Neuropsychiatric Genetics of African Populations-Psychosis (NeuroGAP-Psychosis): A case-control study protocol and GWAS in Ethiopia, Kenya, South Africa and Uganda

BMJ Open

Volumn 9, Issue 2, 2019, Pages

  Stevenson, Anne ^a,b   Akena, Dickens ^c   Stroud, Rocky E ^a,b   Atwoli, Lukoye ^d   Campbell, Megan M ^e   Chibnik, Lori B ^a,b   Kwobah, Edith ^f   Kariuki, Symon M ^g,h   Martin, Alicia R ^b,i   De Menil, Victoria ^a,b   Newton, Charles R J C ^g,h   Sibeko, Goodman ^e   Stein, Dan J ^e   Teferra, Solomon ^j   Zingela, Zukiswa ^k   Koenen, Karestan C ^a,b  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^c MAKERERE UNIVERSITY   (Uganda)

^d MOI UNIVERSITY   (Kenya)

^e UNIVERSITY OF CAPE TOWN   (South Africa)

^f MOI TEACHING AND REFERRAL HOSPITAL   (Kenya)

^g KEMRI WELLCOME TRUST RESEARCH PROGRAMME   (Kenya)

^h UNIVERSITY OF OXFORD   (United Kingdom)

ⁱ MASSACHUSETTS GENERAL HOSPITAL   (United States)

^j ADDIS ABABA UNIVERSITY   (Ethiopia)

^k WALTER SISULU UNIVERSITY   (South Africa)

more..

Author keywords

Africa; genetics; mental Health

Indexed keywords

ANCESTRY GROUP; ARTICLE; BIPOLAR DISORDER; CASE CONTROL STUDY; CONTROLLED STUDY; DNA EXTRACTION; ENVIRONMENTAL FACTOR; ETHIOPIA; GENETIC CORRELATION; GENETIC DIFFERENCE; GENETIC RISK; GENETIC VARIABILITY; GENOME-WIDE ASSOCIATION STUDY; HERITABILITY; HUMAN; KENYA; MAJOR CLINICAL STUDY; MEDICAL HISTORY; MINI INTERNATIONAL NEUROPSYCHIATRIC INTERVIEW; MULTICENTER STUDY; NEUROPSYCHIATRY; POPULATION GENETICS; RISK FACTOR; SALIVA ANALYSIS; SCHIZOPHRENIA; SINGLE NUCLEOTIDE POLYMORPHISM; SOUTH AFRICA; SUBSTANCE USE; UGANDA; GENETIC PREDISPOSITION; GENETICS; METHODOLOGY; PHENOTYPE; PSYCHOLOGICAL RATING SCALE;

BIPOLAR DISORDER; CASE-CONTROL STUDIES; ETHIOPIA; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; KENYA; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; PSYCHIATRIC STATUS RATING SCALES; RESEARCH DESIGN; SCHIZOPHRENIA; SOUTH AFRICA; UGANDA;

EID: 85061314386     PISSN: None     EISSN: 20446055     Source Type: Journal    
DOI: 10.1136/bmjopen-2018-025469     Document Type: Article

References (41)

1. Whiteford HA, Ferrari AJ, Degenhardt L, et al. Global Burden of Mental, Neurological, and Substance Use Disorders: An Analysis from the Global Burden of Disease Study 2010. In: Patel V, Chisholm D, Dua T, eds. Mental, neurological, and substance use disorders: disease control priorities. 3rd edn. Washington (DC): The International Bank for Reconstruction and Development/The World Bank (c) 2016 International Bank for Reconstruction and Development/The World Bank, 2016.
2. Whiteford HA, Degenhardt L, Rehm J, et al. Global burden of disease attributable to mental and substance use disorders: findings from the Global Burden of Disease Study 2010. Lancet 2013;382:1575-86. doi:10.1016/S0140-6736(13)61611-6
3. Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 2014;511:421-7. doi:10.1038/nature13595
4. Pardiñas AF, Holmans P, Pocklington AJ, et al. Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection. Nat Genet 2018;50:381-9. doi:10.1038/s41588-018-0059-2
5. Zeggini E, Ioannidis JP. Meta-analysis in genome-wide association studies. Pharmacogenomics 2009;10:191-201. doi:10.2217/14622416.10.2.191
6. Popejoy AB, Fullerton SM. Genomics is failing on diversity. Nature 2016;538:161-4. doi:10.1038/538161a
7. Li Z, Chen J, Yu H, et al. Genome-wide association analysis identifies 30 new susceptibility loci for schizophrenia. Nat Genet 2017;49:1576-83. doi:10.1038/ng.3973
8. Dalvie S, Koen N, Duncan L, et al. Large scale genetic research on neuropsychiatric disorders in African populations is needed. EBioMedicine 2015;2:1259-61. doi:10.1016/j.ebiom.2015.10.002
9. Martin AR, Gignoux CR, Walters RK, et al. Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations. Am J Hum Genet 2017;100:635-49. doi:10.1016/j.ajhg.2017.03.004
10. Auton A, Brooks LD, Durbin RM, et al. A global reference for human genetic variation. Nature 2015;526:68-74. doi:10.1038/nature15393
11. Wojcik G, Graff M, Nishimura KK, et al. Genetic diversity turns a new page in our understanding of complex traits. bioRxiv 2017.
12. Campbell MC, Tishkoff SA. African genetic diversity: implications for human demographic history, modern human origins, and complex disease mapping. Annu Rev Genomics Hum Genet 2008;9:403-33. doi:10.1146/annurev.genom.9.081307.164258
13. Cardno AG, Owen MJ. Genetic relationships between schizophrenia, bipolar disorder, and schizoaffective disorder. Schizophr Bull 2014;40:504-15. doi:10.1093/schbul/sbu016
14. Ulrich T. Nations Represented in NeuroGAP-Psychosis: broad communications. 2018.
15. Jeste DV, Palmer BW, Appelbaum PS, et al. A new brief instrument for assessing decisional capacity for clinical research. Arch Gen Psychiatry 2007;64:966-74. doi:10.1001/archpsyc.64.8.966
16. Campbell MM, Susser E, Mall S, et al. Using iterative learning to improve understanding during the informed consent process in a South African psychiatric genomics study. PLoS One 2017;12:e0188466. doi:10.1371/journal.pone.0188466
17. Sheehan DV, Lecrubier Y, Sheehan KH, et al. The Mini-International Neuropsychiatric Interview (M.I.N.I.): the development and validation of a structured diagnostic psychiatric interview for DSM-IV and ICD-10. J Clin Psychiatry 1998;59:22-33.
18. Weathers FW, Blake DD, Schnurr PP, et al. The Life Events Checklist for DSM-5 (LEC-5). Instrument available from the National Center for PTSD. 2013 wwwptsdvagov
19. Humeniuk R, Henry-Edwards S, Ali R, et al. The Alcohol, Smoking and Substance Involvement Screening Test (ASSIST): Amanual for use in primary care, 2010.
20. Kessler RC, Ustün TB. The World Mental Health (WMH) Survey Initiative Version of the World Health Organization (WHO) Composite International Diagnostic Interview (CIDI). Int J Methods Psychiatr Res 2004;13:93-121. doi:10.1002/mpr.168
21. Scott JA, Bauni E, Moisi JC, et al. Profile: The Kilifi Health and Demographic Surveillance System (KHDSS). Int J Epidemiol 2012;41:650-7. doi:10.1093/ije/dys062
22. Kessler RC, Barker PR, Colpe LJ, et al. Screening for serious mental illness in the general population. Arch Gen Psychiatry 2003;60:184-9. doi:10.1001/archpsyc.60.2.184
23. Bebbington P, Nayani T. Psychosis screening questionnaire. Int J of methods in psychiatric research 1995;5:11-19.
24. Skol AD, Scott LJ, Abecasis GR, et al. Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Nat Genet 2006;38:209-13. doi:10.1038/ng1706
25. de Candia TR, Lee SH, Yang J, et al. Additive genetic variation in schizophrenia risk is shared by populations of African and European descent. Am J Hum Genet 2013;93:463-70. doi:10.1016/j.ajhg.2013.07.007
26. Busby GB, Band G, Si Le Q, et al. Admixture into and within sub-Saharan Africa. Elife 2016;5:e15266. doi:10.7554/eLife.15266
27. Gurdasani D, Carstensen T, Tekola-Ayele F, et al. The African Genome Variation Project shapes medical genetics in Africa. Nature 2015;517:327-32. doi:10.1038/nature13997
28. Conomos MP, Miller MB, Thornton TA. Robust inference of population structure for ancestry prediction and correction of stratification in the presence of relatedness. Genet Epidemiol 2015;39:276-93. doi:10.1002/gepi.21896
29. Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res 2009;19:1655-64. doi:10.1101/gr.094052.109
30. Abecasis GR, Auton A, Brooks LD, et al. An integrated map of genetic variation from 1,092 human genomes. Nature 2012;491:56-65. doi:10.1038/nature11632
31. Conomos MP, Reiner AP, Weir BS, et al. Model-free estimation of recent genetic relatedness. Am J Hum Genet 2016;98:127-48. doi:10.1016/j.ajhg.2015.11.022
32. Purcell S, Neale B, Todd-Brown K, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007;81:559-75. doi:10.1086/519795
33. Statistical Computing. R: A language and environment for statistical computing [program. Vienna, Austria: Statistical Computing, 2018.
34. Kanai M, Tanaka T, Okada Y. Empirical estimation of genome-wide significance thresholds based on the 1000 Genomes Project data set. J Hum Genet 2016;61:861-6. doi:10.1038/jhg.2016.72
35. Yang J, Lee SH, Goddard ME, et al. GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet 2011;88:76-82. doi:10.1016/j.ajhg.2010.11.011
36. Brown BC, Ye CJ, Price AL, et al. Transethnic genetic-correlation estimates from summary statistics. Am J Hum Genet 2016;99:76-88. doi:10.1016/j.ajhg.2016.05.001
37. Beiswanger CM, Abimiku Alash'le, Carstens N, et al. Accessing Biospecimens from the H3Africa Consortium. Biopreserv Biobank 2017;15:95-8. doi:10.1089/bio.2017.0008
38. Consortium THA. Enabling the genomic revolution in Africa: H3Africa is developing capacity for health-related genomics research in Africa. Science 2014;344:1346-8.
39. Mulder N, Abimiku A, Adebamowo SN, et al. H3Africa: current perspectives. Pharmgenomics Pers Med 2018;11:59-66. doi:10.2147/PGPM.S141546
40. Band G, Rockett KA, Spencer CC, et al. A novel locus of resistance to severe malaria in a region of ancient balancing selection. Nature 2015;526:253-7. doi:10.1038/nature15390
41. van der Merwe C, Mwesiga EK, McGregor NW, et al. Advancing neuropsychiatric genetics training and collaboration in Africa. Lancet Glob Health 2018;6:e246-7. doi:10.1016/S2214-109X(18)30042-1