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Wang H, Wang LS, Schellenberg G, Lee WP. The role of structural variations in Alzheimer's disease and other neurodegenerative diseases. Front Aging Neurosci 2023; 14:1073905. [PMID: 36846102 PMCID: PMC9944073 DOI: 10.3389/fnagi.2022.1073905] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/31/2022] [Indexed: 02/10/2023] Open
Abstract
Dozens of single nucleotide polymorphisms (SNPs) related to Alzheimer's disease (AD) have been discovered by large scale genome-wide association studies (GWASs). However, only a small portion of the genetic component of AD can be explained by SNPs observed from GWAS. Structural variation (SV) can be a major contributor to the missing heritability of AD; while SV in AD remains largely unexplored as the accurate detection of SVs from the widely used array-based and short-read technology are still far from perfect. Here, we briefly summarized the strengths and weaknesses of available SV detection methods. We reviewed the current landscape of SV analysis in AD and SVs that have been found associated with AD. Particularly, the importance of currently less explored SVs, including insertions, inversions, short tandem repeats, and transposable elements in neurodegenerative diseases were highlighted.
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Affiliation(s)
- Hui Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Gerard Schellenberg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Wan-Ping Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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2
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Hanlon VCT, Lansdorp PM, Guryev V. A survey of current methods to detect and genotype inversions. Hum Mutat 2022; 43:1576-1589. [PMID: 36047337 DOI: 10.1002/humu.24458] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/11/2022]
Abstract
Polymorphic inversions are ubiquitous in humans, and they have been linked to both adaptation and disease. Following their discovery in Drosophila more than a century ago, inversions have proved to be more elusive than other structural variants. A wide variety of methods for the detection and genotyping of inversions have recently been developed: multiple techniques based on selective amplification by PCR, short- and long-read sequencing approaches, principal component analysis of small variant haplotypes, template strand sequencing, optical mapping, and various genome assembly methods. Many methods apply complex wet lab protocols or increasingly refined bioinformatic analyses. This review is an attempt to provide a practical summary and comparison of the methods that are in current use, with a focus on metrics such as the maximum size of segmental duplications at inversion breakpoints that each method can tolerate, the size range of inversions that they recover, their throughput, and whether the locations of putative inversions must be known beforehand. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Peter M Lansdorp
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC, V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, The Netherlands
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3
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Balagué-Dobón L, Cáceres A, González JR. Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure. Brief Bioinform 2022; 23:6535682. [PMID: 35211719 PMCID: PMC8921734 DOI: 10.1093/bib/bbac043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 12/12/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are the most abundant type of genomic variation and the most accessible to genotype in large cohorts. However, they individually explain a small proportion of phenotypic differences between individuals. Ancestry, collective SNP effects, structural variants, somatic mutations or even differences in historic recombination can potentially explain a high percentage of genomic divergence. These genetic differences can be infrequent or laborious to characterize; however, many of them leave distinctive marks on the SNPs across the genome allowing their study in large population samples. Consequently, several methods have been developed over the last decade to detect and analyze different genomic structures using SNP arrays, to complement genome-wide association studies and determine the contribution of these structures to explain the phenotypic differences between individuals. We present an up-to-date collection of available bioinformatics tools that can be used to extract relevant genomic information from SNP array data including population structure and ancestry; polygenic risk scores; identity-by-descent fragments; linkage disequilibrium; heritability and structural variants such as inversions, copy number variants, genetic mosaicisms and recombination histories. From a systematic review of recently published applications of the methods, we describe the main characteristics of R packages, command-line tools and desktop applications, both free and commercial, to help make the most of a large amount of publicly available SNP data.
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4
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Nowling RJ, Fallas-Moya F, Sadovnik A, Emrich S, Aleck M, Leskiewicz D, Peters JG. Fast, low-memory detection and localization of large, polymorphic inversions from SNPs. PeerJ 2022; 10:e12831. [PMID: 35116204 PMCID: PMC8784018 DOI: 10.7717/peerj.12831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/04/2022] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Large (>1 Mb), polymorphic inversions have substantial impacts on population structure and maintenance of genotypes. These large inversions can be detected from single nucleotide polymorphism (SNP) data using unsupervised learning techniques like PCA. Construction and analysis of a feature matrix from millions of SNPs requires large amount of memory and limits the sizes of data sets that can be analyzed. METHODS We propose using feature hashing construct a feature matrix from a VCF file of SNPs for reducing memory usage. The matrix is constructed in a streaming fashion such that the entire VCF file is never loaded into memory at one time. RESULTS When evaluated on Anopheles mosquito and Drosophila fly data sets, our approach reduced memory usage by 97% with minimal reductions in accuracy for inversion detection and localization tasks. CONCLUSION With these changes, inversions in larger data sets can be analyzed easily and efficiently on common laptop and desktop computers. Our method is publicly available through our open-source inversion analysis software, Asaph.
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Affiliation(s)
- Ronald J. Nowling
- Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, Wisconsin, United States of America
| | - Fabian Fallas-Moya
- Electrical Engineering and Computer Science, University of Tennessee-Knoxville, Knoxville, Tennessee, United States
| | - Amir Sadovnik
- Electrical Engineering and Computer Science, University of Tennessee-Knoxville, Knoxville, Tennessee, United States
| | - Scott Emrich
- Electrical Engineering and Computer Science, University of Tennessee-Knoxville, Knoxville, Tennessee, United States
| | - Matthew Aleck
- Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, Wisconsin, United States of America
| | - Daniel Leskiewicz
- Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, Wisconsin, United States of America
| | - John G. Peters
- Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, Wisconsin, United States of America
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5
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Ferrari G, Atmore LM, Jentoft S, Jakobsen KS, Makowiecki D, Barrett JH, Star B. An accurate assignment test for extremely low-coverage whole-genome sequence data. Mol Ecol Resour 2021; 22:1330-1344. [PMID: 34779123 DOI: 10.1111/1755-0998.13551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022]
Abstract
Genomic assignment tests can provide important diagnostic biological characteristics, such as population of origin or ecotype. Yet, assignment tests often rely on moderate- to high-coverage sequence data that can be difficult to obtain for fields such as molecular ecology and ancient DNA. We have developed a novel approach that efficiently assigns biologically relevant information (i.e., population identity or structural variants such as inversions) in extremely low-coverage sequence data. First, we generate databases from existing reference data using a subset of diagnostic single nucleotide polymorphisms (SNPs) associated with a biological characteristic. Low-coverage alignment files are subsequently compared to these databases to ascertain allelic state, yielding a joint probability for each association. To assess the efficacy of this approach, we assigned haplotypes and population identity in Heliconius butterflies, Atlantic herring, and Atlantic cod using chromosomal inversion sites and whole-genome data. We scored both modern and ancient specimens, including the first whole-genome sequence data recovered from ancient Atlantic herring bones. The method accurately assigns biological characteristics, including population membership, using extremely low-coverage data (as low as 0.0001x) based on genome-wide SNPs. This approach will therefore increase the number of samples in evolutionary, ecological and archaeological research for which relevant biological information can be obtained.
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Affiliation(s)
- Giada Ferrari
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Lane M Atmore
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Daniel Makowiecki
- Department of Environmental Archaeology and Human Paleoecology, Institute of Archaeology, Nicolaus Copernicus University, Torun, Poland
| | - James H Barrett
- McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Cambridge, UK.,Department of Archaeology and Cultural History, NTNU University Museum, Trondheim, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
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6
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El Hou A, Rocha D, Venot E, Blanquet V, Philippe R. Long-range linkage disequilibrium in French beef cattle breeds. Genet Sel Evol 2021; 53:63. [PMID: 34301193 PMCID: PMC8306006 DOI: 10.1186/s12711-021-00657-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Linkage disequilibrium (LD) is a key parameter to study the history of populations and to identify and fine map quantitative trait loci (QTL) and it has been studied for many years in animal populations. The advent of new genotyping technologies has allowed whole-genome LD studies in most cattle populations. However, to date, long-range LD (LRLD) between distant variants on the genome has not been investigated in detail in cattle. Here, we present the first comprehensive study of LRLD in French beef cattle by analysing data on 672 Charolais (CHA), 462 Limousine (LIM) and 326 Blonde d'Aquitaine (BLA) individuals that were genotyped on the Illumina BovineHD Beadchip. Furthermore, whole-genome LD and haplotype block structure were analysed in these three breeds. RESULTS We computed linkage disequilibrium (r2) values for 5.9, 5.6 and 6.0 billion pairs of SNPs on the 29 autosomes of CHA, LIM and BLA, respectively. Mean r2 values drop to less than 0.1 for distances between SNPs greater than 120 kb. However, for the first time, we detected the existence of LRLD in the three main French beef breeds. In total, 598, 266, and 795 LRLD events (r2 ≥ 0.6) were detected in CHA, LIM and BLA, respectively. Each breed had predominantly population-specific LRLD interactions, although shared LRLD events occurred in a number of regions (55 LRLD events were shared between two breeds and nine between the three breeds). Examples of possible functional gene interactions and QTL co-location were observed with some of these LRLD events, which suggests epistatic selection. CONCLUSIONS We identified long-range linkage disequilibrium for the first time in French beef cattle populations. Epistatic selection may be the main source of the observed LRLD events, but other forces may also be involved. LRLD information should be accounted for in genome-wide association studies.
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Affiliation(s)
- Abdelmajid El Hou
- INRAE, PEIRENE EA7500, USC1061 GAMAA, Université de Limoges, 87060, Limoges, France
| | - Dominique Rocha
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Eric Venot
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Véronique Blanquet
- INRAE, PEIRENE EA7500, USC1061 GAMAA, Université de Limoges, 87060, Limoges, France
| | - Romain Philippe
- INRAE, PEIRENE EA7500, USC1061 GAMAA, Université de Limoges, 87060, Limoges, France.
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7
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Karimi K, Ngoc Do D, Sargolzaei M, Miar Y. Population Genomics of American Mink Using Whole Genome Sequencing Data. Genes (Basel) 2021; 12:genes12020258. [PMID: 33670138 PMCID: PMC7916864 DOI: 10.3390/genes12020258] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 12/11/2022] Open
Abstract
Characterizing the genetic structure and population history can facilitate the development of genomic breeding strategies for the American mink. In this study, we used the whole genome sequences of 100 mink from the Canadian Centre for Fur Animal Research (CCFAR) at the Dalhousie Faculty of Agriculture (Truro, NS, Canada) and Millbank Fur Farm (Rockwood, ON, Canada) to investigate their population structure, genetic diversity and linkage disequilibrium (LD) patterns. Analysis of molecular variance (AMOVA) indicated that the variation among color-types was significant (p < 0.001) and accounted for 18% of the total variation. The admixture analysis revealed that assuming three ancestral populations (K = 3) provided the lowest cross-validation error (0.49). The effective population size (Ne) at five generations ago was estimated to be 99 and 50 for CCFAR and Millbank Fur Farm, respectively. The LD patterns revealed that the average r2 reduced to <0.2 at genomic distances of >20 kb and >100 kb in CCFAR and Millbank Fur Farm suggesting that the density of 120,000 and 24,000 single nucleotide polymorphisms (SNP) would provide the adequate accuracy of genomic evaluation in these populations, respectively. These results indicated that accounting for admixture is critical for designing the SNP panels for genotype-phenotype association studies of American mink.
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Affiliation(s)
- Karim Karimi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada; (K.K.); (D.N.D.)
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada; (K.K.); (D.N.D.)
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Select Sires Inc., Plain City, OH 43064, USA
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada; (K.K.); (D.N.D.)
- Correspondence:
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8
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Nowling RJ, Manke KR, Emrich SJ. Detecting inversions with PCA in the presence of population structure. PLoS One 2020; 15:e0240429. [PMID: 33119626 PMCID: PMC7595445 DOI: 10.1371/journal.pone.0240429] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 09/28/2020] [Indexed: 12/26/2022] Open
Abstract
Chromosomal inversions can lead to reproductive isolation and adaptation in insects such as Drosophila melanogaster and the non-model malaria vector Anopheles gambiae. Inversions can be detected and characterized using principal component analysis (PCA) of single nucleotide polymorphisms (SNPs). To aid in developing such methods, we formed a new benchmark derived from three publicly-available insect data. We then used this benchmark to perform an extended validation of our software for inversion analysis (Asaph). Through that process, we identified and characterized several problematic test cases liable to misinterpretation that can help guide PCA-based inversion detection. Lastly, we re-analyzed the 2R chromosome arm of 150 An. gambiae and coluzzii samples and observed two inversions (2Rc and 2Rd) that were previously known but not annotated in these particular individuals. The resulting benchmark data set and methods will be useful for future inversion detection based solely on SNP data.
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Affiliation(s)
- Ronald J. Nowling
- Electrical Engineering and Computer Science, Milwaukee School of Engineering, Milwaukee, WI
| | - Krystal R. Manke
- Physics and Chemistry, Milwaukee School of Engineering, Milwaukee, WI
| | - Scott J. Emrich
- Electrical Engineering and Computer Science, University of Tennessee–Knoxville, Knoxville, TN
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9
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Ruiz-Arenas C, Cáceres A, Moreno V, González JR. Common polymorphic inversions at 17q21.31 and 8p23.1 associate with cancer prognosis. Hum Genomics 2019; 13:57. [PMID: 31753042 PMCID: PMC6873427 DOI: 10.1186/s40246-019-0242-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 10/09/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Chromosomal inversions are structural genetic variants where a chromosome segment changes its orientation. While sporadic de novo inversions are known genetic risk factors for cancer susceptibility, it is unknown if common polymorphic inversions are also associated with the prognosis of common tumors, as they have been linked to other complex diseases. We studied the association of two well-characterized human inversions at 17q21.31 and 8p23.1 with the prognosis of lung, liver, breast, colorectal, and stomach cancers. RESULTS Using data from The Cancer Genome Atlas (TCGA), we observed that inv8p23.1 was associated with overall survival in breast cancer and that inv17q21.31 was associated with overall survival in stomach cancer. In the meta-analysis of two independent studies, inv17q21.31 heterozygosity was significantly associated with colorectal disease-free survival. We found that the association was mediated by the de-methylation of cg08283464 and cg03999934, also linked to lower disease-free survival. CONCLUSIONS Our results suggest that chromosomal inversions are important genetic factors of tumor prognosis, likely affecting changes in methylation patterns.
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Affiliation(s)
- Carlos Ruiz-Arenas
- Barcelona Institute for Global Health, ISGlobal, Doctor Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Alejandro Cáceres
- Barcelona Institute for Global Health, ISGlobal, Doctor Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Victor Moreno
- Programa de Prevención y Control del Cáncer, Instituto Catalán de Oncología, L'Hospitalet, Barcelona, Spain
| | - Juan R González
- Barcelona Institute for Global Health, ISGlobal, Doctor Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.
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10
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Gelernter J, Sun N, Polimanti R, Pietrzak RH, Levey DF, Lu Q, Hu Y, Li B, Radhakrishnan K, Aslan M, Cheung KH, Li Y, Rajeevan N, Sayward F, Harrington K, Chen Q, Cho K, Honerlaw J, Pyarajan S, Lencz T, Quaden R, Shi Y, Hunter-Zinck H, Gaziano JM, Kranzler HR, Concato J, Zhao H, Stein MB. Genome-wide Association Study of Maximum Habitual Alcohol Intake in >140,000 U.S. European and African American Veterans Yields Novel Risk Loci. Biol Psychiatry 2019; 86:365-376. [PMID: 31151762 PMCID: PMC6919570 DOI: 10.1016/j.biopsych.2019.03.984] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 03/16/2019] [Accepted: 03/18/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Habitual alcohol use can be an indicator of alcohol dependence, which is associated with a wide range of serious health problems. METHODS We completed a genome-wide association study in 126,936 European American and 17,029 African American subjects in the Veterans Affairs Million Veteran Program for a quantitative phenotype based on maximum habitual alcohol consumption. RESULTS ADH1B, on chromosome 4, was the lead locus for both populations: for the European American sample, rs1229984 (p = 4.9 × 10-47); for African American, rs2066702 (p = 2.3 × 10-12). In the European American sample, we identified three additional genome-wide-significant maximum habitual alcohol consumption loci: on chromosome 17, rs77804065 (p = 1.5 × 10-12), at CRHR1 (corticotropin-releasing hormone receptor 1); the protein product of this gene is involved in stress and immune responses; and on chromosomes 8 and 10. European American and African American samples were then meta-analyzed; the associated region at CRHR1 increased in significance to 1.02 × 10-13, and we identified two additional genome-wide significant loci, FGF14 (p = 9.86 × 10-9) (chromosome 13) and a locus on chromosome 11. Besides ADH1B, none of the five loci have prior genome-wide significant support. Post-genome-wide association study analysis identified genetic correlation to other alcohol-related traits, smoking-related traits, and many others. Replications were observed in UK Biobank data. Genetic correlation between maximum habitual alcohol consumption and alcohol dependence was 0.87 (p = 4.78 × 10-9). Enrichment for cell types included dopaminergic and gamma-aminobutyric acidergic neurons in midbrain, and pancreatic delta cells. CONCLUSIONS The present study supports five novel alcohol-use risk loci, with particularly strong statistical support for CRHR1. Additionally, we provide novel insight regarding the biology of harmful alcohol use.
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Affiliation(s)
- Joel Gelernter
- Psychiatry Service, VA Connecticut Healthcare System, West Haven, Connecticut; Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut.
| | - Ning Sun
- Veterans Affairs (VA) Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, Connecticut; Department of Biostatistics, Yale University School of Medicine, New Haven, Connecticut
| | - Renato Polimanti
- Psychiatry Service, VA Connecticut Healthcare System, West Haven, Connecticut; Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut
| | - Robert H Pietrzak
- Psychiatry Service, VA Connecticut Healthcare System, West Haven, Connecticut; Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut
| | - Daniel F Levey
- Psychiatry Service, VA Connecticut Healthcare System, West Haven, Connecticut; Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut
| | - Qiongshi Lu
- Department of Biostatistics, Yale University School of Medicine, New Haven, Connecticut
| | - Yiming Hu
- Department of Biostatistics, Yale University School of Medicine, New Haven, Connecticut
| | - Boyang Li
- Department of Biostatistics, Yale University School of Medicine, New Haven, Connecticut
| | - Krishnan Radhakrishnan
- Veterans Affairs (VA) Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, Connecticut
| | - Mihaela Aslan
- Veterans Affairs (VA) Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, Connecticut; Department of Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Kei-Hoi Cheung
- Veterans Affairs (VA) Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, Connecticut; Department of Emergency Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Yuli Li
- Veterans Affairs (VA) Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, Connecticut; Yale Center for Medical Informatics, Yale University School of Medicine, New Haven, Connecticut
| | - Nallakkandi Rajeevan
- Veterans Affairs (VA) Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, Connecticut; Yale Center for Medical Informatics, Yale University School of Medicine, New Haven, Connecticut
| | - Fred Sayward
- Veterans Affairs (VA) Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, Connecticut; Yale Center for Medical Informatics, Yale University School of Medicine, New Haven, Connecticut
| | - Kelly Harrington
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, Massachusetts; Department of Psychiatry, Boston University School of Medicine, Boston, Massachusetts
| | - Quan Chen
- Veterans Affairs (VA) Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, Connecticut; Department of Biostatistics, Yale University School of Medicine, New Haven, Connecticut
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, Massachusetts; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jacqueline Honerlaw
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, Massachusetts
| | - Saiju Pyarajan
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, Massachusetts; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Todd Lencz
- Department of Psychiatry, Hofstra Northwell School of Medicine, Hempstead, New York; Department of Molecular Medicine, Hofstra Northwell School of Medicine, Hempstead, New York; Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, New York; Center for Psychiatric Neuroscience, The Feinstein Institute for Medical Research, Manhasset, New York
| | - Rachel Quaden
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, Massachusetts
| | - Yunling Shi
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, Massachusetts
| | - Haley Hunter-Zinck
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, Massachusetts
| | - J Michael Gaziano
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, Massachusetts; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Henry R Kranzler
- Veterans Integrated Services Networks (VISN) 4 Mental Illness Research, Education and Clinical Center, Crescenz VA Medical Center, Philadelphia, Pennsylvania; Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - John Concato
- Veterans Affairs (VA) Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, Connecticut; Department of Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Hongyu Zhao
- Veterans Affairs (VA) Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, Connecticut; Department of Biostatistics, Yale University School of Medicine, New Haven, Connecticut
| | - Murray B Stein
- Psychiatry Service, VA San Diego Healthcare System, San Diego, California; Department of Psychiatry, University of California San Diego, La Jolla, California.
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11
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Gelernter J, Sun N, Polimanti R, Pietrzak R, Levey DF, Bryois J, Lu Q, Hu Y, Li B, Radhakrishnan K, Aslan M, Cheung KH, Li Y, Rajeevan N, Sayward F, Harrington K, Chen Q, Cho K, Pyarajan S, Sullivan PF, Quaden R, Shi Y, Hunter-Zinck H, Gaziano JM, Concato J, Zhao H, Stein MB. Genome-wide association study of post-traumatic stress disorder reexperiencing symptoms in >165,000 US veterans. Nat Neurosci 2019; 22:1394-1401. [PMID: 31358989 PMCID: PMC6953633 DOI: 10.1038/s41593-019-0447-7] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 06/11/2019] [Indexed: 12/20/2022]
Abstract
Post-traumatic stress disorder (PTSD) is a major problem among military veterans and civilians alike, yet its pathophysiology remains poorly understood. We performed a genome-wide association study and bioinformatic analyses, which included 146,660 European Americans and 19,983 African Americans in the US Million Veteran Program, to identify genetic risk factors relevant to intrusive reexperiencing of trauma, which is the most characteristic symptom cluster of PTSD. In European Americans, eight distinct significant regions were identified. Three regions had values of P < 5 × 10-10: CAMKV; chromosome 17 closest to KANSL1, but within a large high linkage disequilibrium region that also includes CRHR1; and TCF4. Associations were enriched with respect to the transcriptomic profiles of striatal medium spiny neurons. No significant associations were observed in the African American cohort of the sample. Results in European Americans were replicated in the UK Biobank data. These results provide new insights into the biology of PTSD in a well-powered genome-wide association study.
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Affiliation(s)
- Joel Gelernter
- Psychiatry Service, VA Connecticut Healthcare System, West Haven, CT, USA.
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA.
| | - Ning Sun
- VA Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Renato Polimanti
- Psychiatry Service, VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Robert Pietrzak
- Psychiatry Service, VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Daniel F Levey
- Psychiatry Service, VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Julien Bryois
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Qiongshi Lu
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Yiming Hu
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Boyang Li
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Krishnan Radhakrishnan
- VA Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Mihaela Aslan
- VA Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Kei-Hoi Cheung
- VA Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Emergency Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Yuli Li
- VA Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Yale Center for Medical Informatics, Yale University School of Medicine, New Haven, CT, USA
| | - Nallakkandi Rajeevan
- VA Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Yale Center for Medical Informatics, Yale University School of Medicine, New Haven, CT, USA
| | - Frederick Sayward
- VA Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Yale Center for Medical Informatics, Yale University School of Medicine, New Haven, CT, USA
| | - Kelly Harrington
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Quan Chen
- VA Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Saiju Pyarajan
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Patrick F Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - Rachel Quaden
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
| | - Yunling Shi
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
| | - Haley Hunter-Zinck
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
| | - J Michael Gaziano
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - John Concato
- VA Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Hongyu Zhao
- VA Clinical Epidemiology Research Center (CERC), VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA
| | - Murray B Stein
- Psychiatry Service, VA San Diego Healthcare System, San Diego, CA, USA
- Departments of Psychiatry and of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
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12
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Ruiz-Arenas C, Cáceres A, López-Sánchez M, Tolosana I, Pérez-Jurado L, González JR. scoreInvHap: Inversion genotyping for genome-wide association studies. PLoS Genet 2019; 15:e1008203. [PMID: 31269027 PMCID: PMC6608898 DOI: 10.1371/journal.pgen.1008203] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/17/2019] [Indexed: 02/02/2023] Open
Abstract
Polymorphic inversions contribute to adaptation and phenotypic variation. However, large multi-centric association studies of inversions remain challenging. We present scoreInvHap, a method to genotype inversions from SNP data for genome-wide association studies (GWASs), overcoming important limitations of current methods and outperforming them in accuracy and applicability. scoreInvHap calls individual inversion-genotypes from a similarity score to the SNPs of experimentally validated references. It can be used on different sources of SNP data, including those with low SNP coverage such as exome sequencing, and is easily adaptable to genotype new inversions, either in humans or in other species. We present 20 human inversions that can be reliably and easily genotyped with scoreInvHap to discover their role in complex human traits, and illustrate a first genome-wide association study of experimentally-validated human inversions. scoreInvHap is implemented in R and it is freely available from Bioconductor. Chromosomal inversions are structural variants consisting on an orientation change of a chromosome segment. Inversions have been linked to some phenotypic differences between individuals and to genetic divergence. However, their overall contribution to complex diseases is largely underdetermined as there are no high-throughput methods to call inversion-genotypes in large cohort studies. Here, we propose a new method, scoreInvHap, to call individual inversion genotypes from their haplotype similarity. We show that scoreInvHap has a high performance when analyzing heterogeneous sources of SNP data. Our current implementation contains 20 human inversions that can be readily genotyped in existing GWAS datasets. We exemplify the utility of scoreInvHap by running the first-genome wide association of experimentally validated inversions and a multi-centric inversion association study. All in all, scoreInvHap can substantially contribute to increase our knowledge of the role of chromosomal inversions in complex diseases by re-analyzing data from existing genetic association studies.
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Affiliation(s)
- Carlos Ruiz-Arenas
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Alejandro Cáceres
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Marcos López-Sánchez
- Genetics Unit, Universitat Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Ignacio Tolosana
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Luis Pérez-Jurado
- Genetics Unit, Universitat Pompeu Fabra, Barcelona, Spain
- Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- SA Clinical Genetics, Women's and Children's Hospital & University of Adelaide, Adelaide, South Australia Australia
- South Australian Health and Medical Research Institute, Adelaide, South Australia Australia
| | - Juan R. González
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
- * E-mail:
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13
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Lehnert SJ, Bentzen P, Kess T, Lien S, Horne JB, Clément M, Bradbury IR. Chromosome polymorphisms track trans‐Atlantic divergence and secondary contact in Atlantic salmon. Mol Ecol 2019; 28:2074-2087. [DOI: 10.1111/mec.15065] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/12/2019] [Accepted: 02/19/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Sarah J. Lehnert
- Fisheries and Oceans Canada Northwest Atlantic Fisheries Centre St. John's Newfoundland Canada
| | - Paul Bentzen
- Biology Department Dalhousie University Halifax Nova Scotia Canada
| | - Tony Kess
- Fisheries and Oceans Canada Northwest Atlantic Fisheries Centre St. John's Newfoundland Canada
| | - Sigbjørn Lien
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences Norwegian University of Life Sciences Ås Norway
| | - John B. Horne
- Gulf Coast Research Laboratory University of Southern Mississippi Ocean Springs Mississippi USA
| | - Marie Clément
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute Memorial University of Newfoundland St. John's Newfoundland Canada
- Labrador Institute Memorial University of Newfoundland Happy Valley‐Goose Bay Newfoundland Canada
| | - Ian R. Bradbury
- Fisheries and Oceans Canada Northwest Atlantic Fisheries Centre St. John's Newfoundland Canada
- Biology Department Dalhousie University Halifax Nova Scotia Canada
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14
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Wellband K, Mérot C, Linnansaari T, Elliott JAK, Curry RA, Bernatchez L. Chromosomal fusion and life history-associated genomic variation contribute to within-river local adaptation of Atlantic salmon. Mol Ecol 2018; 28:1439-1459. [PMID: 30506831 DOI: 10.1111/mec.14965] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 12/30/2022]
Abstract
Chromosomal inversions have been implicated in facilitating adaptation in the face of high levels of gene flow, but whether chromosomal fusions also have similar potential remains poorly understood. Atlantic salmon are usually characterized by population structure at multiple spatial scales; however, this is not the case for tributaries of the Miramichi River in North America. To resolve genetic relationships between populations in this system and the potential for known chromosomal fusions to contribute to adaptation, we genotyped 728 juvenile salmon using a 50 K SNP array. Consistent with previous work, we report extremely weak overall population structuring (Global FST = 0.004) and failed to support hierarchical structure between the river's two main branches. We provide the first genomic characterization of a previously described polymorphic fusion between chromosomes 8 and 29. Fusion genomic characteristics included high LD, reduced heterozygosity in the fused homokaryotes, and strong divergence between the fused and the unfused rearrangement. Population structure based on fusion karyotype was five times stronger than neutral variation (FST = 0.019), and the frequency of the fusion was associated with summer precipitation supporting a hypothesis that this rearrangement may contribute local adaptation despite weak neutral differentiation. Additionally, both outlier variation among populations and a polygenic framework for characterizing adaptive variation in relation to climate identified a 250-Kb region of chromosome 9, including the gene six6 that has previously been linked to age-at-maturity and run-timing for this species. Overall, our results indicate that adaptive processes, independent of major river branching, are more important than neutral processes for structuring these populations.
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Affiliation(s)
- Kyle Wellband
- Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
| | - Tommi Linnansaari
- Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - J A K Elliott
- Cooke Aquaculture Inc, Oak Bay, New Brunswick, Canada
| | - R Allen Curry
- Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
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15
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Shao H, Ganesamoorthy D, Duarte T, Cao MD, Hoggart CJ, Coin LJM. npInv: accurate detection and genotyping of inversions using long read sub-alignment. BMC Bioinformatics 2018; 19:261. [PMID: 30001702 PMCID: PMC6044046 DOI: 10.1186/s12859-018-2252-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 06/18/2018] [Indexed: 11/21/2022] Open
Abstract
Background Detection of genomic inversions remains challenging. Many existing methods primarily target inzversions with a non repetitive breakpoint, leaving inverted repeat (IR) mediated non-allelic homologous recombination (NAHR) inversions largely unexplored. Result We present npInv, a novel tool specifically for detecting and genotyping NAHR inversion using long read sub-alignment of long read sequencing data. We benchmark npInv with other tools in both simulation and real data. We use npInv to generate a whole-genome inversion map for NA12878 consisting of 30 NAHR inversions (of which 15 are novel), including all previously known NAHR mediated inversions in NA12878 with flanking IR less than 7kb. Our genotyping accuracy on this dataset was 94%. We used PCR to confirm the presence of two of these novel inversions. We show that there is a near linear relationship between the length of flanking IR and the minimum inversion size, without inverted repeats. Conclusion The application of npInv shows high accuracy in both simulation and real data. The results give deeper insight into understanding inversion. Electronic supplementary material The online version of this article (10.1186/s12859-018-2252-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haojing Shao
- Genomics of Development and Disease Division, Institute for Molecular Bioscience, University of Queensland, 306 Carmody Rd, St Lucia, Brisbane, 4067, Australia
| | - Devika Ganesamoorthy
- Genomics of Development and Disease Division, Institute for Molecular Bioscience, University of Queensland, 306 Carmody Rd, St Lucia, Brisbane, 4067, Australia
| | - Tania Duarte
- Genomics of Development and Disease Division, Institute for Molecular Bioscience, University of Queensland, 306 Carmody Rd, St Lucia, Brisbane, 4067, Australia
| | - Minh Duc Cao
- Genomics of Development and Disease Division, Institute for Molecular Bioscience, University of Queensland, 306 Carmody Rd, St Lucia, Brisbane, 4067, Australia
| | - Clive J Hoggart
- Department of Medicine, Imperial College London, Level 2, Faculty Building South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Lachlan J M Coin
- Genomics of Development and Disease Division, Institute for Molecular Bioscience, University of Queensland, 306 Carmody Rd, St Lucia, Brisbane, 4067, Australia.
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16
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Sinclair-Waters M, Bradbury IR, Morris CJ, Lien S, Kent MP, Bentzen P. Ancient chromosomal rearrangement associated with local adaptation of a postglacially colonized population of Atlantic Cod in the northwest Atlantic. Mol Ecol 2017; 27:339-351. [PMID: 29193392 DOI: 10.1111/mec.14442] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/19/2017] [Accepted: 11/13/2017] [Indexed: 12/28/2022]
Abstract
Intraspecific diversity is central to the management and conservation of exploited species, yet knowledge of how this diversity is distributed and maintained in the genome of many marine species is lacking. Recent advances in genomic analyses allow for genome-wide surveys of intraspecific diversity and offer new opportunities for exploring genomic patterns of divergence. Here, we analysed genome-wide polymorphisms to measure genetic differentiation between an offshore migratory and a nonmigratory population and to define conservation units of Atlantic Cod (Gadus morhua) in coastal Labrador. A total of 141 individuals, collected from offshore sites and from a coastal site within Gilbert Bay, Labrador, were genotyped using an ~11k single nucleotide polymorphism array. Analyses of population structure revealed strong genetic differentiation between migratory offshore cod and nonmigratory Gilbert Bay cod. Genetic differentiation was elevated for loci within a chromosomal rearrangement found on linkage group 1 (LG1) that coincides with a previously found double inversion associated with migratory and nonmigratory ecotype divergence of cod in the northeast Atlantic. This inverted region includes several genes potentially associated with adaptation to differences in salinity and temperature, as well as influencing migratory behaviour. Our work provides evidence that a chromosomal rearrangement on LG1 is associated with parallel patterns of divergence between migratory and nonmigratory ecotypes on both sides of the Atlantic Ocean.
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Affiliation(s)
| | - Ian R Bradbury
- Biology Department, Dalhousie University, Halifax, NS, Canada.,Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Corey J Morris
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Centre for Integrative Genetics, Norwegian University of Life Sciences, Ås, Norway
| | - Matthew P Kent
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Centre for Integrative Genetics, Norwegian University of Life Sciences, Ås, Norway
| | - Paul Bentzen
- Biology Department, Dalhousie University, Halifax, NS, Canada
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17
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Demaerel W, Hestand MS, Vergaelen E, Swillen A, López-Sánchez M, Pérez-Jurado LA, McDonald-McGinn DM, Zackai E, Emanuel BS, Morrow BE, Breckpot J, Devriendt K, Vermeesch JR. Nested Inversion Polymorphisms Predispose Chromosome 22q11.2 to Meiotic Rearrangements. Am J Hum Genet 2017; 101:616-622. [PMID: 28965848 DOI: 10.1016/j.ajhg.2017.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 08/16/2017] [Indexed: 11/17/2022] Open
Abstract
Inversion polymorphisms between low-copy repeats (LCRs) might predispose chromosomes to meiotic non-allelic homologous recombination (NAHR) events and thus lead to genomic disorders. However, for the 22q11.2 deletion syndrome (22q11.2DS), the most common genomic disorder, no such inversions have been uncovered as of yet. Using fiber-FISH, we demonstrate that parents transmitting the de novo 3 Mb LCR22A-D 22q11.2 deletion, the reciprocal duplication, and the smaller 1.5 Mb LCR22A-B 22q11.2 deletion carry inversions of LCR22B-D or LCR22C-D. Hence, the inversions predispose chromosome 22q11.2 to meiotic rearrangements and increase the individual risk for transmitting rearrangements. Interestingly, the inversions are nested or flanking rather than coinciding with the deletion or duplication sizes. This finding raises the possibility that inversions are a prerequisite not only for 22q11.2 rearrangements but also for all NAHR-mediated genomic disorders.
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Affiliation(s)
- Wolfram Demaerel
- Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Matthew S Hestand
- Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Elfi Vergaelen
- Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Ann Swillen
- Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Marcos López-Sánchez
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain; Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain
| | - Luis A Pérez-Jurado
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain; Institut Hospital del Mar d'Investigacions Mèdiques, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Barcelona, Spain
| | - Donna M McDonald-McGinn
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Elaine Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Beverly S Emanuel
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Bernice E Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jeroen Breckpot
- Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Koenraad Devriendt
- Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Joris R Vermeesch
- Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium.
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18
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Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions. Heredity (Edinb) 2017; 119:418-428. [PMID: 28930288 PMCID: PMC5677996 DOI: 10.1038/hdy.2017.54] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 07/13/2017] [Accepted: 08/05/2017] [Indexed: 01/03/2023] Open
Abstract
Chromosomal rearrangements such as inversions can play a crucial role in maintaining polymorphism underlying complex traits and contribute to the process of speciation. In Atlantic cod (Gadus morhua), inversions of several megabases have been identified that dominate genomic differentiation between migratory and nonmigratory ecotypes in the Northeast Atlantic. Here, we show that the same genomic regions display elevated divergence and contribute to ecotype divergence in the Northwest Atlantic as well. The occurrence of these inversions on both sides of the Atlantic Ocean reveals a common evolutionary origin, predating the >100 000-year-old trans-Atlantic separation of Atlantic cod. The long-term persistence of these inversions indicates that they are maintained by selection, possibly facilitated by coevolution of genes underlying complex traits. Our data suggest that migratory behaviour is derived from more stationary, ancestral ecotypes. Overall, we identify several large genomic regions—each containing hundreds of genes—likely involved in the maintenance of genomic divergence in Atlantic cod on both sides of the Atlantic Ocean.
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19
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Barth JMI, Berg PR, Jonsson PR, Bonanomi S, Corell H, Hemmer-Hansen J, Jakobsen KS, Johannesson K, Jorde PE, Knutsen H, Moksnes PO, Star B, Stenseth NC, Svedäng H, Jentoft S, André C. Genome architecture enables local adaptation of Atlantic cod despite high connectivity. Mol Ecol 2017. [DOI: 10.1111/mec.14207] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Julia M. I. Barth
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
| | - Paul R. Berg
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
- Faculty of Medicine; Centre for Molecular Medicine Norway (NCMM); University of Oslo; Oslo Norway
| | - Per R. Jonsson
- Department of Marine Sciences - Tjärnö; University of Gothenburg; Strömstad Sweden
| | - Sara Bonanomi
- Section for Marine Living Resources; National Institute of Aquatic Resources; Technical University of Denmark; Silkeborg Denmark
- National Research Council (CNR); Fisheries Section; Institute of Marine Sciences (ISMAR); Ancona Italy
| | - Hanna Corell
- Department of Marine Sciences - Tjärnö; University of Gothenburg; Strömstad Sweden
| | - Jakob Hemmer-Hansen
- Section for Marine Living Resources; National Institute of Aquatic Resources; Technical University of Denmark; Silkeborg Denmark
| | - Kjetill S. Jakobsen
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
| | - Kerstin Johannesson
- Department of Marine Sciences - Tjärnö; University of Gothenburg; Strömstad Sweden
| | - Per Erik Jorde
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
| | - Halvor Knutsen
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
- Institute of Marine Research; Flødevigen; His Norway
- Department of Natural Sciences; Centre for Coastal Research; University of Agder; Kristiansand Norway
| | - Per-Olav Moksnes
- Department of Marine Sciences; University of Gothenburg; Gothenburg Sweden
| | - Bastiaan Star
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
| | - Nils Chr. Stenseth
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
- Department of Natural Sciences; Centre for Coastal Research; University of Agder; Kristiansand Norway
| | - Henrik Svedäng
- Swedish Institute for the Marine Environment (SIME); Gothenburg Sweden
| | - Sissel Jentoft
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; Oslo Norway
- Department of Natural Sciences; Centre for Coastal Research; University of Agder; Kristiansand Norway
| | - Carl André
- Department of Marine Sciences - Tjärnö; University of Gothenburg; Strömstad Sweden
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20
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Cáceres A, Esko T, Pappa I, Gutiérrez A, Lopez-Espinosa MJ, Llop S, Bustamante M, Tiemeier H, Metspalu A, Joshi PK, Wilsonx JF, Reina-Castillón J, Shin J, Pausova Z, Paus T, Sunyer J, Pérez-Jurado LA, González JR. Ancient Haplotypes at the 15q24.2 Microdeletion Region Are Linked to Brain Expression of MAN2C1 and Children's Intelligence. PLoS One 2016; 11:e0157739. [PMID: 27355585 PMCID: PMC4927142 DOI: 10.1371/journal.pone.0157739] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 06/05/2016] [Indexed: 11/26/2022] Open
Abstract
The chromosome bands 15q24.1-15q24.3 contain a complex region with numerous segmental duplications that predispose to regional microduplications and microdeletions, both of which have been linked to intellectual disability, speech delay and autistic features. The region may also harbour common inversion polymorphisms whose functional and phenotypic manifestations are unknown. Using single nucleotide polymorphism (SNP) data, we detected four large contiguous haplotype-genotypes at 15q24 with Mendelian inheritance in 2,562 trios, African origin, high population stratification and reduced recombination rates. Although the haplotype-genotypes have been most likely generated by decreased or absent recombination among them, we could not confirm that they were the product of inversion polymorphisms in the region. One of the blocks was composed of three haplotype-genotypes (N1a, N1b and N2), which significantly correlated with intelligence quotient (IQ) in 2,735 children of European ancestry from three independent population cohorts. Homozygosity for N2 was associated with lower verbal IQ (2.4-point loss, p-value = 0.01), while homozygosity for N1b was associated with 3.2-point loss in non-verbal IQ (p-value = 0.0006). The three alleles strongly correlated with expression levels of MAN2C1 and SNUPN in blood and brain. Homozygosity for N2 correlated with over-expression of MAN2C1 over many brain areas but the occipital cortex where N1b homozygous highly under-expressed. Our population-based analyses suggest that MAN2C1 may contribute to the verbal difficulties observed in microduplications and to the intellectual disability of microdeletion syndromes, whose characteristic dosage increment and removal may affect different brain areas.
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Affiliation(s)
- Alejandro Cáceres
- ISGlobal, Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- * E-mail: (AC); (JRG)
| | - Tõnu Esko
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute, Cambridge, Massachusetts, United States of America
- Division of Endocrinology, Children’s Hospital Boston, Boston, Massachusetts, United States of America
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Irene Pappa
- School of Pedagogical and Educational Sciences, Erasmus University Rotterdam, Rotterdam, The Netherlands
- Generation R Study Group, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Armand Gutiérrez
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Maria-Jose Lopez-Espinosa
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO–Universitat Jaume I–Universitat de València, Valencia, Spain
| | - Sabrina Llop
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO–Universitat Jaume I–Universitat de València, Valencia, Spain
| | - Mariona Bustamante
- ISGlobal, Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Genomics and Disease Group, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center-Sophia Children’s Hospital, Rotterdam, The Netherlands
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Peter K. Joshi
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland
| | - James F. Wilsonx
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland
| | - Judith Reina-Castillón
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Jean Shin
- Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Zdenka Pausova
- Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Tomáš Paus
- Rotman Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Jordi Sunyer
- ISGlobal, Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Luis A. Pérez-Jurado
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Juan R. González
- ISGlobal, Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Mathematics, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
- * E-mail: (AC); (JRG)
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21
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Sodeland M, Jorde PE, Lien S, Jentoft S, Berg PR, Grove H, Kent MP, Arnyasi M, Olsen EM, Knutsen H. "Islands of Divergence" in the Atlantic Cod Genome Represent Polymorphic Chromosomal Rearrangements. Genome Biol Evol 2016; 8:1012-22. [PMID: 26983822 PMCID: PMC4860689 DOI: 10.1093/gbe/evw057] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In several species genetic differentiation across environmental gradients or between geographically separate populations has been reported to center at "genomic islands of divergence," resulting in heterogeneous differentiation patterns across genomes. Here, genomic regions of elevated divergence were observed on three chromosomes of the highly mobile fish Atlantic cod (Gadus morhua) within geographically fine-scaled coastal areas. The "genomic islands" extended at least 5, 9.5, and 13 megabases on linkage groups 2, 7, and 12, respectively, and coincided with large blocks of linkage disequilibrium. For each of these three chromosomes, pairs of segregating, highly divergent alleles were identified, with little or no gene exchange between them. These patterns of recombination and divergence mirror genomic signatures previously described for large polymorphic inversions, which have been shown to repress recombination across extensive chromosomal segments. The lack of genetic exchange permits divergence between noninverted and inverted chromosomes in spite of gene flow. For the rearrangements on linkage groups 2 and 12, allelic frequency shifts between coastal and oceanic environments suggest a role in ecological adaptation, in agreement with recently reported associations between molecular variation within these genomic regions and temperature, oxygen, and salinity levels. Elevated genetic differentiation in these genomic regions has previously been described on both sides of the Atlantic Ocean, and we therefore suggest that these polymorphisms are involved in adaptive divergence across the species distributional range.
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Affiliation(s)
- Marte Sodeland
- Institute of Marine Research, Flødevigen, Norway Department of Natural Sciences, Faculty of Engineering and Science, University of Agder, Kristiansand, Norway
| | - Per Erik Jorde
- Centre for Ecological and Evolutionary Syntheses, Department of Biosciences, University of Oslo, Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Norway
| | - Sissel Jentoft
- Department of Natural Sciences, Faculty of Engineering and Science, University of Agder, Kristiansand, Norway Centre for Ecological and Evolutionary Syntheses, Department of Biosciences, University of Oslo, Norway
| | - Paul R Berg
- Centre for Ecological and Evolutionary Syntheses, Department of Biosciences, University of Oslo, Norway
| | - Harald Grove
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Norway
| | - Matthew P Kent
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Norway
| | - Mariann Arnyasi
- Centre for Integrative Genetics, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Norway
| | - Esben Moland Olsen
- Institute of Marine Research, Flødevigen, Norway Department of Natural Sciences, Faculty of Engineering and Science, University of Agder, Kristiansand, Norway
| | - Halvor Knutsen
- Institute of Marine Research, Flødevigen, Norway Department of Natural Sciences, Faculty of Engineering and Science, University of Agder, Kristiansand, Norway Centre for Ecological and Evolutionary Syntheses, Department of Biosciences, University of Oslo, Norway
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22
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Berg PR, Star B, Pampoulie C, Sodeland M, Barth JMI, Knutsen H, Jakobsen KS, Jentoft S. Three chromosomal rearrangements promote genomic divergence between migratory and stationary ecotypes of Atlantic cod. Sci Rep 2016; 6:23246. [PMID: 26983361 PMCID: PMC4794648 DOI: 10.1038/srep23246] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/02/2016] [Indexed: 12/15/2022] Open
Abstract
Identification of genome-wide patterns of divergence provides insight on how genomes are influenced by selection and can reveal the potential for local adaptation in spatially structured populations. In Atlantic cod – historically a major marine resource – Northeast-Arctic- and Norwegian coastal cod are recognized by fundamental differences in migratory and non-migratory behavior, respectively. However, the genomic architecture underlying such behavioral ecotypes is unclear. Here, we have analyzed more than 8.000 polymorphic SNPs distributed throughout all 23 linkage groups and show that loci putatively under selection are localized within three distinct genomic regions, each of several megabases long, covering approximately 4% of the Atlantic cod genome. These regions likely represent genomic inversions. The frequency of these distinct regions differ markedly between the ecotypes, spawning in the vicinity of each other, which contrasts with the low level of divergence in the rest of the genome. The observed patterns strongly suggest that these chromosomal rearrangements are instrumental in local adaptation and separation of Atlantic cod populations, leaving footprints of large genomic regions under selection. Our findings demonstrate the power of using genomic information in further understanding the population dynamics and defining management units in one of the world’s most economically important marine resources.
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Affiliation(s)
- Paul R Berg
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
| | | | - Marte Sodeland
- Institute of Marine Research, Flødevigen, N-4817 His, Norway.,Department of Natural Sciences, University of Agder, N-4604 Kristiansand, Norway
| | - Julia M I Barth
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
| | - Halvor Knutsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway.,Institute of Marine Research, Flødevigen, N-4817 His, Norway.,Department of Natural Sciences, University of Agder, N-4604 Kristiansand, Norway
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway.,Department of Natural Sciences, University of Agder, N-4604 Kristiansand, Norway
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23
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Abstract
Polymorphic inversions are a type of structural variants that are difficult to analyze owing to their balanced nature and the location of breakpoints within complex repeated regions. So far, only a handful of inversions have been studied in detail in humans and current knowledge about their possible functional effects is still limited. However, inversions have been related to phenotypic changes and adaptation in multiple species. In this review, we summarize the evidences of the functional impact of inversions in the human genome. First, given that inversions have been shown to inhibit recombination in heterokaryotes, chromosomes displaying different orientation are expected to evolve independently and this may lead to distinct gene-expression patterns. Second, inversions have a role as disease-causing mutations both by directly affecting gene structure or regulation in different ways, and by predisposing to other secondary arrangements in the offspring of inversion carriers. Finally, several inversions show signals of being selected during human evolution. These findings illustrate the potential of inversions to have phenotypic consequences also in humans and emphasize the importance of their inclusion in genome-wide association studies.
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24
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Amador C, Huffman J, Trochet H, Campbell A, Porteous D, Wilson JF, Hastie N, Vitart V, Hayward C, Navarro P, Haley CS. Recent genomic heritage in Scotland. BMC Genomics 2015; 16:437. [PMID: 26048416 PMCID: PMC4458001 DOI: 10.1186/s12864-015-1605-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 05/01/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Generation Scotland Scottish Family Health Study (GS:SFHS) includes 23,960 participants from across Scotland with records for many health-related traits and environmental covariates. Genotypes at ~700 K SNPs are currently available for 10,000 participants. The cohort was designed as a resource for genetic and health related research and the study of complex traits. In this study we developed a suite of analyses to disentangle the genomic differentiation within GS:SFHS individuals to describe and optimise the sample and methods for future analyses. RESULTS We combined the genotypic information of GS:SFHS with 1092 individuals from the 1000 Genomes project and estimated their genomic relationships. Then, we performed Principal Component Analyses of the resulting relationships to investigate the genomic origin of different groups. We characterised two groups of individuals: those with a few sparse rare markers in the genome, and those with several large rare haplotypes which might represent relatively recent exogenous ancestors. We identified some individuals with likely Italian ancestry and a group with some potential African/Asian ancestry. An analysis of homozygosity in the GS:SFHS sample revealed a very similar pattern to other European populations. We also identified an individual carrying a chromosome 1 uniparental disomy. We found evidence of local geographic stratification within the population having impact on the genomic structure. CONCLUSIONS These findings illuminate the history of the Scottish population and have implications for further analyses such as the study of the contributions of common and rare variants to trait heritabilities and the evaluation of genomic and phenotypic prediction of disease.
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Affiliation(s)
- Carmen Amador
- MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK.
| | | | - Holly Trochet
- MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK.
| | | | - David Porteous
- MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK.
| | | | - James F Wilson
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, EH8 9AG, UK.
| | - Nick Hastie
- MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK.
| | | | | | - Pau Navarro
- MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK.
| | - Chris S Haley
- MRC IGMM, University of Edinburgh, Edinburgh, EH4 2XU, UK. .,Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, UK.
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25
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Hernandez-Ferrer C, Quintela Garcia I, Danielski K, Carracedo Á, Pérez-Jurado LA, González JR. affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling. BMC Bioinformatics 2015; 16:167. [PMID: 25991004 PMCID: PMC4438530 DOI: 10.1186/s12859-015-0608-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 04/30/2015] [Indexed: 12/02/2022] Open
Abstract
Background The well-known Genome-Wide Association Studies (GWAS) had led to many scientific discoveries using SNP data. Even so, they were not able to explain the full heritability of complex diseases. Now, other structural variants like copy number variants or DNA inversions, either germ-line or in mosaicism events, are being studies. We present the R package affy2sv to pre-process Affymetrix CytoScan HD/750k array (also for Genome-Wide SNP 5.0/6.0 and Axiom) in structural variant studies. Results We illustrate the capabilities of affy2sv using two different complete pipelines on real data. The first one performing a GWAS and a mosaic alterations detection study, and the other detecting CNVs and performing an inversion calling. Conclusion Both examples presented in the article show up how affy2sv can be used as part of more complex pipelines aimed to analyze Affymetrix SNP arrays data in genetic association studies, where different types of structural variants are considered. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0608-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Carles Hernandez-Ferrer
- Center for Research in Environmental Epidemiology (CREAL), Doctor Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.
| | - Ines Quintela Garcia
- Grupo de Medicina Xenómica - Universidade de Santiago de Compostela, Santiago de Compostela, Spain. .,Centro Nacional de Genotipado - Instituto Carlos III, Santiago de Compostela, Spain.
| | | | - Ángel Carracedo
- Grupo de Medicina Xenómica - Universidade de Santiago de Compostela, Santiago de Compostela, Spain. .,CIBER Enfermedades Raras (CIBERER), Madrid, Spain. .,Fundación Pública Galega de Medicina Xenómica (SERGAS), Santiago de Compostela, Spain. .,King Abdulaziz University, Center of Excellence in Genomic Medicine Research, Jeddah, Saudi Arabia.
| | - Luis A Pérez-Jurado
- CIBER Enfermedades Raras (CIBERER), Madrid, Spain. .,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain.
| | - Juan R González
- Center for Research in Environmental Epidemiology (CREAL), Doctor Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.
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26
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Escaramís G, Docampo E, Rabionet R. A decade of structural variants: description, history and methods to detect structural variation. Brief Funct Genomics 2015; 14:305-14. [PMID: 25877305 DOI: 10.1093/bfgp/elv014] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In the past decade, the view on genomic structural variation (SV) has been changed completely. SVs, previously considered rare events, are now recognized as the largest source of interindividual genetic variation affecting more bases than single nucleotide polymorphisms, variable number of tandem repeats and other small genetic variants. They have also been shown to play a role in phenotypic variation and in disease. In this review, the authors will provide an introduction to SV; a short historical perspective on the research of this source of genomic variation; a description of the types of structural variants, and on how they may have arisen; and an overview on methods of detecting structural variants, focusing on the analysis of high-throughput sequencing data.
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27
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Cáceres A, González JR. Following the footprints of polymorphic inversions on SNP data: from detection to association tests. Nucleic Acids Res 2015; 43:e53. [PMID: 25672393 PMCID: PMC4417146 DOI: 10.1093/nar/gkv073] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 01/20/2015] [Indexed: 11/12/2022] Open
Abstract
Inversion polymorphisms have important phenotypic and evolutionary consequences in humans. Two different methodologies have been used to infer inversions from SNP dense data, enabling the use of large cohorts for their study. One approach relies on the differences in linkage disequilibrium across breakpoints; the other one captures the internal haplotype groups that tag the inversion status of chromosomes. In this article, we assessed the convergence of the two methods in the detection of 20 human inversions that have been reported in the literature. The methods converged in four inversions including inv-8p23, for which we studied its association with low-BMI in American children. Using a novel haplotype tagging method with control on inversion ancestry, we computed the frequency of inv-8p23 in two American cohorts and observed inversion haplotype admixture. Accounting for haplotype ancestry, we found that the European inverted allele in children carries a recessive risk of underweight, validated in an independent Spanish cohort (combined: OR= 2.00, P = 0.001). While the footprints of inversions on SNP data are complex, we show that systematic analyses, such as convergence of different methods and controlling for ancestry, can reveal the contribution of inversions to the ancestral composition of populations and to the heritability of human disease.
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Affiliation(s)
- Alejandro Cáceres
- Center for Research in Environmental Epidemiology (CREAL), Doctor Aiguader 88, Barcelona 08003, Spain IMIM (Hospital del Mar Research Institute), Doctor Aiguader 88, Barcelona 08003, Spain
| | - Juan R González
- Center for Research in Environmental Epidemiology (CREAL), Doctor Aiguader 88, Barcelona 08003, Spain IMIM (Hospital del Mar Research Institute), Doctor Aiguader 88, Barcelona 08003, Spain Centro de Investigacion Biomedica en Red en Epidemiologia y Salud Publica (CIBERESP), Barcelona 08036, Spain Department of Mathematics, Universitat Autonoma de Barcelona (UAB), Barcelona 08193, Spain
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28
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Poelstra JW, Vijay N, Bossu CM, Lantz H, Ryll B, Muller I, Baglione V, Unneberg P, Wikelski M, Grabherr MG, Wolf JBW. The genomic landscape underlying phenotypic integrity in the face of gene flow in crows. Science 2014; 344:1410-4. [DOI: 10.1126/science.1253226] [Citation(s) in RCA: 411] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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29
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Genome-wide association tests of inversions with application to psoriasis. Hum Genet 2014; 133:967-74. [PMID: 24623382 DOI: 10.1007/s00439-014-1437-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 03/04/2014] [Indexed: 01/28/2023]
Abstract
Although inversions have occasionally been found to be associated with disease susceptibility through interrupting a gene or its regulatory region, or by increasing the risk for deleterious secondary rearrangements, no association study has been specifically conducted for risks associated with inversions, mainly because existing approaches to detecting and genotyping inversions do not readily scale to a large number of samples. Based on our recently proposed approach to identifying and genotyping inversions using principal components analysis (PCA), we herein develop a method of detecting association between inversions and disease in a genome-wide fashion. Our method uses genotype data for single nucleotide polymorphisms (SNPs), and is thus cost-efficient and computationally fast. For an inversion polymorphism, local PCA around the inversion region is performed to infer the inversion genotypes of all samples. For many inversions, we found that some of the SNPs inside an inversion region are fixed in the two lineages of different orientations and thus can serve as surrogate markers. Our method can be applied to case-control and quantitative trait association studies to identify inversions that may interrupt a gene or the connection between a gene and its regulatory agents. Our method also offers a new venue to identify inversions that are responsible for disease-causing secondary rearrangements. We illustrated our proposed approach to case-control data for psoriasis and identified novel associations with a few inversion polymorphisms.
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30
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González JR, Cáceres A, Esko T, Cuscó I, Puig M, Esnaola M, Reina J, Siroux V, Bouzigon E, Nadif R, Reinmaa E, Milani L, Bustamante M, Jarvis D, Antó JM, Sunyer J, Demenais F, Kogevinas M, Metspalu A, Cáceres M, Pérez-Jurado LA. A common 16p11.2 inversion underlies the joint susceptibility to asthma and obesity. Am J Hum Genet 2014; 94:361-72. [PMID: 24560518 PMCID: PMC3951940 DOI: 10.1016/j.ajhg.2014.01.015] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 01/28/2014] [Indexed: 12/21/2022] Open
Abstract
The prevalence of asthma and obesity is increasing worldwide, and obesity is a well-documented risk factor for asthma. The mechanisms underlying this association and parallel time trends remain largely unknown but genetic factors may be involved. Here, we report on a common ~0.45 Mb genomic inversion at 16p11.2 that can be accurately genotyped via SNP array data. We show that the inversion allele protects against the joint occurrence of asthma and obesity in five large independent studies (combined sample size of 317 cases and 543 controls drawn from a total of 5,809 samples; combined OR = 0.48, p = 5.5 × 10(-6)). Allele frequencies show remarkable worldwide population stratification, ranging from 10% in East Africa to 49% in Northern Europe, consistent with discordant and extreme genetic drifts or adaptive selections after human migration out of Africa. Inversion alleles strongly correlate with expression levels of neighboring genes, especially TUFM (p = 3.0 × 10(-40)) that encodes a mitochondrial protein regulator of energy balance and inhibitor of type 1 interferon, and other candidates for asthma (IL27) and obesity (APOB48R and SH2B1). Therefore, by affecting gene expression, the ~0.45 Mb 16p11.2 inversion provides a genetic basis for the joint susceptibility to asthma and obesity, with a population attributable risk of 39.7%. Differential mitochondrial function and basal energy balance of inversion alleles might also underlie the potential selection signature that led to their uneven distribution in world populations.
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Affiliation(s)
- Juan R González
- Center for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Department of Mathematics, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain.
| | - Alejandro Cáceres
- Center for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain
| | - Tonu Esko
- Estonian Genome Center, University of Tartu, Tartu 50090, Estonia; Institute of Molecular and Cell Biology, University of Tartu, Tartu 50090, Estonia
| | - Ivon Cuscó
- Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona 08003, Spain
| | - Marta Puig
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain
| | - Mikel Esnaola
- Center for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain
| | - Judith Reina
- Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona 08003, Spain
| | - Valerie Siroux
- INSERM-UJF, U823, Institut Albert Bonniot, 38042 Grenoble, France; Université Joseph Fourier - BP 53, 38041 Grenoble, France
| | - Emmanuelle Bouzigon
- INSERM, UMRS-946, Genetic Variation of Human Diseases Unit, 75010 Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, 75010 Paris, France
| | - Rachel Nadif
- INSERM, U1018, CESP Centre for Research in Epidemiology and Population Health, Respiratory and Environmental Epidemiology Team, 94807 Villejuif, France; Université Paris-Sud 11, UMRS 1018, 94807 Villejuif, France
| | - Eva Reinmaa
- Estonian Genome Center, University of Tartu, Tartu 50090, Estonia
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu 50090, Estonia
| | - Mariona Bustamante
- Center for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Genes and Disease Group, Centre for Genomic Regulation (CRG), Barcelona 08003, Spain
| | - Deborah Jarvis
- National Heart and Lung Institute, Imperial College, London SW7 2AZ, UK
| | - Josep M Antó
- Center for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Department of Mathematics, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Jordi Sunyer
- Center for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Department of Mathematics, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Florence Demenais
- INSERM, UMRS-946, Genetic Variation of Human Diseases Unit, 75010 Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, 75010 Paris, France
| | - Manolis Kogevinas
- Center for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; National School of Public Health, Athens 115 21, Greece
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu 50090, Estonia; Institute of Molecular and Cell Biology, University of Tartu, Tartu 50090, Estonia
| | - Mario Cáceres
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain; Institució Catalana de Recerca i Estudis Avancats (ICREA), Barcelona 08010, Spain
| | - Luis A Pérez-Jurado
- Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona 08003, Spain.
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31
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Aguado C, Gayà-Vidal M, Villatoro S, Oliva M, Izquierdo D, Giner-Delgado C, Montalvo V, García-González J, Martínez-Fundichely A, Capilla L, Ruiz-Herrera A, Estivill X, Puig M, Cáceres M. Validation and genotyping of multiple human polymorphic inversions mediated by inverted repeats reveals a high degree of recurrence. PLoS Genet 2014; 10:e1004208. [PMID: 24651690 PMCID: PMC3961182 DOI: 10.1371/journal.pgen.1004208] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 01/14/2014] [Indexed: 01/17/2023] Open
Abstract
In recent years different types of structural variants (SVs) have been discovered in the human genome and their functional impact has become increasingly clear. Inversions, however, are poorly characterized and more difficult to study, especially those mediated by inverted repeats or segmental duplications. Here, we describe the results of a simple and fast inverse PCR (iPCR) protocol for high-throughput genotyping of a wide variety of inversions using a small amount of DNA. In particular, we analyzed 22 inversions predicted in humans ranging from 5.1 kb to 226 kb and mediated by inverted repeat sequences of 1.6-24 kb. First, we validated 17 of the 22 inversions in a panel of nine HapMap individuals from different populations, and we genotyped them in 68 additional individuals of European origin, with correct genetic transmission in ∼ 12 mother-father-child trios. Global inversion minor allele frequency varied between 1% and 49% and inversion genotypes were consistent with Hardy-Weinberg equilibrium. By analyzing the nucleotide variation and the haplotypes in these regions, we found that only four inversions have linked tag-SNPs and that in many cases there are multiple shared SNPs between standard and inverted chromosomes, suggesting an unexpected high degree of inversion recurrence during human evolution. iPCR was also used to check 16 of these inversions in four chimpanzees and two gorillas, and 10 showed both orientations either within or between species, providing additional support for their multiple origin. Finally, we have identified several inversions that include genes in the inverted or breakpoint regions, and at least one disrupts a potential coding gene. Thus, these results represent a significant advance in our understanding of inversion polymorphism in human populations and challenge the common view of a single origin of inversions, with important implications for inversion analysis in SNP-based studies.
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Affiliation(s)
- Cristina Aguado
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Magdalena Gayà-Vidal
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Sergi Villatoro
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Meritxell Oliva
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - David Izquierdo
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Carla Giner-Delgado
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Víctor Montalvo
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Judit García-González
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | | | - Laia Capilla
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Aurora Ruiz-Herrera
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
- Departament de Biologia Celular, Fisiologia i Immunologia. Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Xavier Estivill
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marta Puig
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Mario Cáceres
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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32
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Koch E, Ristroph M, Kirkpatrick M. Long range linkage disequilibrium across the human genome. PLoS One 2013; 8:e80754. [PMID: 24349013 PMCID: PMC3861250 DOI: 10.1371/journal.pone.0080754] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/17/2013] [Indexed: 11/19/2022] Open
Abstract
Long-range linkage disequilibria (LRLD) between sites that are widely separated on chromosomes may suggest that population admixture, epistatic selection, or other evolutionary forces are at work. We quantified patterns of LRLD on a chromosome-wide level in the YRI population of the HapMap dataset of single nucleotide polymorphisms (SNPs). We calculated the disequilibrium between all pairs of SNPs on each chromosome (a total of >2×10(11) values) and evaluated significance of overall disequilibrium using randomization. The results show an excess of associations between pairs of distant sites (separated by >0.25 cM) on all of the 22 autosomes. We discuss possible explanations for this observation.
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Affiliation(s)
- Evan Koch
- Department of Integrative Biology, University of Texas, Austin, Texas, United States of America
| | - Mickey Ristroph
- Department of Integrative Biology, University of Texas, Austin, Texas, United States of America
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, Texas, United States of America
- * E-mail:
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33
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Ma J, Amos CI. Investigation of inversion polymorphisms in the human genome using principal components analysis. PLoS One 2012; 7:e40224. [PMID: 22808122 PMCID: PMC3392271 DOI: 10.1371/journal.pone.0040224] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 06/02/2012] [Indexed: 11/18/2022] Open
Abstract
Despite the significant advances made over the last few years in mapping inversions with the advent of paired-end sequencing approaches, our understanding of the prevalence and spectrum of inversions in the human genome has lagged behind other types of structural variants, mainly due to the lack of a cost-efficient method applicable to large-scale samples. We propose a novel method based on principal components analysis (PCA) to characterize inversion polymorphisms using high-density SNP genotype data. Our method applies to non-recurrent inversions for which recombination between the inverted and non-inverted segments in inversion heterozygotes is suppressed due to the loss of unbalanced gametes. Inside such an inversion region, an effect similar to population substructure is thus created: two distinct “populations” of inversion homozygotes of different orientations and their 1∶1 admixture, namely the inversion heterozygotes. This kind of substructure can be readily detected by performing PCA locally in the inversion regions. Using simulations, we demonstrated that the proposed method can be used to detect and genotype inversion polymorphisms using unphased genotype data. We applied our method to the phase III HapMap data and inferred the inversion genotypes of known inversion polymorphisms at 8p23.1 and 17q21.31. These inversion genotypes were validated by comparing with literature results and by checking Mendelian consistency using the family data whenever available. Based on the PCA-approach, we also performed a preliminary genome-wide scan for inversions using the HapMap data, which resulted in 2040 candidate inversions, 169 of which overlapped with previously reported inversions. Our method can be readily applied to the abundant SNP data, and is expected to play an important role in developing human genome maps of inversions and exploring associations between inversions and susceptibility of diseases.
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Affiliation(s)
- Jianzhong Ma
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America.
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