Whole Genome Sequencing of Four Representatives From the Admixed Population of the United Arab Emirates
Whole genome sequences (WGS) of four nationals of the United Arab Emirates (UAE) at an average coverage of 33X have been completed and described. The selection of suitable subpopulation representatives was informed by a preceding comprehensive population structure analysis. Representatives were chos...
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Published in | Frontiers in genetics Vol. 11; p. 681 |
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Main Authors | , , , |
Format | Journal Article |
Language | English |
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Abstract | Whole genome sequences (WGS) of four nationals of the United Arab Emirates (UAE) at an average coverage of 33X have been completed and described. The selection of suitable subpopulation representatives was informed by a preceding comprehensive population structure analysis. Representatives were chosen based on their central location within the subpopulation on a principal component analysis (PCA) and the degree to which they were admixed. Novel genomic variations among the different subgroups of the UAE population are reported here. Specifically, the WGS analysis identified 4,161,067–4,798,806 variants in the four individual samples, where approximately 80% were single nucleotide polymorphisms (SNPs) and 20% were insertions or deletions (indels). An average of 2.75% was found to be novel variants according to dbSNP (build 151). This is the first report of structural variants (SV) from WGS data from UAE nationals. There were 15,677–20,339 called SVs, of which around 13.5% were novel. The four samples shared 1,399,178 variants, each with distinct variants as follows: 1,085,524 (for the individual denoted as UAE S011), 1,228,559 (UAE S012), 791,072 (UAE S013), and 906,818 (UAE S014). These results show a previously unappreciated population diversity in the region. The synergy of WGS and genotype array data was demonstrated through variant annotation of the former using 2.3 million allele frequencies for the local population derived from the latter technology platform. This novel approach of combining breadth and depth of array and WGS technologies has guided the choice of population genetic representatives and provides complementary, regionalized allele frequency annotation to new genomes comprising millions of loci. |
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AbstractList | Whole genome sequences (WGS) of four nationals of the United Arab Emirates (UAE) at an average coverage of 33X have been completed and described. The selection of suitable subpopulation representatives was informed by a preceding comprehensive population structure analysis. Representatives were chosen based on their central location within the subpopulation on a principal component analysis (PCA) and the degree to which they were admixed. Novel genomic variations among the different subgroups of the UAE population are reported here. Specifically, the WGS analysis identified 4,161,067–4,798,806 variants in the four individual samples, where approximately 80% were single nucleotide polymorphisms (SNPs) and 20% were insertions or deletions (indels). An average of 2.75% was found to be novel variants according to dbSNP (build 151). This is the first report of structural variants (SV) from WGS data from UAE nationals. There were 15,677–20,339 called SVs, of which around 13.5% were novel. The four samples shared 1,399,178 variants, each with distinct variants as follows: 1,085,524 (for the individual denoted as UAE S011), 1,228,559 (UAE S012), 791,072 (UAE S013), and 906,818 (UAE S014). These results show a previously unappreciated population diversity in the region. The synergy of WGS and genotype array data was demonstrated through variant annotation of the former using 2.3 million allele frequencies for the local population derived from the latter technology platform. This novel approach of combining breadth and depth of array and WGS technologies has guided the choice of population genetic representatives and provides complementary, regionalized allele frequency annotation to new genomes comprising millions of loci. |
Author | Henschel, Andreas Al Safar, Habiba S. Tay, Guan K. Daw Elbait, Gihan |
AuthorAffiliation | 2 Department of Computer Science, Khalifa University of Science and Technology , Abu Dhabi , United Arab Emirates 5 School of Medical and Health Sciences, Edith Cowan University , Joondalup, WA , Australia 6 Department of Genetics and Molecular Biology, Collage of Medicine and Health Sciences, Khalifa University of Science and Technology , Abu Dhabi , United Arab Emirates 3 Department of Biomedical Engineering, Khalifa University of Science and Technology , Abu Dhabi , United Arab Emirates 1 Center for Biotechnology, Khalifa University of Science and Technology , Abu Dhabi , United Arab Emirates 4 Division of Psychiatry, Faculty of Health and Medical Sciences, The University of Western Australia , Crawley, WA , Australia |
AuthorAffiliation_xml | – name: 1 Center for Biotechnology, Khalifa University of Science and Technology , Abu Dhabi , United Arab Emirates – name: 5 School of Medical and Health Sciences, Edith Cowan University , Joondalup, WA , Australia – name: 2 Department of Computer Science, Khalifa University of Science and Technology , Abu Dhabi , United Arab Emirates – name: 4 Division of Psychiatry, Faculty of Health and Medical Sciences, The University of Western Australia , Crawley, WA , Australia – name: 6 Department of Genetics and Molecular Biology, Collage of Medicine and Health Sciences, Khalifa University of Science and Technology , Abu Dhabi , United Arab Emirates – name: 3 Department of Biomedical Engineering, Khalifa University of Science and Technology , Abu Dhabi , United Arab Emirates |
Author_xml | – sequence: 1 givenname: Gihan surname: Daw Elbait fullname: Daw Elbait, Gihan – sequence: 2 givenname: Andreas surname: Henschel fullname: Henschel, Andreas – sequence: 3 givenname: Guan K. surname: Tay fullname: Tay, Guan K. – sequence: 4 givenname: Habiba S. surname: Al Safar fullname: Al Safar, Habiba S. |
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CitedBy_id | crossref_primary_10_3389_fgwh_2021_708410 crossref_primary_10_1016_j_ebiom_2021_103695 crossref_primary_10_1038_s41598_022_11256_y crossref_primary_10_1007_s00439_021_02323_x crossref_primary_10_3389_fgene_2021_660428 |
Cites_doi | 10.1093/bioinformatics/btu668 10.1093/molbev/msz005 10.1126/science.8430313 10.1016/j.ajhg.2014.04.004 10.1186/1471-2156-10-49 10.1093/nar/gkw233 10.3389/fgene.2013.00127 10.1093/bioinformatics/btp394 10.1371/journal.pgen.1001111 10.1093/nar/gkr201 10.1353/hub.2002.0054 10.1038/nature07517 10.1086/382286 10.1186/s12864-015-1233-x 10.1038/s41598-019-50876-9 10.4161/fly.19695 10.1159/000093774 10.1016/j.ygeno.2018.02.003 10.1093/bib/bbv051 10.1093/bioinformatics/btu170 10.3389/fgene.2020.00608 10.1159/000083333 10.1093/nar/gkt1113 10.1093/bioinformatics/btv566 10.1016/j.gdata.2014.11.016 10.1186/1471-2156-10-59 10.1038/nature19057 10.1371/journal.pone.0099069 10.1093/bioinformatics/bty304 10.1186/1750-1172-5-29 10.3402/gha.v6i0.20100 10.1186/1471-2156-10-125 10.1002/humu.22376 10.1101/cshperspect.a008581 10.1086/519795 10.1126/science.296.5566.261b 10.1038/13779 10.1371/journal.pone.0075619 10.1101/088716 10.1093/nar/gkt958 10.1093/nar/gkq963 10.1093/bioinformatics/btp698 10.1038/ng.3592 10.1093/bioinformatics/btr330 10.1038/hgv.2016.16 10.1101/gr.094052.109 10.1101/gr.107524.110 10.1101/gr.191478.115 10.1038/nature08211 10.1186/1471-2148-10-138 10.1038/Nmeth.1363 10.1038/s10038-017-0402-y 10.1038/nature09534 10.1038/nbt.1596 10.1111/j.1469-8749.2011.04032.x 10.1093/nar/29.1.308 10.1038/538161a 10.1038/35057062 10.1038/ng.691 10.1101/015909 |
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Copyright | Copyright © 2020 Daw Elbait, Henschel, Tay and Al Safar. 2020 Daw Elbait, Henschel, Tay and Al Safar |
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Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 This article was submitted to Evolutionary and Population Genetics, a section of the journal Frontiers in Genetics These authors share first authorship Edited by: TingFung Chan, The Chinese University of Hong Kong, China Reviewed by: Magdalena Gayà-Vidal, University of Porto, Portugal; Andrés Pérez-Figueroa, University of Porto, Portugal |
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References | Wang (B63) 2014; 94 Danecek (B19) 2011; 27 Cavalli-Sforza (B16) 1993; 259 Abu-Amero (B1) 2009; 10 Cann (B14) 2002; 296 Lu (B43) 2014; 4 Thareja (B61) 2015; 16 Julier (B31) 2010; 5 Rodriguez-Flores (B55) 2016; 26 Fujimoto (B23) 2010; 42 Almal (B6) 2019; 111 Purcell (B53) 2007; 81 Loney (B41) 2013; 6 Omberg (B49) 2012; 13 Cingolani (B18) 2012; 6 Geoffroy (B26) 2018; 34 Sherry (B57) 2001; 29 Alexander (B4) 2009; 19 Al-Ali (B3) 2018; 63 Alsmadi (B8) 2014; 9 Bey (B12) 1996 Liu (B39) 2013; 8 Lek (B35) 2016; 536 (B29) 2018 Luis (B44) 2004; 74 Teebi (B60) 2010; 8 Popejoy (B51) 2016; 538 Hart (B28) 2015; 17 Poznik (B52) 2016 Regueiro (B54) 2006; 61 Carson (B15) 2014; 15 Bentley (B11) 2008; 456 Almal (B5) 2018; 111 Li (B38) 2010; 28 Alabdulkareem (B2) 2015 Weissensteiner (B65) 2016; 44 Van der Auwera (B62) 2013; 11 Ye (B66) 2009; 25 Lander (B33) 2001; 409 Harich (B27) 2010; 10 Scott (B56) 2016; 48 Fakhro (B20) 2016; 3 Manni (B46) 2002; 74 Andrews (B9) 1999; 23 Chen (B17) 2009; 6 AlSafar (B7) 2019; 9 Lu (B42) 2013; 4 Tay (B59) 2020; 11 Kim (B32) 2009; 460 Genomes Project Consortium, Abecasis (B25) 2010; 467 Okonechnikov (B48) 2016; 32 Tadmouri (B58) 1987; 36 Pelak (B50) 2010; 6 John (B30) 2015; 3 Firth (B22) 2011; 53 Bolger (B13) 2014; 30 Fujita (B24) 2010; 39 Landrum (B34) 2014; 42 MacDonald (B45) 2013; 42 Li (B37) 2010; 26 Fernandes (B21) 2019; 36 Letunic (B36) 2011; 39 Liu (B40) 2013; 34 Wang (B64) 2015; 31 Andrews (B10) 2010 McKenna (B47) 2010; 20 |
References_xml | – volume: 31 start-page: 318 year: 2015 ident: B64 article-title: Genome measures used for quality control are dependent on gene function and ancestry. publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu668 contributor: fullname: Wang – volume: 36 start-page: 575 year: 2019 ident: B21 article-title: Genome-wide characterization of arabian peninsula populations: shedding light on the history of a fundamental bridge between continents. publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msz005 contributor: fullname: Fernandes – volume: 259 start-page: 639 year: 1993 ident: B16 article-title: Demic expansions and human evolution. publication-title: Science doi: 10.1126/science.8430313 contributor: fullname: Cavalli-Sforza – volume: 94 start-page: 770 year: 2014 ident: B63 article-title: Variant association tools for quality control and analysis of large-scale sequence and genotyping array data. publication-title: Am. J. Hum. Genet. doi: 10.1016/j.ajhg.2014.04.004 contributor: fullname: Wang – volume: 13 year: 2012 ident: B49 article-title: Inferring genome-wide patterns of admixture in Qataris using fifty-five ancestral populations. publication-title: BMC Genet. doi: 10.1186/1471-2156-10-49 contributor: fullname: Omberg – year: 2010 ident: B10 publication-title: FastQC A Quality Control Tool for High Throughput Sequence Data contributor: fullname: Andrews – volume: 44 start-page: W58 year: 2016 ident: B65 article-title: HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkw233 contributor: fullname: Weissensteiner – volume: 4 year: 2013 ident: B42 article-title: Principal component analysis reveals the 1000 genomes project does not sufficiently cover the human genetic diversity in Asia. publication-title: Front. Genet. doi: 10.3389/fgene.2013.00127 contributor: fullname: Lu – volume: 25 start-page: 2865 year: 2009 ident: B66 article-title: Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp394 contributor: fullname: Ye – volume: 6 year: 2010 ident: B50 article-title: The characterization of twenty sequenced human genomes. publication-title: PLoS Genet. doi: 10.1371/journal.pgen.1001111 contributor: fullname: Pelak – year: 1996 ident: B12 publication-title: From Trucial States to United Arab Emirates. contributor: fullname: Bey – volume: 39 start-page: W475 year: 2011 ident: B36 article-title: Interactive tree of life v2: online annotation and display of phylogenetic trees made easy. publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkr201 contributor: fullname: Letunic – volume: 74 start-page: 645 year: 2002 ident: B46 article-title: Y-chromosome analysis in Egypt suggests a genetic regional continuity in Northeastern Africa. publication-title: Hum. Biol. doi: 10.1353/hub.2002.0054 contributor: fullname: Manni – volume: 456 start-page: 53 year: 2008 ident: B11 article-title: Accurate whole human genome sequencing using reversible terminator chemistry. publication-title: Nature doi: 10.1038/nature07517 contributor: fullname: Bentley – volume: 74 start-page: 532 year: 2004 ident: B44 article-title: The levant versus the Horn of Africa: evidence for bidirectional corridors of human migrations. publication-title: Am. J. Hum. Genet. doi: 10.1086/382286 contributor: fullname: Luis – volume: 16 year: 2015 ident: B61 article-title: Sequence and analysis of a whole genome from Kuwaiti population subgroup of Persian ancestry. publication-title: BMC Genomics doi: 10.1186/s12864-015-1233-x contributor: fullname: Thareja – volume: 9 year: 2019 ident: B7 article-title: Introducing the first whole genomes of nationals from the United Arab Emirates. publication-title: Sci. Rep. doi: 10.1038/s41598-019-50876-9 contributor: fullname: AlSafar – volume: 6 start-page: 80 year: 2012 ident: B18 article-title: A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. publication-title: Fly doi: 10.4161/fly.19695 contributor: fullname: Cingolani – volume: 61 start-page: 132 year: 2006 ident: B54 article-title: Iran: tricontinental nexus for Y-chromosome driven migration. publication-title: Hum. Hered. doi: 10.1159/000093774 contributor: fullname: Regueiro – volume: 111 start-page: 196 year: 2018 ident: B5 article-title: Sequencing and analysis of the whole genome of Indian Gujarati male. publication-title: Genomics doi: 10.1016/j.ygeno.2018.02.003 contributor: fullname: Almal – volume: 17 start-page: 346 year: 2015 ident: B28 article-title: VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files. publication-title: Brief. Bioinform. doi: 10.1093/bib/bbv051 contributor: fullname: Hart – volume: 30 start-page: 2114 year: 2014 ident: B13 article-title: Trimmomatic: a flexible trimmer for Illumina sequence data. publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu170 contributor: fullname: Bolger – volume: 11 year: 2020 ident: B59 article-title: Genetic diversity and low stratification of the population of the united arab emirates. publication-title: Front. Genet. doi: 10.3389/fgene.2020.00608 contributor: fullname: Tay – volume: 8 start-page: 21 year: 2010 ident: B60 article-title: Introduction: genetic diversity among arabs. publication-title: Commun. Genet. doi: 10.1159/000083333 contributor: fullname: Teebi – volume: 42 start-page: D980 year: 2014 ident: B34 article-title: ClinVar: public archive of relationships among sequence variation and human phenotype. publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkt1113 contributor: fullname: Landrum – volume: 32 start-page: 292 year: 2016 ident: B48 article-title: Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv566 contributor: fullname: Okonechnikov – volume: 3 start-page: 116 year: 2015 ident: B30 article-title: Kuwaiti population subgroup of nomadic Bedouin ancestry-Whole genome sequence and analysis. publication-title: Genom Data doi: 10.1016/j.gdata.2014.11.016 contributor: fullname: John – volume: 10 year: 2009 ident: B1 article-title: Saudi arabian Y-chromosome diversity and its relationship with nearby regions. publication-title: BMC Genet. doi: 10.1186/1471-2156-10-59 contributor: fullname: Abu-Amero – volume: 536 start-page: 285 year: 2016 ident: B35 article-title: Analysis of protein-coding genetic variation in 60,706 humans. publication-title: Nature doi: 10.1038/nature19057 contributor: fullname: Lek – volume: 9 year: 2014 ident: B8 article-title: Genome at juncture of early human migration: a systematic analysis of two whole genomes and thirteen exomes from Kuwaiti population subgroup of inferred Saudi Arabian tribe ancestry. publication-title: PLoS One doi: 10.1371/journal.pone.0099069 contributor: fullname: Alsmadi – volume: 34 start-page: 3572 year: 2018 ident: B26 article-title: AnnotSV: an integrated tool for structural variations annotation. publication-title: Bioinformatics doi: 10.1093/bioinformatics/bty304 contributor: fullname: Geoffroy – volume: 5 year: 2010 ident: B31 article-title: Wolcott-Rallison syndrome. publication-title: Orphanet. J. Rare Dis. doi: 10.1186/1750-1172-5-29 contributor: fullname: Julier – volume: 6 year: 2013 ident: B41 article-title: An analysis of the health status of the United Arab Emirates: the ‘Big 4’ public health issues. publication-title: Glob. Health Action doi: 10.3402/gha.v6i0.20100 contributor: fullname: Loney – volume: 15 year: 2014 ident: B15 article-title: Effective filtering strategies to improve data quality from population-based whole exome sequencing studies. publication-title: BMC Bioinform. doi: 10.1186/1471-2156-10-125 contributor: fullname: Carson – volume: 34 start-page: E2393 year: 2013 ident: B40 article-title: dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. publication-title: Hum. Mutat. doi: 10.1002/humu.22376 contributor: fullname: Liu – volume: 4 year: 2014 ident: B43 article-title: Personalized medicine and human genetic diversity. publication-title: Cold Spring Harb. Perspect. Med. doi: 10.1101/cshperspect.a008581 contributor: fullname: Lu – volume: 81 start-page: 559 year: 2007 ident: B53 article-title: PLINK: a tool set for whole-genome association and population-based linkage analyses. publication-title: Am. J. Hum. Genet. doi: 10.1086/519795 contributor: fullname: Purcell – volume: 296 start-page: 261 year: 2002 ident: B14 article-title: A human genome diversity cell line panel. publication-title: Science doi: 10.1126/science.296.5566.261b contributor: fullname: Cann – volume: 23 year: 1999 ident: B9 article-title: Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. publication-title: Nat. Genet. doi: 10.1038/13779 contributor: fullname: Andrews – volume: 111 start-page: 196 year: 2019 ident: B6 article-title: Sequencing and analysis of the whole genome of Indian Gujarati male. publication-title: Genomics doi: 10.1016/j.ygeno.2018.02.003 contributor: fullname: Almal – volume: 8 year: 2013 ident: B39 article-title: Variant callers for next-generation sequencing data: a comparison study. publication-title: PLoS One doi: 10.1371/journal.pone.0075619 contributor: fullname: Liu – year: 2016 ident: B52 article-title: Identifying Y-chromosome haplogroups in arbitrarily large samples of sequenced or genotyped men. publication-title: bioRxiv doi: 10.1101/088716 contributor: fullname: Poznik – volume: 42 start-page: D986 year: 2013 ident: B45 article-title: The database of genomic variants: a curated collection of structural variation in the human genome. publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkt958 contributor: fullname: MacDonald – volume: 39 start-page: D876 year: 2010 ident: B24 article-title: The UCSC genome browser database: update 2011. publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkq963 contributor: fullname: Fujita – volume: 11 year: 2013 ident: B62 article-title: From FastQ data to high-confidence variant calls: the genome analysis toolkit best practices pipeline. publication-title: Curr. Protoc. Bioinform. contributor: fullname: Van der Auwera – volume: 26 start-page: 589 year: 2010 ident: B37 article-title: Fast and accurate long-read alignment with burrows–wheeler transform. publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp698 contributor: fullname: Li – volume: 48 start-page: 1071 year: 2016 ident: B56 article-title: Characterization of Greater Middle Eastern genetic variation for enhanced disease gene discovery. publication-title: Nat. Genet. doi: 10.1038/ng.3592 contributor: fullname: Scott – volume: 36 year: 1987 ident: B58 article-title: Genetic disorders in the united arab emirates. publication-title: Hemoglobin contributor: fullname: Tadmouri – volume: 27 start-page: 2156 year: 2011 ident: B19 article-title: The variant call format and VCFtools. publication-title: Bioinformatics doi: 10.1093/bioinformatics/btr330 contributor: fullname: Danecek – volume: 3 year: 2016 ident: B20 article-title: The qatar genome: a population-specific tool for precision medicine in the middle East. publication-title: Hum. Genome Var. doi: 10.1038/hgv.2016.16 contributor: fullname: Fakhro – volume: 19 start-page: 1655 year: 2009 ident: B4 article-title: Fast model-based estimation of ancestry in unrelated individuals. publication-title: Genome Res. doi: 10.1101/gr.094052.109 contributor: fullname: Alexander – volume: 20 start-page: 1297 year: 2010 ident: B47 article-title: The Genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data. publication-title: Genome Res. doi: 10.1101/gr.107524.110 contributor: fullname: McKenna – volume: 26 start-page: 151 year: 2016 ident: B55 article-title: Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations. publication-title: Genome Res. doi: 10.1101/gr.191478.115 contributor: fullname: Rodriguez-Flores – volume: 460 start-page: 1011 year: 2009 ident: B32 article-title: A highly annotated whole-genome sequence of a Korean individual. publication-title: Nature doi: 10.1038/nature08211 contributor: fullname: Kim – volume: 10 year: 2010 ident: B27 article-title: The trans-Saharan slave trade - clues from interpolation analyses and high-resolution characterization of mitochondrial DNA lineages. publication-title: BMC Evol. Biol. doi: 10.1186/1471-2148-10-138 contributor: fullname: Harich – volume: 6 start-page: 677 year: 2009 ident: B17 article-title: BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. publication-title: Nat. Methods doi: 10.1038/Nmeth.1363 contributor: fullname: Chen – volume: 63 start-page: 533 year: 2018 ident: B3 article-title: A 1000 Arab genome project to study the emirati population. publication-title: J. Hum. Genet. doi: 10.1038/s10038-017-0402-y contributor: fullname: Al-Ali – volume: 467 start-page: 1061 year: 2010 ident: B25 article-title: A map of human genome variation from population-scale sequencing. publication-title: Nature doi: 10.1038/nature09534 contributor: fullname: Genomes Project Consortium, Abecasis – volume: 28 start-page: 57 year: 2010 ident: B38 article-title: Building the sequence map of the human pan-genome. publication-title: Nat. Biotechnol. doi: 10.1038/nbt.1596 contributor: fullname: Li – volume: 53 start-page: 702 year: 2011 ident: B22 article-title: The deciphering developmental disorders (DDD) study. publication-title: Dev. Med. Child Neurol. doi: 10.1111/j.1469-8749.2011.04032.x contributor: fullname: Firth – volume: 29 start-page: 308 year: 2001 ident: B57 article-title: dbSNP: the NCBI database of genetic variation. publication-title: Nucleic Acids Res. doi: 10.1093/nar/29.1.308 contributor: fullname: Sherry – volume: 538 start-page: 161 year: 2016 ident: B51 article-title: Genomics is failing on diversity. publication-title: Nature doi: 10.1038/538161a contributor: fullname: Popejoy – volume: 409 start-page: 860 year: 2001 ident: B33 article-title: Initial sequencing and analysis of the human genome. publication-title: Nature doi: 10.1038/35057062 contributor: fullname: Lander – volume: 42 start-page: 931 year: 2010 ident: B23 article-title: Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. publication-title: Nat. Genet. doi: 10.1038/ng.691 contributor: fullname: Fujimoto – year: 2015 ident: B2 article-title: Distinctive features of a saudi genome. publication-title: bioRxiv doi: 10.1101/015909 contributor: fullname: Alabdulkareem – year: 2018 ident: B29 publication-title: Stanford HGDP SNP Genotyping Data. |
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Snippet | Whole genome sequences (WGS) of four nationals of the United Arab Emirates (UAE) at an average coverage of 33X have been completed and described. The selection... |
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SubjectTerms | Genetics next generation sequence analysis population admixture population-specific allele frequencies United Arab Emirates whole genome sequencing |
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Title | Whole Genome Sequencing of Four Representatives From the Admixed Population of the United Arab Emirates |
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