Introduction to deep sequencing and its application to drug addiction research with a focus on rare variants

Molecular Neurobiology

Volumn 49, Issue 1, 2014, Pages 601-614

  Wang, Shaolin ^a   Yang, Zhongli ^a,b   Ma, Jennie Z ^a   Payne, Thomas J ^c   Li, Ming D ^a  

^a UNIVERSITY OF VIRGINIA   (United States)

^b SHANXI AGRICULTURAL UNIVERSITY   (China)

^c UNIVERSITY OF MISSISSIPPI SCHOOL OF MEDICINE   (United States)

Author keywords

Drug addiction; Next generation sequencing; Rare variants

Indexed keywords

ALCOHOLISM; ALDH2 GENE; AMPLICON; DRUG DEPENDENCE; EXOME; GENE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCATION; GENETIC ASSOCIATION; GENETIC LINKAGE; GENETIC PROCEDURES; GENETIC RISK; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOTYPE; HIGH THROUGHPUT SEQUENCING; HUMAN; NACH RECEPTOR GENE; NEXT GENERATION SEQUENCING; NONHUMAN; PHENOTYPE; REVIEW; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; BEHAVIOR, ADDICTIVE; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; SUBSTANCE-RELATED DISORDERS;

EID: 84894307307     PISSN: 08937648     EISSN: 15591182     Source Type: Journal    
DOI: 10.1007/s12035-013-8541-4     Document Type: Review

References (130)

1. WHO (2008) Report on the global tobacco epidemic, 2008: the MPOWER package. World Health Organization, Geneva
2. Mokdad AH, Marks JS, Stroup DF, Gerberding JL (2004) Actual causes of death in the United States, 2000. JAMA 291:1238-1245
3. Centers for Disease, Control and Prevention (2008) Smoking-attributable mortality, years of potential life lost, and productivity losses - United States, 2000-2004. MMWR 57:1226-1228
4. Rhee SH, Hewitt JK, Young SE, Corley RP, Crowley TJ, Stallings MC (2003) Genetic and environmental influences on substance initiation, use, and problem use in adolescents. Arch Gen Psychiatry 60:1256-1264
5. Palmer RHC, Young SE, Hopfer CJ, Corley RP, Stallings MC, Crowley TJ, Hewitt JK (2009) Developmental epidemiology of drug use and abuse in adolescence and young adulthood: evidence of generalized risk. Drug Alcohol Depend 102:78-87
6. Li MD, Burmeister M (2009) New insights into the genetics of addiction. Nat Rev Genet 10:225-231
7. Bierut LJ, Dinwiddie SH, Begleiter H, Crowe RR, Hesselbrock V, Nurnberger JI Jr, Porjesz B, Schuckit MA, Reich T (1998) Familial transmission of substance dependence: alcohol, marijuana, cocaine, and habitual smoking: a report from the Collaborative Study on the Genetics of Alcoholism. Arch Gen Psychiatry 55:982-988
8. Agrawal A, Lynskey MT (2008) Are there genetic influences on addiction: evidence from family, adoption and twin studies. Addiction 103:1069-1081
9. Li MD, Cheng R, Ma JZ, Swan GE (2003) A meta-analysis of estimated genetic and environmental effects on smoking behavior in male and female adult twins. Addiction 98:23-31
10. Tsuang MT, Bar JL, Harley RM, Lyons MJ (2001) The Harvard twin study of substance abuse: what we have learned. Harv Rev Psychiatry 9:267-279
11. Agrawal A, Lynskey MT, Hinrichs A, Grucza R, Saccone SF, Krueger R, Neuman R, Howells W, Fisher S, Fox L et al (2011) A genome-wide association study of DSM-IV cannabis dependence. Addict Biol 16:514-518
12. Long JC, Knowler WC, Hanson RL, Robin RW, Urbanek M, Moore E, Bennett PH, Goldman D (1998) Evidence for genetic linkage to alcohol dependence on chromosomes 4 and 11 from an autosome-wide scan in an American Indian population. Am J Med Genet 81:216-221
13. Reich T, Edenberg HJ, Goate A, Williams JT, Rice JP, Van Eerdewegh P, Foroud T, Hesselbrock V, Schuckit MA, Bucholz K et al (1998) Genome-wide search for genes affecting the risk for alcohol dependence. Am J Med Genet 81:207-215
14. Foroud T, Edenberg HJ, Goate A, Rice J, Flury L, Koller DL, Bierut LJ, Conneally PM, Nurnberger JI, Bucholz KK et al (2000) Alcoholism susceptibility loci: confirmation studies in a replicate sample and further mapping. Alcohol Clin Exp Res 24:933-945
15. Cui WY, Seneviratne C, Gu J, Li MD (2012) Genetics of GABAergic signaling in nicotine and alcohol dependence. Hum Genet 131:843-855
16. Gelernter J, Kranzler HR (2009) Genetics of alcohol dependence. Hum Genet 126:91-99
17. Goldman D, Oroszi G, Ducci F (2005) The genetics of addictions: uncovering the genes. Nat Rev Genet 6:521-532
18. Treutlein J, Cichon S, Ridinger M, Wodarz N, Soyka M, Zill P, Maier W, Moessner R, Gaebel W, Dahmen N et al (2009) Genome-wide association study of alcohol dependence. Arch Gen Psychiatry 66:773-784
19. Li D, Zhao H, Gelernter J (2011) Strong association of the alcohol dehydrogenase 1B gene (ADH1B) with alcohol dependence and alcohol-induced medical diseases. Biol Psychiatry 70:504-512
20. Guo H, Zhang G, Mai R (2012) Alcohol dehydrogenase-1B Arg47His polymorphism and upper aerodigestive tract cancer risk: a meta-analysis including 24,252 subjects. Alcohol Clin Exp Res 36:272-278
21. Li D, Zhao H, Gelernter J (2012) Further clarification of the contribution of the ADH1C gene to vulnerability of alcoholism and selected liver diseases. Hum Genet 131:1361-1374
22. Li D, Zhao H, Gelernter J (2012) Strong protective effect of the aldehyde dehydrogenase gene (ALDH2) 504lys (2) allele against alcoholism and alcohol-induced medical diseases in Asians. Hum Genet 131:725-737
23. Li MD (2008) Identifying susceptibility loci for nicotine dependence: 2008 update based on recent genome-wide linkage analyses. Hum Genet 123:119-131
24. Li MD, Ma JZ, Payne TJ, Lou XY, Zhang D, Dupont RT, Elston RC (2008) Genome-wide linkage scan for nicotine dependence in European Americans and its converging results with African Americans in the mid-South tobacco family sample. Mol Psychiatry 13:407-416
25. Gelernter J, Liu X, Hesselbrock V, Page GP, Goddard A, Zhang H (2004) Results of a genomewide linkage scan: support for chromosomes 9 and 11 loci increasing risk for cigarette smoking. Am J Med Genet B Neuropsychiatr Genet Off Publ Int Soc Psychiatr Gen 128B:94-101
26. Morley KI, Medland SE, Ferreira MA, Lynskey MT, Montgomery GW, Heath AC, Madden PA, Martin NG (2006) A possible smoking susceptibility locus on chromosome 11p12: evidence from sex-limitation linkage analyses in a sample of Australian twin families. Behav Genet 36:87-99
27. Vink JM, Posthuma D, Neale MC, Eline Slagboom P, Boomsma DI (2006) Genome-wide linkage scan to identify loci for age at first cigarette in Dutch sibling pairs. Behav Benet 36:100-111
28. Saccone SF, Pergadia ML, Loukola A, Broms U, Montgomery GW, Wang JC, Agrawal A, Dick DM, Heath AC, Todorov AA et al (2007) Genetic linkage to chromosome 22q12 for a heavy-smoking quantitative trait in two independent samples. Am J Hum Genet 80:856-866
29. Loukola A, Broms U, Maunu H, Widen E, Heikkila K, Siivola M, Salo A, Pergadia ML, Nyman E, Sammalisto S et al (2008) Linkage of nicotine dependence and smoking behavior on 10q, 7q and 11p in twins with homogeneous genetic background. Pharmacogenomics J 8:209-219
30. Morabia A, Cayanis E, Costanza MC, Ross BM, Bernstein MS, Flaherty MS, Alvin GB, Das K, Morris MA, Penchaszadeh GK et al (2003) Association between lipoprotein lipase (LPL) gene and blood lipids: a common variant for a common trait? Genet Epidemiol 24:309-321
31. Wang D, Ma JZ, Li MD (2005) Mapping and verification of susceptibility loci for smoking quantity using permutation linkage analysis. Pharmacogenomics J 5:166-172
32. Li MD, Payne TJ, Ma JZ, Lou XY, Zhang D, Dupont RT, Crews KM, Somes G, Williams NJ, Elston RC (2006) A genomewide search finds major susceptibility Loci for nicotine dependence on chromosome 10 in African Americans. Am J Hum Genet 79:745-751
33. Swan GE, Hops H, Wilhelmsen KC, Lessov-Schlaggar CN, Cheng LS, Hudmon KS, Amos CI, Feiler HS, Ring HZ, Andrews JA et al (2006) A genome-wide screen for nicotine dependence susceptibility loci. Am J Med Genet B Neuropsychiatr Genet 141:354-360
34. Gelernter J, Panhuysen C, Weiss R, Brady K, Poling J, Krauthammer M, Farrer L, Kranzler HR (2007) Genomewide linkage scan for nicotine dependence: identification of a chromosome 5 risk locus. Biol Psychiatry 61:119-126
35. Li MD, Sun D, Lou XY, Beuten J, Payne TJ, Ma JZ (2007) Linkage and association studies in African- and Caucasian-American populations demonstrate that SHC3 is a novel susceptibility locus for nicotine dependence. Mol Psychiatry 12:462-473
36. Bierut LJ, Stitzel JA, Wang JC, Hinrichs AL, Grucza RA, Xuei X, Saccone NL, Saccone SF, Bertelsen S, Fox L et al (2008) Variants in nicotinic receptors and risk for nicotine dependence. Am J Psychiatry 165:1163-1171
37. Li MD, Xu Q, Lou XY, Payne TJ, Niu T, Ma JZ (2010) Association and interaction analysis of variants in CHRNA5/CHRNA3/CHRNB4 gene cluster with nicotine dependence in African and European Americans. Am J Med Genet B Neuropsychiatr Genet 153B:745-756
38. Li MD, Yoon D, Lee JY, Han BG, Niu T, Payne TJ, Ma JZ, Park T (2010) Associations of variants in CHRNA5/A3/B4 gene cluster with smoking behaviors in a Korean population. PLoS One 5:e12183
39. Liu JZ, Tozzi F, Waterworth DM, Pillai SG, Muglia P, Middleton L, Berrettini W, Knouff CW, Yuan X, Waeber G et al (2010) Meta-analysis and imputation refines the association of 15q25 with smoking quantity. Nat Genet 42:436-440
40. Saccone NL, Culverhouse RC, Schwantes-An TH, Cannon DS, Chen X, Cichon S, Giegling I, Han S, Han Y, Keskitalo-Vuokko K et al (2010) Multiple independent loci at chromosome 15q25.1 affect smoking quantity: a meta-analysis and comparison with lung cancer and COPD. PLoS Genet 6
41. Thorgeirsson TE, Gudbjartsson DF, Surakka I, Vink JM, Amin N, Geller F, Sulem P, Rafnar T, Esko T, Walter S et al (2010) Sequence variants at CHRNB3-CHRNA6 and CYP2A6 affect smoking behavior. Nat Genet 42:448-453
42. Tobacco & Genetics Consortium (2010) Genome-wide meta-analyses identify multiple loci associated with smoking behavior. Nat Genet 42:441-447
43. Truong T, Hung RJ, Amos CI, Wu X, Bickeboller H, Rosenberger A, Sauter W, Illig T, Wichmann HE, Risch A et al (2010) Replication of lung cancer susceptibility loci at chromosomes 15q25, 5p15, and 6p21: a pooled analysis from the International Lung Cancer Consortium. J Natl Cancer Inst 102:959-971
44. Saccone NL, Schwantes-An TH, Wang JC, Grucza RA, Breslau N, Hatsukami D, Johnson EO, Rice JP, Goate AM, Bierut LJ (2010) Multiple cholinergic nicotinic receptor genes affect nicotine dependence risk in African and European Americans. Genes Brain Behav 9:741-750
45. Cui WY, Wang S, Yang J, Yi SG, Yoon D, Kim YJ, Payne TJ, Ma JZ, Park T, Li MD (2013) Significant association of CHRNB3 variants with nicotine dependence in multiple ethnic populations. Mol Psychiatry. doi: 10.1038/mp.2012.190
46. Gelernter J, Yu Y, Weiss R, Brady K, Panhuysen C, Yang BZ, Kranzler HR, Farrer L (2006) Haplotype spanning TTC12 and ANKK1, flanked by the DRD2 and NCAM1 loci, is strongly associated to nicotine dependence in two distinct American populations. Hum Mol Genet 15:3498-3507
47. Huang W, Payne TJ, Ma JZ, Beuten J, Dupont RT, Inohara N, Li MD (2009) Significant association of ANKK1 and detection of a functional polymorphism with nicotine dependence in an African-American sample. Neuropsychopharmacology 34:319-330
48. Saccone NL, Saccone SF, Hinrichs AL, Stitzel JA, Duan W, Pergadia ML, Agrawal A, Breslau N, Grucza RA, Hatsukami D et al (2009) Multiple distinct risk loci for nicotine dependence identified by dense coverage of the complete family of nicotinic receptor subunit (CHRN) genes. Am J Med Genet B Neuropsychiatr Genet 150B:453-466
49. Bierut LJ, Madden PA, Breslau N, Johnson EO, Hatsukami D, Pomerleau OF, Swan GE, Rutter J, Bertelsen S, Fox L et al (2007) Novel genes identified in a high-density genome wide association study for nicotine dependence. Hum Mol Genet 16:24-35
50. Nussbaum J, Xu Q, Payne TJ, Ma JZ, Huang W, Gelernter J, Li MD (2008) Significant association of the neurexin-1 gene (NRXN1) with nicotine dependence in European- and African-American smokers. Hum Mol Genet 17:1569-1577
51. TAG (2010) Genome-wide meta-analyses identify multiple loci associated with smoking behavior. Nat Genet 42:441-447
52. Beuten J, Ma JZ, Payne TJ, Dupont RT, Quezada P, Huang W, Crews KM, Li MD (2005) Significant association of BDNF haplotypes in European-American male smokers but not in European-American female or African-American smokers. Am J Med Genet B Neuropsychiatr Genet 139:73-80
53. Hopfer CJ, Lessem JM, Hartman CA, Stallings MC, Cherny SS, Corley RP, Hewitt JK, Krauter KS, Mikulich-Gilbertson SK, Rhee SH et al (2007) A genome-wide scan for loci influencing adolescent cannabis dependence symptoms: evidence for linkage on chromosomes 3 and 9. Drug Alcohol Depend 89:34-41
54. Ehlers CL, Gilder DA, Gizer IR, Wilhelmsen KC (2009) Heritability and a genome-wide linkage analysis of a Type II/B cluster construct for cannabis dependence in an American Indian community. Addict Biol 14:338-348
55. Gelernter J, Panhuysen C, Weiss R, Brady K, Hesselbrock V, Rounsaville B, Poling J, Wilcox M, Farrer L, Kranzler HR (2005) Genomewide linkage scan for cocaine dependence and related traits: significant linkages for a cocaine-related trait and cocaine-induced paranoia. Am J Med Genet B Neuropsychiatr Genet 136B:45-52
56. Gelernter J, Panhuysen C, Wilcox M, Hesselbrock V, Rounsaville B, Poling J, Weiss R, Sonne S, Zhao H, Farrer L et al (2006) Genomewide linkage scan for opioid dependence and related traits. Am J Hum Genet 78:759-769
57. Lachman HM, Fann CS, Bartzis M, Evgrafov OV, Rosenthal RN, Nunes EV, Miner C, Santana M, Gaffney J, Riddick A et al (2007) Genomewide suggestive linkage of opioid dependence to chromosome 14q. Hum Mol Genet 16:1327-1334
58. Levran O, Awolesi O, Linzy S, Adelson M, Kreek MJ (2011) Haplotype block structure of the genomic region of the mu opioid receptor gene. J Hum Genet 56:147-155
59. Levran O, Yuferov V, Kreek MJ (2012) The genetics of the opioid system and specific drug addictions. Hum Genet 131:823-842
60. Zhang H, Kranzler HR, Yang BZ, Luo X, Gelernter J (2008) The OPRD1 and OPRK1 loci in alcohol or drug dependence: OPRD1 variation modulates substance dependence risk. Mol Psychiatry 13:531-543
61. Bart G, Heilig M, LaForge KS, Pollak L, Leal SM, Ott J, Kreek MJ (2004) Substantial attributable risk related to a functional mu-opioid receptor gene polymorphism in association with heroin addiction in central Sweden. Mol Psychiatry 9:547-549
62. Tan EC, Tan CH, Karupathivan U, Yap EP (2003) Mu opioid receptor gene polymorphisms and heroin dependence in Asian populations. Neuroreport 14:569-572
63. Levran O, Londono D, O'Hara K, Nielsen DA, Peles E, Rotrosen J, Casadonte P, Linzy S, Randesi M, Ott J et al (2008) Genetic susceptibility to heroin addiction: a candidate gene association study. Genes Brain Behav 7:720-729
64. Nielsen DA, Ji F, Yuferov V, Ho A, He C, Ott J, Kreek MJ (2010) Genome-wide association study identifies genes that may contribute to risk for developing heroin addiction. Psychiatr Genet 20:207-214
65. Nishizawa D, Fukuda K, Kasai S, Hasegawa J, Aoki Y, Nishi A, Saita N, Koukita Y, Nagashima M, Katoh R et al (2012) Genome-wide association study identifies a potent locus associated with human opioid sensitivity. Mol Psychiatry. doi: 10.1038/mp.2012.164
66. Feinberg AP (2007) Phenotypic plasticity and the epigenetics of human disease. Nature 447:433-440
67. Mackay TF, Stone EA, Ayroles JF (2009) The genetics of quantitative traits: challenges and prospects. Nat Rev Genet 10:565-577
68. Shi J, Levinson DF, Duan J, Sanders AR, Zheng Y, Pe'er I, Dudbridge F, Holmans PA, Whittemore AS, Mowry BJ et al (2009) Common variants on chromosome 6p22.1 are associated with schizophrenia. Nature 460:753-757
69. Visscher PM, Hill WG, Wray NR (2008) Heritability in the genomics era - concepts and misconceptions. Nat Rev Genet 9:255-266
70. Cirulli ET, Goldstein DB (2010) Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet 11:415-425
71. Feldman MW, Lewontin RC (1975) The heritability hang-up. Science 190:1163-1168
72. Eichler EE, Flint J, Gibson G, Kong A, Leal SM, Moore JH, Nadeau JH (2010) Missing heritability and strategies for finding the underlying causes of complex disease. Nat Rev Genet 11:446-450
73. Mackay TF (2001) The genetic architecture of quantitative traits. Annu Rev Genet 35:303-339
74. Gibson G (2011) Rare and common variants: twenty arguments. Nat Rev Genet 13:135-145
75. Lupski JR, Belmont JW, Boerwinkle E, Gibbs RA (2011) Clan genomics and the complex architecture of human disease. Cell 147:32-43
76. Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE et al (2009) Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461:272-276
77. Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA (2010) A map of human genome variation from population-scale sequencing. Nature 467:1061-1073
78. Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491:56-65
79. Altshuler DM, Gibbs RA, Peltonen L, Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu F, Peltonen L et al (2010) Integrating common and rare genetic variation in diverse human populations. Nature 467:52-58
80. Li Y, Sidore C, Kang HM, Boehnke M, Abecasis GR (2011) Low-coverage sequencing: implications for design of complex trait association studies. Genome Res 21:940-951
81. Flanigan KM, Gastier-Foster J, Pyatt R, Rosales XQ, Thrush DL, Kneile K, Mendell JR, Kelly B, Newsom D, Hu P et al (2012) Comparison of commercially-available exome capture kits in the diagnosis of neuromuscular disorders. Neuromuscul Disord 22:808
82. Ewing CM, Ray AM, Lange EM, Zuhlke KA, Robbins CM, Tembe WD, Wiley KE, Isaacs SD, Johng D, Wang Y et al (2012) Germline mutations in HOXB13 and prostate-cancer risk. New Engl J Med 366:141-149
83. Mondal K, Ramachandran D, Patel VC, Hagen KR, Bose P, Cutler DJ, Zwick ME (2012) Excess variants in AFF2 detected by massively parallel sequencing of males with autism spectrum disorder. Hum Mol Genet 21:4356-4364
84. Myllykangas S, Buenrostro JD, Natsoulis G, Bell JM, Ji HP (2011) Efficient targeted resequencing of human germline and cancer genomes by oligonucleotide-selective sequencing. Nat Biotechnol 29:1024-1027
85. Sham P, Bader JS, Craig I, O'Donovan M, Owen M (2002) DNA Pooling: a tool for large-scale association studies. Nat Rev Genet 3:862-871
86. Norton N, Williams NM, O'Donovan MC, Owen MJ (2004) DNA pooling as a tool for large-scale association studies in complex traits. Ann Med 36:146-152
87. Nejentsev S, Walker N, Riches D, Egholm M, Todd JA (2009) Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes. Science 324:387-389
88. Calvo SE, Tucker EJ, Compton AG, Kirby DM, Crawford G, Burtt NP, Rivas M, Guiducci C, Bruno DL, Goldberger OA et al (2010) High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency. Nat Genet 42:851-858
89. Marchini J, Howie B (2010) Genotype imputation for genome-wide association studies. Nat Rev Genet 11:499-511
90. Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM et al (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449:851-861
91. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760
92. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M et al (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297-1303
93. Li H (2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27:2987-2993
94. Scott LJ, Mohlke KL, Bonnycastle LL, Willer CJ, Li Y, Duren WL, Erdos MR, Stringham HM, Chines PS, Jackson AU et al (2007) A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science 316:1341-1345
95. Liu EY, Li M, Wang W, Li Y (2013) MaCH-admix: genotype imputation for admixed populations. Genet Epidemiol 37:25-37
96. Marchini J, Howie B, Myers S, McVean G, Donnelly P (2007) A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet 39:906-913
97. Howie BN, Donnelly P, Marchini J (2009) A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 5:e1000529
98. Browning SR, Browning BL (2011) Haplotype phasing: existing methods and new developments. Nat Rev Genet 12:703-714
99. Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR (2012) Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat Genet 44:955-959
100. Browning SR, Browning BL (2007) Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet 81:1084-1097
101. Browning BL, Browning SR (2009) A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet 84:210-223
102. Li B, Leal SM (2008) Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet 83:311-321
103. Morgenthaler S, Thilly WG (2007) A strategy to discover genes that carry multi-allelic or mono-allelic risk for common diseases: a cohort allelic sums test (CAST). Mutat Res 615:28-56
104. Madsen BE, Browning SR (2009) A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet 5:e1000384
105. Morris AP, Zeggini E (2010) An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genet Epidemiol 34:188-193
106. Cohen JC, Kiss RS, Pertsemlidis A, Marcel YL, McPherson R, Hobbs HH (2004) Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science 305:869-872
107. Fearnhead NS, Wilding JL, Winney B, Tonks S, Bartlett S, Bicknell DC, Tomlinson IP, Mortensen NJ, Bodmer WF (2004) Multiple rare variants in different genes account for multifactorial inherited susceptibility to colorectal adenomas. Proc Natl Acad Sci U S A 101:15992-15997
108. Price AL, Kryukov GV, de Bakker PI, Purcell SM, Staples J, Wei LJ, Sunyaev SR (2010) Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet 86:832-838
109. Neale BM, Rivas MA, Voight BF, Altshuler D, Devlin B, Orho-Melander M, Kathiresan S, Purcell SM, Roeder K, Daly MJ (2011) Testing for an unusual distribution of rare variants. PLoS Genet 7:e1001322
110. Wu Michael C, Lee S, Cai T, Li Y, Boehnke M, Lin X (2011) Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet 89:82-93
111. Basu S, Pan W (2011) Comparison of statistical tests for disease association with rare variants. Genet Epidemiol 35:606-619
112. Lin DY, Tang ZZ (2011) A general framework for detecting disease associations with rare variants in sequencing studies. Am J Hum Genet 89:354-367
113. Lee S, Emond MJ, Bamshad MJ, Barnes KC, Rieder MJ, Nickerson DA, NHLBI GO Exome Sequencing Project - ESP Lung Project Team, Christiani DC, Wurfel MM, Lin X (2012) Optimal unified approach for rare-variant association testing with application to small-sample case-control whole-exome sequencing studies. Am J Hum Genet 91:224-237
114. Chen H, Meigs JB, Dupuis J (2013) Sequence kernel association test for quantitative traits in family samples. Genet Epidemiol 37:196-204
115. Conneely KN, Boehnke M (2007) So many correlated tests, so little time! Rapid adjustment of P values for multiple correlated tests. Am J Hum Genet 81:1158-1168
116. Chapman J, Whittaker J (2008) Analysis of multiple SNPs in a candidate gene or region. Genet Epidemiol 32:560-566
117. Pan W (2009) Asymptotic tests of association with multiple SNPs in linkage disequilibrium. Genet Epidemiol 33:497-507
118. Wessel J, McDonald SM, Hinds DA, Stokowski RP, Javitz HS, Kennemer M, Krasnow R, Dirks W, Hardin J, Pitts SJ et al (2010) Resequencing of nicotinic acetylcholine receptor genes and association of common and rare variants with the Fagerstrom test for nicotine dependence. Neuropsychopharmacology 35:2392-2402
119. Xie P, Kranzler HR, Krauthammer M, Cosgrove KP, Oslin D, Anton RF, Farrer LA, Picciotto MR, Krystal JH, Zhao H et al (2011) Rare nonsynonymous variants in alpha-4 nicotinic acetylcholine receptor gene protect against nicotine dependence. Biol Psychiat 70:528-536
120. Haller G, Druley T, Vallania FL, Mitra RD, Li P, Akk G, Steinbach JH, Breslau N, Johnson E, Hatsukami D et al (2012) Rare missense variants in CHRNB4 are associated with reduced risk of nicotine dependence. Hum Mol Genet 21:647-655
121. Ho MK, Goldman D, Heinz A, Kaprio J, Kreek MJ, Li MD, Munafo MR, Tyndale RF (2010) Breaking barriers in the genomics and pharmacogenetics of drug addiction. Clin Pharmacol Ther 88:779-791
122. Salas R, Orr-Urtreger A, Broide RS, Beaudet A, Paylor R, De Biasi M (2003) The nicotinic acetylcholine receptor subunit alpha 5 mediates short-term effects of nicotine in vivo. Mol Pharmacol 63:1059-1066
123. Salas R, Pieri F, De Biasi M (2004) Decreased signs of nicotine withdrawal in mice null for the beta4 nicotinic acetylcholine receptor subunit. J Neurosci 24:10035-10039
124. Salas R, Cook KD, Bassetto L, De Biasi M (2004) The alpha3 and beta4 nicotinic acetylcholine receptor subunits are necessary for nicotine-induced seizures and hypolocomotion in mice. Neuropharmacology 47:401-407
125. Fowler CD, Lu Q, Johnson PM, Marks MJ, Kenny PJ (2011) Habenular alpha5 nicotinic receptor subunit signalling controls nicotine intake. Nature 471:597-601
126. Hong LE, Hodgkinson CA, Yang Y, Sampath H, Ross TJ, Buchholz B, Salmeron BJ, Srivastava V, Thaker GK, Goldman D et al (2010) A genetically modulated, intrinsic cingulate circuit supports human nicotine addiction. Proc Natl Acad Sci U S A 107:13509-13514
127. Bierut LJ (2010) Convergence of genetic findings for nicotine dependence and smoking related diseases with chromosome 15q24-25. Trends Pharmacol Sci 31:46-51
128. Wang JC, Kapoor M, Goate AM (2012) The genetics of substance dependence. Annu Rev Genom Hum Genet 13:241-261
129. Munafo MR, Matheson IJ, Flint J (2007) Association of the DRD2 gene Taq1A polymorphism and alcoholism: a meta-analysis of case-control studies and evidence of publication bias. Mol Psychiatry 12:454-461
130. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ et al (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81:559-575