia
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, California 94720, USA
| | - Mattias Jakobsson
- 1] Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, Uppsala 752 36, Sweden [2] Science for Life Laboratory, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
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28
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Joshi PK, Prendergast J, Fraser RM, Huffman JE, Vitart V, Hayward C, McQuillan R, Glodzik D, Polašek O, Hastie ND, Rudan I, Campbell H, Wright AF, Haley CS, Wilson JF, Navarro P. Local exome sequences facilitate imputation of less common variants and increase power of genome wide association studies. PLoS One 2013; 8:e68604. [PMID: 23874685 PMCID: PMC3712964 DOI: 10.1371/journal.pone.0068604] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 05/30/2013] [Indexed: 11/18/2022] Open
Abstract
The analysis of less common variants in genome-wide association studies promises to elucidate complex trait genetics but is hampered by low power to reliably detect association. We show that addition of population-specific exome sequence data to global reference data allows more accurate imputation, particularly of less common SNPs (minor allele frequency 1-10%) in two very different European populations. The imputation improvement corresponds to an increase in effective sample size of 28-38%, for SNPs with a minor allele frequency in the range 1-3%.
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Affiliation(s)
- Peter K. Joshi
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - James Prendergast
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Ross M. Fraser
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Jennifer E. Huffman
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Veronique Vitart
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Caroline Hayward
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Ruth McQuillan
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Dominik Glodzik
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Ozren Polašek
- Department of Public Health, University of Split, Split, Croatia
- Centre for Global Health, University of Split, Split, Croatia
| | - Nicholas D. Hastie
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Igor Rudan
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Alan F. Wright
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Chris S. Haley
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- Roslin Institute, University of Edinburgh, Scotland, United Kingdom
| | - James F. Wilson
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Pau Navarro
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, Scotland, United Kingdom
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29
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Okser S, Pahikkala T, Aittokallio T. Genetic variants and their interactions in disease risk prediction - machine learning and network perspectives. BioData Min 2013; 6:5. [PMID: 23448398 PMCID: PMC3606427 DOI: 10.1186/1756-0381-6-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 02/11/2013] [Indexed: 12/31/2022] Open
Abstract
A central challenge in systems biology and medical genetics is to understand how interactions among genetic loci contribute to complex phenotypic traits and human diseases. While most studies have so far relied on statistical modeling and association testing procedures, machine learning and predictive modeling approaches are increasingly being applied to mining genotype-phenotype relationships, also among those associations that do not necessarily meet statistical significance at the level of individual variants, yet still contributing to the combined predictive power at the level of variant panels. Network-based analysis of genetic variants and their interaction partners is another emerging trend by which to explore how sub-network level features contribute to complex disease processes and related phenotypes. In this review, we describe the basic concepts and algorithms behind machine learning-based genetic feature selection approaches, their potential benefits and limitations in genome-wide setting, and how physical or genetic interaction networks could be used as a priori information for providing improved predictive power and mechanistic insights into the disease networks. These developments are geared toward explaining a part of the missing heritability, and when combined with individual genomic profiling, such systems medicine approaches may also provide a principled means for tailoring personalized treatment strategies in the future.
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30
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Jay F, Sjödin P, Jakobsson M, Blum MGB. Anisotropic isolation by distance: the main orientations of human genetic differentiation. Mol Biol Evol 2012; 30:513-25. [PMID: 23171862 PMCID: PMC3563970 DOI: 10.1093/molbev/mss259] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genetic differentiation among human populations is greatly influenced by geography due to the accumulation of local allele frequency differences. However, little is known about the possibly different increment of genetic differentiation along the different geographical axes (north–south, east–west, etc.). Here, we provide new methods to examine the asymmetrical patterns of genetic differentiation. We analyzed genome-wide polymorphism data from populations in Africa (n = 29), Asia (n = 26), America (n = 9), and Europe (n = 38), and we found that the major orientations of genetic differentiation are north–south in Europe and Africa, and east–west in Asia, but no preferential orientation was found in the Americas. Additionally, we showed that the localization of the individual geographic origins based on single nucleotide polymorphism data was not equally precise along all orientations. Confirming our findings, we obtained that, in each continent, the orientation along which the precision is maximal corresponds to the orientation of maximum differentiation. Our results have implications for interpreting human genetic variation in terms of isolation by distance and spatial range expansion processes. In Europe, for instance, the precise northnorthwest–southsoutheast axis of main European differentiation cannot be explained by a simple Neolithic demic diffusion model without admixture with the local populations because in that case the orientation of greatest differentiation should be perpendicular to the direction of expansion. In addition to humans, anisotropic analyses can guide the description of genetic differentiation for other organisms and provide information on expansions of invasive species or the processes of plant dispersal.
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Affiliation(s)
- Flora Jay
- Department of Integrative Biology, University of California, Berkeley, CA, USA
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31
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Genotype imputation in a coalescent model with infinitely-many-sites mutation. Theor Popul Biol 2012; 87:62-74. [PMID: 23079542 DOI: 10.1016/j.tpb.2012.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 09/09/2012] [Accepted: 09/28/2012] [Indexed: 11/20/2022]
Abstract
Empirical studies have identified population-genetic factors as important determinants of the properties of genotype-imputation accuracy in imputation-based disease association studies. Here, we develop a simple coalescent model of three sequences that we use to explore the theoretical basis for the influence of these factors on genotype-imputation accuracy, under the assumption of infinitely-many-sites mutation. Employing a demographic model in which two populations diverged at a given time in the past, we derive the approximate expectation and variance of imputation accuracy in a study sequence sampled from one of the two populations, choosing between two reference sequences, one sampled from the same population as the study sequence and the other sampled from the other population. We show that, under this model, imputation accuracy-as measured by the proportion of polymorphic sites that are imputed correctly in the study sequence-increases in expectation with the mutation rate, the proportion of the markers in a chromosomal region that are genotyped, and the time to divergence between the study and reference populations. Each of these effects derives largely from an increase in information available for determining the reference sequence that is genetically most similar to the sequence targeted for imputation. We analyze as a function of divergence time the expected gain in imputation accuracy in the target using a reference sequence from the same population as the target rather than from the other population. Together with a growing body of empirical investigations of genotype imputation in diverse human populations, our modeling framework lays a foundation for extending imputation techniques to novel populations that have not yet been extensively examined.
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32
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Utilizing extended pedigree information for discovery and confirmation of copy number variable regions among Mexican Americans. Eur J Hum Genet 2012; 21:404-9. [PMID: 22909773 DOI: 10.1038/ejhg.2012.188] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Copy number variation (CNV) remains poorly defined in many populations, including Mexican Americans. We report the discovery and genetic confirmation of copy number variable regions (CNVRs) in subjects of the San Antonio Family Heart and the San Antonio Family Diabetes Gallbladder Studies, both comprised of multigenerational pedigrees of Mexican American descent. In a discovery group of 1677 participants genotyped using Illumina Infinium Beadchips, we identified 2937 unique CNVRs, some with observation frequencies as low as 0.002, using a process that integrates pedigree information with CNV calls made by PennCNV and/or QuantiSNP. Quantitative copy number values had statistically significant (P ≤ 1.792e-5) heritability estimates ranging from 0.139 to 0.863 for 2776 CNVRs. Additionally, 920 CNVRs showed evidence of linkage to their genomic location, providing strong genetic confirmation. Linked CNVRs were enriched in a set of independently identified CNVRs from a second group of 380 samples, confirming that these CNVRs can be used as predefined CNVRs of high confidence. Interestingly, we identified 765 putatively novel variants that do not overlap with the Database of Genomic Variants. This study is the first to use linkage and heritability in multigenerational pedigrees as a confirmation approach for the discovery of CNVRs, and the largest study to date investigating copy number variation on a genome-wide scale in individuals of Mexican American descent. These results provide insight to the structural variation present in Mexican Americans and show the strength of multigenerational pedigrees to elucidate structural variation in the human genome.
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33
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Skoglund P, Malmstrom H, Raghavan M, Stora J, Hall P, Willerslev E, Gilbert MTP, Gotherstrom A, Jakobsson M. Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe. Science 2012; 336:466-9. [DOI: 10.1126/science.1216304] [Citation(s) in RCA: 405] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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34
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Intracranial aneurysm risk locus 5q23.2 is associated with elevated systolic blood pressure. PLoS Genet 2012; 8:e1002563. [PMID: 22438818 PMCID: PMC3305343 DOI: 10.1371/journal.pgen.1002563] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 01/13/2012] [Indexed: 01/19/2023] Open
Abstract
Although genome-wide association studies (GWAS) have identified hundreds of complex trait loci, the pathomechanisms of most remain elusive. Studying the genetics of risk factors predisposing to disease is an attractive approach to identify targets for functional studies. Intracranial aneurysms (IA) are rupture-prone pouches at cerebral artery branching sites. IA is a complex disease for which GWAS have identified five loci with strong association and a further 14 loci with suggestive association. To decipher potential underlying disease mechanisms, we tested whether there are IA loci that convey their effect through elevating blood pressure (BP), a strong risk factor of IA. We performed a meta-analysis of four population-based Finnish cohorts (nFIN = 11 266) not selected for IA, to assess the association of previously identified IA candidate loci (n = 19) with BP. We defined systolic BP (SBP), diastolic BP, mean arterial pressure, and pulse pressure as quantitative outcome variables. The most significant result was further tested for association in the ICBP-GWAS cohort of 200 000 individuals. We found that the suggestive IA locus at 5q23.2 in PRDM6 was significantly associated with SBP in individuals of European descent (pFIN = 3.01E-05, pICBP-GWAS = 0.0007, pALL = 8.13E-07). The risk allele of IA was associated with higher SBP. PRDM6 encodes a protein predominantly expressed in vascular smooth muscle cells. Our study connects a complex disease (IA) locus with a common risk factor for the disease (SBP). We hypothesize that common variants in PRDM6 can contribute to altered vascular wall structure, hence increasing SBP and predisposing to IA. True positive associations often fail to reach genome-wide significance in GWAS. Our findings show that analysis of traditional risk factors as intermediate phenotypes is an effective tool for deciphering hidden heritability. Further, we demonstrate that common disease loci identified in a population isolate may bear wider significance. When multiple genes or genetic regions contribute to the inherited risk of a disease, it is referred to as a complex disease. Genome-wide association studies (GWAS) aim to detect common genetic variations that associate with complex traits or diseases. Although GWAS have been successful in identifying strongly associated genetic loci, they lack the means to point out true, but less strong, associations. Studying conditions that are related to the disease of interest can help sort out less strong associations. Intracranial aneurysms (IA) are berry-like dilations in cerebral arteries. Most IAs do not give symptoms until they bleed, causing a highly fatal form of stroke. Half of the people who suffer bleeding of an IA die. IA is a complex disease. Both inherited risk and environmental factors contribute to the risk of developing IA. Women, smokers, those with high alcohol intake or high blood pressure are more prone to develop IA and bleeding. GWAS found 19 genetic regions increasing the risk of IA. Here we show that one of these loci, on the long arm of chromosome 5, in addition to raising IA risk also increases systolic blood pressure. We speculate that the cause is modified vascular wall structure.
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35
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A common variant near the KCNJ2 gene is associated with T-peak to T-end interval. Heart Rhythm 2012; 9:1099-103. [PMID: 22342860 DOI: 10.1016/j.hrthm.2012.02.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Indexed: 11/21/2022]
Abstract
BACKGROUND T-peak to T-end (TPE) interval on the electrocardiogram is a measure of myocardial dispersion of repolarization and is associated with an increased risk of ventricular arrhythmias. The genetic factors affecting the TPE interval are largely unknown. OBJECTIVE To identify common genetic variants that affect the duration of the TPE interval in the general population. METHODS We performed a genome-wide association study on 1870 individuals of Finnish origin participating in the Health 2000 Study. The TPE interval was measured from T-peak to T-wave end in leads II, V(2), and V(5) on resting electrocardiograms, and the mean of these TPE intervals was adjusted for age, sex, and Cornell voltage-duration product. We sought replication for a genome-wide significant result in the 3745 subjects from the Framingham Heart Study. RESULTS We identified a locus on 17q24 that was associated with the TPE interval. The minor allele of the common variant rs7219669 was associated with a 1.8-ms shortening of the TPE interval (P = 1.1 × 10(-10)). The association was replicated in the Framingham Heart Study (-1.5 ms; P = 1.3 × 10(-4)). The overall effect estimate of rs7219669 in the 2 studies was -1.7 ms (P = 5.7 × 10(-14)). The common variant rs7219669 maps downstream of the KCNJ2 gene, in which rare mutations cause congenital long and short QT syndromes. CONCLUSION The common variant rs7219669 is associated with the TPE interval and is thus a candidate to modify repolarization-related arrhythmia susceptibility in individuals carrying the major allele of this polymorphism.
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36
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Kettunen J, Tukiainen T, Sarin AP, Ortega-Alonso A, Tikkanen E, Lyytikäinen LP, Kangas AJ, Soininen P, Würtz P, Silander K, Dick DM, Rose RJ, Savolainen MJ, Viikari J, Kähönen M, Lehtimäki T, Pietiläinen KH, Inouye M, McCarthy MI, Jula A, Eriksson J, Raitakari OT, Salomaa V, Kaprio J, Järvelin MR, Peltonen L, Perola M, Freimer NB, Ala-Korpela M, Palotie A, Ripatti S. Genome-wide association study identifies multiple loci influencing human serum metabolite levels. Nat Genet 2012; 44:269-76. [PMID: 22286219 PMCID: PMC3605033 DOI: 10.1038/ng.1073] [Citation(s) in RCA: 420] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 12/13/2011] [Indexed: 12/12/2022]
Abstract
Nuclear magnetic resonance assays allow for measurement of a wide range of metabolic phenotypes. We report here the results of a GWAS on 8,330 Finnish individuals genotyped and imputed at 7.7 million SNPs for a range of 216 serum metabolic phenotypes assessed by NMR of serum samples. We identified significant associations (P < 2.31 × 10(-10)) at 31 loci, including 11 for which there have not been previous reports of associations to a metabolic trait or disorder. Analyses of Finnish twin pairs suggested that the metabolic measures reported here show higher heritability than comparable conventional metabolic phenotypes. In accordance with our expectations, SNPs at the 31 loci associated with individual metabolites account for a greater proportion of the genetic component of trait variance (up to 40%) than is typically observed for conventional serum metabolic phenotypes. The identification of such associations may provide substantial insight into cardiometabolic disorders.
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Affiliation(s)
- Johannes Kettunen
- Institute for Molecular Medicine Finland, University of Helsinki, Finland
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37
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Peltola T, Marttinen P, Jula A, Salomaa V, Perola M, Vehtari A. Bayesian variable selection in searching for additive and dominant effects in genome-wide data. PLoS One 2012; 7:e29115. [PMID: 22235263 PMCID: PMC3250410 DOI: 10.1371/journal.pone.0029115] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 11/21/2011] [Indexed: 01/19/2023] Open
Abstract
Although complex diseases and traits are thought to have multifactorial genetic basis, the common methods in genome-wide association analyses test each variant for association independent of the others. This computational simplification may lead to reduced power to identify variants with small effect sizes and requires correcting for multiple hypothesis tests with complex relationships. However, advances in computational methods and increase in computational resources are enabling the computation of models that adhere more closely to the theory of multifactorial inheritance. Here, a Bayesian variable selection and model averaging approach is formulated for searching for additive and dominant genetic effects. The approach considers simultaneously all available variants for inclusion as predictors in a linear genotype-phenotype mapping and averages over the uncertainty in the variable selection. This leads to naturally interpretable summary quantities on the significances of the variants and their contribution to the genetic basis of the studied trait. We first characterize the behavior of the approach in simulations. The results indicate a gain in the causal variant identification performance when additive and dominant variation are simulated, with a negligible loss of power in purely additive case. An application to the analysis of high- and low-density lipoprotein cholesterol levels in a dataset of 3895 Finns is then presented, demonstrating the feasibility of the approach at the current scale of single-nucleotide polymorphism data. We describe a Markov chain Monte Carlo algorithm for the computation and give suggestions on the specification of prior parameters using commonly available prior information. An open-source software implementing the method is available at http://www.lce.hut.fi/research/mm/bmagwa/ and https://github.com/to-mi/.
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Affiliation(s)
- Tomi Peltola
- Department of Biomedical Engineering and Computational Science, Aalto University School of Science, Espoo, Finland.
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38
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Tukiainen T, Kettunen J, Kangas AJ, Lyytikainen LP, Soininen P, Sarin AP, Tikkanen E, O'Reilly PF, Savolainen MJ, Kaski K, Pouta A, Jula A, Lehtimaki T, Kahonen M, Viikari J, Taskinen MR, Jauhiainen M, Eriksson JG, Raitakari O, Salomaa V, Jarvelin MR, Perola M, Palotie A, Ala-Korpela M, Ripatti S. Detailed metabolic and genetic characterization reveals new associations for 30 known lipid loci. Hum Mol Genet 2011; 21:1444-55. [DOI: 10.1093/hmg/ddr581] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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39
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Tikkanen E, Tuovinen T, Widén E, Lehtimäki T, Viikari J, Kähönen M, Peltonen L, Raitakari OT, Ripatti S. Association of Known Loci With Lipid Levels Among Children and Prediction of Dyslipidemia in Adults. ACTA ACUST UNITED AC 2011; 4:673-80. [DOI: 10.1161/circgenetics.111.960369] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background—
Recent genome-wide association studies have found 95 distinct genetic loci associated with high-density (HDL-C) and low-density (LDL-C) lipoprotein cholesterol, total cholesterol (TC), and triglycerides (TG), using adult samples. It is not known if these variants are associated with lipid levels in children and adolescents and if the genetic risk score (GRS), based on these variants, could improve adulthood dyslipidemia prediction over the childhood lipid measurements.
Methods and Results—
We used 2443 participants of the Cardiovascular Risk in Young Finns study cohort with up to 5 measurements of serum lipids taken between ages 3 and 45 years to estimate the effect of individual single-nucleotide polymorphisms and the GRS on lipids. The GRSs were strongly associated with lipids in all age groups (1.5×10
−20
<
P
<8.7×10
−12
for HDL-C, 3.5×10
−27
<
P
<5.6×10
−09
for LDL-C, 2.0×10
−25
<
P
<5.2×10
−09
for TC, and 4.1×10
−20
<
P
<8.4×10
−05
for TG). Jointly, the lipid loci explained 11.8–26.7% of the total variance in lipids among 3- to 6-year-old children, and the proportion dropped over age, except for TG. The discrimination of adult hypertriglyceridemia improved when GRS was added to childhood lipid measurement (
C
statistic=0.04,
P
=0.01).
Conclusions—
Previously identified lipid loci are associated with lipid levels in children and adolescents and explain up to more than 2 times of the lipid variation in children compared with adults. The TG-GRS improves the risk discrimination over childhood lipid measurement for adult hypertriglyceridemia.
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Affiliation(s)
- Emmi Tikkanen
- From the Institute for Molecular Medicine, Finland FIMM, University of Helsinki, Helsinki, Finland (E.T., T.T., E.W., L.P., S.R.); National Institute for Health and Welfare, Helsinki, Finland (E.T., T.T., L.P., S.R.); the Department of Clinical Chemistry, Tampere University Hospital and University of Tampere, Tampere, Finland (T.L.); the Department of Medicine, University of Turku and Turku University Hospital, Turku, Finland (J.V.); the Department of Clinical Physiology, Tampere University Hospital
| | - Tarja Tuovinen
- From the Institute for Molecular Medicine, Finland FIMM, University of Helsinki, Helsinki, Finland (E.T., T.T., E.W., L.P., S.R.); National Institute for Health and Welfare, Helsinki, Finland (E.T., T.T., L.P., S.R.); the Department of Clinical Chemistry, Tampere University Hospital and University of Tampere, Tampere, Finland (T.L.); the Department of Medicine, University of Turku and Turku University Hospital, Turku, Finland (J.V.); the Department of Clinical Physiology, Tampere University Hospital
| | - Elisabeth Widén
- From the Institute for Molecular Medicine, Finland FIMM, University of Helsinki, Helsinki, Finland (E.T., T.T., E.W., L.P., S.R.); National Institute for Health and Welfare, Helsinki, Finland (E.T., T.T., L.P., S.R.); the Department of Clinical Chemistry, Tampere University Hospital and University of Tampere, Tampere, Finland (T.L.); the Department of Medicine, University of Turku and Turku University Hospital, Turku, Finland (J.V.); the Department of Clinical Physiology, Tampere University Hospital
| | - Terho Lehtimäki
- From the Institute for Molecular Medicine, Finland FIMM, University of Helsinki, Helsinki, Finland (E.T., T.T., E.W., L.P., S.R.); National Institute for Health and Welfare, Helsinki, Finland (E.T., T.T., L.P., S.R.); the Department of Clinical Chemistry, Tampere University Hospital and University of Tampere, Tampere, Finland (T.L.); the Department of Medicine, University of Turku and Turku University Hospital, Turku, Finland (J.V.); the Department of Clinical Physiology, Tampere University Hospital
| | - Jorma Viikari
- From the Institute for Molecular Medicine, Finland FIMM, University of Helsinki, Helsinki, Finland (E.T., T.T., E.W., L.P., S.R.); National Institute for Health and Welfare, Helsinki, Finland (E.T., T.T., L.P., S.R.); the Department of Clinical Chemistry, Tampere University Hospital and University of Tampere, Tampere, Finland (T.L.); the Department of Medicine, University of Turku and Turku University Hospital, Turku, Finland (J.V.); the Department of Clinical Physiology, Tampere University Hospital
| | - Mika Kähönen
- From the Institute for Molecular Medicine, Finland FIMM, University of Helsinki, Helsinki, Finland (E.T., T.T., E.W., L.P., S.R.); National Institute for Health and Welfare, Helsinki, Finland (E.T., T.T., L.P., S.R.); the Department of Clinical Chemistry, Tampere University Hospital and University of Tampere, Tampere, Finland (T.L.); the Department of Medicine, University of Turku and Turku University Hospital, Turku, Finland (J.V.); the Department of Clinical Physiology, Tampere University Hospital
| | - Leena Peltonen
- From the Institute for Molecular Medicine, Finland FIMM, University of Helsinki, Helsinki, Finland (E.T., T.T., E.W., L.P., S.R.); National Institute for Health and Welfare, Helsinki, Finland (E.T., T.T., L.P., S.R.); the Department of Clinical Chemistry, Tampere University Hospital and University of Tampere, Tampere, Finland (T.L.); the Department of Medicine, University of Turku and Turku University Hospital, Turku, Finland (J.V.); the Department of Clinical Physiology, Tampere University Hospital
| | - Olli T. Raitakari
- From the Institute for Molecular Medicine, Finland FIMM, University of Helsinki, Helsinki, Finland (E.T., T.T., E.W., L.P., S.R.); National Institute for Health and Welfare, Helsinki, Finland (E.T., T.T., L.P., S.R.); the Department of Clinical Chemistry, Tampere University Hospital and University of Tampere, Tampere, Finland (T.L.); the Department of Medicine, University of Turku and Turku University Hospital, Turku, Finland (J.V.); the Department of Clinical Physiology, Tampere University Hospital
| | - Samuli Ripatti
- From the Institute for Molecular Medicine, Finland FIMM, University of Helsinki, Helsinki, Finland (E.T., T.T., E.W., L.P., S.R.); National Institute for Health and Welfare, Helsinki, Finland (E.T., T.T., L.P., S.R.); the Department of Clinical Chemistry, Tampere University Hospital and University of Tampere, Tampere, Finland (T.L.); the Department of Medicine, University of Turku and Turku University Hospital, Turku, Finland (J.V.); the Department of Clinical Physiology, Tampere University Hospital
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40
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An obesity-related FTO variant and the risk of preeclampsia in a Finnish study population. J Pregnancy 2011; 2011:251470. [PMID: 22132335 PMCID: PMC3216321 DOI: 10.1155/2011/251470] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 08/31/2011] [Accepted: 08/31/2011] [Indexed: 01/09/2023] Open
Abstract
Previous studies have demonstrated a common variant of the obesity and fat mass-related FTO gene, rs9939609, to be associated with obesity, type 2 diabetes, and elevated blood pressure. We investigated whether the FTO SNP rs9939609 is associated with the risk of preeclampsia (PE) in a Finnish study population. 485 women with prior PE and 449 women who had given birth after a normotensive pregnancy were genotyped (TaqMan) for the SNP rs9939609. The prevalences of genotypes AA, AT, and TT were 15%, 53%, and 32%, respectively, among the PE cases, and 16%, 47%, and 37%, respectively, among the controls (P = 0.199). We found no evidence of an association between the FTO SNP rs9939609 and PE. However, our cases were dominated by severe, early-onset PE. Thus, we are unable to exclude an association with the milder, later-onset form of the disease in which the role of maternal metabolic predisposition could be more significant.
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Abstract
Recent studies of ancient genomes have suggested that gene flow from archaic hominin groups to the ancestors of modern humans occurred on two separate occasions during the modern human expansion out of Africa. At the same time, decreasing levels of human genetic diversity have been found at increasing distance from Africa as a consequence of human expansion out of Africa. We analyzed the signal of archaic ancestry in modern human populations, and we investigated how serial founder models of human expansion affect the signal of archaic ancestry using simulations. For descendants of an archaic admixture event, we show that genetic drift coupled with ascertainment bias for common alleles can cause artificial but largely predictable differences in similarity to archaic genomes. In genotype data from non-Africans, this effect results in a biased genetic similarity to Neandertals with increasing distance from Africa. However, in addition to the previously reported gene flow between Neandertals and non-Africans as well as gene flow between an archaic human population from Siberia ("Denisovans") and Oceanians, we found a significant affinity between East Asians, particularly Southeast Asians, and the Denisova genome--a pattern that is not expected under a model of solely Neandertal admixture in the ancestry of East Asians. These results suggest admixture between Denisovans or a Denisova-related population and the ancestors of East Asians, and that the history of anatomically modern and archaic humans might be more complex than previously proposed.
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Huang YT, Wu MH. Inference of chromosome-specific copy numbers using population haplotypes. BMC Bioinformatics 2011; 12:194. [PMID: 21605463 PMCID: PMC3128032 DOI: 10.1186/1471-2105-12-194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Accepted: 05/24/2011] [Indexed: 12/28/2022] Open
Abstract
Background Using microarray and sequencing platforms, a large number of copy number variations (CNVs) have been identified in humans. In practice, because our human genome is a diploid, these platforms are limited to or more accurate for detecting total copy numbers rather than chromosome-specific copy numbers at each of the two homologous chromosomes. Nevertheless, the analysis of linkage disequilibrium (LD) between CNVs and SNPs indicates that distinct copy numbers often sit on their own background haplotypes. Results We propose new computational models for inferring chromosome-specific copy numbers by distinguishing background haplotypes of each copy number. The formulated problems are shown to be NP-hard and approximation/heuristic algorithms are developed. Simulation indicates that our method is accurate and outperforms the existing approach. By testing the program in 60 parent-offspring trios, the inferred chromosome-specific copy numbers are highly consistent with the law of Mendelian inheritance. The distributions of copy numbers at chromosomal level are provided for 270 individuals in three HapMap panels. Conclusions The estimation of chromosome-specific copy numbers using microarray or sequencing platforms was often confounded by a number of factors. This study showed that the integration of background haplotypes is able to improve the accuracies of copy number estimation at chromosome level, especially for the CNVs having strong LD with SNPs in proximity.
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Affiliation(s)
- Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan.
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