1501
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Yew CW, Hoque MZ, Pugh-Kitingan J, Minsong A, Voo CLY, Ransangan J, Lau STY, Wang X, Saw WY, Ong RTH, Teo YY, Xu S, Hoh BP, Phipps ME, Kumar SV. Genetic relatedness of indigenous ethnic groups in northern Borneo to neighboring populations from Southeast Asia, as inferred from genome-wide SNP data. Ann Hum Genet 2018. [PMID: 29521412 DOI: 10.1111/ahg.12246] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The region of northern Borneo is home to the current state of Sabah, Malaysia. It is located closest to the southern Philippine islands and may have served as a viaduct for ancient human migration onto or off of Borneo Island. In this study, five indigenous ethnic groups from Sabah were subjected to genome-wide SNP genotyping. These individuals represent the "North Borneo"-speaking group of the great Austronesian family. They have traditionally resided in the inland region of Sabah. The dataset was merged with public datasets, and the genetic relatedness of these groups to neighboring populations from the islands of Southeast Asia, mainland Southeast Asia and southern China was inferred. Genetic structure analysis revealed that these groups formed a genetic cluster that was independent of the clusters of neighboring populations. Additionally, these groups exhibited near-absolute proportions of a genetic component that is also common among Austronesians from Taiwan and the Philippines. They showed no genetic admixture with Austro-Melanesian populations. Furthermore, phylogenetic analysis showed that they are closely related to non-Austro-Melansian Filipinos as well as to Taiwan natives but are distantly related to populations from mainland Southeast Asia. Relatively lower heterozygosity and higher pairwise genetic differentiation index (FST ) values than those of nearby populations indicate that these groups might have experienced genetic drift in the past, resulting in their differentiation from other Austronesians. Subsequent formal testing suggested that these populations have received no gene flow from neighboring populations. Taken together, these results imply that the indigenous ethnic groups of northern Borneo shared a common ancestor with Taiwan natives and non-Austro-Melanesian Filipinos and then isolated themselves on the inland of Sabah. This isolation presumably led to no admixture with other populations, and these individuals therefore underwent strong genetic differentiation. This report contributes to addressing the paucity of genetic data on representatives from this strategic region of ancient human migration event(s).
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Affiliation(s)
- Chee Wei Yew
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
| | - Mohd Zahirul Hoque
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
| | | | - Alexander Minsong
- Faculty of Humanities, Arts & Heritage, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
| | | | - Julian Ransangan
- Borneo Marine Research Institute, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
| | - Sophia Tiek Ying Lau
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
| | - Xu Wang
- Department of Statistics and Applied Probability, Faculty of Science, National University of Singapore, Singapore
| | - Woei Yuh Saw
- Department of Statistics and Applied Probability, Faculty of Science, National University of Singapore, Singapore
| | - Rick Twee-Hee Ong
- Department of Statistics and Applied Probability, Faculty of Science, National University of Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Yik-Ying Teo
- Department of Statistics and Applied Probability, Faculty of Science, National University of Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Shuhua Xu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology (PICB), Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTec University, Shanghai, China.,Collaborative Innovation Centre of Genetics and Development, Shanghai, China
| | - Boon-Peng Hoh
- Institute for Molecular Medical Biotechnology, Universiti Teknologi MARA, Selangor, Malaysia.,Faculty of Medicine and Health Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Maude E Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor, Malaysia
| | - S Vijay Kumar
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
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1502
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Mo SK, Ren ZL, Yang YR, Liu YC, Zhang JJ, Wu HJ, Li Z, Bo XC, Wang SQ, Yan JW, Ni M. A 472-SNP panel for pairwise kinship testing of second-degree relatives. Forensic Sci Int Genet 2018; 34:178-185. [PMID: 29510334 DOI: 10.1016/j.fsigen.2018.02.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 02/22/2018] [Accepted: 02/25/2018] [Indexed: 10/17/2022]
Abstract
Kinship testing based on genetic markers, as forensic short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), has valuable practical applications. Paternity and first-degree relationship can be accurately identified by current commonly-used forensic STRs and reported SNP markers. However, second-degree and more distant relationships remain challenging. Although ∼105-106 SNPs can be used to estimate relatedness of higher degrees, genome-wide genotyping and analysis may be impractical for forensic use. With rapid growth of human genome data sets, it is worthwhile to explore additional markers, especially SNPs, for kinship analysis. Here, we reported an autosomal SNP panel consisted of 342 SNP selected from >84 million SNPs and 131 SNPs from previous systems. We genotyped these SNPs in 136 Chinese individuals by multiplex amplicon Massively Parallel Sequencing, and performed pairwise gender-independent kinship testing. The specificity and sensitivity of these SNPs to distinguish second-degree relatives and the unrelated was 99.9% and 100%, respectively, compared with 53.7% and 99.9% of 19 commonly-used forensic STRs. Moreover, the specificity increased to 100% by the combined use of these STRs and SNPs. The 472-SNP panel could also greatly facilitate the discrimination among different relationships. We estimated that the power of ∼6.45 SNPs were equivalent to one forensic STR in the scenario of 2nd-degree relative pedigree. Altogether, we proposed a panel of 472 SNP markers for kinship analysis, which could be important supplementary of current forensic STRs to solve the problem of second-degree relative testing.
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Affiliation(s)
- Shao-Kang Mo
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China; Department of Reproductive Center, General Hospital of Lanzhou Military Region, Lanzhou 730050, China.
| | - Zi-Lin Ren
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Ya-Ran Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ya-Cheng Liu
- Department of Genetics, Beijing Tongda Shoucheng Institute of Forensic Science, Beijing 100192, China.
| | - Jing-Jing Zhang
- Department of Biotechnology, Beijing Center for Physical and Chemical Analysis, Beijing 100089, China.
| | - Hui-Juan Wu
- Department of Biotechnology, Beijing Center for Physical and Chemical Analysis, Beijing 100089, China.
| | - Zhen Li
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Xiao-Chen Bo
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Sheng-Qi Wang
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Jiang-Wei Yan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ming Ni
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China.
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1503
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Kutkowska-Kaźmierczak A, Rydzanicz M, Chlebowski A, Kłosowska-Kosicka K, Mika A, Gruchota J, Jurkiewicz E, Kowalewski C, Pollak A, Stradomska TJ, Kmieć T, Jakubowski R, Gasperowicz P, Walczak A, Śladowski D, Jankowska-Steifer E, Korniszewski L, Kosińska J, Obersztyn E, Nowak W, Śledziński T, Dziembowski A, Płoski R. Dominant ELOVL1 mutation causes neurological disorder with ichthyotic keratoderma, spasticity, hypomyelination and dysmorphic features. J Med Genet 2018; 55:408-414. [PMID: 29496980 DOI: 10.1136/jmedgenet-2017-105172] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/02/2018] [Accepted: 02/05/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Ichthyosis and neurological involvement occur in relatively few known Mendelian disorders caused by mutations in genes relevant both for epidermis and neural function. OBJECTIVES To identify the cause of a similar phenotype of ichthyotic keratoderma, spasticity, mild hypomyelination (on MRI) and dysmorphic features (IKSHD) observed in two unrelated paediatric probands without family history of disease. METHODS Whole exome sequencing was performed in both patients. The functional effect of prioritised variant in ELOVL1 (very-long-chain fatty acids (VLCFAs) elongase) was analysed by VLCFA profiling by gas chromatography-mass spectrometry in stably transfected HEK2932 cells and in cultured patient's fibroblasts. RESULTS Probands shared novel heterozygous ELOVL1 p.Ser165Phe mutation (de novo in one family, while in the other family, father could not be tested). In transfected cells p.Ser165Phe: (1) reduced levels of FAs C24:0-C28:0 and C26:1 with the most pronounced effect for C26:0 (P=7.8×10-6 vs HEK293 cells with wild type (wt) construct, no difference vs naïve HEK293) and (2) increased levels of C20:0 and C22:0 (P=6.3×10-7, P=1.2×10-5, for C20:0 and C22:0, respectively, comparison vs HEK293 cells with wt construct; P=2.2×10-7, P=1.9×10-4, respectively, comparison vs naïve HEK293). In skin fibroblasts, there was decrease of C26:1 (P=0.014), C28:0 (P=0.001) and increase of C20:0 (P=0.033) in the patient versus controls. There was a strong correlation (r=0.92, P=0.008) between the FAs profile of patient's fibroblasts and that of p.Ser165Phe transfected HEK293 cells. Serum levels of C20:0-C26:0 FAs were normal, but the C24:0/C22:0 ratio was decreased. CONCLUSION The ELOVL1 p.Ser165Phe mutation is a likely cause of IKSHD.
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Affiliation(s)
| | | | - Aleksander Chlebowski
- Laboratory of RNA Biology and Functional Genomics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Adriana Mika
- Department of Environmental Analysis, Faculty of Chemistry, University of Gdansk, Gdansk, Poland.,Department of Pharmaceutical Biochemistry, Medical University of Gdansk, Gdansk, Poland
| | - Jakub Gruchota
- Laboratory of RNA Biology and Functional Genomics, Polish Academy of Sciences, Warsaw, Poland
| | - Elżbieta Jurkiewicz
- Department of Diagnostic Imaging, The Children's Memorial Health Institute, Warsaw, Poland
| | - Cezary Kowalewski
- Department of Dermatology and Immunodermatology, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Pollak
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw, Poland
| | - Teresa Joanna Stradomska
- Department of Biochemistry, Radioimmunology and Experimental Medicine, Children's Memorial Health Institute, Warsaw, Poland
| | - Tomasz Kmieć
- Child Neurology Department, The Children's Memorial Health Institute, Warsaw, Poland
| | - Rafał Jakubowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Torun, Poland.,Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Piotr Gasperowicz
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Anna Walczak
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Dariusz Śladowski
- Department of Transplantology and Central Tissue Bank, Centre for Biostructure, Medical University of Warsaw, Warsaw, Poland
| | | | - Lech Korniszewski
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw, Poland
| | - Joanna Kosińska
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Ewa Obersztyn
- Department of Medical Genetics, Institute of the Mother and Child, Warsaw, Poland
| | - Wieslaw Nowak
- Institue of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Torun, Poland
| | - Tomasz Śledziński
- Department of Pharmaceutical Biochemistry, Medical University of Gdansk, Gdansk, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology and Functional Genomics, Polish Academy of Sciences, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
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1504
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Tsoi LC, Patrick MT, Elder JT. Research Techniques Made Simple: Using Genome-Wide Association Studies to Understand Complex Cutaneous Disorders. J Invest Dermatol 2018; 138:e23-e29. [PMID: 29477192 PMCID: PMC5903459 DOI: 10.1016/j.jid.2018.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Complex cutaneous disorders result from the combined effect of many different genes and environmental factors, with individual genetic variants often having only a modest effect on disease risk. The ability to examine large numbers of samples is required for correlating genetic variants with diseases/traits. Technological advances in high-throughput genotyping, along with mapping of the human genome and its associated inter-individual variation, have allowed genetic variants to be analyzed at high density in large case-control cohorts for many diseases, including several major skin diseases. These genome-wide association studies focus on showing differences in the frequencies of variants between case and control groups, rather than co-transmission of a variant and disease through a family, as is done in linkage studies. In this review, we provide overall guidance for genome-wide association study analysis and interpreting the results. Additionally, we discuss challenges and future directions for genome-wide association studies, focusing on translation of findings to provide biological and clinical implications for dermatology.
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Affiliation(s)
- Lam C Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA; Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
| | - Matthew T Patrick
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - James T Elder
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, Michigan, USA; Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, USA.
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1505
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Environment dominates over host genetics in shaping human gut microbiota. Nature 2018; 555:210-215. [PMID: 29489753 DOI: 10.1038/nature25973] [Citation(s) in RCA: 1649] [Impact Index Per Article: 274.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 01/16/2018] [Indexed: 02/06/2023]
Abstract
Human gut microbiome composition is shaped by multiple factors but the relative contribution of host genetics remains elusive. Here we examine genotype and microbiome data from 1,046 healthy individuals with several distinct ancestral origins who share a relatively common environment, and demonstrate that the gut microbiome is not significantly associated with genetic ancestry, and that host genetics have a minor role in determining microbiome composition. We show that, by contrast, there are significant similarities in the compositions of the microbiomes of genetically unrelated individuals who share a household, and that over 20% of the inter-person microbiome variability is associated with factors related to diet, drugs and anthropometric measurements. We further demonstrate that microbiome data significantly improve the prediction accuracy for many human traits, such as glucose and obesity measures, compared to models that use only host genetic and environmental data. These results suggest that microbiome alterations aimed at improving clinical outcomes may be carried out across diverse genetic backgrounds.
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1506
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Muthusamy B, Selvan LDN, Nguyen TT, Manoj J, Stawiski EW, Jaiswal BS, Wang W, Raja R, Ramprasad VL, Gupta R, Murugan S, Kadandale JS, Prasad TSK, Reddy K, Peterson A, Pandey A, Seshagiri S, Girimaji SC, Gowda H. Next-Generation Sequencing Reveals Novel Mutations in X-linked Intellectual Disability. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 21:295-303. [PMID: 28481730 DOI: 10.1089/omi.2017.0009] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Robust diagnostics for many human genetic disorders are much needed in the pursuit of global personalized medicine. Next-generation sequencing now offers new promise for biomarker and diagnostic discovery, in developed as well as resource-limited countries. In this broader global health context, X-linked intellectual disability (XLID) is an inherited genetic disorder that is associated with a range of phenotypes impacting societies in both developed and developing countries. Although intellectual disability arises due to diverse causes, a substantial proportion is caused by genomic alterations. Studies have identified causal XLID genomic alterations in more than 100 protein-coding genes located on the X-chromosome. However, the causes for a substantial number of intellectual disability and associated phenotypes still remain unknown. Identification of causative genes and novel mutations will help in early diagnosis as well as genetic counseling of families. Advent of next-generation sequencing methods has accelerated the discovery of new genes involved in mental health disorders. In this study, we analyzed the exomes of three families from India with nonsyndromic XLID comprising seven affected individuals. The affected individuals had varying degrees of intellectual disability, microcephaly, and delayed motor and language milestones. We identified potential causal variants in three XLID genes, including PAK3 (V294M), CASK (complex structural variant), and MECP2 (P354T). Our findings reported in this study extend the spectrum of mutations and phenotypes associated with XLID, and calls for further studies of intellectual disability and mental health disorders with use of next-generation sequencing technologies.
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Affiliation(s)
- Babylakshmi Muthusamy
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India .,2 Centre for Bioinformatics, Pondicherry University , Puducherry, India
| | | | - Thong T Nguyen
- 3 Molecular Biology Department, Genentech, Inc. , South San Francisco, California
| | - Jesna Manoj
- 4 Department of Child and Adolescent Psychiatry, NIMHANS , Bangalore, India
| | - Eric W Stawiski
- 3 Molecular Biology Department, Genentech, Inc. , South San Francisco, California.,5 Department of Bioinformatics and Computational Biology, Genentech, Inc. , South San Francisco, California
| | - Bijay S Jaiswal
- 3 Molecular Biology Department, Genentech, Inc. , South San Francisco, California
| | - Weiru Wang
- 6 Department of Structural Biology, Genentech, Inc. , South San Francisco, California
| | - Remya Raja
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India
| | | | | | | | | | - T S Keshava Prasad
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India .,9 YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore, India .,10 NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences , Bangalore, India
| | - Kavita Reddy
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India
| | - Andrew Peterson
- 3 Molecular Biology Department, Genentech, Inc. , South San Francisco, California
| | - Akhilesh Pandey
- 11 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine , Baltimore, Maryland.,12 Department of Biological Chemistry, Johns Hopkins University School of Medicine , Baltimore, Maryland.,13 Department of Pathology, Johns Hopkins University School of Medicine , Baltimore, Maryland
| | - Somasekar Seshagiri
- 3 Molecular Biology Department, Genentech, Inc. , South San Francisco, California
| | | | - Harsha Gowda
- 1 Institute of Bioinformatics , International Technology Park, Bangalore, India .,9 YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University , Mangalore, India
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1507
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Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors. Nat Immunol 2018; 19:302-314. [PMID: 29476184 DOI: 10.1038/s41590-018-0049-7] [Citation(s) in RCA: 174] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 01/12/2018] [Indexed: 12/21/2022]
Abstract
The quantification and characterization of circulating immune cells provide key indicators of human health and disease. To identify the relative effects of environmental and genetic factors on variation in the parameters of innate and adaptive immune cells in homeostatic conditions, we combined standardized flow cytometry of blood leukocytes and genome-wide DNA genotyping of 1,000 healthy, unrelated people of Western European ancestry. We found that smoking, together with age, sex and latent infection with cytomegalovirus, were the main non-genetic factors that affected variation in parameters of human immune cells. Genome-wide association studies of 166 immunophenotypes identified 15 loci that showed enrichment for disease-associated variants. Finally, we demonstrated that the parameters of innate cells were more strongly controlled by genetic variation than were those of adaptive cells, which were driven by mainly environmental exposure. Our data establish a resource that will generate new hypotheses in immunology and highlight the role of innate immunity in susceptibility to common autoimmune diseases.
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1508
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Sung C, Bell KL, Nice CC, Martin NH. Integrating Bayesian genomic cline analyses and association mapping of morphological and ecological traits to dissect reproductive isolation and introgression in a Louisiana Iris hybrid zone. Mol Ecol 2018; 27:959-978. [DOI: 10.1111/mec.14481] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 12/14/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Cheng‐Jung Sung
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos TX USA
| | - Katherine L. Bell
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos TX USA
| | - Chris C. Nice
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos TX USA
| | - Noland H. Martin
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos TX USA
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1509
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Shinde P, Sarkar C, Jalan S. Codon based co-occurrence network motifs in human mitochondria. Sci Rep 2018; 8:3060. [PMID: 29449618 PMCID: PMC5814444 DOI: 10.1038/s41598-018-21454-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 02/05/2018] [Indexed: 11/09/2022] Open
Abstract
The nucleotide polymorphism in the human mitochondrial genome (mtDNA) tolled by codon position bias plays an indispensable role in human population dispersion and expansion. Herein, genome-wide nucleotide co-occurrence networks were constructed using data comprised of five different geographical regions and around 3000 samples for each region. We developed a powerful network model to describe complex mitochondrial evolutionary patterns among codon and non-codon positions. We found evidence that the evolution of human mitochondria DNA is dominated by adaptive forces, particularly mutation and selection, which was supported by many previous studies. The diversity observed in the mtDNA was compared with mutations, co-occurring mutations, network motifs considering codon positions as causing agent. This comparison showed that long-range nucleotide co-occurrences have a large effect on genomic diversity. Most notably, codon motifs apparently underpinned the preferences among codon positions for co-evolution which is probably highly biased during the origin of the genetic code. Our analysis also showed that variable nucleotide positions of different human sub-populations implemented the independent mtDNA evolution to its geographical dispensation. Ergo, this study has provided both a network framework and a codon glance to investigate co-occurring genomic variations that are critical in underlying complex mitochondrial evolution.
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Affiliation(s)
- Pramod Shinde
- Centre for Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Camellia Sarkar
- Centre for Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Sarika Jalan
- Centre for Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India.
- Complex Systems Lab, Discipline of Physics, Indian Institute of Technology Indore, Simrol, Indore, 453552, India.
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1510
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Gandal MJ, Haney JR, Parikshak NN, Leppa V, Ramaswami G, Hartl C, Schork AJ, Appadurai V, Buil A, Werge TM, Liu C, White KP, Horvath S, Geschwind DH. Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap. Science 2018; 359:693-697. [PMID: 29439242 PMCID: PMC5898828 DOI: 10.1126/science.aad6469] [Citation(s) in RCA: 659] [Impact Index Per Article: 109.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 06/21/2017] [Accepted: 11/20/2017] [Indexed: 12/26/2022]
Abstract
The predisposition to neuropsychiatric disease involves a complex, polygenic, and pleiotropic genetic architecture. However, little is known about how genetic variants impart brain dysfunction or pathology. We used transcriptomic profiling as a quantitative readout of molecular brain-based phenotypes across five major psychiatric disorders-autism, schizophrenia, bipolar disorder, depression, and alcoholism-compared with matched controls. We identified patterns of shared and distinct gene-expression perturbations across these conditions. The degree of sharing of transcriptional dysregulation is related to polygenic (single-nucleotide polymorphism-based) overlap across disorders, suggesting a substantial causal genetic component. This comprehensive systems-level view of the neurobiological architecture of major neuropsychiatric illness demonstrates pathways of molecular convergence and specificity.
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Affiliation(s)
- Michael J. Gandal
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - Jillian R. Haney
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Neelroop N. Parikshak
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Virpi Leppa
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Gokul Ramaswami
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Chris Hartl
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Andrew J. Schork
- Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen, Denmark
| | - Vivek Appadurai
- Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen, Denmark
| | - Alfonso Buil
- Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen, Denmark
| | - Thomas M. Werge
- Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Chunyu Liu
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60607, USA
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Kevin P. White
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Tempus Labs, 600 W. Chicago Ave., Chicago IL 60654
| | | | | | | | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Daniel H. Geschwind
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
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1511
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Laucou V, Launay A, Bacilieri R, Lacombe T, Adam-Blondon AF, Bérard A, Chauveau A, de Andrés MT, Hausmann L, Ibáñez J, Le Paslier MC, Maghradze D, Martinez-Zapater JM, Maul E, Ponnaiah M, Töpfer R, Péros JP, Boursiquot JM. Extended diversity analysis of cultivated grapevine Vitis vinifera with 10K genome-wide SNPs. PLoS One 2018; 13:e0192540. [PMID: 29420602 PMCID: PMC5805323 DOI: 10.1371/journal.pone.0192540] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 01/25/2018] [Indexed: 12/18/2022] Open
Abstract
Grapevine is a very important crop species that is mainly cultivated worldwide for fruits, wine and juice. Identification of the genetic bases of performance traits through association mapping studies requires a precise knowledge of the available diversity and how this diversity is structured and varies across the whole genome. An 18k SNP genotyping array was evaluated on a panel of Vitis vinifera cultivars and we obtained a data set with no missing values for a total of 10207 SNPs and 783 different genotypes. The average inter-SNP spacing was ~47 kbp, the mean minor allele frequency (MAF) was 0.23 and the genetic diversity in the sample was high (He = 0.32). Fourteen SNPs, chosen from those with the highest MAF values, were sufficient to identify each genotype in the sample. Parentage analysis revealed 118 full parentages and 490 parent-offspring duos, thus confirming the close pedigree relationships within the cultivated grapevine. Structure analyses also confirmed the main divisions due to an eastern-western gradient and human usage (table vs. wine). Using a multivariate approach, we refined the structure and identified a total of eight clusters. Both the genetic diversity (He, 0.26-0.32) and linkage disequilibrium (LD, 28.8-58.2 kbp) varied between clusters. Despite the short span LD, we also identified some non-recombining haplotype blocks that may complicate association mapping. Finally, we performed a genome-wide association study that confirmed previous works and also identified new regions for important performance traits such as acidity. Taken together, all the results contribute to a better knowledge of the genetics of the cultivated grapevine.
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Affiliation(s)
- Valérie Laucou
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Amandine Launay
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Roberto Bacilieri
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Thierry Lacombe
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.,INRA Unité Expérimentale de Vassal, Centre de Ressources Biologiques de la Vigne, Marseillan-plage, France
| | | | - Aurélie Bérard
- EPGV, Univ Paris-Saclay, CEA, IG-CNG, INRA, Evry, France
| | | | | | - Ludger Hausmann
- JKI, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Javier Ibáñez
- ICVV, CSIC, Universidad de La Rioja, Gobierno de la Rioja, Logroño, Spain
| | | | | | | | - Erika Maul
- JKI, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Maharajah Ponnaiah
- EPGV, Univ Paris-Saclay, CEA, IG-CNG, INRA, Evry, France.,LBD, Univ UPMC, CNRS, INSERM, Paris, France
| | - Reinhard Töpfer
- JKI, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Jean-Pierre Péros
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Jean-Michel Boursiquot
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.,INRA Unité Expérimentale de Vassal, Centre de Ressources Biologiques de la Vigne, Marseillan-plage, France
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1512
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Rubinstein M, Patowary A, Stanaway IB, McCord E, Nesbitt RR, Archer M, Scheuer T, Nickerson D, Raskind WH, Wijsman EM, Bernier R, Catterall WA, Brkanac Z. Association of rare missense variants in the second intracellular loop of Na V1.7 sodium channels with familial autism. Mol Psychiatry 2018; 23:231-239. [PMID: 27956748 PMCID: PMC5468514 DOI: 10.1038/mp.2016.222] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 10/07/2016] [Accepted: 10/17/2016] [Indexed: 01/21/2023]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder often accompanied by intellectual disability, language impairment and medical co-morbidities. The heritability of autism is high and multiple genes have been implicated as causal. However, most of these genes have been identified in de novo cases. To further the understanding of familial autism, we performed whole-exome sequencing on five families in which second- and third-degree relatives were affected. By focusing on novel and protein-altering variants, we identified a small set of candidate genes. Among these, a novel private missense C1143F variant in the second intracellular loop of the voltage-gated sodium channel NaV1.7, encoded by the SCN9A gene, was identified in one family. Through electrophysiological analysis, we show that NaV1.7C1143F exhibits partial loss-of-function effects, resulting in slower recovery from inactivation and decreased excitability in cultured cortical neurons. Furthermore, for the same intracellular loop of NaV1.7, we found an excess of rare variants in a case-control variant-burden study. Functional analysis of one of these variants, M932L/V991L, also demonstrated reduced firing in cortical neurons. However, although this variant is rare in Caucasians, it is frequent in Latino population, suggesting that genetic background can alter its effects on phenotype. Although the involvement of the SCN1A and SCN2A genes encoding NaV1.1 and NaV1.2 channels in de novo ASD has previously been demonstrated, our study indicates the involvement of inherited SCN9A variants and partial loss-of-function of NaV1.7 channels in the etiology of rare familial ASD.
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Affiliation(s)
- M Rubinstein
- Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - A Patowary
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - I B Stanaway
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - E McCord
- Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - R R Nesbitt
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - M Archer
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - T Scheuer
- Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - D Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - W H Raskind
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA,Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - E M Wijsman
- Department of Genome Sciences, University of Washington, Seattle, WA, USA,Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA,Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - R Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - W A Catterall
- Department of Pharmacology, University of Washington, Seattle, WA, USA,Department of Pharmacology, University of Washington, Seattle, WA 98195, USA E-mail:
| | - Z Brkanac
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA,Department of Psychiatry and Behavioral Science, University of Washington, 1959N.E. Pacific Street, Room BB1526, Seattle, WA 98195-6560, USA. E-mail:
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1513
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Doyle SR, Laing R, Bartley DJ, Britton C, Chaudhry U, Gilleard JS, Holroyd N, Mable BK, Maitland K, Morrison AA, Tait A, Tracey A, Berriman M, Devaney E, Cotton JA, Sargison ND. A Genome Resequencing-Based Genetic Map Reveals the Recombination Landscape of an Outbred Parasitic Nematode in the Presence of Polyploidy and Polyandry. Genome Biol Evol 2018; 10:396-409. [PMID: 29267942 PMCID: PMC5793844 DOI: 10.1093/gbe/evx269] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2017] [Indexed: 12/27/2022] Open
Abstract
The parasitic nematode Haemonchus contortus is an economically and clinically important pathogen of small ruminants, and a model system for understanding the mechanisms and evolution of traits such as anthelmintic resistance. Anthelmintic resistance is widespread and is a major threat to the sustainability of livestock agriculture globally; however, little is known about the genome architecture and parameters such as recombination that will ultimately influence the rate at which resistance may evolve and spread. Here, we performed a genetic cross between two divergent strains of H. contortus, and subsequently used whole-genome resequencing of a female worm and her brood to identify the distribution of genome-wide variation that characterizes these strains. Using a novel bioinformatic approach to identify variants that segregate as expected in a pseudotestcross, we characterized linkage groups and estimated genetic distances between markers to generate a chromosome-scale F1 genetic map. We exploited this map to reveal the recombination landscape, the first for any helminth species, demonstrating extensive variation in recombination rate within and between chromosomes. Analyses of these data also revealed the extent of polyandry, whereby at least eight males were found to have contributed to the genetic variation of the progeny analyzed. Triploid offspring were also identified, which we hypothesize are the result of nondisjunction during female meiosis or polyspermy. These results expand our knowledge of the genetics of parasitic helminths and the unusual life-history of H. contortus, and enhance ongoing efforts to understand the genetic basis of resistance to the drugs used to control these worms and for related species that infect livestock and humans throughout the world. This study also demonstrates the feasibility of using whole-genome resequencing data to directly construct a genetic map in a single generation cross from a noninbred nonmodel organism with a complex lifecycle.
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Affiliation(s)
- Stephen R Doyle
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Roz Laing
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - David J Bartley
- Moredun Research Institute, Pentlands Science Park, Penicuik, United Kingdom
| | - Collette Britton
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Umer Chaudhry
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom
| | - John S Gilleard
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Alberta, Canada
| | - Nancy Holroyd
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Barbara K Mable
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Kirsty Maitland
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Alison A Morrison
- Moredun Research Institute, Pentlands Science Park, Penicuik, United Kingdom
| | - Andy Tait
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Alan Tracey
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Eileen Devaney
- Institute of Biodiversity Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - James A Cotton
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Neil D Sargison
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom
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1514
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Grant RC, Denroche RE, Borgida A, Virtanen C, Cook N, Smith AL, Connor AA, Wilson JM, Peterson G, Roberts NJ, Klein AP, Grimmond SM, Biankin A, Cleary S, Moore M, Lemire M, Zogopoulos G, Stein L, Gallinger S. Exome-Wide Association Study of Pancreatic Cancer Risk. Gastroenterology 2018; 154:719-722.e3. [PMID: 29074453 PMCID: PMC5811358 DOI: 10.1053/j.gastro.2017.10.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/04/2017] [Accepted: 10/12/2017] [Indexed: 12/20/2022]
Abstract
We conducted a case-control exome-wide association study to discover germline variants in coding regions that affect risk for pancreatic cancer, combining data from 5 studies. We analyzed exome and genome sequencing data from 437 patients with pancreatic cancer (cases) and 1922 individuals not known to have cancer (controls). In the primary analysis, BRCA2 had the strongest enrichment for rare inactivating variants (17/437 cases vs 3/1922 controls) (P = 3.27x10-6; exome-wide statistical significance threshold P < 2.5x10-6). Cases had more rare inactivating variants in DNA repair genes than controls, even after excluding 13 genes known to predispose to pancreatic cancer (adjusted odds ratio, 1.35; P = .045). At the suggestive threshold (P < .001), 6 genes were enriched for rare damaging variants (UHMK1, AP1G2, DNTA, CHST6, FGFR3, and EPHA1) and 7 genes had associations with pancreatic cancer risk, based on the sequence-kernel association test. We confirmed variants in BRCA2 as the most common high-penetrant genetic factor associated with pancreatic cancer and we also identified candidate pancreatic cancer genes. Large collaborations and novel approaches are needed to overcome the genetic heterogeneity of pancreatic cancer predisposition.
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Affiliation(s)
| | | | | | | | - Natalie Cook
- Princess Margaret Genomics Centre, Toronto, Canada
| | - Alyssa L Smith
- Research Institute of the McGill University Health Centre, Montreal, Canada
| | | | | | - Gloria Peterson
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Nicholas J Roberts
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Alison P Klein
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Baltimore, Maryland; Department of Pathology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Sean M Grimmond
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne, Australia
| | - Andrew Biankin
- Wohl Cancer Research Centre, Institute of, Cancer Sciences, University of Glasgow, Glasgow, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom; South Western Sydney Clinical School, Faculty of Medicine, University of NSW, Liverpool, Australia
| | - Sean Cleary
- Ontario Institute for Cancer Research, Toronto, Canada; Ontario Pancreas Cancer Study, Toronto, Canada
| | | | | | - George Zogopoulos
- Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Lincoln Stein
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, Canada; Ontario Pancreas Cancer Study, Toronto, Canada.
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1515
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Fadista J, Lund M, Skotte L, Geller F, Nandakumar P, Chatterjee S, Matsson H, Granström AL, Wester T, Salo P, Virtanen V, Carstensen L, Bybjerg-Grauholm J, Hougaard DM, Pakarinen M, Perola M, Nordenskjöld A, Chakravarti A, Melbye M, Feenstra B. Genome-wide association study of Hirschsprung disease detects a novel low-frequency variant at the RET locus. Eur J Hum Genet 2018; 26:561-569. [PMID: 29379196 DOI: 10.1038/s41431-017-0053-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 10/03/2017] [Accepted: 11/07/2017] [Indexed: 12/22/2022] Open
Abstract
Hirschsprung disease (HSCR) is a congenital disorder with a population incidence of ~1/5000 live births, defined by an absence of enteric ganglia along variable lengths of the colon. HSCR genome-wide association studies (GWAS) have found common associated variants at RET, SEMA3, and NRG1, but they still fail to explain all of its heritability. To enhance gene discovery, we performed a GWAS of 170 cases identified from the Danish nationwide pathology registry with 4717 controls, based on 6.2 million variants imputed from the haplotype reference consortium panel. We found a novel low-frequency variant (rs144432435), which, when conditioning on the lead RET single-nucleotide polymorphism (SNP), was of genome-wide significance in the discovery analysis. This conditional association signal was replicated in a Swedish HSCR cohort with discovery plus replication meta-analysis conditional odds ratio of 6.6 (P = 7.7 × 10-10; 322 cases and 4893 controls). The conditional signal was, however, not replicated in two HSCR cohorts from USA and Finland, leading to the hypothesis that rs144432435 tags a rare haplotype present in Denmark and Sweden. Using the genome-wide complex trait analysis method, we estimated the SNP heritability of HSCR to be 88%, close to estimates based on classical family studies. Moreover, by using Lasso (least absolute shrinkage and selection operator) regression we were able to construct a genetic HSCR predictor with a area under the receiver operator characteristics curve of 76% in an independent validation set. In conclusion, we combined the largest collection of sporadic Hirschsprung cases to date (586 cases) to further elucidate HSCR's genetic architecture.
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Affiliation(s)
- João Fadista
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.
| | - Marie Lund
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Line Skotte
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Priyanka Nandakumar
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sumantra Chatterjee
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hans Matsson
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Anna Löf Granström
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Paediatric Surgery, Astrid Lindgren Children Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Tomas Wester
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Paediatric Surgery, Astrid Lindgren Children Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Perttu Salo
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Valtter Virtanen
- Pediatric Surgery, Children's Hospital, University of Helsinki, Helsinki, Finland
| | - Lisbeth Carstensen
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- Department of Congenital Disorders, Danish Centre for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - David Michael Hougaard
- Department of Congenital Disorders, Danish Centre for Neonatal Screening, Statens Serum Institut, Copenhagen, Denmark
| | - Mikko Pakarinen
- Pediatric Surgery, Children's Hospital, University of Helsinki, Helsinki, Finland
| | - Markus Perola
- Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Agneta Nordenskjöld
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Paediatric Surgery, Astrid Lindgren Children Hospital, Karolinska University Hospital, Stockholm, Sweden.,Center of Molecular Medicine, Karolinska institutet, Stockholm, Sweden
| | - Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
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1516
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Kolde R, Franzosa EA, Rahnavard G, Hall AB, Vlamakis H, Stevens C, Daly MJ, Xavier RJ, Huttenhower C. Host genetic variation and its microbiome interactions within the Human Microbiome Project. Genome Med 2018; 10:6. [PMID: 29378630 PMCID: PMC5789541 DOI: 10.1186/s13073-018-0515-8] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/04/2018] [Indexed: 02/07/2023] Open
Abstract
Background Despite the increasing recognition that microbial communities within the human body are linked to health, we have an incomplete understanding of the environmental and molecular interactions that shape the composition of these communities. Although host genetic factors play a role in these interactions, these factors have remained relatively unexplored given the requirement for large population-based cohorts in which both genotyping and microbiome characterization have been performed. Methods We performed whole-genome sequencing of 298 donors from the Human Microbiome Project (HMP) healthy cohort study to accompany existing deep characterization of their microbiomes at various body sites. This analysis yielded an average sequencing depth of 32x, with which we identified 27 million (M) single nucleotide variants and 2.3 M insertions-deletions. Results Taxonomic composition and functional potential of the microbiome covaried significantly with genetic principal components in the gastrointestinal tract and oral communities, but not in the nares or vaginal microbiota. Example associations included validation of known associations between FUT2 secretor status, as well as a variant conferring hypolactasia near the LCT gene, with Bifidobacterium longum abundance in stool. The associations of microbial features with both high-level genetic attributes and single variants were specific to particular body sites, highlighting the opportunity to find unique genetic mechanisms controlling microbiome properties in the microbial communities from multiple body sites. Conclusions This study adds deep sequencing of host genomes to the body-wide microbiome sequences already extant from the HMP healthy cohort, creating a unique, versatile, and well-controlled reference for future studies seeking to identify host genetic modulators of the microbiome. Electronic supplementary material The online version of this article (10.1186/s13073-018-0515-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Raivo Kolde
- Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge St, Boston, MA, 02114, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA.,The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Gholamali Rahnavard
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA.,The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | | | - Hera Vlamakis
- The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Christine Stevens
- The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Mark J Daly
- The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.,Center for Human Genetic Research, Massachusetts General Hospital, 185 Cambridge St, Boston, MA, 02114, USA
| | - Ramnik J Xavier
- Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge St, Boston, MA, 02114, USA. .,The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA. .,Center for Microbiome Informatics & Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, Boston, MA, 02115, USA. .,The Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
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1517
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Investigating the origins of eastern Polynesians using genome-wide data from the Leeward Society Isles. Sci Rep 2018; 8:1823. [PMID: 29379068 PMCID: PMC5789021 DOI: 10.1038/s41598-018-20026-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/11/2018] [Indexed: 12/14/2022] Open
Abstract
The debate concerning the origin of the Polynesian speaking peoples has been recently reinvigorated by genetic evidence for secondary migrations to western Polynesia from the New Guinea region during the 2nd millennium BP. Using genome-wide autosomal data from the Leeward Society Islands, the ancient cultural hub of eastern Polynesia, we find that the inhabitants' genomes also demonstrate evidence of this episode of admixture, dating to 1,700-1,200 BP. This supports a late settlement chronology for eastern Polynesia, commencing ~1,000 BP, after the internal differentiation of Polynesian society. More than 70% of the autosomal ancestry of Leeward Society Islanders derives from Island Southeast Asia with the lowland populations of the Philippines as the single largest potential source. These long-distance migrants into Polynesia experienced additional admixture with northern Melanesians prior to the secondary migrations of the 2nd millennium BP. Moreover, the genetic diversity of mtDNA and Y chromosome lineages in the Leeward Society Islands is consistent with linguistic evidence for settlement of eastern Polynesia proceeding from the central northern Polynesian outliers in the Solomon Islands. These results stress the complex demographic history of the Leeward Society Islands and challenge phylogenetic models of cultural evolution predicated on eastern Polynesia being settled from Samoa.
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1518
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Domingue BW, Belsky DW, Fletcher JM, Conley D, Boardman JD, Harris KM. The social genome of friends and schoolmates in the National Longitudinal Study of Adolescent to Adult Health. Proc Natl Acad Sci U S A 2018; 115:702-707. [PMID: 29317533 PMCID: PMC5789914 DOI: 10.1073/pnas.1711803115] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Humans tend to form social relationships with others who resemble them. Whether this sorting of like with like arises from historical patterns of migration, meso-level social structures in modern society, or individual-level selection of similar peers remains unsettled. Recent research has evaluated the possibility that unobserved genotypes may play an important role in the creation of homophilous relationships. We extend this work by using data from 5,500 adolescents from the National Longitudinal Study of Adolescent to Adult Health (Add Health) to examine genetic similarities among pairs of friends. Although there is some evidence that friends have correlated genotypes, both at the whole-genome level as well as at trait-associated loci (via polygenic scores), further analysis suggests that meso-level forces, such as school assignment, are a principal source of genetic similarity between friends. We also observe apparent social-genetic effects in which polygenic scores of an individual's friends and schoolmates predict the individual's own educational attainment. In contrast, an individual's height is unassociated with the height genetics of peers.
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Affiliation(s)
| | - Daniel W Belsky
- Department of Population Health Sciences, School of Medicine, Duke University, Durham, NC 27710
- Social Science Research Institute, Duke University, Durham, NC 27710
| | - Jason M Fletcher
- La Follette School of Public Affairs, University of Wisconsin-Madison, Madison, WI 53706
- Department of Sociology, University of Wisconsin-Madison, Madison, WI 53706
- Center for Demography and Ecology, University of Wisconsin-Madison, Madison, WI 53706
| | - Dalton Conley
- Department of Sociology, Princeton University, Princeton, NJ 08544
| | - Jason D Boardman
- Institute of Behavioral Science, University of Colorado Boulder, Boulder, CO 80309
- Sociology Department, University of Colorado Boulder, Boulder, CO 80302
| | - Kathleen Mullan Harris
- Department of Sociology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599;
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516
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1519
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Prediction of inherited genomic susceptibility to 20 common cancer types by a supervised machine-learning method. Proc Natl Acad Sci U S A 2018; 115:1322-1327. [PMID: 29358382 PMCID: PMC5819441 DOI: 10.1073/pnas.1717960115] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Prevention and early intervention are the most effective ways of avoiding or minimizing psychological, physical, and financial suffering from cancer. However, such proactive action requires the ability to predict the individual's susceptibility to cancer with a measure of probability. Of the triad of cancer-causing factors (inherited genomic susceptibility, environmental factors, and lifestyle factors), the inherited genomic component may be derivable from the recent public availability of a large body of whole-genome variation data. However, genome-wide association studies have so far showed limited success in predicting the inherited susceptibility to common cancers. We present here a multiple classification approach for predicting individuals' inherited genomic susceptibility to acquire the most likely phenotype among a panel of 20 major common cancer types plus 1 "healthy" type by application of a supervised machine-learning method under competing conditions among the cohorts of the 21 types. This approach suggests that, depending on the phenotypes of 5,919 individuals of "white" ethnic population in this study, (i) the portion of the cohort of a cancer type who acquired the observed type due to mostly inherited genomic susceptibility factors ranges from about 33 to 88% (or its corollary: the portion due to mostly environmental and lifestyle factors ranges from 12 to 67%), and (ii) on an individual level, the method also predicts individuals' inherited genomic susceptibility to acquire the other types ranked with associated probabilities. These probabilities may provide practical information for individuals, heath professionals, and health policymakers related to prevention and/or early intervention of cancer.
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1520
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Patin E, Lopez M, Grollemund R, Verdu P, Harmant C, Quach H, Laval G, Perry GH, Barreiro LB, Froment A, Heyer E, Massougbodji A, Fortes-Lima C, Migot-Nabias F, Bellis G, Dugoujon JM, Pereira JB, Fernandes V, Pereira L, Van der Veen L, Mouguiama-Daouda P, Bustamante CD, Hombert JM, Quintana-Murci L. Dispersals and genetic adaptation of Bantu-speaking populations in Africa and North America. Science 2018; 356:543-546. [PMID: 28473590 DOI: 10.1126/science.aal1988] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 04/11/2017] [Indexed: 12/12/2022]
Abstract
Bantu languages are spoken by about 310 million Africans, yet the genetic history of Bantu-speaking populations remains largely unexplored. We generated genomic data for 1318 individuals from 35 populations in western central Africa, where Bantu languages originated. We found that early Bantu speakers first moved southward, through the equatorial rainforest, before spreading toward eastern and southern Africa. We also found that genetic adaptation of Bantu speakers was facilitated by admixture with local populations, particularly for the HLA and LCT loci. Finally, we identified a major contribution of western central African Bantu speakers to the ancestry of African Americans, whose genomes present no strong signals of natural selection. Together, these results highlight the contribution of Bantu-speaking peoples to the complex genetic history of Africans and African Americans.
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Affiliation(s)
- Etienne Patin
- Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France. .,Centre National de la Recherche Scientifique URA3012, 75015 Paris, France.,Center of Bioinformatics, Biostatistics, and Integrative Biology, Institut Pasteur, 75015 Paris, France
| | - Marie Lopez
- Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France.,Centre National de la Recherche Scientifique URA3012, 75015 Paris, France.,Center of Bioinformatics, Biostatistics, and Integrative Biology, Institut Pasteur, 75015 Paris, France
| | - Rebecca Grollemund
- Evolutionary Biology Group, School of Biological Sciences, University of Reading, Reading RG6 6BX, England.,Departments of English and Anthropology, University of Missouri, Columbia, Missouri, MO 65211, USA
| | - Paul Verdu
- Centre National de la Recherche Scientifique UMR7206, Muséum National d'Histoire Naturelle, Université Paris Diderot, Sorbonne Paris Cité, 75016 Paris, France
| | - Christine Harmant
- Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France.,Centre National de la Recherche Scientifique URA3012, 75015 Paris, France.,Center of Bioinformatics, Biostatistics, and Integrative Biology, Institut Pasteur, 75015 Paris, France
| | - Hélène Quach
- Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France.,Centre National de la Recherche Scientifique URA3012, 75015 Paris, France.,Center of Bioinformatics, Biostatistics, and Integrative Biology, Institut Pasteur, 75015 Paris, France
| | - Guillaume Laval
- Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France.,Centre National de la Recherche Scientifique URA3012, 75015 Paris, France.,Center of Bioinformatics, Biostatistics, and Integrative Biology, Institut Pasteur, 75015 Paris, France
| | - George H Perry
- Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Luis B Barreiro
- Université de Montréal, Centre de Recherche CHU Sainte-Justine, Montréal, Québec H3T 1C5, Canada
| | - Alain Froment
- Institut de Recherche pour le Développement, UMR 208, Muséum National d'Histoire Naturelle, 75005 Paris, France
| | - Evelyne Heyer
- Centre National de la Recherche Scientifique UMR7206, Muséum National d'Histoire Naturelle, Université Paris Diderot, Sorbonne Paris Cité, 75016 Paris, France
| | - Achille Massougbodji
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et l'Enfance (CERPAGE), Cotonou, Bénin.,Institut de Recherche Clinique du Bénin (IRCB), 01 BP 188 Cotonou, Bénin
| | - Cesar Fortes-Lima
- Centre National de la Recherche Scientifique UMR7206, Muséum National d'Histoire Naturelle, Université Paris Diderot, Sorbonne Paris Cité, 75016 Paris, France.,Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique UMR 5288/Université Paul Sabatier Toulouse 3, 31073 Toulouse Cedex 3, France
| | - Florence Migot-Nabias
- Institut de Recherche pour le Développement, UMR 216, 75006 Paris, France.,Communautés d'Universités et Etablissements (COMUE) Sorbonne Paris Cité, Faculté de Pharmacie, Université Paris Descartes, 75006 Paris, France
| | - Gil Bellis
- Institut National d'Etudes Démographiques, 75020 Paris, France
| | - Jean-Michel Dugoujon
- Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique UMR 5288/Université Paul Sabatier Toulouse 3, 31073 Toulouse Cedex 3, France
| | - Joana B Pereira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal
| | - Verónica Fernandes
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal
| | - Luisa Pereira
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal.,Faculdade de Medicina da Universidade do Porto, Porto 4200-319, Portugal
| | - Lolke Van der Veen
- Centre National de la Recherche Scientifique UMR 5596, Dynamique du Langage, Université Lumière-Lyon 2, 69007 Lyon, France
| | - Patrick Mouguiama-Daouda
- Centre National de la Recherche Scientifique UMR 5596, Dynamique du Langage, Université Lumière-Lyon 2, 69007 Lyon, France.,Laboratoire Langue, Culture et Cognition (LCC), Université Omar Bongo, 13131 Libreville, Gabon
| | - Carlos D Bustamante
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.,Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Jean-Marie Hombert
- Centre National de la Recherche Scientifique UMR 5596, Dynamique du Langage, Université Lumière-Lyon 2, 69007 Lyon, France
| | - Lluís Quintana-Murci
- Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France. .,Centre National de la Recherche Scientifique URA3012, 75015 Paris, France.,Center of Bioinformatics, Biostatistics, and Integrative Biology, Institut Pasteur, 75015 Paris, France
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1521
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Hall LS, Adams MJ, Arnau-Soler A, Clarke TK, Howard DM, Zeng Y, Davies G, Hagenaars SP, Maria Fernandez-Pujals A, Gibson J, Wigmore EM, Boutin TS, Hayward C, Scotland G, Porteous DJ, Deary IJ, Thomson PA, Haley CS, McIntosh AM. Genome-wide meta-analyses of stratified depression in Generation Scotland and UK Biobank. Transl Psychiatry 2018; 8:9. [PMID: 29317602 PMCID: PMC5802463 DOI: 10.1038/s41398-017-0034-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/28/2017] [Accepted: 08/25/2017] [Indexed: 11/10/2022] Open
Abstract
Few replicable genetic associations for Major Depressive Disorder (MDD) have been identified. Recent studies of MDD have identified common risk variants by using a broader phenotype definition in very large samples, or by reducing phenotypic and ancestral heterogeneity. We sought to ascertain whether it is more informative to maximize the sample size using data from all available cases and controls, or to use a sex or recurrent stratified subset of affected individuals. To test this, we compared heritability estimates, genetic correlation with other traits, variance explained by MDD polygenic score, and variants identified by genome-wide meta-analysis for broad and narrow MDD classifications in two large British cohorts - Generation Scotland and UK Biobank. Genome-wide meta-analysis of MDD in males yielded one genome-wide significant locus on 3p22.3, with three genes in this region (CRTAP, GLB1, and TMPPE) demonstrating a significant association in gene-based tests. Meta-analyzed MDD, recurrent MDD and female MDD yielded equivalent heritability estimates, showed no detectable difference in association with polygenic scores, and were each genetically correlated with six health-correlated traits (neuroticism, depressive symptoms, subjective well-being, MDD, a cross-disorder phenotype and Bipolar Disorder). Whilst stratified GWAS analysis revealed a genome-wide significant locus for male MDD, the lack of independent replication, and the consistent pattern of results in other MDD classifications suggests that phenotypic stratification using recurrence or sex in currently available sample sizes is currently weakly justified. Based upon existing studies and our findings, the strategy of maximizing sample sizes is likely to provide the greater gain.
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Affiliation(s)
- Lynsey S. Hall
- 0000 0004 1936 7988grid.4305.2Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, EH10 5HF Edinburgh, UK ,0000 0001 0462 7212grid.1006.7Institute of Genetic Medicine, Newcastle University, NE1 7RU Newcastle upon Tyne, UK
| | - Mark J. Adams
- 0000 0004 1936 7988grid.4305.2Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, EH10 5HF Edinburgh, UK
| | - Aleix Arnau-Soler
- 0000 0004 1936 7988grid.4305.2Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH8 9YL Edinburgh, UK
| | - Toni-Kim Clarke
- 0000 0004 1936 7988grid.4305.2Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, EH10 5HF Edinburgh, UK
| | - David M. Howard
- 0000 0004 1936 7988grid.4305.2Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, EH10 5HF Edinburgh, UK
| | - Yanni Zeng
- 0000 0004 1936 7988grid.4305.2Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, EH10 5HF Edinburgh, UK ,0000 0004 1936 7988grid.4305.2Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH8 9YL Edinburgh, UK
| | - Gail Davies
- 0000 0004 1936 7988grid.4305.2Department of Psychology, University of Edinburgh, EH8 9YL Edinburgh, UK ,0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, EH8 9YL Edinburgh, UK
| | - Saskia P. Hagenaars
- 0000 0004 1936 7988grid.4305.2Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, EH10 5HF Edinburgh, UK ,0000 0004 1936 7988grid.4305.2Department of Psychology, University of Edinburgh, EH8 9YL Edinburgh, UK ,0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, EH8 9YL Edinburgh, UK
| | - Ana Maria Fernandez-Pujals
- 0000 0004 1936 7988grid.4305.2Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, EH10 5HF Edinburgh, UK
| | - Jude Gibson
- 0000 0004 1936 7988grid.4305.2Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, EH10 5HF Edinburgh, UK
| | - Eleanor M. Wigmore
- 0000 0004 1936 7988grid.4305.2Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, EH10 5HF Edinburgh, UK
| | - Thibaud S. Boutin
- 0000 0004 1936 7988grid.4305.2Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH8 9YL Edinburgh, UK
| | - Caroline Hayward
- 0000 0004 1936 7988grid.4305.2Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH8 9YL Edinburgh, UK ,A collaboration between the University Medical Schools and National Health Service in Aberdeen, Dundee, Edinburgh and Glasgow UK
| | - Generation Scotland
- A collaboration between the University Medical Schools and National Health Service in Aberdeen, Dundee, Edinburgh and Glasgow UK
| | | | - David J. Porteous
- 0000 0004 1936 7988grid.4305.2Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH8 9YL Edinburgh, UK
| | - Ian J. Deary
- 0000 0004 1936 7988grid.4305.2Department of Psychology, University of Edinburgh, EH8 9YL Edinburgh, UK ,0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, EH8 9YL Edinburgh, UK
| | - Pippa A. Thomson
- 0000 0004 1936 7988grid.4305.2Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH8 9YL Edinburgh, UK ,0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, EH8 9YL Edinburgh, UK
| | - Chris S. Haley
- 0000 0004 1936 7988grid.4305.2Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH8 9YL Edinburgh, UK
| | - Andrew M. McIntosh
- 0000 0004 1936 7988grid.4305.2Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, EH10 5HF Edinburgh, UK ,0000 0004 1936 7988grid.4305.2Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, EH8 9YL Edinburgh, UK
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1522
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Triska P, Chekanov N, Stepanov V, Khusnutdinova EK, Kumar GPA, Akhmetova V, Babalyan K, Boulygina E, Kharkov V, Gubina M, Khidiyatova I, Khitrinskaya I, Khrameeva EE, Khusainova R, Konovalova N, Litvinov S, Marusin A, Mazur AM, Puzyrev V, Ivanoshchuk D, Spiridonova M, Teslyuk A, Tsygankova S, Triska M, Trofimova N, Vajda E, Balanovsky O, Baranova A, Skryabin K, Tatarinova TV, Prokhortchouk E. Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe. BMC Genet 2017; 18:110. [PMID: 29297395 PMCID: PMC5751809 DOI: 10.1186/s12863-017-0578-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The history of human populations occupying the plains and mountain ridges separating Europe from Asia has been eventful, as these natural obstacles were crossed westward by multiple waves of Turkic and Uralic-speaking migrants as well as eastward by Europeans. Unfortunately, the material records of history of this region are not dense enough to reconstruct details of population history. These considerations stimulate growing interest to obtain a genetic picture of the demographic history of migrations and admixture in Northern Eurasia. RESULTS We genotyped and analyzed 1076 individuals from 30 populations with geographical coverage spanning from Baltic Sea to Baikal Lake. Our dense sampling allowed us to describe in detail the population structure, provide insight into genomic history of numerous European and Asian populations, and significantly increase quantity of genetic data available for modern populations in region of North Eurasia. Our study doubles the amount of genome-wide profiles available for this region. We detected unusually high amount of shared identical-by-descent (IBD) genomic segments between several Siberian populations, such as Khanty and Ket, providing evidence of genetic relatedness across vast geographic distances and between speakers of different language families. Additionally, we observed excessive IBD sharing between Khanty and Bashkir, a group of Turkic speakers from Southern Urals region. While adding some weight to the "Finno-Ugric" origin of Bashkir, our studies highlighted that the Bashkir genepool lacks the main "core", being a multi-layered amalgamation of Turkic, Ugric, Finnish and Indo-European contributions, which points at intricacy of genetic interface between Turkic and Uralic populations. Comparison of the genetic structure of Siberian ethnicities and the geography of the region they inhabit point at existence of the "Great Siberian Vortex" directing genetic exchanges in populations across the Siberian part of Asia. Slavic speakers of Eastern Europe are, in general, very similar in their genetic composition. Ukrainians, Belarusians and Russians have almost identical proportions of Caucasus and Northern European components and have virtually no Asian influence. We capitalized on wide geographic span of our sampling to address intriguing question about the place of origin of Russian Starovers, an enigmatic Eastern Orthodox Old Believers religious group relocated to Siberia in seventeenth century. A comparative reAdmix analysis, complemented by IBD sharing, placed their roots in the region of the Northern European Plain, occupied by North Russians and Finno-Ugric Komi and Karelian people. Russians from Novosibirsk and Russian Starover exhibit ancestral proportions close to that of European Eastern Slavs, however, they also include between five to 10 % of Central Siberian ancestry, not present at this level in their European counterparts. CONCLUSIONS Our project has patched the hole in the genetic map of Eurasia: we demonstrated complexity of genetic structure of Northern Eurasians, existence of East-West and North-South genetic gradients, and assessed different inputs of ancient populations into modern populations.
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MESH Headings
- Algorithms
- Asia
- DNA
- Datasets as Topic
- Emigration and Immigration/history
- Ethnicity/genetics
- Europe
- Female
- Genetic Variation
- Genetics, Population
- Genotyping Techniques
- History, 15th Century
- History, 16th Century
- History, 17th Century
- History, 18th Century
- History, 19th Century
- History, 20th Century
- History, 21st Century
- History, Ancient
- History, Medieval
- Humans
- Male
- Russia
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Affiliation(s)
- Petr Triska
- Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Nikolay Chekanov
- Federal State Institution "Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences", Moscow, Russia
- "Genoanalytica" CJSC, Moscow, Russia
| | - Vadim Stepanov
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
- Bashkir State University, Ufa, Russia
| | | | - Vita Akhmetova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
| | - Konstantin Babalyan
- Moscow Institute of Physics and Technology, Department of Molecular and Bio-Physics, Moscow, Russia
| | | | - Vladimir Kharkov
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Marina Gubina
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Irina Khidiyatova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
- Bashkir State University, Ufa, Russia
| | - Irina Khitrinskaya
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Ekaterina E Khrameeva
- "Genoanalytica" CJSC, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Moscow, Russia
| | - Rita Khusainova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
- Bashkir State University, Ufa, Russia
| | | | - Sergey Litvinov
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
| | - Andrey Marusin
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Alexandr M Mazur
- Federal State Institution "Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences", Moscow, Russia
| | - Valery Puzyrev
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Dinara Ivanoshchuk
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Maria Spiridonova
- Institute of Medical Genetics, Tomsk National Medical Research Center, Russian Academy of Sciences, Siberian Branch, Tomsk, Russia
| | - Anton Teslyuk
- Moscow Institute of Physics and Technology, Department of Molecular and Bio-Physics, Moscow, Russia
| | - Svetlana Tsygankova
- Moscow Institute of Physics and Technology, Department of Molecular and Bio-Physics, Moscow, Russia
| | - Martin Triska
- Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Natalya Trofimova
- Institute of Biochemistry and Genetics, Russian Academy of Sciences, Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
| | - Edward Vajda
- Department of Modern and Classical Languages, Western Washington University, Bellingham, WA, USA
| | - Oleg Balanovsky
- Research Centre for Medical Genetics, Moscow, Russia
- Vavilov Institute of General Genetics, Moscow, Russia
| | - Ancha Baranova
- Research Centre for Medical Genetics, Moscow, Russia
- School of Systems Biology, George Mason University, Fairfax, VA, USA
- Atlas Biomed Group, Moscow, Russia
| | - Konstantin Skryabin
- Federal State Institution "Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences", Moscow, Russia
- Russian Scientific Centre "Kurchatov Institute", Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana V Tatarinova
- Vavilov Institute of General Genetics, Moscow, Russia.
- School of Systems Biology, George Mason University, Fairfax, VA, USA.
- Atlas Biomed Group, Moscow, Russia.
- Department of Biology, University of La Verne, La Verne, CA, USA.
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
| | - Egor Prokhortchouk
- Federal State Institution "Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences", Moscow, Russia.
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia.
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1523
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Laso-Jadart R, Harmant C, Quach H, Zidane N, Tyler-Smith C, Mehdi Q, Ayub Q, Quintana-Murci L, Patin E. The Genetic Legacy of the Indian Ocean Slave Trade: Recent Admixture and Post-admixture Selection in the Makranis of Pakistan. Am J Hum Genet 2017; 101:977-984. [PMID: 29129317 DOI: 10.1016/j.ajhg.2017.09.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 09/27/2017] [Indexed: 12/20/2022] Open
Abstract
From the eighth century onward, the Indian Ocean was the scene of extensive trade of sub-Saharan African slaves via sea routes controlled by Muslim Arab and Swahili traders. Several populations in present-day Pakistan and India are thought to be the descendants of such slaves, yet their history of admixture and natural selection remains largely undefined. Here, we studied the genome-wide diversity of the African-descent Makranis, who reside on the Arabian Sea coast of Pakistan, as well that of four neighboring Pakistani populations, to investigate the genetic legacy, population dynamics, and tempo of the Indian Ocean slave trade. We show that the Makranis are the result of an admixture event between local Baluch tribes and Bantu-speaking populations from eastern or southeastern Africa; we dated this event to ∼300 years ago during the Omani Empire domination. Levels of parental relatedness, measured through runs of homozygosity, were found to be similar across Pakistani populations, suggesting that the Makranis rapidly adopted the traditional practice of endogamous marriages. Finally, we searched for signatures of post-admixture selection at traits evolving under positive selection, including skin color, lactase persistence, and resistance to malaria. We demonstrate that the African-specific Duffy-null blood group-believed to confer resistance against Plasmodium vivax infection-was recently introduced to Pakistan through the slave trade and evolved adaptively in this P. vivax malaria-endemic region. Our study reconstructs the genetic and adaptive history of a neglected episode of the African Diaspora and illustrates the impact of recent admixture on the diffusion of adaptive traits across human populations.
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1524
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Kling D. SNP analyzer – A tool to analyze large sets of genetic markers accounting for linkage. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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1525
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Kling D, Tillmar A. Kinship inference for males with identical Y-STR profiles using whole genome SNP data provides a deeper understanding about the level of coancestry in the Swedish male population. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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1526
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Weng LC, Choi SH, Klarin D, Smith JG, Loh PR, Chaffin M, Roselli C, Hulme OL, Lunetta KL, Dupuis J, Benjamin EJ, Newton-Cheh C, Kathiresan S, Ellinor PT, Lubitz SA. Heritability of Atrial Fibrillation. CIRCULATION. CARDIOVASCULAR GENETICS 2017; 10:e001838. [PMID: 29237688 PMCID: PMC5966046 DOI: 10.1161/circgenetics.117.001838] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 09/25/2017] [Indexed: 12/22/2022]
Abstract
BACKGROUND Previous reports have implicated multiple genetic loci associated with AF, but the contributions of genome-wide variation to AF susceptibility have not been quantified. METHODS AND RESULTS We assessed the contribution of genome-wide single-nucleotide polymorphism variation to AF risk (single-nucleotide polymorphism heritability, h2g ) using data from 120 286 unrelated individuals of European ancestry (2987 with AF) in the population-based UK Biobank. We ascertained AF based on self-report, medical record billing codes, procedure codes, and death records. We estimated h2g using a variance components method with variants having a minor allele frequency ≥1%. We evaluated h2g in age, sex, and genomic strata of interest. The h2g for AF was 22.1% (95% confidence interval, 15.6%-28.5%) and was similar for early- versus older-onset AF (≤65 versus >65 years of age), as well as for men and women. The proportion of AF variance explained by genetic variation was mainly accounted for by common (minor allele frequency, ≥5%) variants (20.4%; 95% confidence interval, 15.1%-25.6%). Only 6.4% (95% confidence interval, 5.1%-7.7%) of AF variance was attributed to variation within known AF susceptibility, cardiac arrhythmia, and cardiomyopathy gene regions. CONCLUSIONS Genetic variation contributes substantially to AF risk. The risk for AF conferred by genomic variation is similar to that observed for several other cardiovascular diseases. Established AF loci only explain a moderate proportion of disease risk, suggesting that further genetic discovery, with an emphasis on common variation, is warranted to understand the causal genetic basis of AF.
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Affiliation(s)
- Lu-Chen Weng
- From the Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA (L.-C.W., S.H.C., D.K., J.G.S. P.-R.L., M.C., C.R., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.); Department of Cardiology, Clinical Sciences, Lund University, Sweden (J.G.S.); Department of Heart Failure and Valvular Disease, Skane University Hospital, Lund, Sweden (J.G.S.); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA (P.-R.L.); Boston University and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA (K.L.L., J.D., E.J.B.); Boston University School of Public Health, Boston, MA (K.L.L., J.D., E.J.B.); Boston University School of Medicine, Boston, MA (E.J.B.); and Cardiovascular Research Center (L.-C.W., D.K., J.G.S., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.) and Cardiac Arrhythmia Service (P.T.E., S.A.L.), Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Seung Hoan Choi
- From the Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA (L.-C.W., S.H.C., D.K., J.G.S. P.-R.L., M.C., C.R., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.); Department of Cardiology, Clinical Sciences, Lund University, Sweden (J.G.S.); Department of Heart Failure and Valvular Disease, Skane University Hospital, Lund, Sweden (J.G.S.); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA (P.-R.L.); Boston University and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA (K.L.L., J.D., E.J.B.); Boston University School of Public Health, Boston, MA (K.L.L., J.D., E.J.B.); Boston University School of Medicine, Boston, MA (E.J.B.); and Cardiovascular Research Center (L.-C.W., D.K., J.G.S., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.) and Cardiac Arrhythmia Service (P.T.E., S.A.L.), Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Derek Klarin
- From the Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA (L.-C.W., S.H.C., D.K., J.G.S. P.-R.L., M.C., C.R., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.); Department of Cardiology, Clinical Sciences, Lund University, Sweden (J.G.S.); Department of Heart Failure and Valvular Disease, Skane University Hospital, Lund, Sweden (J.G.S.); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA (P.-R.L.); Boston University and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA (K.L.L., J.D., E.J.B.); Boston University School of Public Health, Boston, MA (K.L.L., J.D., E.J.B.); Boston University School of Medicine, Boston, MA (E.J.B.); and Cardiovascular Research Center (L.-C.W., D.K., J.G.S., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.) and Cardiac Arrhythmia Service (P.T.E., S.A.L.), Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - J Gustav Smith
- From the Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA (L.-C.W., S.H.C., D.K., J.G.S. P.-R.L., M.C., C.R., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.); Department of Cardiology, Clinical Sciences, Lund University, Sweden (J.G.S.); Department of Heart Failure and Valvular Disease, Skane University Hospital, Lund, Sweden (J.G.S.); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA (P.-R.L.); Boston University and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA (K.L.L., J.D., E.J.B.); Boston University School of Public Health, Boston, MA (K.L.L., J.D., E.J.B.); Boston University School of Medicine, Boston, MA (E.J.B.); and Cardiovascular Research Center (L.-C.W., D.K., J.G.S., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.) and Cardiac Arrhythmia Service (P.T.E., S.A.L.), Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Po-Ru Loh
- From the Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA (L.-C.W., S.H.C., D.K., J.G.S. P.-R.L., M.C., C.R., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.); Department of Cardiology, Clinical Sciences, Lund University, Sweden (J.G.S.); Department of Heart Failure and Valvular Disease, Skane University Hospital, Lund, Sweden (J.G.S.); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA (P.-R.L.); Boston University and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA (K.L.L., J.D., E.J.B.); Boston University School of Public Health, Boston, MA (K.L.L., J.D., E.J.B.); Boston University School of Medicine, Boston, MA (E.J.B.); and Cardiovascular Research Center (L.-C.W., D.K., J.G.S., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.) and Cardiac Arrhythmia Service (P.T.E., S.A.L.), Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Mark Chaffin
- From the Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA (L.-C.W., S.H.C., D.K., J.G.S. P.-R.L., M.C., C.R., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.); Department of Cardiology, Clinical Sciences, Lund University, Sweden (J.G.S.); Department of Heart Failure and Valvular Disease, Skane University Hospital, Lund, Sweden (J.G.S.); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA (P.-R.L.); Boston University and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA (K.L.L., J.D., E.J.B.); Boston University School of Public Health, Boston, MA (K.L.L., J.D., E.J.B.); Boston University School of Medicine, Boston, MA (E.J.B.); and Cardiovascular Research Center (L.-C.W., D.K., J.G.S., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.) and Cardiac Arrhythmia Service (P.T.E., S.A.L.), Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Carolina Roselli
- From the Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA (L.-C.W., S.H.C., D.K., J.G.S. P.-R.L., M.C., C.R., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.); Department of Cardiology, Clinical Sciences, Lund University, Sweden (J.G.S.); Department of Heart Failure and Valvular Disease, Skane University Hospital, Lund, Sweden (J.G.S.); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA (P.-R.L.); Boston University and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA (K.L.L., J.D., E.J.B.); Boston University School of Public Health, Boston, MA (K.L.L., J.D., E.J.B.); Boston University School of Medicine, Boston, MA (E.J.B.); and Cardiovascular Research Center (L.-C.W., D.K., J.G.S., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.) and Cardiac Arrhythmia Service (P.T.E., S.A.L.), Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Olivia L Hulme
- From the Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA (L.-C.W., S.H.C., D.K., J.G.S. P.-R.L., M.C., C.R., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.); Department of Cardiology, Clinical Sciences, Lund University, Sweden (J.G.S.); Department of Heart Failure and Valvular Disease, Skane University Hospital, Lund, Sweden (J.G.S.); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA (P.-R.L.); Boston University and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA (K.L.L., J.D., E.J.B.); Boston University School of Public Health, Boston, MA (K.L.L., J.D., E.J.B.); Boston University School of Medicine, Boston, MA (E.J.B.); and Cardiovascular Research Center (L.-C.W., D.K., J.G.S., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.) and Cardiac Arrhythmia Service (P.T.E., S.A.L.), Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Kathryn L Lunetta
- From the Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA (L.-C.W., S.H.C., D.K., J.G.S. P.-R.L., M.C., C.R., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.); Department of Cardiology, Clinical Sciences, Lund University, Sweden (J.G.S.); Department of Heart Failure and Valvular Disease, Skane University Hospital, Lund, Sweden (J.G.S.); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA (P.-R.L.); Boston University and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA (K.L.L., J.D., E.J.B.); Boston University School of Public Health, Boston, MA (K.L.L., J.D., E.J.B.); Boston University School of Medicine, Boston, MA (E.J.B.); and Cardiovascular Research Center (L.-C.W., D.K., J.G.S., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.) and Cardiac Arrhythmia Service (P.T.E., S.A.L.), Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Josée Dupuis
- From the Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA (L.-C.W., S.H.C., D.K., J.G.S. P.-R.L., M.C., C.R., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.); Department of Cardiology, Clinical Sciences, Lund University, Sweden (J.G.S.); Department of Heart Failure and Valvular Disease, Skane University Hospital, Lund, Sweden (J.G.S.); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA (P.-R.L.); Boston University and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA (K.L.L., J.D., E.J.B.); Boston University School of Public Health, Boston, MA (K.L.L., J.D., E.J.B.); Boston University School of Medicine, Boston, MA (E.J.B.); and Cardiovascular Research Center (L.-C.W., D.K., J.G.S., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.) and Cardiac Arrhythmia Service (P.T.E., S.A.L.), Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Emelia J Benjamin
- From the Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA (L.-C.W., S.H.C., D.K., J.G.S. P.-R.L., M.C., C.R., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.); Department of Cardiology, Clinical Sciences, Lund University, Sweden (J.G.S.); Department of Heart Failure and Valvular Disease, Skane University Hospital, Lund, Sweden (J.G.S.); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA (P.-R.L.); Boston University and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA (K.L.L., J.D., E.J.B.); Boston University School of Public Health, Boston, MA (K.L.L., J.D., E.J.B.); Boston University School of Medicine, Boston, MA (E.J.B.); and Cardiovascular Research Center (L.-C.W., D.K., J.G.S., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.) and Cardiac Arrhythmia Service (P.T.E., S.A.L.), Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Christopher Newton-Cheh
- From the Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA (L.-C.W., S.H.C., D.K., J.G.S. P.-R.L., M.C., C.R., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.); Department of Cardiology, Clinical Sciences, Lund University, Sweden (J.G.S.); Department of Heart Failure and Valvular Disease, Skane University Hospital, Lund, Sweden (J.G.S.); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA (P.-R.L.); Boston University and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA (K.L.L., J.D., E.J.B.); Boston University School of Public Health, Boston, MA (K.L.L., J.D., E.J.B.); Boston University School of Medicine, Boston, MA (E.J.B.); and Cardiovascular Research Center (L.-C.W., D.K., J.G.S., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.) and Cardiac Arrhythmia Service (P.T.E., S.A.L.), Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Sekar Kathiresan
- From the Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA (L.-C.W., S.H.C., D.K., J.G.S. P.-R.L., M.C., C.R., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.); Department of Cardiology, Clinical Sciences, Lund University, Sweden (J.G.S.); Department of Heart Failure and Valvular Disease, Skane University Hospital, Lund, Sweden (J.G.S.); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA (P.-R.L.); Boston University and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA (K.L.L., J.D., E.J.B.); Boston University School of Public Health, Boston, MA (K.L.L., J.D., E.J.B.); Boston University School of Medicine, Boston, MA (E.J.B.); and Cardiovascular Research Center (L.-C.W., D.K., J.G.S., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.) and Cardiac Arrhythmia Service (P.T.E., S.A.L.), Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Patrick T Ellinor
- From the Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA (L.-C.W., S.H.C., D.K., J.G.S. P.-R.L., M.C., C.R., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.); Department of Cardiology, Clinical Sciences, Lund University, Sweden (J.G.S.); Department of Heart Failure and Valvular Disease, Skane University Hospital, Lund, Sweden (J.G.S.); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA (P.-R.L.); Boston University and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA (K.L.L., J.D., E.J.B.); Boston University School of Public Health, Boston, MA (K.L.L., J.D., E.J.B.); Boston University School of Medicine, Boston, MA (E.J.B.); and Cardiovascular Research Center (L.-C.W., D.K., J.G.S., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.) and Cardiac Arrhythmia Service (P.T.E., S.A.L.), Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Steven A Lubitz
- From the Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA (L.-C.W., S.H.C., D.K., J.G.S. P.-R.L., M.C., C.R., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.); Department of Cardiology, Clinical Sciences, Lund University, Sweden (J.G.S.); Department of Heart Failure and Valvular Disease, Skane University Hospital, Lund, Sweden (J.G.S.); Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA (P.-R.L.); Boston University and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA (K.L.L., J.D., E.J.B.); Boston University School of Public Health, Boston, MA (K.L.L., J.D., E.J.B.); Boston University School of Medicine, Boston, MA (E.J.B.); and Cardiovascular Research Center (L.-C.W., D.K., J.G.S., O.L.H., C.N.-C., S.K., P.T.E., S.A.L.) and Cardiac Arrhythmia Service (P.T.E., S.A.L.), Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, MA.
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1527
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Martin AR, Lin M, Granka JM, Myrick JW, Liu X, Sockell A, Atkinson EG, Werely CJ, Möller M, Sandhu MS, Kingsley DM, Hoal EG, Liu X, Daly MJ, Feldman MW, Gignoux CR, Bustamante CD, Henn BM. An Unexpectedly Complex Architecture for Skin Pigmentation in Africans. Cell 2017; 171:1340-1353.e14. [PMID: 29195075 PMCID: PMC5884124 DOI: 10.1016/j.cell.2017.11.015] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 08/13/2017] [Accepted: 11/08/2017] [Indexed: 01/17/2023]
Abstract
Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than previously assumed, with genetic architecture varying by latitude. We investigate polygenicity in the KhoeSan populations indigenous to southern Africa who have considerably lighter skin than equatorial Africans. We demonstrate that skin pigmentation is highly heritable, but known pigmentation loci explain only a small fraction of the variance. Rather, baseline skin pigmentation is a complex, polygenic trait in the KhoeSan. Despite this, we identify canonical and non-canonical skin pigmentation loci, including near SLC24A5, TYRP1, SMARCA2/VLDLR, and SNX13, using a genome-wide association approach complemented by targeted resequencing. By considering diverse, under-studied African populations, we show how the architecture of skin pigmentation can vary across humans subject to different local evolutionary pressures.
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Affiliation(s)
- Alicia R Martin
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02141, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA 02141, USA.
| | - Meng Lin
- Department of Ecology and Evolution, SUNY Stony Brook, NY 11794, USA
| | - Julie M Granka
- Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Justin W Myrick
- Department of Ecology and Evolution, SUNY Stony Brook, NY 11794, USA
| | | | - Alexandra Sockell
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Cedric J Werely
- SA MRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Marlo Möller
- SA MRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | | | - David M Kingsley
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Eileen G Hoal
- SA MRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02141, USA; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA 02141, USA
| | - Marcus W Feldman
- Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
| | | | | | - Brenna M Henn
- Department of Ecology and Evolution, SUNY Stony Brook, NY 11794, USA.
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1528
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Zhu X, Padmanabhan R, Copeland B, Bridgers J, Ren Z, Kamalakaran S, O'Driscoll-Collins A, Berkovic SF, Scheffer IE, Poduri A, Mei D, Guerrini R, Lowenstein DH, Allen AS, Heinzen EL, Goldstein DB. A case-control collapsing analysis identifies epilepsy genes implicated in trio sequencing studies focused on de novo mutations. PLoS Genet 2017; 13:e1007104. [PMID: 29186148 PMCID: PMC5724893 DOI: 10.1371/journal.pgen.1007104] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 12/11/2017] [Accepted: 11/07/2017] [Indexed: 12/22/2022] Open
Abstract
Trio exome sequencing has been successful in identifying genes with de novo mutations (DNMs) causing epileptic encephalopathy (EE) and other neurodevelopmental disorders. Here, we evaluate how well a case-control collapsing analysis recovers genes causing dominant forms of EE originally implicated by DNM analysis. We performed a genome-wide search for an enrichment of "qualifying variants" in protein-coding genes in 488 unrelated cases compared to 12,151 unrelated controls. These "qualifying variants" were selected to be extremely rare variants predicted to functionally impact the protein to enrich for likely pathogenic variants. Despite modest sample size, three known EE genes (KCNT1, SCN2A, and STXBP1) achieved genome-wide significance (p<2.68×10−6). In addition, six of the 10 most significantly associated genes are known EE genes, and the majority of the known EE genes (17 out of 25) originally implicated in trio sequencing are nominally significant (p<0.05), a proportion significantly higher than the expected (Fisher’s exact p = 2.33×10−17). Our results indicate that a case-control collapsing analysis can identify several of the EE genes originally implicated in trio sequencing studies, and clearly show that additional genes would be implicated with larger sample sizes. The case-control analysis not only makes discovery easier and more economical in early onset disorders, particularly when large cohorts are available, but also supports the use of this approach to identify genes in diseases that present later in life when parents are not readily available. Trio exome sequencing and de novo mutation (DNM) analysis has been the main approach to discovering genes responsible for severe sporadic disorders, including a range of neurodevelopmental disorders. This approach requires sequencing parents, identifying DNMs from trio sequence data, and comparing the observed rate of DNMs to the expected. In this study, we adopted a case-control design, performed a gene-based collapsing analysis, and rediscovered several of the epileptic encephalopathy (EE) genes originally implicated by DNM analysis of EE trios. Our collapsing analysis focused on ultra-rare, highly impactful variants (“qualifying variants”) by filtering against large-scale population datasets, and this approach revealed that most of the standing variation can be filtered out and DNMs are enriched in “qualifying variants”. Our study suggests that a case-control analysis approach can be used to identify disease genes with causal mutations that are predominantly de novo in place of trio-based analysis methods. This offers an efficient and cost effective alternative approach when large-scale trio sequencing is not possible.
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Affiliation(s)
- Xiaolin Zhu
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Raghavendra Padmanabhan
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Brett Copeland
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Joshua Bridgers
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Zhong Ren
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Sitharthan Kamalakaran
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | | | - Samuel F. Berkovic
- Epilepsy Research Centre, Department of Medicine, University of Melbourne at Austin Health, Heidelberg, Australia
| | - Ingrid E. Scheffer
- Epilepsy Research Centre, Department of Medicine, University of Melbourne at Austin Health, Heidelberg, Australia
- Florey Institute for Neuroscience and Mental Health, University of Melbourne, Heidelberg, Australia
- Departments of Paediatrics and Neurology, Royal Children's Hospital, University of Melbourne, Melbourne, Australia
| | - Annapurna Poduri
- Epilepsy Genetics Program and Department of Neurology, Harvard Medical School, Boston, MA, United States of America
| | - Davide Mei
- Pediatric Neurology Unit and Laboratories, Meyer Children’s Hospital, University of Florence, Florence, Italy
| | - Renzo Guerrini
- Pediatric Neurology Unit and Laboratories, Meyer Children’s Hospital, University of Florence, Florence, Italy
- IRCCS Stella Maris Foundation, Pisa, Italy
| | - Daniel H. Lowenstein
- Department of Neurology, University of California, San Francisco, San Francisco, California, United States of America
| | - Andrew S. Allen
- Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina, United States of America
| | - Erin L. Heinzen
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, United States of America
- Department of Medicine, Royal College of Surgeons in Ireland, St Stephen's Green, Dublin, Ireland
- * E-mail:
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1529
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Hudjashov G, Karafet TM, Lawson DJ, Downey S, Savina O, Sudoyo H, Lansing JS, Hammer MF, Cox MP. Complex Patterns of Admixture across the Indonesian Archipelago. Mol Biol Evol 2017; 34:2439-2452. [PMID: 28957506 PMCID: PMC5850824 DOI: 10.1093/molbev/msx196] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Indonesia, an island nation as large as continental Europe, hosts a sizeable proportion of global human diversity, yet remains surprisingly undercharacterized genetically. Here, we substantially expand on existing studies by reporting genome-scale data for nearly 500 individuals from 25 populations in Island Southeast Asia, New Guinea, and Oceania, notably including previously unsampled islands across the Indonesian archipelago. We use high-resolution analyses of haplotype diversity to reveal fine detail of regional admixture patterns, with a particular focus on the Holocene. We find that recent population history within Indonesia is complex, and that populations from the Philippines made important genetic contributions in the early phases of the Austronesian expansion. Different, but interrelated processes, acted in the east and west. The Austronesian migration took several centuries to spread across the eastern part of the archipelago, where genetic admixture postdates the archeological signal. As with the Neolithic expansion further east in Oceania and in Europe, genetic mixing with local inhabitants in eastern Indonesia lagged behind the arrival of farming populations. In contrast, western Indonesia has a more complicated admixture history shaped by interactions with mainland Asian and Austronesian newcomers, which for some populations occurred more than once. Another layer of complexity in the west was introduced by genetic contact with South Asia and strong demographic events in isolated local groups.
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Affiliation(s)
- Georgi Hudjashov
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Estonian Biocentre, 51010 Tartu, Estonia
| | | | - Daniel J Lawson
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Sean Downey
- Department of Anthropology, University of Maryland, College Park, MD
| | - Olga Savina
- ARL Division of Biotechnology, University of Arizona, Tucson, AZ
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.,Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | | | | | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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1530
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Anderson C, Cunha L, Sechi P, Kille P, Spurgeon D. Genetic variation in populations of the earthworm, Lumbricus rubellus, across contaminated mine sites. BMC Genet 2017; 18:97. [PMID: 29149838 PMCID: PMC5693503 DOI: 10.1186/s12863-017-0557-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 10/03/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Populations of the earthworm, Lumbricus rubellus, are commonly found across highly contaminated former mine sites and are considered to have under-gone selection for mitigating metal toxicity. Comparison of adapted populations with those found on less contaminated soils can provide insights into ecological processes that demonstrate the long-term effects of soil contamination. Contemporary sequencing methods allow for portrayal of demographic inferences and highlight genetic variation indicative of selection at specific genes. Furthermore, the occurrence of L. rubellus lineages across the UK allows for inferences of mechanisms associated with drivers of speciation and local adaptation. RESULTS Using RADseq, we were able to define population structure between the two lineages through the use of draft genomes for each, demonstrating an absence of admixture between lineages and that populations over extensive geographic distances form discrete populations. Between the two British lineages, we were able to provide evidence for selection near to genes associated with epigenetic and morphological functions, as well as near a gene encoding a pheromone. Earthworms inhabiting highly contaminated soils bare close genomic resemblance to those from proximal control soils. We were able to define a number of SNPs that largely segregate populations and are indicative of genes that are likely under selection for managing metal toxicity. This includes calcium and phosphate-handling mechanisms linked to lead and arsenic contaminants, respectively, while we also observed evidence for glutathione-related mechanisms, including metallothionein, across multiple populations. Population genomic end points demonstrate no consistent reduction in nucleotide diversity, or increase in inbreeding coefficient, relative to history of exposure. CONCLUSIONS Though we can clearly define lineage membership using genomic markers, as well as population structure between geographic localities, it is difficult to resolve markers that segregate entirely between populations in response to soil metal concentrations. This may represent a highly variable series of traits in response to the heterogenous nature of the soil environment, but ultimately demonstrates the maintenance of lineage-specific genetic variation among local populations. L. rubellus appears to provide an exemplary system for exploring drivers for speciation, with a continuum of lineages coexisting across continental Europe, while distinct lineages exist in isolation throughout the UK.
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Affiliation(s)
- Craig Anderson
- Biological and Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA UK
- Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Wallingford, OX10 8BB UK
- School of Biosciences, University of Cardiff, Main Building, Museum Avenue, Cardiff, CF10 3AT UK
| | - Luis Cunha
- School of Biosciences, University of Cardiff, Main Building, Museum Avenue, Cardiff, CF10 3AT UK
- Embrapa Florestas, Estrada da Ribeira km. 111, Colombo, PR 83411-000 Brazil
| | - Pierfrancesco Sechi
- School of Biosciences, University of Cardiff, Main Building, Museum Avenue, Cardiff, CF10 3AT UK
| | - Peter Kille
- School of Biosciences, University of Cardiff, Main Building, Museum Avenue, Cardiff, CF10 3AT UK
| | - David Spurgeon
- Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Wallingford, OX10 8BB UK
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1531
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Next-generation sequencing of patients with congenital anosmia. Eur J Hum Genet 2017; 25:1377-1387. [PMID: 29255181 DOI: 10.1038/s41431-017-0014-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 08/10/2017] [Accepted: 09/09/2017] [Indexed: 02/05/2023] Open
Abstract
We performed whole exome or genome sequencing in eight multiply affected families with ostensibly isolated congenital anosmia. Hypothesis-free analyses based on the assumption of fully penetrant recessive/dominant/X-linked models obtained no strong single candidate variant in any of these families. In total, these eight families showed 548 rare segregating variants that were predicted to be damaging, in 510 genes. Three Kallmann syndrome genes (FGFR1, SEMA3A, and CHD7) were identified. We performed permutation-based analysis to test for overall enrichment of these 510 genes carrying these 548 variants with genes mutated in Kallmann syndrome and with a control set of genes mutated in hypogonadotrophic hypogonadism without anosmia. The variants were found to be enriched for Kallmann syndrome genes (3 observed vs. 0.398 expected, p = 0.007), but not for the second set of genes. Among these three variants, two have been already reported in genes related to syndromic anosmia (FGFR1 (p.(R250W)), CHD7 (p.(L2806V))) and one was novel (SEMA3A (p.(T717I))). To replicate these findings, we performed targeted sequencing of 16 genes involved in Kallmann syndrome and hypogonadotrophic hypogonadism in 29 additional families, mostly singletons. This yielded an additional 6 variants in 5 Kallmann syndrome genes (PROKR2, SEMA3A, CHD7, PROK2, ANOS1), two of them already reported to cause Kallmann syndrome. In all, our study suggests involvement of 6 syndromic Kallmann genes in isolated anosmia. Further, we report a yet unreported appearance of di-genic inheritance in a family with congenital isolated anosmia. These results are consistent with a complex molecular basis of congenital anosmia.
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1532
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Kistler L, Johnson SM, Irwin MT, Louis EE, Ratan A, Perry GH. A massively parallel strategy for STR marker development, capture, and genotyping. Nucleic Acids Res 2017; 45:e142. [PMID: 28666376 PMCID: PMC5587753 DOI: 10.1093/nar/gkx574] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 06/21/2017] [Indexed: 12/11/2022] Open
Abstract
Short tandem repeat (STR) variants are highly polymorphic markers that facilitate powerful population genetic analyses. STRs are especially valuable in conservation and ecological genetic research, yielding detailed information on population structure and short-term demographic fluctuations. Massively parallel sequencing has not previously been leveraged for scalable, efficient STR recovery. Here, we present a pipeline for developing STR markers directly from high-throughput shotgun sequencing data without a reference genome, and an approach for highly parallel target STR recovery. We employed our approach to capture a panel of 5000 STRs from a test group of diademed sifakas (Propithecus diadema, n = 3), endangered Malagasy rainforest lemurs, and we report extremely efficient recovery of targeted loci—97.3–99.6% of STRs characterized with ≥10x non-redundant sequence coverage. We then tested our STR capture strategy on P. diadema fecal DNA, and report robust initial results and suggestions for future implementations. In addition to STR targets, this approach also generates large, genome-wide single nucleotide polymorphism (SNP) panels from flanking regions. Our method provides a cost-effective and scalable solution for rapid recovery of large STR and SNP datasets in any species without needing a reference genome, and can be used even with suboptimal DNA more easily acquired in conservation and ecological studies.
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Affiliation(s)
- Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.,Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Stephen M Johnson
- Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL 60115, USA
| | - Edward E Louis
- Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107, USA
| | - Aakrosh Ratan
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - George H Perry
- Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA 16802, USA
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1533
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Fortes-Lima C, Gessain A, Ruiz-Linares A, Bortolini MC, Migot-Nabias F, Bellis G, Moreno-Mayar JV, Restrepo BN, Rojas W, Avendaño-Tamayo E, Bedoya G, Orlando L, Salas A, Helgason A, Gilbert MTP, Sikora M, Schroeder H, Dugoujon JM. Genome-wide Ancestry and Demographic History of African-Descendant Maroon Communities from French Guiana and Suriname. Am J Hum Genet 2017; 101:725-736. [PMID: 29100086 DOI: 10.1016/j.ajhg.2017.09.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/22/2017] [Indexed: 01/30/2023] Open
Abstract
The transatlantic slave trade was the largest forced migration in world history. However, the origins of the enslaved Africans and their admixture dynamics remain unclear. To investigate the demographic history of African-descendant Marron populations, we generated genome-wide data (4.3 million markers) from 107 individuals from three African-descendant populations in South America, as well as 124 individuals from six west African populations. Throughout the Americas, thousands of enslaved Africans managed to escape captivity and establish lasting communities, such as the Noir Marron. We find that this population has the highest proportion of African ancestry (∼98%) of any African-descendant population analyzed to date, presumably because of centuries of genetic isolation. By contrast, African-descendant populations in Brazil and Colombia harbor substantially more European and Native American ancestry as a result of their complex admixture histories. Using ancestry tract-length analysis, we detect different dates for the European admixture events in the African-Colombian (1749 CE; confidence interval [CI]: 1737-1764) and African-Brazilian (1796 CE; CI: 1789-1804) populations in our dataset, consistent with the historically attested earlier influx of Africans into Colombia. Furthermore, we find evidence for sex-specific admixture patterns, resulting from predominantly European paternal gene flow. Finally, we detect strong genetic links between the African-descendant populations and specific source populations in Africa on the basis of haplotype sharing patterns. Although the Noir Marron and African-Colombians show stronger affinities with African populations from the Bight of Benin and the Gold Coast, the African-Brazilian population from Rio de Janeiro has greater genetic affinity with Bantu-speaking populations from the Bight of Biafra and west central Africa.
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Affiliation(s)
- Cesar Fortes-Lima
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, AMIS UMR5288, Centre National de la Recherche Scientifique (CNRS) -Université Paul Sabatier Toulouse III, Toulouse 31000, France; Laboratory Eco-Anthropology and Ethno-Biology, UMR7206, CNRS-MNHN-University Paris Diderot, Musée de l'Homme, 17 Place du Trocadéro, 75016 Paris, France
| | - Antoine Gessain
- Oncogenic Virus Epidemiology and Pathophysiology Group, Department of Virology, CNRS UMR3569, Pasteur Institute, Paris 75015, France
| | - Andres Ruiz-Linares
- Department of Genetics, Evolution, and Environment, University College London, London WC1E 6BT, United Kingdom; Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China; Laboratory of Biocultural Anthropology, Law, Ethics, and Health, CNRS/EFS ADES UMR7268, Aix-Marseille University, Marseille 13824, France
| | - Maria-Cátira Bortolini
- Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Florence Migot-Nabias
- Mother and Child Facing Tropical Infections (MERIT), Research Institute for Development, Paris 5 University, Sorbonne Paris Cité, Paris 75006, France
| | - Gil Bellis
- French Institute for Demographic Studies, Paris 75020, France
| | - J Víctor Moreno-Mayar
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - Berta Nelly Restrepo
- Instituto Colombiano de Medicina Tropical, Universidad CES, Sabaneta, Antioquia 055450, Colombia
| | - Winston Rojas
- Laboratory of Molecular Genetics, Institute of Biology, University of Antioquia, Medellín 050010, Colombia
| | - Efren Avendaño-Tamayo
- Laboratory of Molecular Genetics, Institute of Biology, University of Antioquia, Medellín 050010, Colombia; Grupo de Ciencias Básicas Aplicadas del Tecnológico de Antioquia, Tecnológico de Antioquia - Institución Universitaria, Medellín 050034, Colombia
| | - Gabriel Bedoya
- Laboratory of Molecular Genetics, Institute of Biology, University of Antioquia, Medellín 050010, Colombia
| | - Ludovic Orlando
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, AMIS UMR5288, Centre National de la Recherche Scientifique (CNRS) -Université Paul Sabatier Toulouse III, Toulouse 31000, France; Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia 15782, Spain; GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago, Galicia 15782, Spain
| | | | - M Thomas P Gilbert
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark; Norwegian University of Science and Technology, University Museum, Trondheim 7491, Norway
| | - Martin Sikora
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - Hannes Schroeder
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark; Faculty of Archaeology, Leiden University, Leiden 2333, the Netherlands.
| | - Jean-Michel Dugoujon
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, AMIS UMR5288, Centre National de la Recherche Scientifique (CNRS) -Université Paul Sabatier Toulouse III, Toulouse 31000, France.
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1534
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Dand N, Mucha S, Tsoi LC, Mahil SK, Stuart PE, Arnold A, Baurecht H, Burden AD, Callis Duffin K, Chandran V, Curtis CJ, Das S, Ellinghaus D, Ellinghaus E, Enerback C, Esko T, Gladman DD, Griffiths CEM, Gudjonsson JE, Hoffman P, Homuth G, Hüffmeier U, Krueger GG, Laudes M, Lee SH, Lieb W, Lim HW, Löhr S, Mrowietz U, Müller-Nurayid M, Nöthen M, Peters A, Rahman P, Reis A, Reynolds NJ, Rodriguez E, Schmidt CO, Spain SL, Strauch K, Tejasvi T, Voorhees JJ, Warren RB, Weichenthal M, Weidinger S, Zawistowski M, Nair RP, Capon F, Smith CH, Trembath RC, Abecasis GR, Elder JT, Franke A, Simpson MA, Barker JN. Exome-wide association study reveals novel psoriasis susceptibility locus at TNFSF15 and rare protective alleles in genes contributing to type I IFN signalling. Hum Mol Genet 2017; 26:4301-4313. [PMID: 28973304 PMCID: PMC5886170 DOI: 10.1093/hmg/ddx328] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 08/15/2017] [Accepted: 08/18/2017] [Indexed: 02/06/2023] Open
Abstract
Psoriasis is a common inflammatory skin disorder for which multiple genetic susceptibility loci have been identified, but few resolved to specific functional variants. In this study, we sought to identify common and rare psoriasis-associated gene-centric variation. Using exome arrays we genotyped four independent cohorts, totalling 11 861 psoriasis cases and 28 610 controls, aggregating the dataset through statistical meta-analysis. Single variant analysis detected a previously unreported risk locus at TNFSF15 (rs6478108; P = 1.50 × 10-8, OR = 1.10), and association of common protein-altering variants at 11 loci previously implicated in psoriasis susceptibility. We validate previous reports of protective low-frequency protein-altering variants within IFIH1 (encoding an innate antiviral receptor) and TYK2 (encoding a Janus kinase), in each case establishing a further series of protective rare variants (minor allele frequency < 0.01) via gene-wide aggregation testing (IFIH1: pburden = 2.53 × 10-7, OR = 0.707; TYK2: pburden = 6.17 × 10-4, OR = 0.744). Both genes play significant roles in type I interferon (IFN) production and signalling. Several of the protective rare and low-frequency variants in IFIH1 and TYK2 disrupt conserved protein domains, highlighting potential mechanisms through which their effect may be exerted.
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Affiliation(s)
- Nick Dand
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Sören Mucha
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Lam C Tsoi
- Department of Dermatology
- Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Satveer K Mahil
- St John's Institute of Dermatology, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | | | - Andreas Arnold
- Clinic and Polyclinic of Dermatology, University Medicine Greifswald, Greifswald, Germany
| | - Hansjörg Baurecht
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - A David Burden
- Institute of Infection, Inflammation and Immunity, University of Glasgow, Glasgow, UK
| | | | - Vinod Chandran
- Department of Medicine
- Department of Laboratory Medicine and Pathobiology
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Charles J Curtis
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Sayantan Das
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Charlotta Enerback
- Division of Cell Biology and Dermatology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Tõnu Esko
- Estonian Biobank, Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Dafna D Gladman
- Department of Medicine
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Christopher E M Griffiths
- Dermatology Centre, Salford Royal Hospital, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | | | - Per Hoffman
- Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Ulrike Hüffmeier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Gerald G Krueger
- Department of Dermatology, University of Utah, Salt Lake City, UT, USA
| | | | - Sang Hyuck Lee
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, UK
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank PopGen, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Henry W Lim
- Department of Dermatology, Henry Ford Hospital, Detroit, MI, USA
| | - Sabine Löhr
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Ulrich Mrowietz
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | | | - Markus Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Annette Peters
- Institute of Genetic Epidemiology, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Proton Rahman
- Memorial University of Newfoundland, St. John's, NL, Canada
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Nick J Reynolds
- Dermatological Sciences, Institute of Cellular Medicine, Newcastle University Medical School, Newcastle upon Tyne, UK
- Department of Dermatology, Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Elke Rodriguez
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Carsten O Schmidt
- Institute for Community Medicine, Study of Health in Pomerania/KEF, University Medicine Greifswald, Greifswald, Germany
| | - Sarah L Spain
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum Munich, Neuherberg, Germany
| | | | | | - Richard B Warren
- Dermatology Centre, Salford Road NHS Foundation Trust, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Michael Weichenthal
- Department of Dermatology, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Stephan Weidinger
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Matthew Zawistowski
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | | | - Francesca Capon
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Catherine H Smith
- St John's Institute of Dermatology, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Richard C Trembath
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Goncalo R Abecasis
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - James T Elder
- Department of Dermatology
- Ann Arbor Veterans Hospital, Ann Arbor, MI, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Michael A Simpson
- Division of Genetics and Molecular Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Jonathan N Barker
- St John's Institute of Dermatology, Faculty of Life Sciences & Medicine, King's College London, London, UK
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1535
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Turner TN, Coe BP, Dickel DE, Hoekzema K, Nelson BJ, Zody MC, Kronenberg ZN, Hormozdiari F, Raja A, Pennacchio LA, Darnell RB, Eichler EE. Genomic Patterns of De Novo Mutation in Simplex Autism. Cell 2017; 171:710-722.e12. [PMID: 28965761 PMCID: PMC5679715 DOI: 10.1016/j.cell.2017.08.047] [Citation(s) in RCA: 228] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/03/2017] [Accepted: 08/25/2017] [Indexed: 12/22/2022]
Abstract
To further our understanding of the genetic etiology of autism, we generated and analyzed genome sequence data from 516 idiopathic autism families (2,064 individuals). This resource includes >59 million single-nucleotide variants (SNVs) and 9,212 private copy number variants (CNVs), of which 133,992 and 88 are de novo mutations (DNMs), respectively. We estimate a mutation rate of ∼1.5 × 10-8 SNVs per site per generation with a significantly higher mutation rate in repetitive DNA. Comparing probands and unaffected siblings, we observe several DNM trends. Probands carry more gene-disruptive CNVs and SNVs, resulting in severe missense mutations and mapping to predicted fetal brain promoters and embryonic stem cell enhancers. These differences become more pronounced for autism genes (p = 1.8 × 10-3, OR = 2.2). Patients are more likely to carry multiple coding and noncoding DNMs in different genes, which are enriched for expression in striatal neurons (p = 3 × 10-3), suggesting a path forward for genetically characterizing more complex cases of autism.
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Affiliation(s)
- Tychele N Turner
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Bradley P Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Diane E Dickel
- Functional Genomics Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | - Zev N Kronenberg
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Fereydoun Hormozdiari
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA 95817, USA
| | - Archana Raja
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Len A Pennacchio
- Functional Genomics Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Robert B Darnell
- New York Genome Center, New York, NY 10013, USA; Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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1536
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Rosshart SP, Vassallo BG, Angeletti D, Hutchinson DS, Morgan AP, Takeda K, Hickman HD, McCulloch JA, Badger JH, Ajami NJ, Trinchieri G, Pardo-Manuel de Villena F, Yewdell JW, Rehermann B. Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance. Cell 2017; 171:1015-1028.e13. [PMID: 29056339 DOI: 10.1016/j.cell.2017.09.016] [Citation(s) in RCA: 500] [Impact Index Per Article: 71.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 06/12/2017] [Accepted: 09/09/2017] [Indexed: 12/14/2022]
Abstract
Laboratory mice, while paramount for understanding basic biological phenomena, are limited in modeling complex diseases of humans and other free-living mammals. Because the microbiome is a major factor in mammalian physiology, we aimed to identify a naturally evolved reference microbiome to better recapitulate physiological phenomena relevant in the natural world outside the laboratory. Among 21 distinct mouse populations worldwide, we identified a closely related wild relative to standard laboratory mouse strains. Its bacterial gut microbiome differed significantly from its laboratory mouse counterpart and was transferred to and maintained in laboratory mice over several generations. Laboratory mice reconstituted with natural microbiota exhibited reduced inflammation and increased survival following influenza virus infection and improved resistance against mutagen/inflammation-induced colorectal tumorigenesis. By demonstrating the host fitness-promoting traits of natural microbiota, our findings should enable the discovery of protective mechanisms relevant in the natural world and improve the modeling of complex diseases of free-living mammals. VIDEO ABSTRACT.
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Affiliation(s)
- Stephan P Rosshart
- Immunology Section, Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.
| | - Brian G Vassallo
- Immunology Section, Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Davide Angeletti
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Diane S Hutchinson
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrew P Morgan
- Department of Genetics, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kazuyo Takeda
- Microscopy and Imaging Core Facility, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993-0002, USA
| | - Heather D Hickman
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - John A McCulloch
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Jonathan H Badger
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Giorgio Trinchieri
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jonathan W Yewdell
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
| | - Barbara Rehermann
- Immunology Section, Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA.
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1537
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Demographic history and biologically relevant genetic variation of Native Mexicans inferred from whole-genome sequencing. Nat Commun 2017; 8:1005. [PMID: 29044207 PMCID: PMC5647344 DOI: 10.1038/s41467-017-01194-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 08/25/2017] [Indexed: 11/16/2022] Open
Abstract
Understanding the genetic structure of Native American populations is important to clarify their diversity, demographic history, and to identify genetic factors relevant for biomedical traits. Here, we show a demographic history reconstruction from 12 Native American whole genomes belonging to six distinct ethnic groups representing the three main described genetic clusters of Mexico (Northern, Southern, and Maya). Effective population size estimates of all Native American groups remained below 2,000 individuals for up to 10,000 years ago. The proportion of missense variants predicted as damaging is higher for undescribed (~ 30%) than for previously reported variants (~ 15%). Several variants previously associated with biological traits are highly frequent in the Native American genomes. These findings suggest that the demographic and adaptive processes that occurred in these groups shaped their genetic architecture and could have implications in biological processes of the Native Americans and Mestizos of today. People of Mexico have diverse historical and genetic background. Here, Romero-Hidalgo and colleagues sequence whole genomes of Native Americans of Mexico, and show demographic history and genetic variation shared among subgroups of Native Americans.
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1538
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Ainsworth HC, Marion MC, Bertero T, Brucato A, Cimaz R, Costedoat-Chalumeau N, Fredi M, Gaffney P, Kelly J, Levesque K, Maltret A, Morel N, Ramoni V, Ruffatti A, Langefeld CD, Buyon JP, Clancy RM. Association of Natural Killer Cell Ligand Polymorphism HLA-C Asn80Lys With the Development of Anti-SSA/Ro-Associated Congenital Heart Block. Arthritis Rheumatol 2017; 69:2170-2174. [PMID: 29045069 DOI: 10.1002/art.40228] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 08/08/2017] [Indexed: 01/05/2023]
Abstract
OBJECTIVE Fetal exposure to maternal anti-SSA/Ro antibodies is necessary but not sufficient for the development of autoimmune congenital heart block (CHB), suggesting that other factors, such as fetal genetic predisposition, are important. Given the previously described association between major histocompatibility complex alleles and CHB risk, we undertook the present study to test the hypothesis that a variant form of HLA-C Asn80Lys, which binds with high affinity to an inhibitory killer cell immunoglobulin-like receptor (KIR) and thus renders natural killer (NK) cells incapable of restricting inflammation, contributes to the development of CHB. METHODS Members of 192 pedigrees in the US and Europe (194 cases of CHB, 91 unaffected siblings, 152 fathers, 167 mothers) and 1,073 out-of-study controls were genotyped on the Immunochip single-nucleotide polymorphism microarray. Imputation was used to identify associations at HLA-C Asn80Lys (Asn, C1; Lys, C2) and KIR. Tests for association were performed using logistic regression. McNemar's test and the pedigree disequilibrium test (PDT) were used for matched analyses between affected and unaffected children. RESULTS Compared with out-of-study controls of the same sex, the C2 allele was less frequent in the mothers (odds ratio [OR] 0.63, P = 0.0014) and more frequent in the fathers (OR 1.40, P = 0.0123), yielding a significant sex-by-C2 interaction (P = 0.0002). The C2 allele was more frequent in affected siblings than in unaffected siblings (OR 3.67, P = 0.0025), which was consistent with the PDT results (P = 0.016); these results were observed in both sexes and across the US and European cohorts. There was no difference in the frequency of the inhibitory KIR genotype (KIR AA) between affected and unaffected children (P = 0.55). CONCLUSION These data establish C2 as a novel genetic risk factor associated with CHB. This observation supports a model in which fetuses with C2 ligand expression and maternal anti-SSA/Ro positivity may have impaired NK cell surveillance, resulting in unchecked cardiac inflammation and scarring.
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Affiliation(s)
| | | | | | | | - Rolando Cimaz
- Meyer Children's Hospital and University of Florence, Florence, Italy
| | | | - Micaela Fredi
- Reumatologia e Immunologia, Spedali Civili e Università di Brescia, Brescia, Italy
| | - Patrick Gaffney
- Oklahoma Medical Research Foundation, University of Oklahoma, Oklahoma City
| | - Jennifer Kelly
- Oklahoma Medical Research Foundation, University of Oklahoma, Oklahoma City
| | - Kateri Levesque
- Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Alice Maltret
- Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Nathalie Morel
- Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | | | | | | | - Jill P Buyon
- New York University Langone Medical Center, New York, New York
| | - Robert M Clancy
- New York University Langone Medical Center, New York, New York
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1539
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McIntosh LA, Marion MC, Sudman M, Comeau ME, Becker ML, Bohnsack JF, Fingerlin TE, Griffin TA, Haas JP, Lovell DJ, Maier LA, Nigrovic PA, Prahalad S, Punaro M, Rosé CD, Wallace CA, Wise CA, Moncrieffe H, Howard TD, Langefeld CD, Thompson SD. Genome-Wide Association Meta-Analysis Reveals Novel Juvenile Idiopathic Arthritis Susceptibility Loci. Arthritis Rheumatol 2017; 69:2222-2232. [PMID: 28719732 DOI: 10.1002/art.40216] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/13/2017] [Indexed: 12/26/2022]
Abstract
OBJECTIVE Juvenile idiopathic arthritis (JIA) is the most common childhood rheumatic disease and has a strong genomic component. To date, JIA genetic association studies have had limited sample sizes, used heterogeneous patient populations, or included only candidate regions. The aim of this study was to identify new associations between JIA patients with oligoarticular disease and those with IgM rheumatoid factor (RF)-negative polyarticular disease, which are clinically similar and the most prevalent JIA disease subtypes. METHODS Three cohorts comprising 2,751 patients with oligoarticular or RF-negative polyarticular JIA were genotyped using the Affymetrix Genome-Wide SNP Array 6.0 or the Illumina HumanCoreExome-12+ Array. Overall, 15,886 local and out-of-study controls, typed on these platforms or the Illumina HumanOmni2.5, were used for association analyses. High-quality single-nucleotide polymorphisms (SNPs) were used for imputation to 1000 Genomes prior to SNP association analysis. RESULTS Meta-analysis showed evidence of association (P < 1 × 10-6 ) at 9 regions: PRR9_LOR (P = 5.12 × 10-8 ), ILDR1_CD86 (P = 6.73 × 10-8 ), WDFY4 (P = 1.79 × 10-7 ), PTH1R (P = 1.87 × 10-7 ), RNF215 (P = 3.09 × 10-7 ), AHI1_LINC00271 (P = 3.48 × 10-7 ), JAK1 (P = 4.18 × 10-7 ), LINC00951 (P = 5.80 × 10-7 ), and HBP1 (P = 7.29 × 10-7 ). Of these, PRR9_LOR, ILDR1_CD86, RNF215, LINC00951, and HBP1 were shown, for the first time, to be autoimmune disease susceptibility loci. Furthermore, associated SNPs included cis expression quantitative trait loci for WDFY4, CCDC12, MTP18, SF3A1, AHI1, COG5, HBP1, and GPR22. CONCLUSION This study provides evidence of both unique JIA risk loci and risk loci overlapping between JIA and other autoimmune diseases. These newly associated SNPs are shown to influence gene expression, and their bounding regions tie into molecular pathways of immunologic relevance. Thus, they likely represent regions that contribute to the pathology of oligoarticular JIA and RF-negative polyarticular JIA.
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Affiliation(s)
- Laura A McIntosh
- Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio
| | - Miranda C Marion
- Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Marc Sudman
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Mary E Comeau
- Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | | | | | | | | | - J Peter Haas
- German Center for Pediatric and Adolescent Rheumatology, Garmisch-Partenkirchen, Germany
| | - Daniel J Lovell
- Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio
| | - Lisa A Maier
- National Jewish Health and University of Colorado, Denver
| | - Peter A Nigrovic
- Boston Children's Hospital and Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | | | - Marilynn Punaro
- Texas Scottish Rite Hospital for Children and UT Southwestern Medical Center, Dallas, Texas
| | | | - Carol A Wallace
- Seattle Children's Hospital and Research Institute, Seattle, Washington
| | - Carol A Wise
- Texas Scottish Rite Hospital for Children, McDermott Center for Human Growth and Development, and UT Southwestern Medical Center, Dallas, Texas
| | - Halima Moncrieffe
- Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio
| | | | | | - Susan D Thompson
- Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio
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1540
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Genome-wide association study and meta-analysis in multiple populations identifies new loci for peanut allergy and establishes C11orf30/EMSY as a genetic risk factor for food allergy. J Allergy Clin Immunol 2017; 141:991-1001. [PMID: 29030101 DOI: 10.1016/j.jaci.2017.09.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 09/05/2017] [Accepted: 09/19/2017] [Indexed: 12/23/2022]
Abstract
BACKGROUND Peanut allergy (PA) is a complex disease with both environmental and genetic risk factors. Previously, PA loci were identified in filaggrin (FLG) and HLA in candidate gene studies, and loci in HLA were identified in a genome-wide association study and meta-analysis. OBJECTIVE We sought to investigate genetic susceptibility to PA. METHODS Eight hundred fifty cases and 926 hyper-control subjects and more than 7.8 million genotyped and imputed single nucleotide polymorphisms (SNPs) were analyzed in a genome-wide association study to identify susceptibility variants for PA in the Canadian population. A meta-analysis of 2 phenotypes (PA and food allergy) was conducted by using 7 studies from the Canadian, American (n = 2), Australian, German, and Dutch (n = 2) populations. RESULTS An SNP near integrin α6 (ITGA6) reached genome-wide significance with PA (P = 1.80 × 10-8), whereas SNPs associated with Src kinase-associated phosphoprotein 1 (SKAP1), matrix metallopeptidase 12 (MMP12)/MMP13, catenin α3 (CTNNA3), rho GTPase-activating protein 24 (ARHGAP24), angiopoietin 4 (ANGPT4), chromosome 11 open reading frame (C11orf30/EMSY), and exocyst complex component 4 (EXOC4) reached a threshold suggestive of association (P ≤ 1.49 × 10-6). In the meta-analysis of PA, loci in or near ITGA6, ANGPT4, MMP12/MMP13, C11orf30, and EXOC4 were significant (P ≤ 1.49 × 10-6). When a phenotype of any food allergy was used for meta-analysis, the C11orf30 locus reached genome-wide significance (P = 7.50 × 10-11), whereas SNPs associated with ITGA6, ANGPT4, MMP12/MMP13, and EXOC4 and additional C11orf30 SNPs were suggestive (P ≤ 1.49 × 10-6). Functional annotation indicated that SKAP1 regulates expression of CBX1, which colocalizes with the EMSY protein coded by C11orf30. CONCLUSION This study identifies multiple novel loci as risk factors for PA and food allergy and establishes C11orf30 as a risk locus for both PA and food allergy. Multiple genes (C11orf30/EMSY, SKAP1, and CTNNA3) identified by this study are involved in epigenetic regulation of gene expression.
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1541
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Ponomarenko P, Ryutov A, Maglinte DT, Baranova A, Tatarinova TV, Gai X. Clinical utility of the low-density Infinium QC genotyping Array in a genomics-based diagnostics laboratory. BMC Med Genomics 2017; 10:57. [PMID: 28985730 PMCID: PMC5639583 DOI: 10.1186/s12920-017-0297-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 10/02/2017] [Indexed: 11/10/2022] Open
Abstract
Background With 15,949 markers, the low-density Infinium QC Array-24 BeadChip enables linkage analysis, HLA haplotyping, fingerprinting, ethnicity determination, mitochondrial genome variations, blood groups and pharmacogenomics. It represents an attractive independent QC option for NGS-based diagnostic laboratories, and provides cost-efficient means for determining gender, ethnic ancestry, and sample kinships, that are important for data interpretation of NGS-based genetic tests. Methods We evaluated accuracy and reproducibility of Infinium QC genotyping calls by comparing them with genotyping data of the same samples from other genotyping platforms, whole genome/exome sequencing. Accuracy and robustness of determining gender, provenance, and kinships were assessed. Results Concordance of genotype calls between Infinium QC and other platforms was above 99%. Here we show that the chip’s ancestry informative markers are sufficient for ethnicity determination at continental and sometimes subcontinental levels, with assignment accuracy varying with the coverage for a particular region and ethnic groups. Mean accuracies of provenance prediction at a regional level were varied from 81% for Asia, to 89% for Americas, 86% for Africa, 97% for Oceania, 98% for Europe, and 100% for India. Mean accuracy of ethnicity assignment predictions was 63%. Pairwise concordances of AFR samples with the samples from any other super populations were the lowest (0.39–0.43), while the concordances within the same population were relatively high (0.55–0.61). For all populations except African, cross-population comparisons were similar in their concordance ranges to the range of within-population concordances (0.54–0.57). Gender determination was correct in all tested cases. Conclusions Our results indicate that the Infinium QC Array-24 chip is suitable for cost-efficient, independent QC assaying in the settings of an NGS-based molecular diagnostic laboratory; hence, we recommend its integration into the standard laboratory workflow. Low-density chips can provide sample-specific measures for variant call accuracy, prevent sample mix-ups, validate self-reported ethnicities, and detect consanguineous cases. Integration of low-density chips into QC procedures aids proper interpretation of candidate sequence variants. To enhance utility of this low-density chip, we recommend expansion of ADME and mitochondrial markers. Inexpensive Infinium-like low-density human chips have a potential to become a “Swiss army knife” among genotyping assays suitable for many applications requiring high-throughput assays. Electronic supplementary material The online version of this article (10.1186/s12920-017-0297-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Petr Ponomarenko
- Department of Biology, University of La Verne, La Verne, CA, USA
| | - Alex Ryutov
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Dennis T Maglinte
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Ancha Baranova
- School of Systems Biology, George Mason University, Fairfax, VA, USA.,Research Center for Medical Genetics, Moscow, Russia.,Atlas Biomed Group, Moscow, Russia
| | - Tatiana V Tatarinova
- Department of Biology, University of La Verne, La Verne, CA, USA. .,School of Systems Biology, George Mason University, Fairfax, VA, USA. .,Atlas Biomed Group, Moscow, Russia.
| | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA. .,Department of Pathology and Laboratory Medicine, USC Keck School of Medicine, Los Angeles, CA, USA.
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1542
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Detecting Pedigree Relationship Errors. Methods Mol Biol 2017. [PMID: 28980240 DOI: 10.1007/978-1-4939-7274-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Pedigree relationship errors often occur in family data collected for genetic studies, and unidentified errors can lead to either increased false positives or decreased power in both linkage and association analyses. Here, we review several allele sharing as well as likelihood-based statistics that were proposed to efficiently extract genealogical information from available genome-wide marker data, and the software package PREST that implements these methods. We provide the detailed analytical steps involved using two application examples, and we discuss various practical issues, including result interpretation.
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1543
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Sikora M, Seguin-Orlando A, Sousa VC, Albrechtsen A, Korneliussen T, Ko A, Rasmussen S, Dupanloup I, Nigst PR, Bosch MD, Renaud G, Allentoft ME, Margaryan A, Vasilyev SV, Veselovskaya EV, Borutskaya SB, Deviese T, Comeskey D, Higham T, Manica A, Foley R, Meltzer DJ, Nielsen R, Excoffier L, Mirazon Lahr M, Orlando L, Willerslev E. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers. Science 2017; 358:659-662. [DOI: 10.1126/science.aao1807] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/25/2017] [Indexed: 01/01/2023]
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1544
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Dou J, Sun B, Sim X, Hughes JD, Reilly DF, Tai ES, Liu J, Wang C. Estimation of kinship coefficient in structured and admixed populations using sparse sequencing data. PLoS Genet 2017; 13:e1007021. [PMID: 28961250 PMCID: PMC5636172 DOI: 10.1371/journal.pgen.1007021] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/11/2017] [Accepted: 09/14/2017] [Indexed: 12/15/2022] Open
Abstract
Knowledge of biological relatedness between samples is important for many genetic studies. In large-scale human genetic association studies, the estimated kinship is used to remove cryptic relatedness, control for family structure, and estimate trait heritability. However, estimation of kinship is challenging for sparse sequencing data, such as those from off-target regions in target sequencing studies, where genotypes are largely uncertain or missing. Existing methods often assume accurate genotypes at a large number of markers across the genome. We show that these methods, without accounting for the genotype uncertainty in sparse sequencing data, can yield a strong downward bias in kinship estimation. We develop a computationally efficient method called SEEKIN to estimate kinship for both homogeneous samples and heterogeneous samples with population structure and admixture. Our method models genotype uncertainty and leverages linkage disequilibrium through imputation. We test SEEKIN on a whole exome sequencing dataset (WES) of Singapore Chinese and Malays, which involves substantial population structure and admixture. We show that SEEKIN can accurately estimate kinship coefficient and classify genetic relatedness using off-target sequencing data down sampled to ~0.15X depth. In application to the full WES dataset without down sampling, SEEKIN also outperforms existing methods by properly analyzing shallow off-target data (~0.75X). Using both simulated and real phenotypes, we further illustrate how our method improves estimation of trait heritability for WES studies. Inference of genetic relatedness from molecular markers has broad applications in many areas, including quantitative genetics, forensics, evolution and ecology. Classic estimators, however, are not suitable for low-coverage sequencing data, which have high levels of genotype uncertainty and missing data. We evaluate existing methods and describe a new method for kinship estimation using sparse sequencing data. Our method leverages correlations between neighboring markers and models genotype uncertainty in kinship estimators for both homogeneous populations and admixed populations. We show that our method can accurately estimate kinship coefficient even when the sequencing depth is as low as ~0.15X, while existing methods have strong downward bias. Our method can be applied to estimate kinship using sparse off-target data and thus enables control of family structure and estimation of heritability in target sequencing studies, in which the deeply sequenced target regions are often too small to infer genetic relatedness. Even for whole exome sequencing, we show that our method can improve kinship and heritability estimation by including off-target data, compared to conventional analyses solely based on the target regions.
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Affiliation(s)
- Jinzhuang Dou
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Baoluo Sun
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, Singapore
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Jason D. Hughes
- Genetics, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States of America
| | - Dermot F. Reilly
- Genetics, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States of America
| | - E. Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jianjun Liu
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Chaolong Wang
- Computational and Systems Biology, Genome Institute of Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
- * E-mail:
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1545
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Matovinovic E, Kho PF, Lea RA, Benton MC, Eccles DA, Haupt LM, Hewitt AW, Sherwin JC, Mackey DA, Griffiths LR. Genome-wide linkage and association analysis of primary open-angle glaucoma endophenotypes in the Norfolk Island isolate. Mol Vis 2017; 23:660-665. [PMID: 28966548 PMCID: PMC5620381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/26/2017] [Indexed: 12/04/2022] Open
Abstract
PURPOSE Primary open-angle glaucoma (POAG) refers to a group of heterogeneous diseases involving optic nerve damage. Two well-established risk factors for POAG are elevated intraocular pressure (IOP) and a thinner central corneal thickness (CCT). These endophenotypes exhibit a high degree of heritability across populations. Large-scale genome-wide association studies (GWASs) of outbred populations have robustly implicated several susceptibility gene variants for both IOP and CCT. Despite this progress, a substantial amount of genetic variance remains unexplained. Population-specific variants that might be rare in outbred populations may also influence POAG endophenotypes. The Norfolk Island population is a founder-effect genetic isolate that has been well characterized for POAG endophenotypes. This population is therefore a suitable candidate for mapping new variants that influence these complex traits. METHODS Three hundred and thirty participants from the Norfolk Island Eye Study (NIES) core pedigree provided DNA. Ocular measurements of CCT and IOP were also taken for analysis. Heritability analyses and genome-wide linkage analyses of short tandem repeats (STRs) were conducted using SOLAR. Pedigree-based GWASs of single-nucleotide polymorphisms (SNPs) were performed using the GenABEL software. RESULTS CCT was the most heritable endophenotype in this cohort (h2 = 0.77, p = 6×10-6), while IOP showed a heritability of 0.39 (p = 0.008). A genome-wide linkage analysis of these POAG phenotypes identified a maximum logarithm of the odds (LOD) score of 1.9 for CCT on chromosome 20 (p = 0.0016) and 1.3 for IOP on chromosome 15 (p = 0.0072). The GWAS results revealed a study-wise significant association for IOP at rs790357, which is located within DLG2 on chr11q14.1 (p = 1.02×10-7). DLG2 is involved in neuronal signaling and development, and while it has not previously been associated with IOP, it has been associated with myopia. An analysis of 12 known SNPs for IOP showed that rs12419342 in RAPSN on chromosome 11 was nominally associated in Norfolk Island (NI; p = 0.0021). For CCT, an analysis of 26 known SNPs showed rs9938149 in BANP-ZNF469 on chromosome 16 was nominally associated in NI (p = 0.002). CONCLUSIONS These study results indicate that CCT and IOP exhibit a substantial degree of heritability in the NI pedigree, indicating a genetic component. A genome-wide linkage analysis of POAG endophenotypes did not reveal any major effect loci, but the GWASs did implicate several known loci, as well as a potential new locus in DLG2, suggesting a role for neuronal signaling in development in IOP and perhaps POAG. These results also highlight the need to target rarer variants via whole genome sequencing in this genetic isolate.
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Affiliation(s)
- Elizabeth Matovinovic
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Pik Fang Kho
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Rodney A. Lea
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Miles C. Benton
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - David A. Eccles
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Larisa M. Haupt
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Alex W. Hewitt
- Centre for Eye Research Australia & Royal Victorian Eye and Ear Hospital, University of Melbourne, East Melbourne, Victoria, Australia,Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Hobart, Australia
| | - Justin C. Sherwin
- Centre for Eye Research Australia & Royal Victorian Eye and Ear Hospital, University of Melbourne, East Melbourne, Victoria, Australia
| | - David A. Mackey
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Hobart, Australia,Lions Eye Institute, Centre for Ophthalmology and Visual Science, University of Western Australia, Perth, Australia
| | - Lyn R. Griffiths
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
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1546
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Glusman G, Mauldin DE, Hood LE, Robinson M. Ultrafast Comparison of Personal Genomes via Precomputed Genome Fingerprints. Front Genet 2017; 8:136. [PMID: 29018478 PMCID: PMC5623000 DOI: 10.3389/fgene.2017.00136] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/12/2017] [Indexed: 01/01/2023] Open
Abstract
We present an ultrafast method for comparing personal genomes. We transform the standard genome representation (lists of variants relative to a reference) into “genome fingerprints” via locality sensitive hashing. The resulting genome fingerprints can be meaningfully compared even when the input data were obtained using different sequencing technologies, processed using different pipelines, represented in different data formats and relative to different reference versions. Furthermore, genome fingerprints are robust to up to 30% missing data. Because of their reduced size, computation on the genome fingerprints is fast and requires little memory. For example, we could compute all-against-all pairwise comparisons among the 2504 genomes in the 1000 Genomes data set in 67 s at high quality (21 μs per comparison, on a single processor), and achieved a lower quality approximation in just 11 s. Efficient computation enables scaling up a variety of important genome analyses, including quantifying relatedness, recognizing duplicative sequenced genomes in a set, population reconstruction, and many others. The original genome representation cannot be reconstructed from its fingerprint, effectively decoupling genome comparison from genome interpretation; the method thus has significant implications for privacy-preserving genome analytics.
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Affiliation(s)
| | | | - Leroy E Hood
- Institute for Systems Biology, Seattle, WA, United States
| | - Max Robinson
- Institute for Systems Biology, Seattle, WA, United States
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1547
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Bergström A, Oppenheimer SJ, Mentzer AJ, Auckland K, Robson K, Attenborough R, Alpers MP, Koki G, Pomat W, Siba P, Xue Y, Sandhu MS, Tyler-Smith C. A Neolithic expansion, but strong genetic structure, in the independent history of New Guinea. Science 2017; 357:1160-1163. [PMID: 28912245 PMCID: PMC5802383 DOI: 10.1126/science.aan3842] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 08/22/2017] [Indexed: 12/27/2022]
Abstract
New Guinea shows human occupation since ~50 thousand years ago (ka), independent adoption of plant cultivation ~10 ka, and great cultural and linguistic diversity today. We performed genome-wide single-nucleotide polymorphism genotyping on 381 individuals from 85 language groups in Papua New Guinea and find a sharp divide originating 10 to 20 ka between lowland and highland groups and a lack of non-New Guinean admixture in the latter. All highlanders share ancestry within the last 10 thousand years, with major population growth in the same period, suggesting population structure was reshaped following the Neolithic lifestyle transition. However, genetic differentiation between groups in Papua New Guinea is much stronger than in comparable regions in Eurasia, demonstrating that such a transition does not necessarily limit the genetic and linguistic diversity of human societies.
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Affiliation(s)
- Anders Bergström
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
| | - Stephen J Oppenheimer
- School of Anthropology and Museum Ethnography, University of Oxford, Oxford OX2 6PE, UK
| | - Alexander J Mentzer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Kathryn Auckland
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Kathryn Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Robert Attenborough
- Biological Anthropology, Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 1QH, UK
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT 2601, Australia
| | - Michael P Alpers
- International Health Research, Curtin University, Perth, WA 6845, Australia
- Papua New Guinea Institute of Medical Research, Post Office Box 60, Goroka, Papua New Guinea
| | - George Koki
- Papua New Guinea Institute of Medical Research, Post Office Box 60, Goroka, Papua New Guinea
| | - William Pomat
- Papua New Guinea Institute of Medical Research, Post Office Box 60, Goroka, Papua New Guinea
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Post Office Box 60, Goroka, Papua New Guinea
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Manjinder S Sandhu
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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1548
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Vyas DN, Al‐Meeri A, Mulligan CJ. Testing support for the northern and southern dispersal routes out of Africa: an analysis of Levantine and southern Arabian populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 164:736-749. [DOI: 10.1002/ajpa.23312] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Deven N. Vyas
- Department of AnthropologyUniversity of Florida, 1112 Turlington Hall, PO Box 117305Gainesville Florida 32611‐7305
- Genetics InstituteUniversity of Florida, Cancer & Genetics Research Complex, PO Box 103610Gainesville Florida 32610‐3610
| | - Ali Al‐Meeri
- Department of Clinical Biochemistry, Faculty of Medicine and Health SciencesUniversity of Sana'aSana'a Yemen
| | - Connie J. Mulligan
- Department of AnthropologyUniversity of Florida, 1112 Turlington Hall, PO Box 117305Gainesville Florida 32611‐7305
- Genetics InstituteUniversity of Florida, Cancer & Genetics Research Complex, PO Box 103610Gainesville Florida 32610‐3610
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1549
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Kale G, Ayday E, Tastan O. A utility maximizing and privacy preserving approach for protecting kinship in genomic databases. Bioinformatics 2017; 34:181-189. [DOI: 10.1093/bioinformatics/btx568] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/20/2017] [Accepted: 09/11/2017] [Indexed: 12/13/2022] Open
Affiliation(s)
- Gulce Kale
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - Erman Ayday
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - Oznur Tastan
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
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1550
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Druet T, Gautier M. A model-based approach to characterize individual inbreeding at both global and local genomic scales. Mol Ecol 2017; 26:5820-5841. [PMID: 28815918 DOI: 10.1111/mec.14324] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 07/31/2017] [Accepted: 08/07/2017] [Indexed: 01/05/2023]
Abstract
Inbreeding results from the mating of related individuals and may be associated with reduced fitness because it brings together deleterious variants in one individual. In general, inbreeding is estimated with respect to an arbitrary base population consisting of ancestors that are assumed unrelated. We herein propose a model-based approach to estimate and characterize individual inbreeding at both global and local genomic scales by assuming the individual genome is a mosaic of homozygous-by-descent (HBD) and non-HBD segments. The HBD segments may originate from ancestors tracing back to different periods in the past defining distinct age-related classes. The lengths of the HBD segments are exponentially distributed with class-specific parameters reflecting that inbreeding of older origin generates on average shorter stretches of observed homozygous markers. The model is implemented in a hidden Markov model framework that uses marker allele frequencies, genetic distances, genotyping error rates and the sequences of observed genotypes. Note that genotyping errors, low-fold sequencing or genotype-by-sequencing data are easily accommodated under this framework. Based on simulations under the inference model, we show that the genomewide inbreeding coefficients and the parameters of the model are accurately estimated. In addition, when several inbreeding classes are simulated, the model captures them if their ages are sufficiently different. Complementary analyses, either on data sets simulated under more realistic models or on human, dog and sheep real data, illustrate the range of applications of the approach and how it can reveal recent demographic histories among populations (e.g., very recent bottlenecks or founder effects). The method also allows to clearly identify individuals resulting from extreme consanguineous matings.
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Affiliation(s)
- T Druet
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - M Gautier
- INRA, UMR CBGP (INRA - IRD - Cirad - Montpellier SupAgro), Montferrier-sur-Lez, France.,Institut de Biologie Computationnelle, Montpellier, France
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