1
|
Browning SR, Waples RK, Browning BL. Fast, accurate local ancestry inference with FLARE. Am J Hum Genet 2023; 110:326-335. [PMID: 36610402 PMCID: PMC9943733 DOI: 10.1016/j.ajhg.2022.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/13/2022] [Indexed: 01/09/2023] Open
Abstract
Local ancestry is the source ancestry at each point in the genome of an admixed individual. Inferred local ancestry is used for admixture mapping and population genetic analyses. We present FLARE (fast local ancestry estimation), a method for local ancestry inference. FLARE achieves high accuracy through the use of an extended Li and Stephens model, and it achieves exceptional computational performance through incorporation of computational techniques developed for genotype imputation. Memory requirements are reduced through on-the-fly compression of reference haplotypes and stored checkpoints. Computation time is reduced through the use of composite reference haplotypes. These techniques allow FLARE to scale to datasets with hundreds of thousands of sequenced individuals and to provide superior accuracy on large-scale data. FLARE is open source and available at https://github.com/browning-lab/flare.
Collapse
Affiliation(s)
- Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA, USA.
| | - Ryan K Waples
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Brian L Browning
- Department of Biostatistics, University of Washington, Seattle, WA, USA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
| |
Collapse
|
2
|
García-Ortiz H, Barajas-Olmos F, Flores-Huacuja M, Morales-Rivera MI, Martínez-Hernández A, Baca V, Contreras-Cubas C, Orozco L. Ancestry-dependent genetic structure of the Xq28 risk haplotype in the Mexican population and its association with childhood-onset systemic lupus erythematosus. Front Med (Lausanne) 2023; 9:1044856. [PMID: 36714151 PMCID: PMC9877425 DOI: 10.3389/fmed.2022.1044856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/27/2022] [Indexed: 01/15/2023] Open
Abstract
Objective Here we aimed to investigate the association of the Xq28 risk haplotype (H1) with susceptibility to childhood-onset systemic lupus erythematosus (SLE), and to compare its frequency and genetic structure in the Mexican population with those in other continental populations. Methods We genotyped 15 single-nucleotide variants (SNVs) that form the H1 haplotype, using TaqMan real-time PCR. The association analysis [case-control and transmission disequilibrium test (TDT)] included 376 cases and 400 adult controls, all of whom were mestizos (MEZ). To identify risk alleles in Mexican Indigenous individuals, SNVs were imputed from whole-exome sequencing data of 1,074 individuals. The allelic frequencies determined in MEZ and Indigenous individuals were compared with those of the continental populations from the 1,000 Genomes database phase 3. Linkage disequilibrium (LD) analysis of risk alleles was performed on all populations. Interleukin-1 receptor associated kinase 1 (IRAK1) and methyl CpG binding protein 2 (MECP2) mRNA levels were determined using real-time PCR. Results Case-control analysis revealed genetic association with childhood-onset SLE for all 15 SNVs (OR = 1.49-1.75; p = 0.0095 to 1.81 × 10-4) and for the Xq28 risk haplotype (OR = 1.97, p = 4 × 10-6). Comparing with individuals of European ancestry (0.14-0.16), the frequencies of the risk alleles were significantly higher in the MEZ individuals (0.55-0.68) and even higher in Indigenous individuals (0.57-0.83). LD analysis indicated a differential haplotype structure within the Indigenous groups, which was inherited to the MEZ population as a result of genetic admixture. Individuals homozygous for the Xq28 risk haplotype exhibited decreased levels of both MECP2A and B transcripts. Conclusion We found that the H1 risk haplotype differs in its conformation in the Mexican population. This difference could be attributed to positive selection within the Indigenous population, with its inheritance now having an autoimmune health impact in both the Mexican Indigenous and MEZ populations.
Collapse
Affiliation(s)
- Humberto García-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico
| | - Marlen Flores-Huacuja
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico
| | - Monserrat I. Morales-Rivera
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico
| | - Angélica Martínez-Hernández
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico
| | - Vicente Baca
- Department of Rheumatology, Hospital de Pediatría, CMN Siglo XXI IMSS, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico,*Correspondence: Cecilia Contreras-Cubas,
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, National Institute of Genomic Medicine, SS, Mexico City, Mexico,Lorena Orozco,
| |
Collapse
|
3
|
vonHoldt BM, Brzeski KE, Aardema ML, Schell CJ, Rutledge LY, Fain SR, Shutt AC, Linderholm A, Murphy WJ. Persistence and expansion of cryptic endangered red wolf genomic ancestry along the American Gulf coast. Mol Ecol 2022; 31:5440-5454. [PMID: 34585803 DOI: 10.1111/mec.16200] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/03/2021] [Accepted: 09/22/2021] [Indexed: 12/24/2022]
Abstract
Admixture and introgression play a critical role in adaptation and genetic rescue that has only recently gained a deeper appreciation. Here, we explored the geographical and genomic landscape of cryptic ancestry of the endangered red wolf that persists within the genome of a ubiquitous sister taxon, the coyote, all while the red wolf has been extinct in the wild since the early 1980s. We assessed admixture across 120,621 single nucleotiode polymorphism (SNP) loci genotyped in 293 canid genomes. We found support for increased red wolf ancestry along a west-to-east gradient across the southern United States associated with historical admixture in the past 100 years. Southwestern Louisiana and southeastern Texas, the geographical zone where the last red wolves were known prior to extinction in the wild, contained the highest and oldest levels of red wolf ancestry. Further, given the paucity of inferences based on chromosome types, we compared patterns of ancestry on the X chromosome and autosomes. We additionally aimed to explore the relationship between admixture timing and recombination rate variation to investigate gene flow events. We found that X-linked regions of low recombination rates were depleted of introgression, relative to the autosomes, consistent with the large X effect and enrichment with loci involved in maintaining reproductive isolation. Recombination rate was positively correlated with red wolf ancestry across coyote genomes, consistent with theoretical predictions. The geographical and genomic extent of cryptic red wolf ancestry can provide novel genomic resources for recovery plans targeting the conservation of the endangered red wolf.
Collapse
Affiliation(s)
- Bridgett M vonHoldt
- Ecology & Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Kristin E Brzeski
- College of Forest Resources and Environment Science, Michigan Technological University, Houghton, Michigan, USA
| | - Matthew L Aardema
- Department of Biology, Montclair State University, Montclair, New Jersey, USA.,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
| | - Christopher J Schell
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA
| | - Linda Y Rutledge
- Biology Department, Trent University, Peterborough, Ontario, Canada
| | - Steven R Fain
- USFWS, Clark R. Bavin National Forensics Laboratory, Ashland, Oregon, USA
| | | | - Anna Linderholm
- Department of Anthropology, Texas A&M University, College Station, Texas, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, USA
| |
Collapse
|
4
|
Avadhanam S, Williams AL. Simultaneous inference of parental admixture proportions and admixture times from unphased local ancestry calls. Am J Hum Genet 2022; 109:1405-1420. [PMID: 35908549 PMCID: PMC9388397 DOI: 10.1016/j.ajhg.2022.06.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/24/2022] [Indexed: 02/06/2023] Open
Abstract
Population genetic analyses of local ancestry tracts routinely assume that the ancestral admixture process is identical for both parents of an individual, an assumption that may be invalid when considering recent admixture. Here, we present Parental Admixture Proportion Inference (PAPI), a Bayesian tool for inferring the admixture proportions and admixture times for each parent of a single admixed individual. PAPI analyzes unphased local ancestry tracts and has two components: a binomial model that leverages genome-wide ancestry fractions to infer parental admixture proportions and a hidden Markov model (HMM) that infers admixture times from tract lengths. Crucially, the HMM accounts for unobserved within-ancestry recombination by approximating the pedigree crossover dynamics, enabling inference of parental admixture times. In simulations, we find that PAPI's admixture proportion estimates deviate from the truth by 0.047 on average, outperforming ANCESTOR and PedMix by 46.0% and 57.6%, respectively. Moreover, PAPI's admixture time estimates were strongly correlated with the truth (R=0.76) but have an average downward bias of 1.01 generations that is partly attributable to inaccuracies in local ancestry inference. As an illustration of its utility, we ran PAPI on African American genotypes from the PAGE study (N = 5,786) and found strong evidence of assortative mating by ancestry proportion: couples' ancestry proportions are highly correlated (R = 0.87) and are closer to each other than expected under random mating (p < 10-6). We anticipate that PAPI will be useful in studying the population dynamics of admixture and will also be of interest to individuals seeking to learn about their personal genealogies.
Collapse
Affiliation(s)
- Siddharth Avadhanam
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA
| | - Amy L Williams
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
5
|
vonHoldt BM, Hinton JW, Shutt AC, Murphy SM, Karlin ML, Adams JR, Waits LP, Brzeski KE. Reviving ghost alleles: Genetically admixed coyotes along the American Gulf Coast are critical for saving the endangered red wolf. SCIENCE ADVANCES 2022; 8:eabn7731. [PMID: 35767623 PMCID: PMC9242586 DOI: 10.1126/sciadv.abn7731] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
The last known red wolves were captured in southwestern Louisiana and eastern Texas in 1980 to establish a captive breeding population. Before their extirpation, gene flow with coyotes resulted in the persistence of endangered red wolf genetic variation in local coyote populations. We assessed genomic ancestry and morphology of coyotes in southwestern Louisiana. We detected that 38 to 62% of the coyote genomes contained red wolf ancestry acquired in the past 30 years and have an admixture profile similar to that of the canids captured before the extirpation of red wolves. We further documented a positive correlation between ancestry and weight. Our findings highlight the importance of hybrids and admixed genomes as a reservoir of endangered species ancestry for innovative conservation efforts. Together, this work presents an unprecedented system that conservation can leverage to enrich the recovery program of an endangered species.
Collapse
Affiliation(s)
- Bridgett M. vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | | | | | - Sean M. Murphy
- Forestry and Natural Resources, University of Kentucky, Lexington, KY, USA
| | - Melissa L. Karlin
- Department of Physics and Environmental Science, St. Mary’s University, San Antonio, TX, USA
| | - Jennifer R. Adams
- Laboratory for Ecological, Evolutionary and Conservation Genetics, Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Lisette P. Waits
- Laboratory for Ecological, Evolutionary and Conservation Genetics, Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Kristin E. Brzeski
- College of Forest Resources and Environment Science, Michigan Technological University, Houghton, MI, USA
| |
Collapse
|
6
|
Santander C, Molinaro L, Mutti G, Martínez FI, Mathe J, Ferreira da Silva MJ, Caldon M, Oteo-Garcia G, Aldeias V, Archer W, Bamford M, Biro D, Bobe R, Braun DR, Hammond P, Lüdecke T, Pinto MJ, Meira Paulo L, Stalmans M, Regala FT, Bertolini F, Moltke I, Raveane A, Pagani L, Carvalho S, Capelli C. Genomic variation in baboons from central Mozambique unveils complex evolutionary relationships with other Papio species. BMC Ecol Evol 2022; 22:44. [PMID: 35410131 PMCID: PMC8996594 DOI: 10.1186/s12862-022-01999-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/28/2022] [Indexed: 11/11/2022] Open
Abstract
Background Gorongosa National Park in Mozambique hosts a large population of baboons, numbering over 200 troops. Gorongosa baboons have been tentatively identified as part of Papio ursinus on the basis of previous limited morphological analysis and a handful of mitochondrial DNA sequences. However, a recent morphological and morphometric analysis of Gorongosa baboons pinpointed the occurrence of several traits intermediate between P. ursinus and P. cynocephalus, leaving open the possibility of past and/or ongoing gene flow in the baboon population of Gorongosa National Park. In order to investigate the evolutionary history of baboons in Gorongosa, we generated high and low coverage whole genome sequence data of Gorongosa baboons and compared it to available Papio genomes. Results We confirmed that P. ursinus is the species closest to Gorongosa baboons. However, the Gorongosa baboon genomes share more derived alleles with P. cynocephalus than P. ursinus does, but no recent gene flow between P. ursinus and P. cynocephalus was detected when available Papio genomes were analyzed. Our results, based on the analysis of autosomal, mitochondrial and Y chromosome data, suggest complex, possibly male-biased, gene flow between Gorongosa baboons and P. cynocephalus, hinting to direct or indirect contributions from baboons belonging to the “northern” Papio clade, and signal the presence of population structure within P. ursinus. Conclusions The analysis of genome data generated from baboon samples collected in central Mozambique highlighted a complex set of evolutionary relationships with other baboons. Our results provided new insights in the population dynamics that have shaped baboon diversity. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01999-7.
Collapse
Affiliation(s)
- Cindy Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark. .,Department of Zoology, University of Oxford, Oxford, UK.
| | - Ludovica Molinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Giacomo Mutti
- Department of Biosciences, University of Milan, Milan, Italy.,Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Felipe I Martínez
- Escuela de Antropología, Facultad de Ciencias Sociales, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jacinto Mathe
- School of Anthropology, University of Oxford, Oxford, UK
| | - Maria Joana Ferreira da Silva
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.,CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.,ONE - Organisms and Environment Group, School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff, UK
| | - Matteo Caldon
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gonzalo Oteo-Garcia
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Vera Aldeias
- Interdisciplinary Center for Archaeology and Evolution of Human Behavior (ICArEHB), Universidade do Algarve, Faro, Portugal
| | - Will Archer
- Department of Archaeology, National Museum, Bloemfontein, South Africa
| | - Marion Bamford
- Evolutionary Studies Institute, University of the Witwatersrand, Johannesburg, South Africa
| | - Dora Biro
- Department of Zoology, University of Oxford, Oxford, UK
| | - René Bobe
- School of Anthropology, University of Oxford, Oxford, UK.,Gorongosa National Park, Sofala, Mozambique
| | - David R Braun
- Center for the Advanced Study of Human Paleobiology, George Washington University, Washington, USA
| | | | - Tina Lüdecke
- School of Anthropology, University of Oxford, Oxford, UK.,Emmy Noether Group for Hominin Meat Consumption, Max Planck Institute for Chemistry, Mainz, Germany
| | - Maria José Pinto
- AESDA - Associação de Estudos Subterrâneos e Defesa do Ambiente, Lisbon, Portugal
| | - Luis Meira Paulo
- AESDA - Associação de Estudos Subterrâneos e Defesa do Ambiente, Lisbon, Portugal
| | - Marc Stalmans
- Department of Scientific Services, Gorongosa National Park, Chitengo, Sofala Province, Mozambique
| | - Frederico Tátá Regala
- Interdisciplinary Center for Archaeology and Evolution of Human Behavior (ICArEHB), Universidade do Algarve, Faro, Portugal
| | - Francesco Bertolini
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Alessandro Raveane
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Biology, University of Padua, Padua, Italy
| | - Susana Carvalho
- School of Anthropology, University of Oxford, Oxford, UK. .,Gorongosa National Park, Sofala, Mozambique.
| | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford, UK. .,Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
| |
Collapse
|
7
|
Cuadros-Espinoza S, Laval G, Quintana-Murci L, Patin E. The genomic signatures of natural selection in admixed human populations. Am J Hum Genet 2022; 109:710-726. [PMID: 35259336 DOI: 10.1016/j.ajhg.2022.02.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/14/2022] [Indexed: 12/15/2022] Open
Abstract
Admixture has been a pervasive phenomenon in human history, extensively shaping the patterns of population genetic diversity. There is increasing evidence to suggest that admixture can also facilitate genetic adaptation to local environments, i.e., admixed populations acquire beneficial mutations from source populations, a process that we refer to as "adaptive admixture." However, the role of adaptive admixture in human evolution and the power to detect it remain poorly characterized. Here, we use extensive computer simulations to evaluate the power of several neutrality statistics to detect natural selection in the admixed population, assuming multiple admixture scenarios. We show that statistics based on admixture proportions, Fadm and LAD, show high power to detect mutations that are beneficial in the admixed population, whereas other statistics, including iHS and FST, falsely detect neutral mutations that have been selected in the source populations only. By combining Fadm and LAD into a single, powerful statistic, we scanned the genomes of 15 worldwide, admixed populations for signatures of adaptive admixture. We confirm that lactase persistence and resistance to malaria have been under adaptive admixture in West Africans and in Malagasy, North Africans, and South Asians, respectively. Our approach also uncovers other cases of adaptive admixture, including APOL1 in Fulani nomads and PKN2 in East Indonesians, involved in resistance to infection and metabolism, respectively. Collectively, our study provides evidence that adaptive admixture has occurred in human populations whose genetic history is characterized by periods of isolation and spatial expansions resulting in increased gene flow.
Collapse
|
8
|
Biswas P, Villanueva AL, Soto-Hermida A, Duncan JL, Matsui H, Borooah S, Kurmanov B, Richard G, Khan SY, Branham K, Huang B, Suk J, Bakall B, Goldberg JL, Gabriel L, Khan NW, Raghavendra PB, Zhou J, Devalaraja S, Huynh A, Alapati A, Zawaydeh Q, Weleber RG, Heckenlively JR, Hejtmancik JF, Riazuddin S, Sieving PA, Riazuddin SA, Frazer KA, Ayyagari R. Deciphering the genetic architecture and ethnographic distribution of IRD in three ethnic populations by whole genome sequence analysis. PLoS Genet 2021; 17:e1009848. [PMID: 34662339 PMCID: PMC8589175 DOI: 10.1371/journal.pgen.1009848] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 11/12/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
Patients with inherited retinal dystrophies (IRDs) were recruited from two understudied populations: Mexico and Pakistan as well as a third well-studied population of European Americans to define the genetic architecture of IRD by performing whole-genome sequencing (WGS). Whole-genome analysis was performed on 409 individuals from 108 unrelated pedigrees with IRDs. All patients underwent an ophthalmic evaluation to establish the retinal phenotype. Although the 108 pedigrees in this study had previously been examined for mutations in known IRD genes using a wide range of methodologies including targeted gene(s) or mutation(s) screening, linkage analysis and exome sequencing, the gene mutations responsible for IRD in these 108 pedigrees were not determined. WGS was performed on these pedigrees using Illumina X10 at a minimum of 30X depth. The sequence reads were mapped against hg19 followed by variant calling using GATK. The genome variants were annotated using SnpEff, PolyPhen2, and CADD score; the structural variants (SVs) were called using GenomeSTRiP and LUMPY. We identified potential causative sequence alterations in 61 pedigrees (57%), including 39 novel and 54 reported variants in IRD genes. For 57 of these pedigrees the observed genotype was consistent with the initial clinical diagnosis, the remaining 4 had the clinical diagnosis reclassified based on our findings. In seven pedigrees (12%) we observed atypical causal variants, i.e. unexpected genotype(s), including 4 pedigrees with causal variants in more than one IRD gene within all affected family members, one pedigree with intrafamilial genetic heterogeneity (different affected family members carrying causal variants in different IRD genes), one pedigree carrying a dominant causative variant present in pseudo-recessive form due to consanguinity and one pedigree with a de-novo variant in the affected family member. Combined atypical and large structural variants contributed to about 20% of cases. Among the novel mutations, 75% were detected in Mexican and 50% found in European American pedigrees and have not been reported in any other population while only 20% were detected in Pakistani pedigrees and were not previously reported. The remaining novel IRD causative variants were listed in gnomAD but were found to be very rare and population specific. Mutations in known IRD associated genes contributed to pathology in 63% Mexican, 60% Pakistani and 45% European American pedigrees analyzed. Overall, contribution of known IRD gene variants to disease pathology in these three populations was similar to that observed in other populations worldwide. This study revealed a spectrum of mutations contributing to IRD in three populations, identified a large proportion of novel potentially causative variants that are specific to the corresponding population or not reported in gnomAD and shed light on the genetic architecture of IRD in these diverse global populations.
Collapse
Affiliation(s)
- Pooja Biswas
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
- School of Biotechnology, REVA University, Bengaluru, Karnataka, India
| | - Adda L. Villanueva
- Retina and Genomics Institute, Yucatán, México
- Laboratoire de Diagnostic Moleculaire, Hôpital Maisonneuve Rosemont, Montreal, Quebec, Canada
| | - Angel Soto-Hermida
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Jacque L. Duncan
- Ophthalmology, University of California San Francisco, San Francisco, California, United States of America
| | - Hiroko Matsui
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Shyamanga Borooah
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Berzhan Kurmanov
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | | | - Shahid Y. Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Kari Branham
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, United States of America
| | - Bonnie Huang
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - John Suk
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Benjamin Bakall
- Ophthalmology, University of Arizona College of Medicine Phoenix, Phoenix, Arizona, United States of America
| | - Jeffrey L. Goldberg
- Byers Eye Institute, Stanford, Palo Alto, California, United States of America
| | - Luis Gabriel
- Genetics and Ophthalmology, Genelabor, Goiânia, Brazil
| | - Naheed W. Khan
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, United States of America
| | - Pongali B. Raghavendra
- School of Biotechnology, REVA University, Bengaluru, Karnataka, India
- School of Regenerative Medicine, Manipal University, Bengaluru, Karnataka, India
| | - Jason Zhou
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Sindhu Devalaraja
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Andrew Huynh
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Akhila Alapati
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Qais Zawaydeh
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Richard G. Weleber
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - John R. Heckenlively
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, United States of America
| | - J. Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
| | - Paul A. Sieving
- National Eye Institute, Bethesda, Maryland, United States of America
- Ophthalmology & Vision Science, UC Davis Medical Center, California, United States of America
| | - S. Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Kelly A. Frazer
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, United States of America
- Department of Pediatrics, Rady Children’s Hospital, Division of Genome Information Sciences, San Diego, California, United States of America
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| |
Collapse
|
9
|
Isshiki M, Naka I, Kimura R, Nishida N, Furusawa T, Natsuhara K, Yamauchi T, Nakazawa M, Ishida T, Inaoka T, Matsumura Y, Ohtsuka R, Ohashi J. Admixture with indigenous people helps local adaptation: admixture-enabled selection in Polynesians. BMC Ecol Evol 2021; 21:179. [PMID: 34551727 PMCID: PMC8456657 DOI: 10.1186/s12862-021-01900-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 08/25/2021] [Indexed: 01/08/2023] Open
Abstract
Background Homo sapiens have experienced admixture many times in the last few thousand years. To examine how admixture affects local adaptation, we investigated genomes of modern Polynesians, who are shaped through admixture between Austronesian-speaking people from Southeast Asia (Asian-related ancestors) and indigenous people in Near Oceania (Papuan-related ancestors). Methods In this study local ancestry was estimated across the genome in Polynesians (23 Tongan subjects) to find the candidate regions of admixture-enabled selection contributed by Papuan-related ancestors. Results The mean proportion of Papuan-related ancestry across the Polynesian genome was estimated as 24.6% (SD = 8.63%), and two genomic regions, the extended major histocompatibility complex (xMHC) region on chromosome 6 and the ATP-binding cassette transporter sub-family C member 11 (ABCC11) gene on chromosome 16, showed proportions of Papuan-related ancestry more than 5 SD greater than the mean (> 67.8%). The coalescent simulation under the assumption of selective neutrality suggested that such signals of Papuan-related ancestry enrichment were caused by positive selection after admixture (false discovery rate = 0.045). The ABCC11 harbors a nonsynonymous SNP, rs17822931, which affects apocrine secretory cell function. The approximate Bayesian computation indicated that, in Polynesian ancestors, a strong positive selection (s = 0.0217) acted on the ancestral allele of rs17822931 derived from Papuan-related ancestors. Conclusions Our results suggest that admixture with Papuan-related ancestors contributed to the rapid local adaptation of Polynesian ancestors. Considering frequent admixture events in human evolution history, the acceleration of local adaptation through admixture should be a common event in humans. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01900-y.
Collapse
Affiliation(s)
- Mariko Isshiki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Izumi Naka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, 903-0125, Japan
| | - Nao Nishida
- Genome Medical Science Project, Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, 272-8516, Japan
| | - Takuro Furusawa
- Graduate School of Asian and African Area Studies, Kyoto University, Kyoto, 606-8501, Japan
| | - Kazumi Natsuhara
- Department of International Health and Nursing, Faculty of Nursing, Toho University, Tokyo, 143-0015, Japan
| | - Taro Yamauchi
- Faculty of Health Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Minato Nakazawa
- Graduate School of Health Sciences, Kobe University, Kobe, 654-0142, Japan
| | - Takafumi Ishida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Tsukasa Inaoka
- Department of Human Ecology, Faculty of Agriculture, Saga University, Saga, 840-8502, Japan
| | - Yasuhiro Matsumura
- Faculty of Health and Nutrition, Bunkyo University, Chigasaki, 253-8550, Japan
| | | | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
| |
Collapse
|
10
|
Interface of Human/Wildlife Interactions: An Example of a Bold Coyote (Canis latrans) in Atlanta, GA, USA. DIVERSITY 2021. [DOI: 10.3390/d13080372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
There is arguably no other North American species that better illustrates the complexities of the human-wildlife interface than the coyote. In this study, a melanistic coyote in metropolitan Atlanta, Georgia was exhibiting unusually bold behaviors that included encounters with humans, domestic dogs, and attempts to enter homes. After tracking this coyote (nicknamed Carmine) across a highly urbanized landscape with participatory science, including at least 80 publicly reported sightings, he was captured and relocated to a wildlife sanctuary. Genome-wide analyses revealed 92.8% coyote ancestry, 1.7% gray wolf ancestry, and 5.5% domestic dog ancestry. The dog alleles in Carmine’s genome were estimated to have been acquired by his ancestors 14–29 years ago. Despite his bold behavior, Carmine did not carry any mutations known to shape hypersociability in canines. He did, however, carry a single copy of the dominant mutation responsible for his melanistic coat color. This detailed study of Carmine dispels common assumptions about the reticent coyote personality and the origins of behavior. His unusual bold behavior created a higher level of human-coyote interaction. He now serves as a public ambassador for human-wildlife coexistence, urging the global community to reconsider mythologies about wildlife and promote coexistence with them in landscapes significantly altered by human activity in our rapidly changing world.
Collapse
|
11
|
Genetic Ancestry Inference and Its Application for the Genetic Mapping of Human Diseases. Int J Mol Sci 2021; 22:ijms22136962. [PMID: 34203440 PMCID: PMC8269095 DOI: 10.3390/ijms22136962] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/21/2022] Open
Abstract
Admixed populations arise when two or more ancestral populations interbreed. As a result of this admixture, the genome of admixed populations is defined by tracts of variable size inherited from these parental groups and has particular genetic features that provide valuable information about their demographic history. Diverse methods can be used to derive the ancestry apportionment of admixed individuals, and such inferences can be leveraged for the discovery of genetic loci associated with diseases and traits, therefore having important biomedical implications. In this review article, we summarize the most common methods of global and local genetic ancestry estimation and discuss the use of admixture mapping studies in human diseases.
Collapse
|
12
|
Wu D, Li PY, Pan B, Tiang Z, Dou J, Williantarra I, Pribowo AY, Nurdiansyah R, Foo RSY, Wang C. Genetic admixture in the culturally unique Peranakan Chinese population in Southeast Asia. Mol Biol Evol 2021; 38:4463-4474. [PMID: 34152401 PMCID: PMC8476152 DOI: 10.1093/molbev/msab187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The Peranakan Chinese are culturally unique descendants of immigrants from China who settled in the Malay Archipelago ∼300-500 years ago. Today, among large communities in Southeast Asia, the Peranakans have preserved Chinese traditions with strong influence from the local indigenous Malays. Yet, whether or to what extent genetic admixture co-occurred with the cultural mixture has been a topic of ongoing debate. We performed whole-genome sequencing (WGS) on 177 Singapore (SG) Peranakans and analyzed the data jointly with WGS data of Asian and European populations. We estimated that Peranakan Chinese inherited ∼5.62% (95% confidence interval [CI]: 4.75-6.46%) Malay ancestry, much higher than that in SG Chinese (1.08%, 0.69-1.53%), southern Chinese (0.86%, 0.57-1.31%), and northern Chinese (0.25%, 0.18-0.33%). A sex-biased admixture history, in which the Malay ancestry was contributed primarily by females, was supported by X chromosomal variants, and mitochondrial (MT) and Y haplogroups. Finally, we identified an ancient admixture event shared by Peranakan Chinese and SG Chinese ∼1,612 (95% CI: 1,345-1,923) years ago, coinciding with the settlement history of Han Chinese in southern China, apart from the recent admixture event with Malays unique to Peranakan Chinese ∼190 (159-213) years ago. These findings greatly advance our understanding of the dispersal history of Chinese and their interaction with indigenous populations in Southeast Asia.
Collapse
Affiliation(s)
- Degang Wu
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peter Yiqing Li
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUHS Cardiovascular Diseases Translational Research Program, National University Health System, Singapore, Singapore
| | - Bangfen Pan
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUHS Cardiovascular Diseases Translational Research Program, National University Health System, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Zenia Tiang
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUHS Cardiovascular Diseases Translational Research Program, National University Health System, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jinzhuang Dou
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Ivanna Williantarra
- Department of Anatomy and Medical Imaging, School of Medical Science, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
- Department of Biotechnology, Indonesia International Institute for Life Sciences (i3L), Jakarta, Indonesia
| | - Amadeus Yeremia Pribowo
- Department of Biotechnology, Indonesia International Institute for Life Sciences (i3L), Jakarta, Indonesia
| | - Rizky Nurdiansyah
- Department of Bioinformatics, Indonesia International Institute for Life Sciences (i3L), Jakarta, Indonesia
| | | | - Roger S Y Foo
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUHS Cardiovascular Diseases Translational Research Program, National University Health System, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Corresponding authors: E-mails: ;
| | - Chaolong Wang
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Corresponding authors: E-mails: ;
| |
Collapse
|
13
|
Beltrán JQ, Ogando-Rivas E, Nettel-Rueda B, Velasco-Campos F, Navarro-Olvera JL, Aguado-Carrillo G, Soriano-Sánchez JA, Alpizar-Aguirre A, Carrillo-Ruiz JD. Women in Neurosurgery: First Neurosurgeon in Latin America and Current Mexican Leaders. World Neurosurg 2021; 150:114-120. [PMID: 33781943 DOI: 10.1016/j.wneu.2021.03.102] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND History has taught us that Mexican culture has been largely supported by women, despite gender prejudice from the society. Neurosurgery has not been the exception. Therefore, we investigated the challenges and influence of female neurosurgeons in Mexico. METHODS We conducted a review of the literature and an analysis of the internal database of the Mexican Society of Neurological Surgery focusing on 3 topics: 1) the historical presence of women and gender inequality in Mexico; 2) the life and legacy of the woman who became the first neurosurgeon in Mexico and in Latin America; and 3) the participation of women in neurosurgery in the past 3 decades. RESULTS In Latin America, the first woman in neurosurgery was María Cristina García-Sancho, who completed her neurosurgical training in 1951. Currently, women represent 6.2% of the total members of the Mexican Society of Neurological Surgery (MSNS). This percentage is still low, although data collected in this study suggest that it might increase in the next few years because 16.7% of Board Directors of the MSNS are women, the next elected president is a female neurosurgeon, and 14.5% of neurosurgery residents are women. CONCLUSIONS Although a steady increase has occurred of women in neurosurgery in Mexico, there is still work to do, especially to overcome the barriers related to the old assumptions of the cultural and social roles of women.
Collapse
Affiliation(s)
- Jesús Q Beltrán
- Unit for Stereotactic and Functional Neurosurgery, General Hospital of Mexico, Mexico City, Mexico; Direction of Research, General Hospital of Mexico, Mexico City, Mexico
| | - Elizabeth Ogando-Rivas
- Department of Neurosurgery, University of Florida, Gainesville, Florida, USA; Brain Tumor Immunotherapy Program, University of Florida, Gainesville, Florida, USA
| | - Barbara Nettel-Rueda
- Department of Neurosurgery, Hospital de Especialidades del Centro Médico Nacional Siglo XXI, Mexico City, Mexico
| | - Francisco Velasco-Campos
- Unit for Stereotactic and Functional Neurosurgery, General Hospital of Mexico, Mexico City, Mexico
| | - José L Navarro-Olvera
- Unit for Stereotactic and Functional Neurosurgery, General Hospital of Mexico, Mexico City, Mexico
| | - Gustavo Aguado-Carrillo
- Unit for Stereotactic and Functional Neurosurgery, General Hospital of Mexico, Mexico City, Mexico
| | - José A Soriano-Sánchez
- Spine Clinic, The American-British Cowdray Medical Center IAP, Campus Santa Fe, Mexico City, Mexico
| | | | - José D Carrillo-Ruiz
- Unit for Stereotactic and Functional Neurosurgery, General Hospital of Mexico, Mexico City, Mexico; Direction of Research, General Hospital of Mexico, Mexico City, Mexico; Direction of Faculty of Health Sciences, Anahuac University, Mexico City, Mexico.
| |
Collapse
|
14
|
Abstract
Throughout human history, large-scale migrations have facilitated the formation of populations with ancestry from multiple previously separated populations. This process leads to subsequent shuffling of genetic ancestry through recombination, producing variation in ancestry between populations, among individuals in a population, and along the genome within an individual. Recent methodological and empirical developments have elucidated the genomic signatures of this admixture process, bringing previously understudied admixed populations to the forefront of population and medical genetics. Under this theme, we present a collection of recent PLOS Genetics publications that exemplify recent progress in human genetic admixture studies, and we discuss potential areas for future work.
Collapse
Affiliation(s)
- Katharine L. Korunes
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
| |
Collapse
|
15
|
Póvoa R. New Markers of Carotid Thickening in Hypertension. Arq Bras Cardiol 2021; 116:66-67. [PMID: 33566966 PMCID: PMC8159507 DOI: 10.36660/abc.20201335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rui Póvoa
- Universidade Federal de São Paulo, São Paulo, SP - Brasil
| |
Collapse
|
16
|
Gamboa R, Jaramillo-Estrella MJ, Martínez-Alvarado MDR, Soto ME, Torres-Paz YE, Gonzalo-Calvo DD, Del Valle-Mondragón L, López-Marure R, Llorente-Cortés VC, Huesca-Gómez C. Monocyte Low-Density Lipoprotein Receptor-Related Protein 1 (LRP1) Expression Correlates with cIMT in Mexican Hypertensive Patients. Arq Bras Cardiol 2021; 116:56-65. [PMID: 33566965 PMCID: PMC8159500 DOI: 10.36660/abc.20190535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 03/16/2020] [Indexed: 12/26/2022] Open
Abstract
Fundamento A hipertensão arterial (HTA) representa um grande fator de risco de morbidade e mortalidade cardiovascular. Ainda não se sabe que mecanismos moleculares específicos estão associados ao desenvolvimento de hipertensão essencial. Objetivo Neste trabalho, analisamos a associação entre expressão mRNA de monócito LRP1, expressão de proteína LRP1, e espessura íntima-média de carótida (EIMC) de pacientes com hipertensão essencial. Métodos A expressão mRNA de monócito LRP1 e os níveis de proteína e EIMC foram quantificados em 200 indivíduos mexicanos, sendo 91 normotensos (NT) e 109 hipertensos (HT) A significância estatística foi definida em p < 0,05. Resultados O grupo de pacientes HT tinha EIMC maior altamente significativa em comparação com os pacientes NT (p = 0,002), e isso está relacionado ao aumento na expressão mRNA de LRP1 (6,54 versus. 2,87) (p = 0,002) e expressão de proteína LRP1 (17,83 versus 6,25), respectivamente (p = 0,001). Essas diferenças foram mantidas mesmo quando dividimos nossos grupos de estudo, levando em consideração apenas aqueles que apresentavam dislipidemia na expressão de mRNA (p = 0,041) e de proteínas (p < 0,001). Também se identificou que a indução de LRP1 mediada por LRP1 em monócitos em de maneira dependente de dose e tempo, com diferença significativa em NT versus HT (0,195 ± 0,09 versus 0,226 ± 0,12, p = 0,046). Conclusão Foi encontrado um aumento em EIMC em indivíduos com hipertensão, associada a expressões de proteína LRP1 e mRNA mais altas em monócitos, independente da presença de dislipidemia em pacientes HT. Esses resultados que a upregulation de LRP1 em monócitos de pacientes hipertensos mexicanos poderia estar envolvida na diminuição da EIMC. (Arq Bras Cardiol. 2021; 116(1):56-65)
Collapse
Affiliation(s)
- Ricardo Gamboa
- Instituto Nacional de Cardiologia Ignacio Chavez, Ciudad de México - México
| | | | | | - Maria Elena Soto
- Instituto Nacional de Cardiologia Ignacio Chavez, Ciudad de México - México
| | | | - David de Gonzalo-Calvo
- Hospital de Sant Pau - Lipids and Cardiovascular Pathology Group, Barcelona, Catalunya - Espanha
| | | | | | | | | |
Collapse
|
17
|
Wong ML, Arcos-Burgos M, Liu S, Licinio AW, Yu C, Chin EWM, Yao WD, Lu XY, Bornstein SR, Licinio J. Rare Functional Variants Associated with Antidepressant Remission in Mexican-Americans: Short title: Antidepressant remission and pharmacogenetics in Mexican-Americans. J Affect Disord 2021; 279:491-500. [PMID: 33128939 PMCID: PMC7953425 DOI: 10.1016/j.jad.2020.10.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 08/24/2020] [Accepted: 10/11/2020] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Rare genetic functional variants can contribute to 30-40% of functional variability in genes relevant to drug action. Therefore, we investigated the role of rare functional variants in antidepressant response. METHOD Mexican-American individuals meeting the Diagnostic and Statistical Manual-IV criteria for major depressive disorder (MDD) participated in a prospective randomized, double-blind study with desipramine or fluoxetine. The rare variant analysis was performed using whole-exome genotyping data. Network and pathway analyses were carried out with the list of significant genes. RESULTS The Kernel-Based Adaptive Cluster method identified functional rare variants in 35 genes significantly associated with treatment remission (False discovery rate, FDR <0.01). Pathway analysis of these genes supports the involvement of the following gene ontology processes: olfactory/sensory transduction, regulation of response to cytokine stimulus, and meiotic cell cycleprocess. LIMITATIONS Our study did not have a placebo arm. We were not able to use antidepressant blood level as a covariate. Our study is based on a small sample size of only 65 Mexican-American individuals. Further studies using larger cohorts are warranted. CONCLUSION Our data identified several rare functional variants in antidepressant drug response in MDD patients. These have the potential to serve as genetic markers for predicting drug response. TRIAL REGISTRATION ClinicalTrials.gov NCT00265291.
Collapse
Affiliation(s)
- Ma-Li Wong
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, USA; Department of Neuroscience and Physiology, State University of New York, Upstate Medical University, Syracuse, NY, USA; Mind & Brain Theme, South Australian Health and Medical Research Institute Adelaide, South Australia, Australia; Department of Psychiatry, Flinders University College of Medicine and Public Health, Bedford Park, South Australia, Australia.
| | - Mauricio Arcos-Burgos
- Grupo de Investigación en Psiquiatría, Departamento de Psiquiatría, Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellin, Antioquia, Colombia
| | - Sha Liu
- Mind & Brain Theme, South Australian Health and Medical Research Institute Adelaide, South Australia, Australia
| | - Alice W Licinio
- Mind & Brain Theme, South Australian Health and Medical Research Institute Adelaide, South Australia, Australia
| | - Chenglong Yu
- Mind & Brain Theme, South Australian Health and Medical Research Institute Adelaide, South Australia, Australia; Department of Psychiatry, Flinders University College of Medicine and Public Health, Bedford Park, South Australia, Australia
| | - Eunice W M Chin
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, USA
| | - Wei-Dong Yao
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, USA; Department of Neuroscience and Physiology, State University of New York, Upstate Medical University, Syracuse, NY, USA
| | - Xin-Yun Lu
- Department of Neuroscience & Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Stefan R Bornstein
- Medical Clinic III, Carl Gustav Carus University Hospital, Dresden University of Technology, Dresden, Germany
| | - Julio Licinio
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, USA; Department of Neuroscience and Physiology, State University of New York, Upstate Medical University, Syracuse, NY, USA; Mind & Brain Theme, South Australian Health and Medical Research Institute Adelaide, South Australia, Australia; Department of Psychiatry, Flinders University College of Medicine and Public Health, Bedford Park, South Australia, Australia.
| |
Collapse
|
18
|
Missaggia BO, Reales G, Cybis GB, Hünemeier T, Bortolini MC. Adaptation and co-adaptation of skin pigmentation and vitamin D genes in native Americans. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:1060-1077. [PMID: 33325159 DOI: 10.1002/ajmg.c.31873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/23/2020] [Accepted: 12/02/2020] [Indexed: 11/06/2022]
Abstract
We carried out an exhaustive review regarding human skin color variation and how much it may be related to vitamin D metabolism and other photosensitive molecules. We discuss evolutionary contexts that modulate this variability and hypotheses postulated to explain them; for example, a small amount of melanin in the skin facilitates vitamin D production, making it advantageous to have fair skin in an environment with little radiation incidence. In contrast, more melanin protects folate from degradation in an environment with a high incidence of radiation. Some Native American populations have a skin color at odds with what would be expected for the amount of radiation in the environment in which they live, a finding challenging the so-called "vitamin D-folate hypothesis." Since food is also a source of vitamin D, dietary habits should also be considered. Here we argue that a gene network approach provides tools to explain this phenomenon since it indicates potential alleles co-evolving in a compensatory way. We identified alleles of the vitamin D metabolism and pigmentation pathways segregated together, but in different proportions, in agriculturalists and hunter-gatherers. Finally, we highlight how an evolutionary approach can be useful to understand current topics of medical interest.
Collapse
Affiliation(s)
- Bruna Oliveira Missaggia
- Genetics Departament, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Guillermo Reales
- Genetics Departament, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Gabriela B Cybis
- Statistics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Tábita Hünemeier
- Department of Genetics and Evolutionary Biology, Biosciences Institute, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Maria Cátira Bortolini
- Genetics Departament, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| |
Collapse
|
19
|
Barquera R, Martínez-Álvarez JC, Hernández-Zaragoza DI, Bravo-Acevedo A, Juárez-Nicolás F, Arriaga-Perea AJ, Vega-Martínez MDR, Ortega-Yáñez A, Benítez-Arvizu G, Arrieta-Bolaños E, Clayton S, Juárez-Cortés ED, López-Gil C, García-Álvarez R, Arrazola-García MA, Martínez-Bezies V, Juárez-Barreto V, Ramos-de la Cruz FDR, Macías-Medrano RM, Méndez-Mani P, Escutia-González A, Montiel-Hernández GD, Immel A, Pavón-Vargas MDLÁ, Salgado-Galicia N, Novelo-Garza B, Zúñiga J, Yunis EJ, Bekker-Méndez C, Granados J. Genetic diversity of HLA system in six populations from Mexico City Metropolitan Area, Mexico: Mexico City North, Mexico City South, Mexico City East, Mexico City West, Mexico City Center and rural Mexico City. Hum Immunol 2020; 81:539-543. [DOI: 10.1016/j.humimm.2019.07.297] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/21/2019] [Accepted: 07/22/2019] [Indexed: 11/25/2022]
|
20
|
Mas-Sandoval A, Arauna LR, Gouveia MH, Barreto ML, Horta BL, Lima-Costa MF, Pereira AC, Salzano FM, Hünemeier T, Tarazona-Santos E, Bortolini MC, Comas D. Reconstructed Lost Native American Populations from Eastern Brazil Are Shaped by Differential Jê/Tupi Ancestry. Genome Biol Evol 2020; 11:2593-2604. [PMID: 31328768 PMCID: PMC6756188 DOI: 10.1093/gbe/evz161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2019] [Indexed: 01/19/2023] Open
Abstract
After the colonization of the Americas by Europeans and the consequent Trans-Atlantic Slave Trade, most Native American populations in eastern Brazil disappeared or went through an admixture process that configured a population composed of three main genetic components: the European, the sub-Saharan African, and the Native American. The study of the Native American genetic history is challenged by the lack of availability of genome-wide samples from Native American populations, the technical difficulties to develop ancient DNA studies, and the low proportions of the Native American component in the admixed Brazilian populations (on average 7%). We analyzed genome-wide data of 5,825 individuals from three locations of eastern Brazil: Salvador (North-East), Bambui (South-East), and Pelotas (South) and we reconstructed populations that emulate the Native American groups that were living in the 16th century around the sampling locations. This genetic reconstruction was performed after local ancestry analysis of the admixed Brazilian populations, through the rearrangement of the Native American haplotypes into reconstructed individuals with full Native American ancestry (51 reconstructed individuals in Salvador, 45 in Bambui, and 197 in Pelotas). We compared the reconstructed populations with nonadmixed Native American populations from other regions of Brazil through haplotype-based methods. Our results reveal a population structure shaped by the dichotomy of Tupi-/Jê-speaking ancestry related groups. We also show evidence of a decrease of the diversity of nonadmixed Native American groups after the European contact, in contrast with the reconstructed populations, suggesting a reservoir of the Native American genetic diversity within the admixed Brazilian population.
Collapse
Affiliation(s)
- Alex Mas-Sandoval
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.,Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Lara R Arauna
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Mateus H Gouveia
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Center for Research on Genomics and Global Health, National Institutes of Health, Bethesda, Maryland
| | - Mauricio L Barreto
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Bahia, Brazil.,Center for Data and Knowledge Integration for Health, Institute Gonçalo Muniz, Fundação Oswaldo Cruz, Salvador, Bahia, Brazil
| | - Bernardo L Horta
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Rio Grande do Sul, Brazil
| | | | | | - Francisco M Salzano
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Tábita Hünemeier
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Eduardo Tarazona-Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| |
Collapse
|
21
|
Yelmen B, Mondal M, Marnetto D, Pathak AK, Montinaro F, Gallego Romero I, Kivisild T, Metspalu M, Pagani L. Ancestry-Specific Analyses Reveal Differential Demographic Histories and Opposite Selective Pressures in Modern South Asian Populations. Mol Biol Evol 2020; 36:1628-1642. [PMID: 30952160 PMCID: PMC6657728 DOI: 10.1093/molbev/msz037] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Genetic variation in contemporary South Asian populations follows a northwest to southeast decreasing cline of shared West Eurasian ancestry. A growing body of ancient DNA evidence is being used to build increasingly more realistic models of demographic changes in the last few thousand years. Through high-quality modern genomes, these models can be tested for gene and genome level deviations. Using local ancestry deconvolution and masking, we reconstructed population-specific surrogates of the two main ancestral components for more than 500 samples from 25 South Asian populations and showed our approach to be robust via coalescent simulations. Our f3 and f4 statistics–based estimates reveal that the reconstructed haplotypes are good proxies for the source populations that admixed in the area and point to complex interpopulation relationships within the West Eurasian component, compatible with multiple waves of arrival, as opposed to a simpler one wave scenario. Our approach also provides reliable local haplotypes for future downstream analyses. As one such example, the local ancestry deconvolution in South Asians reveals opposite selective pressures on two pigmentation genes (SLC45A2 and SLC24A5) that are common or fixed in West Eurasians, suggesting post-admixture purifying and positive selection signals, respectively.
Collapse
Affiliation(s)
- Burak Yelmen
- Institute of Genomics, University of Tartu, Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Mayukh Mondal
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Ajai K Pathak
- Institute of Genomics, University of Tartu, Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Francesco Montinaro
- Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Irene Gallego Romero
- Melbourne Integrative Genomics and School of BioSciences, University of Melbourne, Parkville, Australia
| | - Toomas Kivisild
- Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Mait Metspalu
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Luca Pagani
- Institute of Genomics, University of Tartu, Tartu, Estonia.,APE Lab, Department of Biology, University of Padova, Padova, Italy
| |
Collapse
|
22
|
Genetic variability of five ADRB2 polymorphisms among Mexican Amerindian ethnicities and the Mestizo population. PLoS One 2019; 14:e0225030. [PMID: 31790415 PMCID: PMC6886845 DOI: 10.1371/journal.pone.0225030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 10/28/2019] [Indexed: 01/02/2023] Open
Abstract
The Mexican population is characterized by high and particular admixture, and the picture of variants associated with disease remains unclear. Here we investigated the distribution of single nucleotide polymorphisms (SNPs) in the Mexican population. We focused on two non-synonymous and three synonymous SNPs in the beta-2 adrenergic receptor gene (ADRB2), which plays key roles in energy balance regulation. These SNPs were genotyped in 2,011 Mexican Amerindians (MAs) belonging to 62 ethnic groups and in 1,980 geographically matched Mexican Mestizos (MEZs). The frequency distribution of all five ADRB2 variants significantly differed between MAs, MEZs, and other continental populations (CPs) from the 1000 Genomes database. Allele frequencies of the three synonymous SNPs rs1042717A, rs1042718A, and rs1042719C were significantly higher in Mexican individuals, particularly among MAs, compared to in the other analyzed populations (P<0.05). The non-synonymous ADRB2 Glu27 allele (rs1042714G), which is associated with several common conditions, showed the lowest frequency in MAs (0.03) compared to other populations worldwide. Among MEZs, this allele showed a frequency of 0.15, intermediate between that in MAs and in Iberians (0.43). Moreover, Glu27 was the only SNP exhibiting a geographic gradient within the MEZ population (from 0.22 to 0.11), reflecting admixed mestizo ancestry across the country. Population differentiation analysis demonstrated that Glu27 had the highest FST value in MAs compared with Europeans (CEU) (0.71), and the lowest between MAs and Japanese (JPT) (0.01), even lower than that observed between MAs and MEZs (0.08). This analysis demonstrated the genetic diversity among Amerindian ethnicities, with the most extreme FST value (0.34) found between the Nahuatls from Morelos and the Seris. This is the first study of ADRB2 genetic variants among MA ethnicities. Our findings add to our understanding of the genetic contribution to variability in disease susceptibility in admixed populations.
Collapse
|
23
|
Inter-individual genomic heterogeneity within European population isolates. PLoS One 2019; 14:e0214564. [PMID: 31596857 PMCID: PMC6785074 DOI: 10.1371/journal.pone.0214564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 09/24/2019] [Indexed: 12/12/2022] Open
Abstract
A number of studies carried out since the early ‘70s has investigated the effects of isolation on genetic variation within and among human populations in diverse geographical contexts. However, no extensive analysis has been carried out on the heterogeneity among genomes within isolated populations. This issue is worth exploring since events of recent admixture and/or subdivision could potentially disrupt the genetic homogeneity which is to be expected when isolation is prolonged and constant over time. Here, we analyze literature data relative to 87,815 autosomal single-nucleotide polymorphisms, which were obtained from a total of 28 European populations. Our results challenge the traditional paradigm of population isolates as structured as genetically (and genomically) uniform entities. In fact, focusing on the distribution of variance of intra-population diversity measures across individuals, we show that the inter-individual heterogeneity of isolated populations is at least comparable to the open ones. More in particular, three small and highly inbred isolates (Sappada, Sauris and Timau in Northeastern Italy) were found to be characterized by levels of inter-individual heterogeneity largely exceeding that of all other populations, possibly due to relatively recent events of genetic introgression. Finally, we propose a way to monitor the effects of inter-individual heterogeneity in disease-gene association studies.
Collapse
|
24
|
Catalytically Impaired TYK2 Variants are Protective Against Childhood- and Adult-Onset Systemic Lupus Erythematosus in Mexicans. Sci Rep 2019; 9:12165. [PMID: 31434951 PMCID: PMC6704113 DOI: 10.1038/s41598-019-48451-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 08/06/2019] [Indexed: 01/30/2023] Open
Abstract
Type I interferon (IFN-I) pathway plays a central role in the systemic lupus erythematosus (SLE) pathogenesis. Recent data suggest that SLE is associated with variants in IFN-I genes, such as tyrosine kinase 2 (TYK2), which is crucial in anti-viral immunity. Here, five TYK2 single nucleotide polymorphisms (SNPs) were genotyped in 368 childhood-onset SLE Mexican patients and 516 sex-matched healthy controls. Allele frequencies were also estimated in four indigenous groups. SLE protection was associated with TYK2 risk infection variants affecting residually its catalytic domain, rs12720356 (OR = 0.308; p = 0.041) and rs34536443 (OR = 0.370; p = 0.034), but not with rs2304256, rs12720270, and rs280500. This association was replicated in a 506 adult-onset SLE patients sample (OR = 0.250; p = 0.005, and OR = 0.277; p = 0.008, respectively). The minor alleles of both associated SNPs had a lower frequency in Mestizos than in Spaniards and were absent or rare in indigenous, suggesting that the presence of these alleles in the Mexican Mestizo population was derived from the Spaniards. For the first time, we report genetic variants with a protective effect in childhood- and adult-onset SLE Mexican population. Our results suggest that the frequency of IFN-I alleles associated with SLE, may have been shaped in populations exposed to infectious diseases for long periods, and this could be an explanation why Native American ancestry is associated with a higher SLE prevalence and an earlier onset.
Collapse
|
25
|
Mattucci F, Galaverni M, Lyons LA, Alves PC, Randi E, Velli E, Pagani L, Caniglia R. Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations. Sci Rep 2019; 9:11612. [PMID: 31406125 PMCID: PMC6691104 DOI: 10.1038/s41598-019-48002-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 07/25/2019] [Indexed: 12/22/2022] Open
Abstract
The survival of indigenous European wildcat (Felis silvestris silvestris) populations can be locally threatened by introgressive hybridization with free-ranging domestic cats. Identifying pure wildcats and investigating the ancestry of admixed individuals becomes thus a conservation priority. We analyzed 63k cat Single Nucleotide Polymorphisms (SNPs) with multivariate, Bayesian and gene-search tools to better evaluate admixture levels between domestic and wild cats collected in Europe, timing and ancestry proportions of their hybrids and backcrosses, and track the origin (wild or domestic) of the genomic blocks carried by admixed cats, also looking for possible deviations from neutrality in their inheritance patterns. Small domestic ancestry blocks were detected in the genomes of most admixed cats, which likely originated from hybridization events occurring from 6 to 22 generations in the past. We identified about 1,900 outlier coding genes with excess of wild or domestic ancestry compared to random expectations in the admixed individuals. More than 600 outlier genes were significantly enriched for Gene Ontology (GO) categories mainly related to social behavior, functional and metabolic adaptive processes (wild-like genes), involved in cognition and neural crest development (domestic-like genes), or associated with immune system functions and lipid metabolism (parental-like genes). These kinds of genomic ancestry analyses could be reliably applied to unravel the admixture dynamics in European wildcats, as well as in other hybridizing populations, in order to design more efficient conservation plans.
Collapse
Affiliation(s)
- Federica Mattucci
- Area per la Genetica della Conservazione (BIO-CGE), Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell'Emilia, Italy.
| | | | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, USA
| | - Paulo C Alves
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBio - Laboratório Associado, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, USA
| | - Ettore Randi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- Department of Chemistry and Bioscience, Faculty of Engineering and Science, University of Aalborg, Aalborg, Denmark
| | - Edoardo Velli
- Area per la Genetica della Conservazione (BIO-CGE), Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell'Emilia, Italy
| | - Luca Pagani
- Dipartimento di Biologia, Università degli Studi di Padova, Padua, Italy
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Romolo Caniglia
- Area per la Genetica della Conservazione (BIO-CGE), Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell'Emilia, Italy
| |
Collapse
|
26
|
Ortiz-Cruz G, Luna-Muñoz L, Arteaga-Vázquez J, Mutchinick OM. Isolated postaxial polydactyly: Epidemiologic characteristics from a multicenter birth defects study. Am J Med Genet A 2019; 179:1432-1441. [PMID: 31091006 DOI: 10.1002/ajmg.a.61193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 04/24/2019] [Accepted: 04/27/2019] [Indexed: 11/09/2022]
Abstract
Isolated postaxial polydactyly (I-PAP), as a single defect, is a frequent malformation, characterized by an extra digit placed on the ulnar or fibular side of the limbs. Worldwide prevalence varies from as high as 225/10,000 in Nigerians to so low as 6.08/10,000 in Argentinians. Genetic-ethnic background significantly affects worldwide prevalence and type of I-PAP. Herein we describe the epidemiological characteristics of I-PAP in 697 newborns, 383 males and 314 females identified in 1,178,993 examined live births from a multicenter case-control hospital-based population study, the Mexican program of Registry and Epidemiological Surveillance of Congenital Malformations (RYVEMCE). The main characteristics analyzed included total I-PAP, stratified in Types A and B, defined as complete or incomplete extra-digit formation, respectively, sex prevalence, affected limb, laterality, parity, prematurity, delivery-type, twinning, consanguinity, and parental age. Males (6.35/10,000) are significantly more frequently affected than females (5.45/10,000), hands more than feet, left more than right limbs, and Type B (74.50%) more than A (25.50%). Prematurity and forceps use were significantly more frequent in cases than controls. An evident decreasing time-trend prevalence was present. Similar findings with other studies were males, upper and left limbs more frequently affected. Findings that were not previously reported include prematurity, forceps use, a significant decreasing time trend and an inverse ethnic prevalence for Types A (75%) and B (25%) in the Mayan population in contrast to other worldwide ethnic groups.
Collapse
Affiliation(s)
- Gabriela Ortiz-Cruz
- Department of Genetics, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, México City, Mexico
| | - Leonora Luna-Muñoz
- Department of Genetics, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, México City, Mexico
| | - Jazmín Arteaga-Vázquez
- Department of Genetics, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, México City, Mexico
| | - Osvaldo M Mutchinick
- Department of Genetics, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, México City, Mexico
| |
Collapse
|
27
|
Ostrom QT, Egan KM, Nabors LB, Gerke T, Thompson RC, Olson JJ, LaRocca R, Chowdhary S, Eckel-Passow JE, Armstrong G, Wiencke JK, Bernstein JL, Claus EB, Il'yasova D, Johansen C, Lachance DH, Lai RK, Merrell RT, Olson SH, Sadetzki S, Schildkraut JM, Shete S, Houlston RS, Jenkins RB, Wrensch MR, Melin B, Amos CI, Huse JT, Barnholtz-Sloan JS, Bondy ML. Glioma risk associated with extent of estimated European genetic ancestry in African Americans and Hispanics. Int J Cancer 2019; 146:739-748. [PMID: 30963577 DOI: 10.1002/ijc.32318] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/30/2019] [Accepted: 02/14/2019] [Indexed: 12/15/2022]
Abstract
Glioma incidence is highest in non-Hispanic Whites, and to date, glioma genome-wide association studies (GWAS) to date have only included European ancestry (EA) populations. African Americans and Hispanics in the US have varying proportions of EA, African (AA) and Native American ancestries (NAA). It is unknown if identified GWAS loci or increased EA is associated with increased glioma risk. We assessed whether EA was associated with glioma in African Americans and Hispanics. Data were obtained for 832 cases and 675 controls from the Glioma International Case-Control Study and GliomaSE Case-Control Study previously estimated to have <80% EA, or self-identify as non-White. We estimated global and local ancestry using fastStructure and RFMix, respectively, using 1,000 genomes project reference populations. Within groups with ≥40% AA (AFR≥0.4 ), and ≥15% NAA (AMR≥0.15 ), genome-wide association between local EA and glioma was evaluated using logistic regression conditioned on global EA for all gliomas. We identified two regions (7q21.11, p = 6.36 × 10-4 ; 11p11.12, p = 7.0 × 10-4 ) associated with increased EA, and one associated with decreased EA (20p12.13, p = 0.0026) in AFR≥0.4 . In addition, we identified a peak at rs1620291 (p = 4.36 × 10-6 ) in 7q21.3. Among AMR≥0.15 , we found an association between increased EA in one region (12q24.21, p = 8.38 × 10-4 ), and decreased EA in two regions (8q24.21, p = 0. 0010; 20q13.33, p = 6.36 × 10-4 ). No other significant associations were identified. This analysis identified an association between glioma and two regions previously identified in EA populations (8q24.21, 20q13.33) and four novel regions (7q21.11, 11p11.12, 12q24.21 and 20p12.13). The identifications of novel association with EA suggest regions to target for future genetic association studies.
Collapse
Affiliation(s)
- Quinn T Ostrom
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
| | - Kathleen M Egan
- Division of Population Sciences, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - L Burt Nabors
- Neuro-Oncology Program, University of Alabama at Birmingham, Birmingham, AL
| | - Travis Gerke
- Division of Population Sciences, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Reid C Thompson
- Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Jeffrey J Olson
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA
| | - Renato LaRocca
- Department of Hematology-Oncology, Norton Cancer Institute, Louisville, KY
| | | | - Jeanette E Eckel-Passow
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN
| | - Georgina Armstrong
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
| | - John K Wiencke
- Department of Neurological Surgery, School of Medicine, University of California, San Francisco, San Francisco, CA
| | - Jonine L Bernstein
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY, New York
| | - Elizabeth B Claus
- School of Public Health, Yale University, New Haven, CT.,Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA
| | - Dora Il'yasova
- Department of Epidemiology and Biostatistics, School of Public Health, Georgia State University, Atlanta, GA.,Cancer Control and Prevention Program, Department of Community and Family Medicine, Duke University Medical Center, Durham, NC.,Duke Cancer Institute, Duke University Medical Center, Durham, NC
| | - Christoffer Johansen
- Oncology Clinic, Finsen Center, Rigshospitalet and Survivorship Research Unit, The Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Daniel H Lachance
- Department of Neurology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN
| | - Rose K Lai
- Department of Neurology and Preventive Medicine, Keck School of Medicine, University of Southern California, CA, Los Angeles
| | - Ryan T Merrell
- Department of Neurology, NorthShore University HealthSystem, Evanston, IL
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, NY, New York
| | - Siegal Sadetzki
- Cancer and Radiation Epidemiology Unit, Gertner Institute, Chaim Sheba Medical Center, Tel Hashomer, Israel.,Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Joellen M Schildkraut
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA
| | - Sanjay Shete
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research in Sutton, Surrey, United Kingdom
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN
| | - Margaret R Wrensch
- Department of Neurological Surgery, School of Medicine, University of California, San Francisco, San Francisco, CA
| | - Beatrice Melin
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
| | - Jason T Huse
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Melissa L Bondy
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
| |
Collapse
|
28
|
Trujillo-Cáceres SJ, Torres-Sánchez L, Burguete-García AI, Orbe Orihuela YC, Vázquez-Salas RA, Álvarez-Topete E, Gómez R. Contribution of MSMB promoter region gene polymorphism to early-onset prostate cancer risk in Mexican males. Oncotarget 2019; 10:738-748. [PMID: 30774776 PMCID: PMC6366823 DOI: 10.18632/oncotarget.26592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/16/2018] [Indexed: 11/25/2022] Open
Abstract
Sexually transmitted infections and its contribution to prostate cancer (PC) development have been relevant in different populations. MSMB gene polymorphism (rs10993994) has exhibited an association both with PC as well as the susceptibility to sexually transmitted infections. Hitherto, these conditions have been not studied in Mexico yet, neither if sexually transmitted infections could modify the MSMB and PC association. Herein, socio-demographic features, sexually transmitted infections records, the reproductive backgrounds, and the genetic characterisation were analysed in 322 incident PC cases and 628 population healthy controls from Mexico City. Whole PC, early-onset PC (PC at < 60 years old), late-onset PC (≥ 60 years old), and PC aggressiveness were used to evaluate the genetic variants contribution to PC risk using unconditional logistic regression models. Overall, none associations between the allelic variants of rs10993994 polymorphisms with whole and PC aggressiveness were found. Howbeit, the TT genotype carriers presented the highest susceptibility to develop early-onset PC (OR = 2.66; 95% CI = 1.41, 5.04; p = 0.03) than CC+CT carriers, both with codominant and recessive models. Although none association between whole PC and MSMB gene polymorphism was found, our results were reinforced by prior studies in European descendent populations, suggesting a contribution between rs10993994 and early-onset PC development.
Collapse
Affiliation(s)
| | - Luisa Torres-Sánchez
- Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, Mexico
| | - Ana I Burguete-García
- Centro de Investigación en Enfermedades Infecciosas, INSP, Cuernavaca, Morelos, Mexico
| | | | | | | | - Rocío Gómez
- Departamento de Toxicología, Cinvestav-IPN, Mexico City, Mexico
| |
Collapse
|
29
|
Soares-Souza G, Borda V, Kehdy F, Tarazona-Santos E. Admixture, Genetics and Complex Diseases in Latin Americans and US Hispanics. CURRENT GENETIC MEDICINE REPORTS 2018. [DOI: 10.1007/s40142-018-0151-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
30
|
Amezcua L, Beecham AH, Delgado SR, Chinea A, Burnett M, Manrique CP, Gomez R, Comabella M, Montalban X, Ortega M, Tornes L, Lund BT, Islam T, Conti D, Oksenberg JR, McCauley JL. Native ancestry is associated with optic neuritis and age of onset in hispanics with multiple sclerosis. Ann Clin Transl Neurol 2018; 5:1362-1371. [PMID: 30480030 PMCID: PMC6243381 DOI: 10.1002/acn3.646] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/19/2018] [Accepted: 08/21/2018] [Indexed: 11/24/2022] Open
Abstract
Background and Objective Hispanics with multiple sclerosis (MS) present younger and more often with optic neuritis (ON) as compared to Whites in the western United States. Regional differences related to Hispanic genetic admixture could be responsible. We investigated the association between global genetic ancestry and ON and age at onset of MS in Hispanics. Methods Data were obtained for 1033 self‐identified Hispanics with MS from four MS‐based registries from four academic institutions across the United States January 2016–April 2017. Multivariate regression models, utilizing genetic ancestry estimates for Native American (NA), African, and European ancestry, were used to assess the relationship between genetic ancestry and ON presentation and age of MS onset, defined as age at first symptom. Results Genetic ancestry and ON proportions varied by region where NA ancestry and ON proportions were highest among Hispanics in the southwestern United States (40% vs. 19% overall for NA and 38% vs. 25% overall for ON). A strong inverse correlation was observed between NA and European ancestry (r = −0.83). ON presentation was associated with younger age of onset (OR: 0.98; 95% CI: 0.96–0.99; P = 7.80 × 10−03) and increased NA ancestry (OR: 2.35 for the highest versus the lowest quartile of NA ancestry; 95% CI: 1.35–4.10; P = 2.60 × 10−03). Younger age of onset was found to be associated with a higher proportion NA (Beta: −5.58; P = 3.49 × 10−02) and African ancestry (Beta: −10.07; P = 1.39 × 10−03). Interpretation Ethnic differences associated with genetic admixture could influence clinical presentation in Hispanics with MS; underscoring the importance of considering genetic substructure in future clinical, genetic, and epigenetic studies in Hispanics.
Collapse
Affiliation(s)
- Lilyana Amezcua
- Department of Neurology Keck School of Medicine University of Southern California Los Angeles California
| | - Ashley H Beecham
- Dr. John T. Macdonald Department of Human Genetics Miller School of Medicine University of Miami Miami Florida.,John P. Hussman Institute of Human Genomics Miller School of Medicine University of Miami Miami Florida
| | - Silvia R Delgado
- Multiple Sclerosis Division Department of Neurology Miller School of Medicine University of Miami Miami Florida
| | - Angel Chinea
- San Juan Multiple Sclerosis Center San Juan Puerto Rico
| | - Margaret Burnett
- Department of Neurology Keck School of Medicine University of Southern California Los Angeles California
| | - Clara Patricia Manrique
- John P. Hussman Institute of Human Genomics Miller School of Medicine University of Miami Miami Florida
| | - Refujia Gomez
- Department of Preventive Medicine Keck School of Medicine University of Southern California Los Angeles California
| | - Manuel Comabella
- Department of Neurology University of San Francisco School of Medicine Los Angeles California
| | - Xavier Montalban
- Department of Neurology University of San Francisco School of Medicine Los Angeles California
| | - Melissa Ortega
- Multiple Sclerosis Division Department of Neurology Miller School of Medicine University of Miami Miami Florida
| | - Leticia Tornes
- Multiple Sclerosis Division Department of Neurology Miller School of Medicine University of Miami Miami Florida
| | - Brett T Lund
- Department of Neurology Keck School of Medicine University of Southern California Los Angeles California
| | - Talat Islam
- Department de Neurología-Neuroinmunología Centre d'Esclerosi Múltiple de Catalunya (Cemcat) Institut de Recerca Vall d'Hebron Hospital Universitari Vall d'Hebron Universitat Autònoma de Barcelona Barcelona Spain
| | - David Conti
- Department de Neurología-Neuroinmunología Centre d'Esclerosi Múltiple de Catalunya (Cemcat) Institut de Recerca Vall d'Hebron Hospital Universitari Vall d'Hebron Universitat Autònoma de Barcelona Barcelona Spain
| | - Jorge R Oksenberg
- Department of Preventive Medicine Keck School of Medicine University of Southern California Los Angeles California
| | - Jacob L McCauley
- Dr. John T. Macdonald Department of Human Genetics Miller School of Medicine University of Miami Miami Florida.,John P. Hussman Institute of Human Genomics Miller School of Medicine University of Miami Miami Florida
| |
Collapse
|
31
|
Caniglia R, Fabbri E, Hulva P, Bolfíková BČ, Jindřichová M, Stronen AV, Dykyy I, Camatta A, Carnier P, Randi E, Galaverni M. Wolf outside, dog inside? The genomic make-up of the Czechoslovakian Wolfdog. BMC Genomics 2018; 19:533. [PMID: 30005602 PMCID: PMC6043967 DOI: 10.1186/s12864-018-4916-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 07/02/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Genomic methods can provide extraordinary tools to explore the genetic background of wild species and domestic breeds, optimize breeding practices, monitor and limit the spread of recessive diseases, and discourage illegal crossings. In this study we analysed a panel of 170k Single Nucleotide Polymorphisms with a combination of multivariate, Bayesian and outlier gene approaches to examine the genome-wide diversity and inbreeding levels in a recent wolf x dog cross-breed, the Czechoslovakian Wolfdog, which is becoming increasingly popular across Europe. RESULTS Pairwise FST values, multivariate and assignment procedures indicated that the Czechoslovakian Wolfdog was significantly differentiated from all the other analysed breeds and also well-distinguished from both parental populations (Carpathian wolves and German Shepherds). Coherently with the low number of founders involved in the breed selection, the individual inbreeding levels calculated from homozygosity regions were relatively high and comparable with those derived from the pedigree data. In contrast, the coefficient of relatedness between individuals estimated from the pedigrees often underestimated the identity-by-descent scores determined using genetic profiles. The timing of the admixture and the effective population size trends estimated from the LD patterns reflected the documented history of the breed. Ancestry reconstruction methods identified more than 300 genes with excess of wolf ancestry compared to random expectations, mainly related to key morphological features, and more than 2000 genes with excess of dog ancestry, playing important roles in lipid metabolism, in the regulation of circadian rhythms, in learning and memory processes, and in sociability, such as the COMT gene, which has been described as a candidate gene for the latter trait in dogs. CONCLUSIONS In this study we successfully applied genome-wide procedures to reconstruct the history of the Czechoslovakian Wolfdog, assess individual wolf ancestry proportions and, thanks to the availability of a well-annotated reference genome, identify possible candidate genes for wolf-like and dog-like phenotypic traits typical of this breed, including commonly inherited disorders. Moreover, through the identification of ancestry-informative markers, these genomic approaches could provide tools for forensic applications to unmask illegal crossings with wolves and uncontrolled trades of recent and undeclared wolfdog hybrids.
Collapse
Affiliation(s)
- Romolo Caniglia
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell’Emilia, Bologna, Italy
| | - Elena Fabbri
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell’Emilia, Bologna, Italy
| | - Pavel Hulva
- Department of Zoology, Charles University in Prague, Prague, Czech Republic
- Department of Biology and Ecology, Ostrava University, Ostrava, Czech Republic
| | - Barbora Černá Bolfíková
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Milena Jindřichová
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Astrid Vik Stronen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg Øst, Denmark
| | - Ihor Dykyy
- Department of Zoology, Ivan Franko National University of Lviv, Lviv, Ukraine
| | | | - Paolo Carnier
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Ettore Randi
- Dipartimento BIGEA, Università di Bologna, Bologna, Italy
- Department 18/ Section of Environmental Engineering, Aalborg University, Aalborg Øst, Denmark
| | - Marco Galaverni
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell’Emilia, Bologna, Italy
- Area Conservazione, WWF Italia, Rome, Italy
| |
Collapse
|
32
|
Quinto-Cortés CD, Woerner AE, Watkins JC, Hammer MF. Modeling SNP array ascertainment with Approximate Bayesian Computation for demographic inference. Sci Rep 2018; 8:10209. [PMID: 29977040 PMCID: PMC6033855 DOI: 10.1038/s41598-018-28539-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 06/20/2018] [Indexed: 11/08/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) in commercial arrays have often been discovered in a small number of samples from selected populations. This ascertainment skews patterns of nucleotide diversity and affects population genetic inferences. We propose a demographic inference pipeline that explicitly models the SNP discovery protocol in an Approximate Bayesian Computation (ABC) framework. We simulated genomic regions according to a demographic model incorporating parameters for the divergence of three well-characterized HapMap populations and recreated the SNP distribution of a commercial array by varying the number of haploid samples and the allele frequency cut-off in the given regions. We then calculated summary statistics obtained from both the ascertained and genomic data and inferred ascertainment and demographic parameters. We implemented our pipeline to study the admixture process that gave rise to the present-day Mexican population. Our estimate of the time of admixture is closer to the historical dates than those in previous works which did not consider ascertainment bias. Although the use of whole genome sequences for demographic inference is becoming the norm, there are still underrepresented areas of the world from where only SNP array data are available. Our inference framework is applicable to those cases and will help with the demographic inference.
Collapse
Affiliation(s)
- Consuelo D Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, 36821, Mexico, Mexico.
| | - August E Woerner
- Center for Human Identification, University of North Texas Health Science Center, Texas, 76107, USA
| | - Joseph C Watkins
- Department of Mathematics, University of Arizona, Tucson, Arizona, 85721, USA
| | - Michael F Hammer
- ARL Division of Biotechnology, University of Arizona, Tucson, Arizona, 85721, USA.
| |
Collapse
|
33
|
Yu C, Baune BT, Wong ML, Licinio J. Investigation of short tandem repeats in major depression using whole-genome sequencing data. J Affect Disord 2018; 232:305-309. [PMID: 29501989 DOI: 10.1016/j.jad.2018.02.046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/02/2018] [Accepted: 02/16/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Major depressive disorder (MDD) is a leading contributor to global disease burden. Recent studies have shown that genetic factors play significant roles in the susceptibility to this condition; however, the underlying genetic basis currently remains largely unknown. Short tandem repeat (STR) has been proposed as an explanatory factor in the "missing heritability" of complex diseases or traits. METHODS We investigated STR variations from 15 MDD patients and 10 ethnically matched healthy controls based on their deep whole-genome sequencing (WGS) data. The lobSTR software was used to computationally determine STRs. RESULTS The results of the Mexican-American sample showed that STRs are significantly richer in healthy controls than in MDD cases on each of the 23 chromosomes (all false discovery rates, FDR P-values < 0.0062); while for the Australian of European-ancestry sample, there was no statistically significant STRs difference between MDD cases and controls. LIMITATIONS High quality WGS costs limited obtaining larger datasets. CONCLUSIONS This preliminary work is the first study that STR variations are applied to investigate MDD based on WGS data. The results on Mexican-American population may imply that within the same ancestry, targeted sequencing on a specific chromosome or region of genome would be sufficient for examining the relationship between STR and MDD. Further studies should examine larger sequencing datasets on other ethnic groups.
Collapse
Affiliation(s)
- Chenglong Yu
- Robinson Research Institute, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5005, Australia; Mind and Brain Theme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA 5000, Australia; School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Bedford Park, SA 5042, Australia.
| | - Bernhard T Baune
- Discipline of Psychiatry, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia
| | - Ma-Li Wong
- Mind and Brain Theme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA 5000, Australia; School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Bedford Park, SA 5042, Australia; Department of Psychiatry, College of Medicine, State University of New York, Upstate Medical University, Syracuse, NY 13210, USA
| | - Julio Licinio
- Department of Psychiatry, College of Medicine, State University of New York, Upstate Medical University, Syracuse, NY 13210, USA; Departments of Pharmacology and Medicine, College of Medicine, State University of New York, Upstate Medical University, Syracuse, NY 13210, USA
| |
Collapse
|
34
|
Martin ER, Tunc I, Liu Z, Slifer SH, Beecham AH, Beecham GW. Properties of global- and local-ancestry adjustments in genetic association tests in admixed populations. Genet Epidemiol 2018; 42:214-229. [PMID: 29288582 PMCID: PMC5811405 DOI: 10.1002/gepi.22103] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 09/24/2017] [Accepted: 10/29/2017] [Indexed: 12/31/2022]
Abstract
Population substructure can lead to confounding in tests for genetic association, and failure to adjust properly can result in spurious findings. Here we address this issue of confounding by considering the impact of global ancestry (average ancestry across the genome) and local ancestry (ancestry at a specific chromosomal location) on regression parameters and relative power in ancestry-adjusted and -unadjusted models. We examine theoretical expectations under different scenarios for population substructure; applying different regression models, verifying and generalizing using simulations, and exploring the findings in real-world admixed populations. We show that admixture does not lead to confounding when the trait locus is tested directly in a single admixed population. However, if there is more complex population structure or a marker locus in linkage disequilibrium (LD) with the trait locus is tested, both global and local ancestry can be confounders. Additionally, we show the genotype parameters of adjusted and unadjusted models all provide tests for LD between the marker and trait locus, but in different contexts. The local ancestry adjusted model tests for LD in the ancestral populations, while tests using the unadjusted and the global ancestry adjusted models depend on LD in the admixed population(s), which may be enriched due to different ancestral allele frequencies. Practically, this implies that global-ancestry adjustment should be used for screening, but local-ancestry adjustment may better inform fine mapping and provide better effect estimates at trait loci.
Collapse
Affiliation(s)
- Eden R. Martin
- John P. Hussman Institute for Human Genetics, University of Miami, Miller School of Medicine, Miami, FL
- John T. MacDonald Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL
| | - Ilker Tunc
- Bioinformatics and Systems Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda MD
| | - Zhi Liu
- Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Susan H. Slifer
- John P. Hussman Institute for Human Genetics, University of Miami, Miller School of Medicine, Miami, FL
| | - Ashley H. Beecham
- John T. MacDonald Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL
| | - Gary W. Beecham
- John P. Hussman Institute for Human Genetics, University of Miami, Miller School of Medicine, Miami, FL
- John T. MacDonald Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL
| |
Collapse
|
35
|
Meyer D, C Aguiar VR, Bitarello BD, C Brandt DY, Nunes K. A genomic perspective on HLA evolution. Immunogenetics 2018; 70:5-27. [PMID: 28687858 PMCID: PMC5748415 DOI: 10.1007/s00251-017-1017-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 06/16/2017] [Indexed: 12/20/2022]
Abstract
Several decades of research have convincingly shown that classical human leukocyte antigen (HLA) loci bear signatures of natural selection. Despite this conclusion, many questions remain regarding the type of selective regime acting on these loci, the time frame at which selection acts, and the functional connections between genetic variability and natural selection. In this review, we argue that genomic datasets, in particular those generated by next-generation sequencing (NGS) at the population scale, are transforming our understanding of HLA evolution. We show that genomewide data can be used to perform robust and powerful tests for selection, capable of identifying both positive and balancing selection at HLA genes. Importantly, these tests have shown that natural selection can be identified at both recent and ancient timescales. We discuss how findings from genomewide association studies impact the evolutionary study of HLA genes, and how genomic data can be used to survey adaptive change involving interaction at multiple loci. We discuss the methodological developments which are necessary to correctly interpret genomic analyses involving the HLA region. These developments include adapting the NGS analysis framework so as to deal with the highly polymorphic HLA data, as well as developing tools and theory to search for signatures of selection, quantify differentiation, and measure admixture within the HLA region. Finally, we show that high throughput analysis of molecular phenotypes for HLA genes-namely transcription levels-is now a feasible approach and can add another dimension to the study of genetic variation.
Collapse
Affiliation(s)
- Diogo Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil.
| | - Vitor R C Aguiar
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Bárbara D Bitarello
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Débora Y C Brandt
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Kelly Nunes
- Department of Genetics and Evolutionary Biology, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| |
Collapse
|
36
|
|
37
|
Sun X, Chandar AK, Canto MI, Thota PN, Brock M, Shaheen NJ, Beer DG, Wang JS, Falk GW, Iyer PG, Abrams JA, Venkat-Ramani M, Veigl M, Miron A, Willis J, Patil DT, Nalbantoglu I, Guda K, Markowitz SD, Zhu X, Elston R, Chak A. Genomic regions associated with susceptibility to Barrett's esophagus and esophageal adenocarcinoma in African Americans: The cross BETRNet admixture study. PLoS One 2017; 12:e0184962. [PMID: 29073141 PMCID: PMC5657624 DOI: 10.1371/journal.pone.0184962] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 09/04/2017] [Indexed: 12/20/2022] Open
Abstract
Background Barrett’s esophagus (BE) and esophageal adenocarcinoma (EAC) are far more prevalent in European Americans than in African Americans. Hypothesizing that this racial disparity in prevalence might represent a genetic susceptibility, we used an admixture mapping approach to interrogate disease association with genomic differences between European and African ancestry. Methods Formalin fixed paraffin embedded samples were identified from 54 African Americans with BE or EAC through review of surgical pathology databases at participating Barrett’s Esophagus Translational Research Network (BETRNet) institutions. DNA was extracted from normal tissue, and genotyped on the Illumina OmniQuad SNP chip. Case-only admixture mapping analysis was performed on the data from both all 54 cases and also on a subset of 28 cases with high genotyping quality. Haplotype phases were inferred with Beagle 3.3.2, and local African and European ancestries were inferred with SABER plus. Disease association was tested by estimating and testing excess European ancestry and contrasting it to excess African ancestry. Results Both datasets, the 54 cases and the 28 cases, identified two admixture regions. An association of excess European ancestry on chromosome 11p reached a 5% genome-wide significance threshold, corresponding to -log10(P) = 4.28. A second peak on chromosome 8q reached -log10(P) = 2.73. The converse analysis examining excess African ancestry found no genetic regions with significant excess African ancestry associated with BE and EAC. On average, the regions on chromosomes 8q and 11p showed excess European ancestry of 15% and 20%, respectively. Conclusions Chromosomal regions on 11p15 and 8q22-24 are associated with excess European ancestry in African Americans with BE and EAC. Because GWAS have not reported any variants in these two regions, low frequency and/or rare disease associated variants that confer susceptibility to developing BE and EAC may be driving the observed European ancestry association evidence.
Collapse
Affiliation(s)
- Xiangqing Sun
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States of America
| | - Apoorva K. Chandar
- Division of Gastroenterology and Hepatology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Marcia I. Canto
- Division of Gastroenterology and Hepatology, Johns Hopkins Medical Institutions, Baltimore, MD, United States of America
| | - Prashanthi N. Thota
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH, United States of America
| | - Malcom Brock
- Department of Cardiology and Thoracic Surgery, Johns Hopkins Medical Institutions, Baltimore, MD, United States of America
| | - Nicholas J. Shaheen
- Center for Esophageal Diseases & Swallowing, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States of America
| | - David G. Beer
- Thoracic Surgery, Department of Surgery, University of Michigan, Ann Arbor, MI, United States of America
| | - Jean S. Wang
- Division of Gastroenterology, Washington University School of Medicine, St Louis, MO, United States of America
| | - Gary W. Falk
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United states of America
| | - Prasad G. Iyer
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, United States of America
| | - Julian A. Abrams
- Department of Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Medha Venkat-Ramani
- Division of Gastroenterology and Hepatology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Martina Veigl
- Division of General Medical Sciences (Oncology), Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Alexander Miron
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Joseph Willis
- Department of Pathology, University Hospitals Case Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Deepa T. Patil
- Department of Pathology, Cleveland Clinic, Cleveland, OH, United States of America
| | - Ilke Nalbantoglu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Kishore Guda
- Division of General Medical Sciences (Oncology), Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Sanford D. Markowitz
- Division of Oncology and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Xiaofeng Zhu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States of America
| | - Robert Elston
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, United States of America
| | - Amitabh Chak
- Division of Gastroenterology and Hepatology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
- Division of General Medical Sciences (Oncology), Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
- * E-mail:
| |
Collapse
|
38
|
Hellwege J, Keaton J, Giri A, Gao X, Velez Edwards DR, Edwards TL. Population Stratification in Genetic Association Studies. CURRENT PROTOCOLS IN HUMAN GENETICS 2017; 95:1.22.1-1.22.23. [PMID: 29044472 PMCID: PMC6007879 DOI: 10.1002/cphg.48] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Population stratification (PS) is a primary consideration in studies of genetic determinants of human traits. Failure to control for PS may lead to confounding, causing a study to fail for lack of significant results, or resources to be wasted following false-positive signals. Here, historical and current approaches for addressing PS when performing genetic association studies in human populations are reviewed. Methods for detecting the presence of PS, including global and local ancestry methods, are described. Also described are approaches for accounting for PS when calculating association statistics, such that measures of association are not confounded. Many traits are being examined for the first time in minority populations, which may inherently feature PS. © 2017 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Jacklyn Hellwege
- Vanderbilt Genetics Institute, Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center,
Nashville, TN 37203, USA
| | - Jacob Keaton
- Vanderbilt Genetics Institute, Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center,
Nashville, TN 37203, USA
| | - Ayush Giri
- Vanderbilt Genetics Institute, Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center,
Nashville, TN 37203, USA
| | - Xiaoyi Gao
- Department of Ophthalmology and Preventive Medicine, Keck School of Medicine, University of Southern California, Los
Angeles, CA 90033, USA
| | - Digna R. Velez Edwards
- Vanderbilt Genetics Institute, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center,
Nashville, TN 37203, USA
| | - Todd L. Edwards
- Vanderbilt Genetics Institute, Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center,
Nashville, TN 37203, USA
| |
Collapse
|
39
|
Investigation of copy number variation in subjects with major depression based on whole-genome sequencing data. J Affect Disord 2017; 220:38-42. [PMID: 28578134 DOI: 10.1016/j.jad.2017.05.044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 04/26/2017] [Accepted: 05/28/2017] [Indexed: 01/12/2023]
Abstract
BACKGROUND Despite recent intensive research using genome-wide association studies, the underlying biological basis of major depressive disorder (MDD) still remains unknown. In contrast to genotyping platforms which identify specific variations, whole-genome sequencing (WGS) allows us to detect all private genetic variations within an individual. So far there have been no studies investigating copy number variations (CNVs) in subjects with MDD using WGS data. METHODS We obtained complete WGS paired-end reads data of 15 MDD patients and 10 ethnically matched healthy controls. We performed alignments for the sequencing reads and used GASV package to call CNVs including deletion, inversion, translocation and divergence for those subjects. RESULTS Our results show that, in the Mexican-American sample, deletion CNVs were significantly richer in MDD cases than healthy controls on each of 23 chromosomes. However, other types of CNVs failed to reach any significance. In the Australian sample, there was no statistically significant difference of CNVs between MDD cases and controls. Furthermore, we found that the Australian group had significantly more deletion CNVs than the Mexican-American group. LIMITATIONS High quality WGS costs limited obtaining larger datasets. The GASV package does not currently support duplication or insertion CNVs. CONCLUSIONS To our knowledge this is the first time that CNVs detected by WGS data are used to study major depression. The conclusion that deletion CNVs are significantly richer in MDD cases than healthy controls is consistent with the previous finding about recurrent depressive disorder by genome-wide association analysis of CNVs on a large genotyping microarray data.
Collapse
|
40
|
Rawlik K, Rowlatt A, Sanabria-Salas MC, Hernández-Suárez G, Serrano López ML, Zabaleta J, Tenesa A. Evidence of epigenetic admixture in the Colombian population. Hum Mol Genet 2017; 26:501-508. [PMID: 28073928 PMCID: PMC5409088 DOI: 10.1093/hmg/ddw407] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 11/23/2016] [Indexed: 01/10/2023] Open
Abstract
DNA methylation (DNAm) measured in lymphoblastoid cell lines has been repeatedly demonstrated to differ between various human populations. Due to the role that DNAm plays in controlling gene expression, these differences could significantly contribute to ethnic phenotypic differences. However, because previous studies have compared distinct ethnic groups where genetic and environmental context are confounded, their relative contribution to phenotypic differences between ethnicities remains unclear. Using DNAm assayed in whole blood and colorectal tissue of 132 admixed individuals from Colombia, we identified sites where differential DNAm levels were associated with the local ancestral genetic context. Our results are consistent with population specific DNAm being primarily driven by between population genetic differences in cis, with little environmental contribution, and with consistent effects across tissues. The findings offer new insights into a possible mechanism driving phenotypic differences among different ethnic groups, and could help explain ethnic differences in colorectal cancer incidence.
Collapse
Affiliation(s)
- Konrad Rawlik
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, UK
| | - Amy Rowlatt
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, UK
| | - María Carolina Sanabria-Salas
- Subdirección de Investigaciones, Instituto Nacional de Cancerología, Bogotá D.C., Colombia.,Departamento de Química, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | | | - Martha Lucía Serrano López
- Subdirección de Investigaciones, Instituto Nacional de Cancerología, Bogotá D.C., Colombia.,Departamento de Química, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Jovanny Zabaleta
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA.,Department of Pediatrics, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Albert Tenesa
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, Scotland, UK.,MRC HGU at the MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, UK
| |
Collapse
|
41
|
Galaverni M, Caniglia R, Pagani L, Fabbri E, Boattini A, Randi E. Disentangling Timing of Admixture, Patterns of Introgression, and Phenotypic Indicators in a Hybridizing Wolf Population. Mol Biol Evol 2017; 34:2324-2339. [PMID: 28549194 PMCID: PMC5850710 DOI: 10.1093/molbev/msx169] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Hybridization is a natural or anthropogenic process that can deeply affect the genetic make-up of populations, possibly decreasing individual fitness but sometimes favoring local adaptations. The population of Italian wolves (Canis lupus), after protracted demographic declines and isolation, is currently expanding in anthropic areas, with documented cases of hybridization with stray domestic dogs. However, identifying admixture patterns in deeply introgressed populations is far from trivial. In this study, we used a panel of 170,000 SNPs analyzed with multivariate, Bayesian and local ancestry reconstruction methods to identify hybrids, estimate their ancestry proportions and timing since admixture. Moreover, we carried out preliminary genotype-phenotype association analyses to identify the genetic bases of three phenotypic traits (black coat, white claws, and spur on the hind legs) putative indicators of hybridization. Results showed no sharp subdivisions between nonadmixed wolves and hybrids, indicating that recurrent hybridization and deep introgression might have started mostly at the beginning of the population reexpansion. In hybrids, we identified a number of genomic regions with excess of ancestry in one of the parental populations, and regions with excess or resistance to introgression compared with neutral expectations. The three morphological traits showed significant genotype-phenotype associations, with a single genomic region for black coats and white claws, and with multiple genomic regions for the spur. In all cases the associated haplotypes were likely derived from dogs. In conclusion, we show that the use of multiple genome-wide ancestry reconstructions allows clarifying the admixture dynamics even in highly introgressed populations, and supports their conservation management.
Collapse
Affiliation(s)
- Marco Galaverni
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
- Area Conservazione, WWF Italia, Rome, Italy
| | - Romolo Caniglia
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
| | - Luca Pagani
- Dipartimento di Biologia, Universita degli Studi di Padova, Padua, Italy
- Estonian Biocentre, Tartu, Estonia
| | - Elena Fabbri
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
| | - Alessio Boattini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Ettore Randi
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
- Department 18/Section of Environmental Engineering, Aalborg Universitet, Aalborg, Denmark
| |
Collapse
|
42
|
|
43
|
Mychaleckyj JC, Havt A, Nayak U, Pinkerton R, Farber E, Concannon P, Lima AA, Guerrant RL. Genome-Wide Analysis in Brazilians Reveals Highly Differentiated Native American Genome Regions. Mol Biol Evol 2017; 34:559-574. [PMID: 28100790 PMCID: PMC5430616 DOI: 10.1093/molbev/msw249] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Despite its population, geographic size, and emerging economic importance, disproportionately little genome-scale research exists into genetic factors that predispose Brazilians to disease, or the population genetics of risk. After identification of suitable proxy populations and careful analysis of tri-continental admixture in 1,538 North-Eastern Brazilians to estimate individual ancestry and ancestral allele frequencies, we computed 400,000 genome-wide locus-specific branch length (LSBL) Fst statistics of Brazilian Amerindian ancestry compared to European and African; and a similar set of differentiation statistics for their Amerindian component compared with the closest Asian 1000 Genomes population (surprisingly, Bengalis in Bangladesh). After ranking SNPs by these statistics, we identified the top 10 highly differentiated SNPs in five genome regions in the LSBL tests of Brazilian Amerindian ancestry compared to European and African; and the top 10 SNPs in eight regions comparing their Amerindian component to the closest Asian 1000 Genomes population. We found SNPs within or proximal to the genes CIITA (rs6498115), SMC6 (rs1834619), and KLHL29 (rs2288697) were most differentiated in the Amerindian-specific branch, while SNPs in the genes ADAMTS9 (rs7631391), DOCK2 (rs77594147), SLC28A1 (rs28649017), ARHGAP5 (rs7151991), and CIITA (rs45601437) were most highly differentiated in the Asian comparison. These genes are known to influence immune function, metabolic and anthropometry traits, and embryonic development. These analyses have identified candidate genes for selection within Amerindian ancestry, and by comparison of the two analyses, those for which the differentiation may have arisen during the migration from Asia to the Americas.
Collapse
Affiliation(s)
- Josyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA.,Department of Public Health Sciences, University of Virginia, Charlottesville, VA
| | - Alexandre Havt
- Departamento de Fisiologia e Farmacologia, Universidade Federal do Ceará, Fortaleza, Brazil.,INCT-Instituto de Biomedicina Universidade Federal do Ceará, Fortaleza, Brazil
| | - Uma Nayak
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Relana Pinkerton
- Center for Global Health, University of Virginia, Charlottesville, VA
| | - Emily Farber
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Patrick Concannon
- Genetics Institute, University of Florida, Gainesville, FL.,Department of Pathology Immunology and Laboratory Medicine, University of Florida, Gainesville, FL
| | - Aldo A Lima
- Departamento de Fisiologia e Farmacologia, Universidade Federal do Ceará, Fortaleza, Brazil.,INCT-Instituto de Biomedicina Universidade Federal do Ceará, Fortaleza, Brazil
| | | |
Collapse
|
44
|
Antony VB, Redlich CA, Pinkerton KE, Balmes J, Harkema JR. National Institute of Environmental Health Sciences: 50 Years of Advancing Science and Improving Lung Health. Am J Respir Crit Care Med 2017; 194:1190-1195. [PMID: 27668911 DOI: 10.1164/rccm.201608-1645pp] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The American Thoracic Society celebrates the 50th anniversary of the National Institute of Environmental Health Sciences (NIEHS). The NIEHS has had enormous impact through its focus on research, training, and translational science on lung health. It has been an advocate for clean air both in the United States and across the world. The cutting-edge science funded by the NIEHS has led to major discoveries that have broadened our understanding of the pathogenesis and treatment for lung disease. Importantly, the NIEHS has developed and fostered mechanisms that require cross-cutting science across the spectrum of areas of inquiry, bringing together environmental and social scientists with clinicians to bring their expertise on specific areas of investigation. The intramural program of the NIEHS nurtures cutting-edge science, and the extramural program encourages investigator-initiated research while at the same time providing broader direction through important initiatives. Under the umbrella of the NIEHS and guided by Dr. Linda Birnbaum, the director of the NIEHS, important collaborative programs, such as the Superfund Program and the National Toxicology Program, work to discover mechanisms to protect from environmental toxins. The American Thoracic Society has overlapping goals with the NIEHS, and the strategic plans of both august bodies converge to synergize on population lung health. These bonds must be tightened and highlighted as we work toward our common goals.
Collapse
Affiliation(s)
- Veena B Antony
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Carrie A Redlich
- 2 Occupational and Environmental Medicine, Internal Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Kent E Pinkerton
- 3 School of Veterinary Medicine, University of California Davis, Davis, California
| | - John Balmes
- 4 Occupational and Environmental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California; and
| | - Jack R Harkema
- 5 Department of Pathology and Diagnostic Investigation, Michigan State University, East Lansing, Michigan
| |
Collapse
|
45
|
Wong ML, Arcos-Burgos M, Liu S, Vélez JI, Yu C, Baune BT, Jawahar MC, Arolt V, Dannlowski U, Chuah A, Huttley GA, Fogarty R, Lewis MD, Bornstein SR, Licinio J. The PHF21B gene is associated with major depression and modulates the stress response. Mol Psychiatry 2017; 22:1015-1025. [PMID: 27777418 PMCID: PMC5461220 DOI: 10.1038/mp.2016.174] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/14/2016] [Accepted: 08/16/2016] [Indexed: 12/04/2022]
Abstract
Major depressive disorder (MDD) affects around 350 million people worldwide; however, the underlying genetic basis remains largely unknown. In this study, we took into account that MDD is a gene-environment disorder, in which stress is a critical component, and used whole-genome screening of functional variants to investigate the 'missing heritability' in MDD. Genome-wide association studies (GWAS) using single- and multi-locus linear mixed-effect models were performed in a Los Angeles Mexican-American cohort (196 controls, 203 MDD) and in a replication European-ancestry cohort (499 controls, 473 MDD). Our analyses took into consideration the stress levels in the control populations. The Mexican-American controls, comprised primarily of recent immigrants, had high levels of stress due to acculturation issues and the European-ancestry controls with high stress levels were given higher weights in our analysis. We identified 44 common and rare functional variants associated with mild to moderate MDD in the Mexican-American cohort (genome-wide false discovery rate, FDR, <0.05), and their pathway analysis revealed that the three top overrepresented Gene Ontology (GO) processes were innate immune response, glutamate receptor signaling and detection of chemical stimulus in smell sensory perception. Rare variant analysis replicated the association of the PHF21B gene in the ethnically unrelated European-ancestry cohort. The TRPM2 gene, previously implicated in mood disorders, may also be considered replicated by our analyses. Whole-genome sequencing analyses of a subset of the cohorts revealed that European-ancestry individuals have a significantly reduced (50%) number of single nucleotide variants compared with Mexican-American individuals, and for this reason the role of rare variants may vary across populations. PHF21b variants contribute significantly to differences in the levels of expression of this gene in several brain areas, including the hippocampus. Furthermore, using an animal model of stress, we found that Phf21b hippocampal gene expression is significantly decreased in animals resilient to chronic restraint stress when compared with non-chronically stressed animals. Together, our results reveal that including stress level data enables the identification of novel rare functional variants associated with MDD.
Collapse
Affiliation(s)
- M-L Wong
- Mind & Brain Theme, South Australian
Health and Medical Research Institute (SAHMRI), Adelaide,
SA, Australia
- Department of Psychiatry, Flinders
University School of Medicine, Bedford Park, SA,
Australia
| | - M Arcos-Burgos
- Department of Genome Sciences, John
Curtin School of Medical Research, Australian National University,
Canberra, ACT, Australia
- University of Rosario International
Institute of Translational Medicine, Bogotá,
Colombia
| | - S Liu
- Mind & Brain Theme, South Australian
Health and Medical Research Institute (SAHMRI), Adelaide,
SA, Australia
- Department of Psychiatry, Flinders
University School of Medicine, Bedford Park, SA,
Australia
| | - J I Vélez
- Department of Genome Sciences, John
Curtin School of Medical Research, Australian National University,
Canberra, ACT, Australia
- Universidad del Norte,
Barranquilla, Colombia
| | - C Yu
- Mind & Brain Theme, South Australian
Health and Medical Research Institute (SAHMRI), Adelaide,
SA, Australia
- Department of Psychiatry, Flinders
University School of Medicine, Bedford Park, SA,
Australia
| | - B T Baune
- Discipline of Psychiatry, University of
Adelaide, Adelaide, SA, Australia
| | - M C Jawahar
- Discipline of Psychiatry, University of
Adelaide, Adelaide, SA, Australia
| | - V Arolt
- Department of Psychiatry and
Psychotherapy, University of Münster, Münster,
Germany
| | - U Dannlowski
- Department of Psychiatry and
Psychotherapy, University of Münster, Münster,
Germany
- Department of Psychiatry and
Psychotherapy, University of Marburg, Marburg,
Germany
| | - A Chuah
- Department of Genome Sciences, John
Curtin School of Medical Research, Australian National University,
Canberra, ACT, Australia
| | - G A Huttley
- Department of Genome Sciences, John
Curtin School of Medical Research, Australian National University,
Canberra, ACT, Australia
| | - R Fogarty
- Mind & Brain Theme, South Australian
Health and Medical Research Institute (SAHMRI), Adelaide,
SA, Australia
| | - M D Lewis
- Mind & Brain Theme, South Australian
Health and Medical Research Institute (SAHMRI), Adelaide,
SA, Australia
- Department of Psychiatry, Flinders
University School of Medicine, Bedford Park, SA,
Australia
| | - S R Bornstein
- Department of Psychiatry and
Psychotherapy, University of Münster, Münster,
Germany
- Medical Clinic III, Carl Gustav Carus
University Hospital, Dresden University of Technology, Dresden,
Germany
| | - J Licinio
- Mind & Brain Theme, South Australian
Health and Medical Research Institute (SAHMRI), Adelaide,
SA, Australia
- Department of Psychiatry, Flinders
University School of Medicine, Bedford Park, SA,
Australia
| |
Collapse
|
46
|
Szulc P, Bogdan M, Frommlet F, Tang H. Joint genotype- and ancestry-based genome-wide association studies in admixed populations. Genet Epidemiol 2017; 41:555-566. [PMID: 28657151 DOI: 10.1002/gepi.22056] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 04/01/2017] [Accepted: 04/25/2017] [Indexed: 12/21/2022]
Abstract
In genome-wide association studies (GWAS) genetic loci that influence complex traits are localized by inspecting associations between genotypes of genetic markers and the values of the trait of interest. On the other hand, admixture mapping, which is performed in case of populations consisting of a recent mix of two ancestral groups, relies on the ancestry information at each locus (locus-specific ancestry). Recently it has been proposed to jointly model genotype and locus-specific ancestry within the framework of single marker tests. Here, we extend this approach for population-based GWAS in the direction of multimarker models. A modified version of the Bayesian information criterion is developed for building a multilocus model that accounts for the differential correlation structure due to linkage disequilibrium (LD) and admixture LD. Simulation studies and a real data example illustrate the advantages of this new approach compared to single-marker analysis or modern model selection strategies based on separately analyzing genotype and ancestry data, as well as to single-marker analysis combining genotypic and ancestry information. Depending on the signal strength, our procedure automatically chooses whether genotypic or locus-specific ancestry markers are added to the model. This results in a good compromise between the power to detect causal mutations and the precision of their localization. The proposed method has been implemented in R and is available at http://www.math.uni.wroc.pl/~mbogdan/admixtures/.
Collapse
Affiliation(s)
- Piotr Szulc
- Faculty of Mathematics, Wroclaw University of Technology, Wroclaw, Poland
| | - Malgorzata Bogdan
- Faculty of Mathematics and Computer Science, University of Wroclaw, Wroclaw, Poland
| | - Florian Frommlet
- Department of Medical Statistics, CEMSIIS, Medical University of Vienna, Vienna, Austria
| | - Hua Tang
- Departments of Genetics and Statistics, Stanford University, Stanford, California, United States of America
| |
Collapse
|
47
|
Yu C, Baune BT, Licinio J, Wong ML. Whole-genome single nucleotide variant distribution on genomic regions and its relationship to major depression. Psychiatry Res 2017; 252:75-79. [PMID: 28258043 PMCID: PMC5730269 DOI: 10.1016/j.psychres.2017.02.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 02/06/2017] [Accepted: 02/19/2017] [Indexed: 11/22/2022]
Abstract
Recent advances in DNA technologies have provided unprecedented opportunities for biological and medical research. In contrast to current popular genotyping platforms which identify specific variations, whole-genome sequencing (WGS) allows for the detection of all private mutations within an individual. Major depressive disorder (MDD) is a chronic condition with enormous medical, social and economic impacts. Genetic analysis, by identifying risk variants and thereby increasing our understanding of how MDD arises, could lead to improved prevention and the development of new and more effective treatments. Here we investigated the distributions of whole-genome single nucleotide variants (SNVs) on 12 different genomic regions for 25 human subjects using the symmetrised Kullback-Leibler divergence to measure the similarity between their SNV distributions. We performed cluster analysis for MDD patients and ethnically matched healthy controls. The results showed that Mexican-American controls grouped closer; in contrast depressed Mexican-American participants grouped away from their ethnically matched controls. This implies that whole-genome SNV distribution on the genomic regions may be related to major depression.
Collapse
Affiliation(s)
- Chenglong Yu
- Mind and Brain Theme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA 5000, Australia; School of Medicine, Flinders University, Bedford Park, SA 5042, Australia.
| | - Bernhard T Baune
- Discipline of Psychiatry, School of Medicine, University of Adelaide, Adelaide, SA 5005, Australia
| | - Julio Licinio
- Mind and Brain Theme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA 5000, Australia; School of Medicine, Flinders University, Bedford Park, SA 5042, Australia
| | - Ma-Li Wong
- Mind and Brain Theme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA 5000, Australia; School of Medicine, Flinders University, Bedford Park, SA 5042, Australia
| |
Collapse
|
48
|
Yu C, Arcos-Burgos M, Licinio J, Wong ML. A latent genetic subtype of major depression identified by whole-exome genotyping data in a Mexican-American cohort. Transl Psychiatry 2017; 7:e1134. [PMID: 28509902 PMCID: PMC5534938 DOI: 10.1038/tp.2017.102] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 04/04/2017] [Accepted: 04/10/2017] [Indexed: 02/07/2023] Open
Abstract
Identifying data-driven subtypes of major depressive disorder (MDD) is an important topic of psychiatric research. Currently, MDD subtypes are based on clinically defined depression symptom patterns. Although a few data-driven attempts have been made to identify more homogenous subgroups within MDD, other studies have not focused on using human genetic data for MDD subtyping. Here we used a computational strategy to identify MDD subtypes based on single-nucleotide polymorphism genotyping data from MDD cases and controls using Hamming distance and cluster analysis. We examined a cohort of Mexican-American participants from Los Angeles, including MDD patients (n=203) and healthy controls (n=196). The results in cluster trees indicate that a significant latent subtype exists in the Mexican-American MDD group. The individuals in this hidden subtype have increased common genetic substrates related to major depression and they also have more anxiety and less middle insomnia, depersonalization and derealisation, and paranoid symptoms. Advances in this line of research to validate this strategy in other patient groups of different ethnicities will have the potential to eventually be translated to clinical practice, with the tantalising possibility that in the future it may be possible to refine MDD diagnosis based on genetic data.
Collapse
Affiliation(s)
- C Yu
- Mind and Brain Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- School of Medicine, Flinders University, Bedford Park, Adelaide, SA, Australia
| | - M Arcos-Burgos
- Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
- University of Rosario International Institute of Translational Medicine, Bogota, Colombia
| | - J Licinio
- Mind and Brain Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- School of Medicine, Flinders University, Bedford Park, Adelaide, SA, Australia
- South Ural State University Biomedical School, Chelyabinsk, Russia
| | - M-L Wong
- Mind and Brain Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- School of Medicine, Flinders University, Bedford Park, Adelaide, SA, Australia
| |
Collapse
|
49
|
Xue J, Lencz T, Darvasi A, Pe’er I, Carmi S. The time and place of European admixture in Ashkenazi Jewish history. PLoS Genet 2017; 13:e1006644. [PMID: 28376121 PMCID: PMC5380316 DOI: 10.1371/journal.pgen.1006644] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 02/18/2017] [Indexed: 12/21/2022] Open
Abstract
The Ashkenazi Jewish (AJ) population is important in genetics due to its high rate of Mendelian disorders. AJ appeared in Europe in the 10th century, and their ancestry is thought to comprise European (EU) and Middle-Eastern (ME) components. However, both the time and place of admixture are subject to debate. Here, we attempt to characterize the AJ admixture history using a careful application of new and existing methods on a large AJ sample. Our main approach was based on local ancestry inference, in which we first classified each AJ genomic segment as EU or ME, and then compared allele frequencies along the EU segments to those of different EU populations. The contribution of each EU source was also estimated using GLOBETROTTER and haplotype sharing. The time of admixture was inferred based on multiple statistics, including ME segment lengths, the total EU ancestry per chromosome, and the correlation of ancestries along the chromosome. The major source of EU ancestry in AJ was found to be Southern Europe (≈60–80% of EU ancestry), with the rest being likely Eastern European. The inferred admixture time was ≈30 generations ago, but multiple lines of evidence suggest that it represents an average over two or more events, pre- and post-dating the founder event experienced by AJ in late medieval times. The time of the pre-bottleneck admixture event, which was likely Southern European, was estimated to ≈25–50 generations ago. The Ashkenazi Jewish population has resided in Europe for much of its 1000-year existence. However, its ethnic and geographic origins are controversial, due to the scarcity of reliable historical records. Previous genetic studies have found links to Middle-Eastern and European ancestries, but the admixture history has not been studied in detail yet, partly due to technical difficulties in disentangling signals from multiple admixture events. Here, we present an in-depth analysis of the sources of European gene flow and the time of admixture events by using multiple new and existing methods and extensive simulations. Our results suggest a model of at least two events of European admixture. One event slightly pre-dated a late medieval founder event and was likely from a Southern European source. Another event post-dated the founder event and likely occurred in Eastern Europe. These results, as well as the methods introduced, will be highly valuable for geneticists and other researchers interested in Ashkenazi Jewish origins.
Collapse
Affiliation(s)
- James Xue
- Department of Computer Science, Columbia University, New York, New York, United States of America
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Todd Lencz
- Center for Psychiatric Neuroscience, The Feinstein Institute for Medical Research, North Shore-Long Island Jewish Health System, Manhasset, New York, United States of America
- Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of the North Shore–Long Island Jewish Health System, Glen Oaks, New York, United States of America
- Departments of Psychiatry and Molecular Medicine, Hofstra Northwell School of Medicine, Hempstead, New York, United States of America
| | - Ariel Darvasi
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Itsik Pe’er
- Department of Computer Science, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
- * E-mail:
| |
Collapse
|
50
|
Yu C, Baune BT, Licinio J, Wong ML. A novel strategy for clustering major depression individuals using whole-genome sequencing variant data. Sci Rep 2017; 7:44389. [PMID: 28287625 PMCID: PMC5347377 DOI: 10.1038/srep44389] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/07/2017] [Indexed: 12/01/2022] Open
Abstract
Major depressive disorder (MDD) is highly prevalent, resulting in an exceedingly high disease burden. The identification of generic risk factors could lead to advance prevention and therapeutics. Current approaches examine genotyping data to identify specific variations between cases and controls. Compared to genotyping, whole-genome sequencing (WGS) allows for the detection of private mutations. In this proof-of-concept study, we establish a conceptually novel computational approach that clusters subjects based on the entirety of their WGS. Those clusters predicted MDD diagnosis. This strategy yielded encouraging results, showing that depressed Mexican-American participants were grouped closer; in contrast ethnically-matched controls grouped away from MDD patients. This implies that within the same ancestry, the WGS data of an individual can be used to check whether this individual is within or closer to MDD subjects or to controls. We propose a novel strategy to apply WGS data to clinical medicine by facilitating diagnosis through genetic clustering. Further studies utilising our method should examine larger WGS datasets on other ethnical groups.
Collapse
Affiliation(s)
- Chenglong Yu
- Mind and Brain Theme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA 5000, Australia
- School of Medicine, Flinders University, Bedford Park, SA 5042, Australia
| | - Bernhard T. Baune
- Discipline of Psychiatry, School of Medicine, University of Adelaide, Adelaide, SA 5005, Australia
| | - Julio Licinio
- Mind and Brain Theme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA 5000, Australia
- School of Medicine, Flinders University, Bedford Park, SA 5042, Australia
| | - Ma-Li Wong
- Mind and Brain Theme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA 5000, Australia
- School of Medicine, Flinders University, Bedford Park, SA 5042, Australia
| |
Collapse
|