Imputation of behavioral candidate gene repeat variants in 486,551 publicly-available UK Biobank individuals

European Journal of Human Genetics

Volumn 27, Issue 6, 2019, Pages 963-969

  Border, Richard ^a   Smolen, Andrew ^a   Corley, Robin P ^a   Stallings, Michael C ^a   Brown, Sandra A ^b,c   Conger, Rand D ^d   Derringer, Jaime ^e   Donnellan, M Brent ^f   Haberstick, Brett C ^a   Hewitt, John K ^a   Hopfer, Christian ^a,g   Krauter, Ken ^a   McQueen, Matthew B ^a   Wall, Tamara L ^b   Keller, Matthew C ^a   Evans, Luke M ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^f MICHIGAN STATE UNIVERSITY   (United States)

^g UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; BIOBANK; FEMALE; HUMAN; HUMAN EXPERIMENT; MAJOR CLINICAL STUDY; MALE; PHENOTYPE; SCIENTIST; SINGLE NUCLEOTIDE POLYMORPHISM; VARIABLE NUMBER OF TANDEM REPEAT; GENE LOCUS; GENETICS; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; MENTAL DISEASE; UNITED KINGDOM;

BIOLOGICAL SPECIMEN BANKS; GENETIC LOCI; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; MENTAL DISORDERS; MINISATELLITE REPEATS; POLYMORPHISM, SINGLE NUCLEOTIDE; UNITED KINGDOM;

EID: 85061201369     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/s41431-019-0349-x     Document Type: Article

References (42)

1. McInnes LA, Freimer NB. Mapping genes for psychiatric disorders and behavioral traits. Curr Opin Genet Dev. 1995;5:376–81.
2. Ramamoorthy S, Bauman AL, Moore KR, et al. Antidepressant and cocaine-sensitive human serotonin transporter: molecular cloning, expression, and chromosomal localization. Proc Natl Acad Sci USA. 1993;90:2542–6.
3. Sabol SZ, Hu S, Hamer D. A functional polymorphism in the monoamine oxidase A gene promoter. Hum Genet. 1998;103:273–9.
4. Tol HHM Van, Wu CM, Guan H-C, et al. Multiple dopamine D4 receptor variants in the human population. Nature. 1992;358:149–52.
5. Vandenbergh DJ, Persico AM, Hawkins AL, et al. Human dopamine transporter gene (DAT1) maps to chromosome 5p15.3 and displays a VNTR. Genomics. 1992;14:1104–6.
6. Lesch KP, Bengel D, Heils A, et al. Association of anxiety-related traits with a polymorphism in the serotonin transporter gene regulatory region. Science. 1996;274:1527–31.
7. Collier DA, Arranz MJ, Sham P. The serotonin transporter gene is a potential susceptibility factor for biplor affective disorder. Neuroreport. 1996;7:1675–9.
8. Hamer DH, Greenberg BD, Sabol SZ, Murphy DL. Role of the serotonin transporter gene in temperament and character. J Pers Disord. 1999;13:312–27.
9. Caspi A, Sugden K, Moffitt TE, et al. Influence of life stress on depression: moderation by a polymorphism in the 5-HTT gene. Science. 2003;301:386–9.
10. Culverhouse RC, Saccone NL, Horton AC, et al. Collaborative meta-Analysis finds no evidence of a strong interaction between stress and 5-HTTLPR genotype contributing to the development of depression. Mol Psychiatry. 2018;23:133–42.
11. Johnson EC, Border R, Melroy-Greif WE, de Leeuw CA, Ehringer MA, Keller MC. No evidence that schizophrenia candidate genes are more associated with schizophrenia than noncandidate genes. Biol Psychiatry. 2017;82:702–8.
12. Duncan LE, Keller MC. A critical review of the first 10 years of candidate gene-by-environment interaction research in psychiatry. Am J Psychiatry. 2011;168:1041–9.
13. Burton PR, Hansell AL, Fortier I, et al. Size matters: just how big is BIG?: quantifying realistic sample size requirements for human genome epidemiology. Int J Epidemiol. 2009;38:263–73.
14. Bosker FJ, Hartman CA, Nolte IM, et al. Poor replication of candidate genes for major depressive disorder using genome-wide association data. Mol Psychiatry. 2011;16:516–32.
15. Farrell MS, Werge T, Sklar P, et al. Evaluating historical candidate genes for schizophrenia. Mol Psychiatry. 2015;20:555–62.
16. Brookes KJ. The VNTR in complex disorders: The forgotten polymorphisms? A functional way forward? Genomics. 2013;101:273–81.
17. Vinkhuyzen AAE, Dumenil T, Ryan L, et al. Identification of tag haplotypes for 5HTTLPR for different genome-wide SNP platforms. Mol Psychiatry. 2011;16:1073–5.
18. Lu AT-H, Bakker S, Janson E, Cichon S, Cantor RM, Ophoff RA. Prediction of serotonin transporter promoter polymorphism genotypes from single nucleotide polymorphism arrays using machine learning methods. Psychiatr Genet. 2012;22:182–8.
19. Assary E, Vincent JP, Keers R, Pluess M. Gene-environment interaction and psychiatric disorders: review and future directions. Semin Cell Dev Biol. 2018;77:133–43.
20. Duncan LE, Pollastri AR, Smoller JW. Mind the gap: why many geneticists and psychological scientists have discrepant views about gene-environment interaction (G × E) research. Am Psychol. 2014;69:249–68.
21. Sudlow C, Gallacher J, Allen N, et al. UK Biobank: an open access resource for identifying the causes of a wide range of complex diseases of middle and old age. PLoS Med. 2015;12:1–10.
22. Conger RD, Schofield TJ, Neppl TK. Intergenerational continuity and discontinuity in harsh parenting. Parenting. 2012;12:222–31.
23. Haberstick BC, Smolen A, Stetler GL, et al. Simple sequence repeats in the national longitudinal study of adolescent health: an ethnically diverse resource for genetic analysis of health and behavior. Behav Genet. 2014;44:487–97.
24. Haberstick BC, Smolen A, Williams RB, et al. Population frequencies of the triallelic 5HTTLPR in six ethnicially diverse samples from North America, Southeast Asia, and Africa. Behav Genet. 2015;96:255–61.
25. Masarik AS, Conger RD, Brent Donnellan M, et al. For better and for worse: genes and parenting interact to predict future behavior in romantic relationships. J Fam Psychol. 2014;28:357–67.
26. Derringer J, Corley RP, Haberstick BC, et al. Genome-wide association study of behavioral disinhibition in a selected adolescent sample. Behav Genet. 2015;45:375–81.
27. Young SE, Stallings MC, Corley RP, Krauter KS, Hewitt JK. Genetic and environmental influences on behavioral disinhibition. Am J Med Genet Part B Neuropsychiatr Genet. 2000;695:684–95.
28. Chang CC, Chow CC, Tellier LC, et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 2015;4:7.
29. Abraham G, Inouye M. Fast principal component analysis of large-scale genome-wide data. PLoS One. 2014;9:e92766.
30. McCarthy S, Das S, Kretzschmar W, et al. A reference panel of 64,976 haplotypes for genotype imputation. Nat Genet. 2016;48:1279–83.
31. Delaneau O, Zagury J-F, Marchini J. Improved whole-chromosome phasing for disease and population genetic studies. Nat Methods. 2013;10:5–6.
32. Das S, Forer L, Schönherr S, et al. Next-generation genotype imputation service and methods. Nat Genet. 2016;48:1287–1287.
33. Drury SS, Theall KP, KB JB, Scheeringa M. The role of the dopamine transporter (DAT) in the development of preschool children. J Trauma Stress. 2009;22:534–9.
34. Yu YWY, Tsai SJ, Hong CJ, Chen TJ, Chen MC, Yang CW. Association study of a Monoamine oxidase A gene promoter polymorphism with major depressive disorder and antidepressant response. Neuropsychopharmacology. 2005;30:1719–23.
35. Hutchison KE, McGeary J, Smolen A, Bryan A, Swift RM. The DRD4 VNTR polymorphism moderates craving after alcohol consumption. Heal Psychol. 2002;21:139–46.
36. Browning BL, Browning SR. Genotype imputation with millions of reference samples. Am J Hum Genet. 2016;98:116–26.
37. Mitt M, Kals M, Pärn K, et al. Improved imputation accuracy of rare and low-frequency variants using population-specific high-coverage WGS-based imputation reference panel. European Journal of Human Genetics. 2017;25:869–76.
38. Bycroft C, Freeman C, Petkova D et al. The UK Biobank resource with deep phenotyping and genomic data. Nature. 2018;562:203–9.
39. Li Y, Willer C, Sanna S, Abecasis GR. Genotype imputation. Annu Rev Genom Hum Genet. 2009;10:387–406.
40. Marchini J, Howie B. Genotype imputation for genome-wide association studies. Nat Rev Genet. 2010;11:499–511.
41. Chang FM, Kidd JR, Livak KJ, Pakstis AJ, Kidd KK. The world-wide distribution of allele frequencies at the human dopamine D4 receptor locus. Hum Genet. 1996;98:91–101.
42. Deelen P, Menelaou A, Leeuwen EM Van et al. Improved imputation quality of low-frequency and rare variants in European samples using the “Genome of The Netherlands”. European Journal of Human Genetics. 2014;1321–6.