Kuwaiti population subgroup of nomadic Bedouin ancestry-Whole genome sequence and analysis

Genomics Data

Volumn 3, Issue , 2015, Pages 116-127

  John, Sumi Elsa ^a   Thareja, Gaurav ^a   Hebbar, Prashantha ^a   Behbehani, Kazem ^a   Thanaraj, Thangavel Alphonse ^a   Alsmadi, Osama ^a  

^a DASMAN DIABETES INSTITUTE   (Kuwait)

Author keywords

"Tent dwelling" Bedouins; Arabian Peninsula; Intergenome distances; Kuwaiti population; Nomadic Bedouin ancestry; Whole genome sequence

Indexed keywords

ARTICLE; BEDOUIN; CHROMOSOME ISOLATION; GENE AND NUCLEIC ACID PARAMETERS; GENETIC ANALYSIS; GENETIC IDENTIFICATION; GENOME ANALYSIS; GENOME ANNOTATION; HUMAN; KUWAIT; MOLECULAR GENETICS; PRIORITY JOURNAL; SAMPLING; SINGLE NUCLEOTIDE POLYMORPHISM; WHOLE GENOME SEQUENCE;

EID: 84922942901     PISSN: 22135960     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gdata.2014.11.016     Document Type: Article

References (77)

1. Casey M.S., Thackeray F.W., Findling J.E. The History of Kuwait 2007, Greenwood Press, Westport, Conn.
2. Alsmadi O., Thareja G., Alkayal F., Rajagopalan R., John S.E., Hebbar P., Behbehani K., Thanaraj T.A. Genetic substructure of Kuwaiti population reveals migration history. PLoS One 2013, 8(9):e74913.
3. Abu-Amero K.K., Larruga J.M., Cabrera V.M., Gonzalez A.M. Mitochondrial DNA structure in the Arabian Peninsula. BMC Evol. Biol. 2008, 8:45.
4. Abu-Amero K.K., Hellani A., Gonzalez A.M., Larruga J.M., Cabrera V.M., Underhill P.A. Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions. BMC Genet. 2009, 10:59.
5. Richards M., Rengo C., Cruciani F., Gratrix F., Wilson J.F., Scozzari R., Macaulay V., Torroni A. Extensive female-mediated gene flow from sub-Saharan Africa into near eastern Arab populations. Am. J. Hum. Genet. 2003, 72(4):1058-1064.
6. Hunter-Zinck H., Musharoff S., Salit J., Al-Ali K.A., Chouchane L., Gohar A., Matthews R., Butler M.W., et al. Population genetic structure of the people of Qatar. Am. J. Hum. Genet. 2010, 87(1):17-25.
7. Hitti P.K. The Arabs: A Short History 1996, Regnery Publishing, Washington, D.C.
8. Chatty D. Nomadic societies in the Middle East and North Africa: entering the 21st century 2006, Brill. Netherlands, Boston.
9. Markus B., Alshafee I., Birk O.S. Deciphering the fine-structure of tribal admixture in the Bedouin population using genomic data. Heredity (Edinburgh) 2014, 112(2):182-189.
10. Alsmadi O., John S.E., Thareja G., Hebbar P., Antony D., Behbehani K., Thanaraj T.A. 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. PLoS One 2014, 9(6):e99069.
11. Thareja G., John S.E., Hebbar P., Behbehani K., Thanaraj T.A., Alsmadi O. Comprehensive analysis of a personal genome of Persian ancestry from Kuwait. BMC Genomics 2015, (in press).
12. Chiaroni J., King R.J., Myres N.M., Henn B.M., Ducourneau A., Mitchell M.J., Boetsch G., Sheikha I., et al. The emergence of Y-chromosome haplogroup J1e among Arabic-speaking populations. Eur. J. Hum. Genet. 2010, 18(3):348-353.
13. Behar D.M., Villems R., Soodyall H., Blue-Smith J., Pereira L., Metspalu E., Scozzari R., Makkan H., et al. The dawn of human matrilineal diversity. Am. J. Hum. Genet. 2008, 82(5):1130-1140.
14. Kivisild T., Reidla M., Metspalu E., Rosa A., Brehm A., Pennarun E., Parik J., Geberhiwot T., et al. Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tears. Am. J. Hum. Genet. 2004, 75(5):752-770.
15. Fendt L., Rock A., Zimmermann B., Bodner M., Thye T., Tschentscher F., Owusu-Dabo E., Gobel T.M., et al. MtDNA diversity of Ghana: a forensic and phylogeographic view. Forensic Sci. Int. Genet. 2012, 6(2):244-249.
16. Allard M.W., Polanskey D., Miller K., Wilson M.R., Monson K.L., Budowle B. Characterization of human control region sequences of the African American SWGDAM forensic mtDNA data set. Forensic Sci. Int. 2005, 148(2-3):169-179.
17. Sherry S.T., Ward M.H., Kholodov M., Baker J., Phan L., Smigielski E.M., Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001, 29(1):308-311.
18. DePristo M.A., Banks E., Poplin R., Garimella K.V., Maguire J.R., Hartl C., Philippakis A.A., del Angel G., et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 2011, 43(5):491-498.
19. Kenna K.P., McLaughlin R.L., Byrne S., Elamin M., Heverin M., Kenny E.M., Cormican P., Morris D.W., et al. Delineating the genetic heterogeneity of ALS using targeted high-throughput sequencing. J. Med. Genet. 2013, 50(11):776-783.
20. Rodriguez-Flores J.L., Fuller J., Hackett N.R., Salit J., Malek J.A., Al-Dous E., Chouchane L., Zirie M., et al. Exome sequencing of only seven Qataris identifies potentially deleterious variants in the Qatari population. PLoS One 2012, 7(11):e47614.
21. Wong L.P., Ong R.T., Poh W.T., Liu X., Chen P., Li R., Lam K.K., Pillai N.E., et al. Deep whole-genome sequencing of 100 southeast Asian Malays. Am. J. Hum. Genet. 2013, 92(1):52-66.
22. Kumar P., Henikoff S., Ng P.C. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc. 2009, 4(7):1073-1081.
23. Adzhubei I.A., Schmidt S., Peshkin L., Ramensky V.E., Gerasimova A., Bork P., Kondrashov A.S., Sunyaev S.R. A method and server for predicting damaging missense mutations. Nat. Methods 2010, 7(4):248-249.
24. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25(1):25-29.
25. Welter D., MacArthur J., Morales J., Burdett T., Hall P., Junkins H., Klemm A., Flicek P., et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 2014, 42(Database issue):D1001-D1006.
26. McKusick V.A. Mendelian Inheritance in Man and its online version, OMIM. Am. J. Hum. Genet. 2007, 80(4):588-604.
27. Landrum M.J., Lee J.M., Riley G.R., Jang W., Rubinstein W.S., Church D.M., Maglott D.R. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014, 42(Database issue):D980-D985.
28. Comuzzie A.G., Cole S.A., Laston S.L., Voruganti V.S., Haack K., Gibbs R.A., Butte N.F. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. PLoS One 2012, 7(12):e51954.
29. Wheeler E., Huang N., Bochukova E.G., Keogh J.M., Lindsay S., Garg S., Henning E., Blackburn H., et al. Genome-wide SNP and CNV analysis identifies common and low-frequency variants associated with severe early-onset obesity. Nat. Genet. 2013, 45(5):513-517.
30. Berndt S.I., Gustafsson S., Magi R., Ganna A., Wheeler E., Feitosa M.F., Justice A.E., Monda K.L., et al. Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. Nat. Genet. 2013, 45(5):501-512.
31. Kraja A.T., Vaidya D., Pankow J.S., Goodarzi M.O., Assimes T.L., Kullo I.J., Sovio U., Mathias R.A., et al. A bivariate genome-wide approach to metabolic syndrome: STAMPEED consortium. Diabetes 2011, 60(4):1329-1339.
32. Hotta K., Nakamura T., Takasaki J., Takahashi H., Takahashi A., Nakata Y., Kamohara S., Kotani K., et al. Screening of 336 single-nucleotide polymorphisms in 85 obesity-related genes revealed McKusick-Kaufman syndrome gene variants are associated with metabolic syndrome. J. Hum. Genet. 2009, 54(4):230-235.
33. Kruse S., Mao X.Q., Heinzmann A., Blattmann S., Roberts M.H., Braun S., Gao P.S., Forster J., et al. The Ile198Thr and Ala379Val variants of plasmatic PAF-acetylhydrolase impair catalytical activities and are associated with atopy and asthma. Am. J. Hum. Genet. 2000, 66(5):1522-1530.
34. Kirin M., Chandra A., Charteris D.G., Hayward C., Campbell S., Celap I., Bencic G., Vatavuk Z., et al. Genome-wide association study identifies genetic risk underlying primary rhegmatogenous retinal detachment. Hum. Mol. Genet. 2013, 22(15):3174-3185.
35. Hameed A., Abid A., Aziz A., Ismail M., Mehdi S.Q., Khaliq S. Evidence of RPGRIP1 gene mutations associated with recessive cone-rod dystrophy. J. Med. Genet. 2003, 40(8):616-619.
36. Thorgeirsson T.E., Gudbjartsson D.F., Surakka I., Vink J.M., Amin N., Geller F., Sulem P., Rafnar T., et al. Sequence variants at CHRNB3-CHRNA6 and CYP2A6 affect smoking behavior. Nat. Genet. 2010, 42(5):448-453.
37. Makela K.M., Seppala I., Hernesniemi J.A., Lyytikainen L.P., Oksala N., Kleber M.E., Scharnagl H., Grammer T.B., et al. Genome-wide association study pinpoints a new functional apolipoprotein B variant influencing oxidized low-density lipoprotein levels but not cardiovascular events: AtheroRemo Consortium. Circ. Cardiovasc. Genet. 2013, 6(1):73-81.
38. Goodloe R., Brown-Gentry K., Gillani N.B., Jin H., Mayo P., Allen M., McClellan B., Boston J., et al. Lipid trait-associated genetic variation is associated with gallstone disease in the diverse Third National Health and Nutrition Examination Survey (NHANES III). BMC Med. Genet. 2013, 14:120.
39. Hoh J., Ott J. Mathematical multi-locus approaches to localizing complex human trait genes. Nat. Rev. Genet. 2003, 4(9):701-709.
40. McCarthy M.I., Hirschhorn J.N. Genome-wide association studies: potential next steps on a genetic journey. Hum. Mol. Genet. 2008, 17(R2):R156-R165.
41. Chavarria-Soley G., Sticht H., Aklillu E., Ingelman-Sundberg M., Pasutto F., Reis A., Rautenstrauss B. Mutations in CYP1B1 cause primary congenital glaucoma by reduction of either activity or abundance of the enzyme. Hum. Mutat. 2008, 29(9):1147-1153.
42. Vreken P., Van Kuilenburg A.B., Meinsma R., van Gennip A.H. Identification of novel point mutations in the dihydropyrimidine dehydrogenase gene. J. Inherit. Metab. Dis. 1997, 20(3):335-338.
43. MacDonald J.R., Ziman R., Yuen R.K., Feuk L., Scherer S.W. The Database of Genomic Variants: a curated collection of structural variation in the human genome. Nucleic Acids Res. 2014, 42(Database issue):D986-D992.
44. Moore B., Hu H., Singleton M., De La Vega F.M., Reese M.G., Yandell M. Global analysis of disease-related DNA sequence variation in 10 healthy individuals: implications for whole genome-based clinical diagnostics. Genet. Med. 2011, 13(3):210-217.
45. Teebi A.S. Autosomal recessive disorders among Arabs: an overview from Kuwait. J. Med. Genet. 1994, 31(3):224-233.
46. Cabrera V., Abu-Amero K., Larruga J., González A. The Arabian Peninsula: Gate for Human Migrations Out of Africa or Cul-de-Sac? A Mitochondrial DNA Phylogeographic Perspective. The Evolution of Human Populations in Arabia 2010, 79-87. Springer, Netherlands. M.D. Petraglia, J.I. Rose (Eds.).
47. Rose J., Petraglia M. Tracking the Origin and Evolution of Human Populations in Arabia. The Evolution of Human Populations in Arabia 2010, 1-12. Springer, Netherlands. M.D. Petraglia, J.I. Rose (Eds.).
48. Slot B. Kuwait: The Growth of a Historic Identity 2003, Arabian Publishing, London.
49. Al-Awadi S.A., Moussa M.A., Naguib K.K., Farag T.I., Teebi A.S., el-Khalifa M., el-Dossary L. Consanguinity among the Kuwaiti population. Clin. Genet. 1985, 27(5):483-486.
50. Al-Nassar K.E., Kelly C.L., EL-Kazimi A. Patterns of consanguinity in the population of Kuwait. Am. J. Hum. Genet. 1989, 45(Suppl. 4):0915A.
51. Shohat M., Halpern G.J. Familial Mediterranean fever-a review. Genet. Med. 2011, 13(6):487-498.
52. Haas B.R., Stewart T.H., Zhang J. Premotor biomarkers for Parkinson's disease-a promising direction of research. Transl. Neurodegener. 2012, 1(1):11-23.
53. Amato R., Pinelli M., Monticelli A., Marino D., Miele G., Cocozza S. Genome-wide scan for signatures of human population differentiation and their relationship with natural selection, functional pathways and diseases. PLoS One 2009, 4(11):e7927.
54. Callaway, E., Ancient European genomes reveal jumbled ancestry: Nature News & Comment. DOI: citeulike-article-id:12904863.
55. Lazaridis I., Patterson N., Mittnik A., Renaud G., Mallick S., Kirsanow K., Sudmant P.H., Schraiber J.G., et al. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 2014, 513(7518):409-413.
56. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., et al. Initial sequencing and analysis of the human genome. Nature 2001, 409(6822):860-921.
57. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079.
58. Van der Auwera G.A., Carneiro M., Hartl C., Poplin R., del Angel G., Levy-Moonshine A., Jordan T., Shakir K., et al. From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline. Current Protocols in Bioinformatics 2013, 43. 11.10.1-11.10.33.
59. McKenna A., Hanna M., Banks E., Sivachenko A., Cibulskis K., Kernytsky A., Garimella K., Altshuler D., et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010, 20(9):1297-1303.
60. Flicek P., Ahmed I., Amode M.R., Barrell D., Beal K., Brent S., Carvalho-Silva D., Clapham P., et al. Ensembl 2013. Nucleic Acids Res. 2013, 41(Database issue):D48-D55.
61. Lam H.Y., Pan C., Clark M.J., Lacroute P., Chen R., Haraksingh R., O'Huallachain M., Gerstein M.B., et al. Detecting and annotating genetic variations using the HugeSeq pipeline. Nat. Biotechnol. 2012, 30(3):226-229.
62. Wang K., Li M., Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010, 38(16):e164.
63. Van Geystelen A., Decorte R., Larmuseau M.H. AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications. BMC Genomics 2013, 14:101.
64. Andrews R.M., Kubacka I., Chinnery P.F., Lightowlers R.N., Turnbull D.M., Howell N. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat. Genet. 1999, 23(2):147.
65. Kloss-Brandstatter A., Pacher D., Schonherr S., Weissensteiner H., Binna R., Specht G., Kronenberg F. HaploGrep: a fast and reliable algorithm for automatic classification of mitochondrial DNA haplogroups. Hum. Mutat. 2011, 32(1):25-32.
66. De La Vega F.M., Hyland F.C.L., McLaughlin S., MacBride A.R., Tsung E.F., Peckham H., Scafe C., Lee C., et al. Functional analysis of the genetic variation within the genomes of three HapMap individuals obtained by whole-genome, second-generation sequencing 2009, (https://tools.lifetechnologies.com/content/sfs/posters/cms_065553.pdf).
67. Bentley D.R., Balasubramanian S., Swerdlow H.P., Smith G.P., Milton J., Brown C.G., Hall K.P., Evers D.J., et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456(7218):53-59.
68. McKernan K.J., Peckham H.E., Costa G.L., McLaughlin S.F., Fu Y., Tsung E.F., Clouser C.R., Duncan C., et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res. 2009, 19(9):1527-1541.
69. Wang J., Wang W., Li R., Li Y., Tian G., Goodman L., Fan W., Zhang J., et al. The diploid genome sequence of an Asian individual. Nature 2008, 456(7218):60-65.
70. Ahn S.M., Kim T.H., Lee S., Kim D., Ghang H., Kim D.S., Kim B.C., Kim S.Y., et al. The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res. 2009, 19(9):1622-1629.
71. Levy S., Sutton G., Ng P.C., Feuk L., Halpern A.L., Walenz B.P., Axelrod N., Huang J., et al. The diploid genome sequence of an individual human. PLoS Biol. 2007, 5(10):e254.
72. Wheeler D.A., Srinivasan M., Egholm M., Shen Y., Chen L., McGuire A., He W., Chen Y.J., et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 2008, 452(7189):872-876.
73. Drmanac R., Sparks A.B., Callow M.J., Halpern A.L., Burns N.L., Kermani B.G., Carnevali P., Nazarenko I., et al. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 2010, 327(5961):78-81.
74. Pushkarev D., Neff N.F., Quake S.R. Single-molecule sequencing of an individual human genome. Nat. Biotechnol. 2009, 27(9):847-850.
75. Felsenstein J. PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics 1989, 5:164-166. (DOI: citeulike-article-id:2344765.
76. Krzywinski M., Schein J., Birol I., Connors J., Gascoyne R., Horsman D., Jones S.J., Marra M.A. Circos: an information aesthetic for comparative genomics. Genome Res. 2009, 19(9):1639-1645.
77. Westesson O., Skinner M., Holmes I. Visualizing next-generation sequencing data with JBrowse. Brief. Bioinform. 2013, 14(2):172-177.