Atlas of human diseases influenced by genetic variants with extreme allele frequency differences

Human Genetics

Volumn 136, Issue 1, 2017, Pages 39-54

  Sulovari, Arvis ^a   Chen, Yolanda H ^b   Hudziak, James J ^a   Li, Dawei ^a,b,c  

^a UNIVERSITY OF VERMONT COLLEGE OF MEDICINE   (United States)

^b UNIVERSITY OF VERMONT   (United States)

^c University of Vermont   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOL CONSUMPTION; ARTICLE; ASTHMA; ATTENTION DEFICIT DISORDER; AUTOIMMUNE THYROIDITIS; CHRONIC HEPATITIS B; CONTROLLED STUDY; DARS GENE; DISEASE CLASSIFICATION; DISEASE PREDISPOSITION; DISEASES; FRONTOTEMPORAL DEMENTIA; GENE; GENE DELETION; GENE FREQUENCY; GENE INSERTION; GENE LINKAGE DISEQUILIBRIUM; GENETIC DIFFERENCE; GENETIC DISTANCE; GENETIC VARIABILITY; HAIR; HEPATITIS C; HUMAN; IMMUNE DEFICIENCY; INDEL MUTATION; INSULIN DEPENDENT DIABETES MELLITUS; KRT71 GENE; KRT75 GENE; KRT83 GENE; KRTAP10 1 GENE; LACTOSE TOLERANCE; MAJOR CLINICAL STUDY; NACA2 GENE; NASOPHARYNX CARCINOMA; NON INSULIN DEPENDENT DIABETES MELLITUS; PIK3R3 GENE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SKIN PIGMENTATION; TBC1D2B GENE; TRIM40 GENE; ASIAN CONTINENTAL ANCESTRY GROUP; BLACK PERSON; CAUCASIAN; GENETIC PREDISPOSITION; GENETIC VARIATION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; PHENOTYPE; THEORETICAL MODEL;

AFRICAN CONTINENTAL ANCESTRY GROUP; ASIAN CONTINENTAL ANCESTRY GROUP; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENE FREQUENCY; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, THEORETICAL; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84989911263     PISSN: 03406717     EISSN: 14321203     Source Type: Journal    
DOI: 10.1007/s00439-016-1734-y     Document Type: Article

References (86)

1. 1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR (2015) A global reference for human genetic variation. Nature 526:68–74
2. Arnold M, Soerjomataram I, Ferlay J, Forman D (2015) Global incidence of oesophageal cancer by histological subtype in 2012. Gut 64:381–387
3. Baik I, Cho NH, Kim SH, Han BG, Shin C (2011) Genome-wide association studies identify genetic loci related to alcohol consumption in Korean men. Am J Clin Nutr 93:809–816
4. Barreiro LB, Laval G, Quach H, Patin E, Quintana-Murci L (2008) Natural selection has driven population differentiation in modern humans. Nat Genet 40:340–345
5. Barrett JH, Iles MM, Harland M, Taylor JC, Aitken JF, Andresen PA, Akslen LA, Armstrong BK, Avril MF, Azizi E, Bakker B, Bergman W, Bianchi-Scarra G, Bressac-de Paillerets B, Calista D, Cannon-Albright LA, Corda E, Cust AE, Debniak T, Duffy D, Dunning AM, Easton DF, Friedman E, Galan P, Ghiorzo P, Giles GG, Hansson J, Hocevar M, Hoiom V, Hopper JL, Ingvar C, Janssen B, Jenkins MA, Jonsson G, Kefford RF, Landi G, Landi MT, Lang J, Lubinski J, Mackie R, Malvehy J, Martin NG, Molven A, Montgomery GW, van Nieuwpoort FA, Novakovic S, Olsson H, Pastorino L, Puig S, Puig-Butille JA, Randerson-Moor J, Snowden H, Tuominen R, Van Belle P, van der Stoep N, Whiteman DC, Zelenika D, Han J, Fang S, Lee JE, Wei Q, Lathrop GM, Gillanders EM, Brown KM, Goldstein AM, Kanetsky PA, Mann GJ, Macgregor S, Elder DE, Amos CI, Hayward NK, Gruis NA, Demenais F, Bishop JA, Bishop DT, Geno MELC (2011) Genome-wide association study identifies three new melanoma susceptibility loci. Nat Genet 43:1108–1113
6. Baughman RP, Teirstein AS, Judson MA, Rossman MD, Yeager H Jr, Bresnitz EA, DePalo L, Hunninghake G, Iannuzzi MC, Johns CJ, McLennan G, Moller DR, Newman LS, Rabin DL, Rose C, Rybicki B, Weinberger SE, Terrin ML, Knatterud GL, Cherniak R, Case Control Etiologic Study of Sarcoidosis research g (2001) Clinical characteristics of patients in a case control study of sarcoidosis. Am J Respir Crit Care Med 164:1885–1889
7. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate—a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 57:289–300
8. Bersaglieri T, Sabeti PC, Patterson N, Vanderploeg T, Schaffner SF, Drake JA, Rhodes M, Reich DE, Hirschhorn JN (2004) Genetic signatures of strong recent positive selection at the lactase gene. Am J Hum Genet 74:1111–1120
9. Bertoni JM, Arlette JP, Fernandez HH, Fitzer-Attas C, Frei K, Hassan MN, Isaacson SH, Lew MF, Molho E, Ondo WG, Phillips TJ, Singer C, Sutton JP, Wolf JE Jr, Ps North American, Melanoma Survey I (2010) Increased melanoma risk in Parkinson disease: a prospective clinicopathological study. Arch Neurol 67:347–352
10. ST: the impact of rare variants. Genome Res 23:1514–1521
11. Boyle P (2012) Triple-negative breast cancer: epidemiological considerations and recommendations. Ann Oncol 23(Suppl 6):vi7–vi12
12. Briscoe VJ, Tate DB, Davis SN (2007) Type 1 diabetes: exercise and hypoglycemia. Appl Physiol Nutr Metab 32:576–582
13. Carrigan MA, Uryasev O, Frye CB, Eckman BL, Myers CR, Hurley TD, Benner SA (2015) Hominids adapted to metabolize ethanol long before human-directed fermentation. Proc Natl Acad Sci USA 112:458–463
14. Castren E, Tanila H (2006) Neurotrophins and dementia—keeping in touch. Neuron 51:1–3
15. Chang ET, Adami HO (2006) The enigmatic epidemiology of nasopharyngeal carcinoma. Cancer Epidemiol Biomarkers Prev 15:1765–1777
16. Cooper GM, Stone EA, Asimenos G, Program NCS, Green ED, Batzoglou S, Sidow A (2005) Distribution and intensity of constraint in mammalian genomic sequence. Genome Res 15:901–913
17. Currier RL, Payne DC, Staat MA, Selvarangan R, Shirley SH, Halasa N, Boom JA, Englund JA, Szilagyi PG, Harrison CJ, Klein EJ, Weinberg GA, Wikswo ME, Parashar U, Vinje J, Morrow AL (2015) Innate susceptibility to norovirus infections influenced by FUT2 genotype in a United States pediatric population. Clin Infect Dis 60:1631–1638
18. Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, Butte AJ, Kumar S (2012) Human genomic disease variants: a neutral evolutionary explanation. Genome Res 22:1383–1394
19. Ezzati M, Riboli E (2013) Behavioral and dietary risk factors for noncommunicable diseases. N Engl J Med 369:954–964
20. Fraser HB (2013) Gene expression drives local adaptation in humans. Genome Res 23:1089–1096
21. Garcia-Barcelo MM, Yeung MY, Miao XP, Tang CS, Cheng G, So MT, Ngan ES, Lui VC, Chen Y, Liu XL, Hui KJ, Li L, Guo WH, Sun XB, Tou JF, Chan KW, Wu XZ, Song YQ, Chan D, Cheung K, Chung PH, Wong KK, Sham PC, Cherny SS, Tam PK (2010) Genome-wide association study identifies a susceptibility locus for biliary atresia on 10q24.2. Hum Mol Genet 19:2917–2925
22. Genetic Analysis of Psoriasis C, the Wellcome Trust Case Control C, Strange A, Capon F, Spencer CC, Knight J, Weale ME, Allen MH, Barton A, Band G, Bellenguez C, Bergboer JG, Blackwell JM, Bramon E, Bumpstead SJ, Casas JP, Cork MJ, Corvin A, Deloukas P, Dilthey A, Duncanson A, Edkins S, Estivill X, Fitzgerald O, Freeman C, Giardina E, Gray E, Hofer A, Huffmeier U, Hunt SE, Irvine AD, Jankowski J, Kirby B, Langford C, Lascorz J, Leman J, Leslie S, Mallbris L, Markus HS, Mathew CG, McLean WH, McManus R, Mossner R, Moutsianas L, Naluai AT, Nestle FO, Novelli G, Onoufriadis A, Palmer CN, Perricone C, Pirinen M, Plomin R, Potter SC, Pujol RM, Rautanen A, Riveira-Munoz E, Ryan AW, Salmhofer W, Samuelsson L, Sawcer SJ, Schalkwijk J, Smith CH, Stahle M, Su Z, Tazi-Ahnini R, Traupe H, Viswanathan AC, Warren RB, Weger W, Wolk K, Wood N, Worthington J, Young HS, Zeeuwen PL, Hayday A, Burden AD, Griffiths CE, Kere J, Reis A, McVean G, Evans DM, Brown MA, Barker JN, Peltonen L, Donnelly P, Trembath RC (2010) A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1. Nat Genet 42:985–990
23. Genome of the Netherlands C (2014) Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nat Genet 46:818–825
24. Genovese G, Friedman DJ, Ross MD, Lecordier L, Uzureau P, Freedman BI, Bowden DW, Langefeld CD, Oleksyk TK, Uscinski Knob AL, Bernhardy AJ, Hicks PJ, Nelson GW, Vanhollebeke B, Winkler CA, Kopp JB, Pays E, Pollak MR (2010) Association of trypanolytic ApoL1 variants with kidney disease in African Americans. Science 329:841–845
25. Greenwood BM, Bradley AK, Wall RA (1985) Meningococcal disease and season in sub-Saharan Africa. Lancet 2:829–830
26. Gregersen JW, Kranc KR, Ke X, Svendsen P, Madsen LS, Thomsen AR, Cardon LR, Bell JI, Fugger L (2006) Functional epistasis on a common MHC haplotype associated with multiple sclerosis. Nature 443:574–577
27. Gronberg H (2003) Prostate cancer epidemiology. Lancet 361:859–864
28. Grossman SR, Shlyakhter I, Karlsson EK, Byrne EH, Morales S, Frieden G, Hostetter E, Angelino E, Garber M, Zuk O, Lander ES, Schaffner SF, Sabeti PC (2010) A composite of multiple signals distinguishes causal variants in regions of positive selection. Science 327:883–886
29. Grossman SR, Andersen KG, Shlyakhter I, Tabrizi S, Winnicki S, Yen A, Park DJ, Griesemer D, Karlsson EK, Wong SH, Cabili M, Adegbola RA, Bamezai RN, Hill AV, Vannberg FO, Rinn JL, 1000 Genomes Project, Lander ES, Schaffner SF, Sabeti PC (2013) Identifying recent adaptations in large-scale genomic data. Cell 152:703–713
30. Grossmann A, Benlasfer N, Birth P, Hegele A, Wachsmuth F, Apelt L, Stelzl U (2015) Phospho-tyrosine dependent protein-protein interaction network. Mol Syst Biol 11:794
31. Hamblin MT, Thompson EE, Di Rienzo A (2002) Complex signatures of natural selection at the Duffy blood group locus. Am J Hum Genet 70:369–383
32. Han J, Kraft P, Nan H, Guo Q, Chen C, Qureshi A, Hankinson SE, Hu FB, Duffy DL, Zhao ZZ, Martin NG, Montgomery GW, Hayward NK, Thomas G, Hoover RN, Chanock S, Hunter DJ (2008) A genome-wide association study identifies novel alleles associated with hair color and skin pigmentation. PLoS Genet 4:e1000074
33. He M, Xu M, Zhang B, Liang J, Chen P, Lee JY, Johnson TA, Li H, Yang X, Dai J, Liang L, Gui L, Qi Q, Huang J, Li Y, Adair LS, Aung T, Cai Q, Cheng CY, Cho MC, Cho YS, Chu M, Cui B, Gao YT, Go MJ, Gu D, Gu W, Guo H, Hao Y, Hong J, Hu Z, Hu Y, Huang J, Hwang JY, Ikram MK, Jin G, Kang DH, Khor CC, Kim BJ, Kim HT, Kubo M, Lee J, Lee J, Lee NR, Li R, Li J, Liu J, Longe J, Lu W, Lu X, Miao X, Okada Y, Ong RT, Qiu G, Seielstad M, Sim X, Song H, Takeuchi F, Tanaka T, Taylor PR, Wang L, Wang W, Wang Y, Wu C, Wu Y, Xiang YB, Yamamoto K, Yang H, Liao M, Yokota M, Young T, Zhang X, Kato N, Wang QK, Zheng W, Hu FB, Lin D, Shen H, Teo YY, Mo Z, Wong TY, Lin X, Mohlke KL, Ning G, Tsunoda T, Han BG, Shu XO, Tai ES, Wu T, Qi L (2015) Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci. Hum Mol Genet 24:1791–1800
34. Heilmann S, Kiefer AK, Fricker N, Drichel D, Hillmer AM, Herold C, Tung JY, Eriksson N, Redler S, Betz RC, Li R, Karason A, Nyholt DR, Song K, Vermeulen SH, Kanoni S, Dedoussis G, Martin NG, Kiemeney LA, Mooser V, Stefansson K, Richards JB, Becker T, Brockschmidt FF, Hinds DA, Nothen MM (2013) Androgenetic alopecia: identification of four genetic risk loci and evidence for the contribution of WNT signaling to its etiology. J Invest Dermatol 133:1489–1496
35. Hoglinger GU, Melhem NM, Dickson DW, Sleiman PM, Wang LS, Klei L, Rademakers R, de Silva R, Litvan I, Riley DE, van Swieten JC, Heutink P, Wszolek ZK, Uitti RJ, Vandrovcova J, Hurtig HI, Gross RG, Maetzler W, Goldwurm S, Tolosa E, Borroni B, Pastor P, Group PSPGS, Cantwell LB, Han MR, Dillman A, van der Brug MP, Gibbs JR, Cookson MR, Hernandez DG, Singleton AB, Farrer MJ, Yu CE, Golbe LI, Revesz T, Hardy J, Lees AJ, Devlin B, Hakonarson H, Muller U, Schellenberg GD (2011) Identification of common variants influencing risk of the tauopathy progressive supranuclear palsy. Nat Genet 43:699–705
36. Holsinger KE, Weir BS (2009) Genetics in geographically structured populations: defining, estimating and interpreting F(ST). Nat Rev Genet 10:639–650
37. Hradetzky S, Balaji H, Roesner LM, Heratizadeh A, Mittermann I, Valenta R, Werfel T (2013) The human skin-associated autoantigen alpha-NAC activates monocytes and dendritic cells via TLR-2 and primes an IL-12-dependent Th1 response. J Invest Dermatol 133:2289–2292
38. Huson DH, Scornavacca C (2012) Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol 61:1061–1067
39. Johnson AD, Handsaker RE, Pulit SL, Nizzari MM, O’Donnell CJ, de Bakker PI (2008) SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap. Bioinformatics 24:2938–2939
40. Kamberov YG, Wang S, Tan J, Gerbault P, Wark A, Tan L, Yang Y, Li S, Tang K, Chen H, Powell A, Itan Y, Fuller D, Lohmueller J, Mao J, Schachar A, Paymer M, Hostetter E, Byrne E, Burnett M, McMahon AP, Thomas MG, Lieberman DE, Jin L, Tabin CJ, Morgan BA, Sabeti PC (2013) Modeling recent human evolution in mice by expression of a selected EDAR variant. Cell 152:691–702
41. Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M (2014) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 42:D199–D205
42. Karlsson EK, Kwiatkowski DP, Sabeti PC (2014) Natural selection and infectious disease in human populations. Nat Rev Genet 15:379–393
43. Key FM, Teixeira JC, de Filippo C, Andres AM (2014) Advantageous diversity maintained by balancing selection in humans. Curr Opin Genet Dev 29:45–51
44. Kircher M, Witten DM, Jain P, O’Roak BJ, Cooper GM, Shendure J (2014) A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 46:310–315
45. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19:1639–1645
46. Lamason RL, Mohideen MA, Mest JR, Wong AC, Norton HL, Aros MC, Jurynec MJ, Mao X, Humphreville VR, Humbert JE, Sinha S, Moore JL, Jagadeeswaran P, Zhao W, Ning G, Makalowska I, McKeigue PM, O’Donnell D, Kittles R, Parra EJ, Mangini NJ, Grunwald DJ, Shriver MD, Canfield VA, Cheng KC (2005) SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science 310:1782–1786
47. Lao O, Andres AM, Mateu E, Bertranpetit J, Calafell F (2003) Spatial patterns of cystic fibrosis mutation spectra in European populations. Eur J Hum Genet 11:385–394
48. Lee JW, Brancati FL, Yeh HC (2011) Trends in the prevalence of type 2 diabetes in Asians versus whites: results from the United States National Health Interview Survey, 1997–2008. Diabetes Care 34:353–357
49. Li H (2011) Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics 27:718–719
50. Liu JZ, Tozzi F, Waterworth DM, Pillai SG, Muglia P, Middleton L, Berrettini W, Knouff CW, Yuan X, Waeber G, Vollenweider P, Preisig M, Wareham NJ, Zhao JH, Loos RJ, Barroso I, Khaw KT, Grundy S, Barter P, Mahley R, Kesaniemi A, McPherson R, Vincent JB, Strauss J, Kennedy JL, Farmer A, McGuffin P, Day R, Matthews K, Bakke P, Gulsvik A, Lucae S, Ising M, Brueckl T, Horstmann S, Wichmann HE, Rawal R, Dahmen N, Lamina C, Polasek O, Zgaga L, Huffman J, Campbell S, Kooner J, Chambers JC, Burnett MS, Devaney JM, Pichard AD, Kent KM, Satler L, Lindsay JM, Waksman R, Epstein S, Wilson JF, Wild SH, Campbell H, Vitart V, Reilly MP, Li M, Qu L, Wilensky R, Matthai W, Hakonarson HH, Rader DJ, Franke A, Wittig M, Schafer A, Uda M, Terracciano A, Xiao X, Busonero F, Scheet P, Schlessinger D, St Clair D, Rujescu D, Abecasis GR, Grabe HJ, Teumer A, Volzke H, Petersmann A, John U, Rudan I, Hayward C, Wright AF, Kolcic I, Wright BJ, Thompson JR, Balmforth AJ, Hall AS, Samani NJ, Anderson CA, Ahmad T, Mathew CG, Parkes M, Satsangi J, Caulfield M, Munroe PB, Farrall M, Dominiczak A, Worthington J et al (2010) Meta-analysis and imputation refines the association of 15q25 with smoking quantity. Nat Genet 42:436–440
51. Love-Gregory L, Sherva R, Sun L, Wasson J, Schappe T, Doria A, Rao DC, Hunt SC, Klein S, Neuman RJ, Permutt MA, Abumrad NA (2008) Variants in the CD36 gene associate with the metabolic syndrome and high-density lipoprotein cholesterol. Hum Mol Genet 17:1695–1704
52. Madhava V, Burgess C, Drucker E (2002) Epidemiology of chronic hepatitis C virus infection in sub-Saharan Africa. Lancet Infect Dis 2:293–302
53. Malnic B, Godfrey PA, Buck LB (2004) The human olfactory receptor gene family. Proc Natl Acad Sci USA 101:2584–2589
54. McCarthy DJ, Humburg P, Kanapin A, Rivas MA, Gaulton K, Cazier JB, Donnelly P (2014) Choice of transcripts and software has a large effect on variant annotation. Genome Med 6(3):26
55. McKay JD, Hung RJ, Gaborieau V, Boffetta P, Chabrier A, Byrnes G, Zaridze D, Mukeria A, Szeszenia-Dabrowska N, Lissowska J, Rudnai P, Fabianova E, Mates D, Bencko V, Foretova L, Janout V, McLaughlin J, Shepherd F, Montpetit A, Narod S, Krokan HE, Skorpen F, Elvestad MB, Vatten L, Njolstad I, Axelsson T, Chen C, Goodman G, Barnett M, Loomis MM, Lubinski J, Matyjasik J, Lener M, Oszutowska D, Field J, Liloglou T, Xinarianos G, Cassidy A, Study E, Vineis P, Clavel-Chapelon F, Palli D, Tumino R, Krogh V, Panico S, Gonzalez CA, Ramon Quiros J, Martinez C, Navarro C, Ardanaz E, Larranaga N, Kham KT, Key T, Bueno-de-Mesquita HB, Peeters PH, Trichopoulou A, Linseisen J, Boeing H, Hallmans G, Overvad K, Tjonneland A, Kumle M, Riboli E, Zelenika D, Boland A, Delepine M, Foglio M, Lechner D, Matsuda F, Blanche H, Gut I, Heath S, Lathrop M, Brennan P (2008) Lung cancer susceptibility locus at 5p15.33. Nat Genet 40:1404–1406
56. McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F (2010) Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26:2069–2070
57. Mozaffarian D, Kabagambe EK, Johnson CO, Lemaitre RN, Manichaikul A, Sun Q, Foy M, Wang L, Wiener H, Irvin MR, Rich SS, Wu H, Jensen MK, Chasman DI, Chu AY, Fornage M, Steffen L, King IB, McKnight B, Psaty BM, Djousse L, Chen IY, Wu JH, Siscovick DS, Ridker PM, Tsai MY, Rimm EB, Hu FB, Arnett DK (2015) Genetic loci associated with circulating phospholipid trans fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium. Am J Clin Nutr 101:398–406
58. Nair RP, Duffin KC, Helms C, Ding J, Stuart PE, Goldgar D, Gudjonsson JE, Li Y, Tejasvi T, Feng BJ, Ruether A, Schreiber S, Weichenthal M, Gladman D, Rahman P, Schrodi SJ, Prahalad S, Guthery SL, Fischer J, Liao W, Kwok PY, Menter A, Lathrop GM, Wise CA, Begovich AB, Voorhees JJ, Elder JT, Krueger GG, Bowcock AM, Abecasis GR, Collaborative Association Study of P (2009) Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. Nat Genet 41:199–204
59. Nikolaou V, Stratigos AJ (2014) Emerging trends in the epidemiology of melanoma. Br J Dermatol 170:11–19
60. Noguchi K, Okumura F, Takahashi N, Kataoka A, Kamiyama T, Todo S, Hatakeyama S (2011) TRIM40 promotes neddylation of IKKgamma and is downregulated in gastrointestinal cancers. Carcinogenesis 32:995–1004
61. Ober C, Yao TC (2011) The genetics of asthma and allergic disease: a 21st century perspective. Immunol Rev 242:10–30
62. Ordonez D, Sanchez AJ, Martinez-Rodriguez JE, Cisneros E, Ramil E, Romo N, Moraru M, Munteis E, Lopez-Botet M, Roquer J, Garcia-Merino A, Vilches C (2009) Multiple sclerosis associates with LILRA3 deletion in Spanish patients. Genes Immun 10:579–585
63. Platt OS, Brambilla DJ, Rosse WF, Milner PF, Castro O, Steinberg MH, Klug PP (1994) Mortality in sickle cell disease. Life expectancy and risk factors for early death. N Engl J Med 330:1639–1644
64. Popovic D, Dikic I (2014) TBC1D5 and the AP2 complex regulate ATG9 trafficking and initiation of autophagy. EMBO Rep 15:392–401
65. Qiu C, Kivipelto M, von Strauss E (2009) Epidemiology of Alzheimer’s disease: occurrence, determinants, and strategies toward intervention. Dialogues Clin Neurosci 11:111–128
66. Ralston SH (2013) Clinical practice. Paget’s disease of bone. N Engl J Med 368:644–650
67. Risch N, Tang H, Katzenstein H, Ekstein J (2003) Geographic distribution of disease mutations in the Ashkenazi Jewish population supports genetic drift over selection. Am J Hum Genet 72:812–822
68. Robert-Gangneux F, Darde ML (2012) Epidemiology of and diagnostic strategies for toxoplasmosis. Clin Microbiol Rev 25:264–296
69. Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GJ, Ackerman HC, Campbell SJ, Altshuler D, Cooper R, Kwiatkowski D, Ward R, Lander ES (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419:832–837
70. Scally SW, Petersen J, Law SC, Dudek NL, Nel HJ, Loh KL, Wijeyewickrema LC, Eckle SB, van Heemst J, Pike RN, McCluskey J, Toes RE, La Gruta NL, Purcell AW, Reid HH, Thomas R, Rossjohn J (2013) A molecular basis for the association of the HLA-DRB1 locus, citrullination, and rheumatoid arthritis. J Exp Med 210:2569–2582
71. Soler Artigas M, Loth DW, Wain LV, Gharib SA, Obeidat M, Tang W, Zhai G, Zhao JH, Smith AV, Huffman JE, Albrecht E, Jackson CM, Evans DM, Cadby G, Fornage M, Manichaikul A, Lopez LM, Johnson T, Aldrich MC, Aspelund T, Barroso I, Campbell H, Cassano PA, Couper DJ, Eiriksdottir G, Franceschini N, Garcia M, Gieger C, Gislason GK, Grkovic I, Hammond CJ, Hancock DB, Harris TB, Ramasamy A, Heckbert SR, Heliovaara M, Homuth G, Hysi PG, James AL, Jankovic S, Joubert BR, Karrasch S, Klopp N, Koch B, Kritchevsky SB, Launer LJ, Liu Y, Loehr LR, Lohman K, Loos RJ, Lumley T, Al Balushi KA, Ang WQ, Barr RG, Beilby J, Blakey JD, Boban M, Boraska V, Brisman J, Britton JR, Brusselle GG, Cooper C, Curjuric I, Dahgam S, Deary IJ, Ebrahim S, Eijgelsheim M, Francks C, Gaysina D, Granell R, Gu X, Hankinson JL, Hardy R, Harris SE, Henderson J, Henry A, Hingorani AD, Hofman A, Holt PG, Hui J, Hunter ML, Imboden M, Jameson KA, Kerr SM, Kolcic I, Kronenberg F, Liu JZ, Marchini J, McKeever T, Morris AD, Olin AC, Porteous DJ, Postma DS, Rich SS, Ring SM, Rivadeneira F, Rochat T, Sayer AA, Sayers I, Sly PD et al (2011) Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function. Nat Genet 43:1082–1090
72. Sulem P, Gudbjartsson DF, Stacey SN, Helgason A, Rafnar T, Magnusson KP, Manolescu A, Karason A, Palsson A, Thorleifsson G, Jakobsdottir M, Steinberg S, Palsson S, Jonasson F, Sigurgeirsson B, Thorisdottir K, Ragnarsson R, Benediktsdottir KR, Aben KK, Kiemeney LA, Olafsson JH, Gulcher J, Kong A, Thorsteinsdottir U, Stefansson K (2007) Genetic determinants of hair, eye and skin pigmentation in Europeans. Nat Genet 39:1443–1452
73. Taft RJ, Vanderver A, Leventer RJ, Damiani SA, Simons C, Grimmond SM, Miller D, Schmidt J, Lockhart PJ, Pope K, Ru K, Crawford J, Rosser T, de Coo IF, Juneja M, Verma IC, Prabhakar P, Blaser S, Raiman J, Pouwels PJ, Bevova MR, Abbink TE, van der Knaap MS, Wolf NI (2013) Mutations in DARS cause hypomyelination with brain stem and spinal cord involvement and leg spasticity. Am J Hum Genet 92:774–780
74. Thorgeirsson TE, Geller F, Sulem P, Rafnar T, Wiste A, Magnusson KP, Manolescu A, Thorleifsson G, Stefansson H, Ingason A, Stacey SN, Bergthorsson JT, Thorlacius S, Gudmundsson J, Jonsson T, Jakobsdottir M, Saemundsdottir J, Olafsdottir O, Gudmundsson LJ, Bjornsdottir G, Kristjansson K, Skuladottir H, Isaksson HJ, Gudbjartsson T, Jones GT, Mueller T, Gottsater A, Flex A, Aben KK, de Vegt F, Mulders PF, Isla D, Vidal MJ, Asin L, Saez B, Murillo L, Blondal T, Kolbeinsson H, Stefansson JG, Hansdottir I, Runarsdottir V, Pola R, Lindblad B, van Rij AM, Dieplinger B, Haltmayer M, Mayordomo JI, Kiemeney LA, Matthiasson SE, Oskarsson H, Tyrfingsson T, Gudbjartsson DF, Gulcher JR, Jonsson S, Thorsteinsdottir U, Kong A, Stefansson K (2008) A variant associated with nicotine dependence, lung cancer and peripheral arterial disease. Nature 452:638–642
75. Tishkoff SA, Varkonyi R, Cahinhinan N, Abbes S, Argyropoulos G, Destro-Bisol G, Drousiotou A, Dangerfield B, Lefranc G, Loiselet J, Piro A, Stoneking M, Tagarelli A, Tagarelli G, Touma EH, Williams SM, Clark AG (2001) Haplotype diversity and linkage disequilibrium at human G6PD: recent origin of alleles that confer malarial resistance. Science 293:455–462
76. Tobacco, Genetics C (2010) Genome-wide meta-analyses identify multiple loci associated with smoking behavior. Nat Genet 42:441–447
77. Voight BF, Kudaravalli S, Wen X, Pritchard JK (2006) A map of recent positive selection in the human genome. PLoS Biol 4:e72
78. Wang K, Li M, Hakonarson H (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucl Acids Res 38:e164
79. Wang J, Duncan D, Shi Z, Zhang B (2013) WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. Nucl Acids Res 41:W77–W83
80. Weir BS, Cockerham CC (1984) Estimating F-Statistics for the Analysis of Population-Structure. Evolution 38:1358–1370
81. Weir BS, Hill WG (2002) Estimating F-statistics. Annu Rev Genet 36:721–750
82. Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, Klemm A, Flicek P, Manolio T, Hindorff L, Parkinson H (2014) The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucl Acids Res 42:D1001–D1006
83. Wong GK, Yang Z, Passey DA, Kibukawa M, Paddock M, Liu CR, Bolund L, Yu J (2003) A population threshold for functional polymorphisms. Genome Res 13:1873–1879
84. Wood AR, Esko T, Yang J, Vedantam S, Pers TH, Gustafsson S, Chu AY, Estrada K, Luan J, Kutalik Z, Amin N, Buchkovich ML, Croteau-Chonka DC, Day FR, Duan Y, Fall T, Fehrmann R, Ferreira T, Jackson AU, Karjalainen J, Lo KS, Locke AE, Magi R, Mihailov E, Porcu E, Randall JC, Scherag A, Vinkhuyzen AA, Westra HJ, Winkler TW, Workalemahu T, Zhao JH, Absher D, Albrecht E, Anderson D, Baron J, Beekman M, Demirkan A, Ehret GB, Feenstra B, Feitosa MF, Fischer K, Fraser RM, Goel A, Gong J, Justice AE, Kanoni S, Kleber ME, Kristiansson K, Lim U, Lotay V, Lui JC, Mangino M, Mateo Leach I, Medina-Gomez C, Nalls MA, Nyholt DR, Palmer CD, Pasko D, Pechlivanis S, Prokopenko I, Ried JS, Ripke S, Shungin D, Stancakova A, Strawbridge RJ, Sung YJ, Tanaka T, Teumer A, Trompet S, van der Laan SW, van Setten J, Van Vliet-Ostaptchouk JV, Wang Z, Yengo L, Zhang W, Afzal U, Arnlov J, Arscott GM, Bandinelli S, Barrett A, Bellis C, Bennett AJ, Berne C, Bluher M, Bolton JL, Bottcher Y, Boyd HA, Bruinenberg M, Buckley BM, Buyske S, Caspersen IH, Chines PS, Clarke R, Claudi-Boehm S, Cooper M, Daw EW, De Jong PA, Deelen J, Delgado G et al (2014) Defining the role of common variation in the genomic and biological architecture of adult human height. Nat Genet 46:1173–1186
85. Yi X, Liang Y, Huerta-Sanchez E, Jin X, Cuo ZX, Pool JE, Xu X, Jiang H, Vinckenbosch N, Korneliussen TS, Zheng H, Liu T, He W, Li K, Luo R, Nie X, Wu H, Zhao M, Cao H, Zou J, Shan Y, Li S, Yang Q, Asan Ni P, Tian G, Xu J, Liu X, Jiang T, Wu R, Zhou G, Tang M, Qin J, Wang T, Feng S, Li G, Huasang Luosang J, Wang W, Chen F, Wang Y, Zheng X, Li Z, Bianba Z, Yang G, Wang X, Tang S, Gao G, Chen Y, Luo Z, Gusang L, Cao Z, Zhang Q, Ouyang W, Ren X, Liang H, Zheng H, Huang Y, Li J, Bolund L, Kristiansen K, Li Y, Zhang Y, Zhang X, Li R, Li S, Yang H, Nielsen R, Wang J, Wang J (2010) Sequencing of 50 human exomes reveals adaptation to high altitude. Science 329:75–78
86. Zhang M, Song F, Liang L, Nan H, Zhang J, Liu H, Wang LE, Wei Q, Lee JE, Amos CI, Kraft P, Qureshi AA, Han J (2013) Genome-wide association studies identify several new loci associated with pigmentation traits and skin cancer risk in European Americans. Hum Mol Genet 22:2948–2959