Ethical and legal implications of whole genome and whole exome sequencing in African populations

BMC Medical Ethics

Volumn 14, Issue 1, 2013, Pages

  Wright, Galen E B ^a   Koornhof, Pieter G J ^a   Adeyemo, Adebowale A ^b   Tiffin, Nicki ^a  

^a UNIVERSITY OF THE WESTERN CAPE   (South Africa)

^b NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

Author keywords

African populations; and societal issues; Ethical; legal; Next generation sequencing; Whole genome and whole exome sequencing

Indexed keywords

AFRICA; ARTICLE; COMPUTER SECURITY; CONFIDENTIALITY; DNA SEQUENCE; EDUCATIONAL STATUS; ETHICS; EXOME; FINANCIAL MANAGEMENT; GENETIC PRIVACY; GENETICS; GENOMICS; HUMAN; HUMAN GENOME; INCIDENTAL FINDING; INFORMATION DISSEMINATION; INFORMED CONSENT; LEGAL ASPECT; NATIONAL HEALTH ORGANIZATION; NEGRO; PARTICIPATORY RESEARCH; PERSONNEL; RESEARCH SUBJECT; RETROSPECTIVE STUDY; UNITED KINGDOM; UNITED STATES; VULNERABLE POPULATION;

AFRICA; AFRICAN CONTINENTAL ANCESTRY GROUP; COMMUNITY-BASED PARTICIPATORY RESEARCH; COMPUTER SECURITY; CONFIDENTIALITY; EDUCATIONAL STATUS; EXOME; GENETIC PRIVACY; GENETIC RESEARCH; GENOME, HUMAN; GENOMICS; GREAT BRITAIN; HUMANS; INCIDENTAL FINDINGS; INFORMATION DISSEMINATION; INFORMED CONSENT; NATIONAL INSTITUTES OF HEALTH (U.S.); RESEARCH PERSONNEL; RESEARCH SUBJECTS; RESEARCH SUPPORT AS TOPIC; RETROSPECTIVE STUDIES; SEQUENCE ANALYSIS, DNA; UNITED STATES; VULNERABLE POPULATIONS;

MLCS; MLOWN;

EID: 84878245443     PISSN: None     EISSN: 14726939     Source Type: Journal    
DOI: 10.1186/1472-6939-14-21     Document Type: Review

References (98)

1. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G, Science 2012 337 64 69 10.1126/science.1219240 22604720
2. Research ethics recommendations for whole-genome research: consensus statement. Caulfield T, McGuire AL, Cho M, Buchanan JA, Burgess MM, Danilczyk U, Diaz CM, Fryer-Edwards K, Green SK, Hodosh MA, PLoS Biol 2008 6 73 10.1371/journal.pbio.0060073 18366258 (Pubitemid 351492451)
3. National Human Genome Research Institute: Charting a course for genomic medicine from base pairs to bedside. Green ED, Guyer MS, Nature 2011 470 204 213 10.1038/nature09764 21307933
4. Genomics really gets personal: how exome and whole genome sequencing challenge the ethical framework of human genetics research. Tabor HK, Berkman BE, Hull SC, Bamshad MJ, Am J Med Genet A 2011 155A 2916 2924 22038764
5. Genetic studies of African populations: an overview on disease susceptibility and response to vaccines and therapeutics. Sirugo G, Hennig BJ, Adeyemo AA, Matimba A, Newport MJ, Ibrahim ME, Ryckman KK, Tacconelli A, Mariani-Costantini R, Novelli G, Soodyall H, Rotimi CN, Ramesar RS, Tishkoff SA, Williams SM, Hum Genet 2008 123 557 598 10.1007/s00439-008-0511-y 18512079
6. Ancestry and disease in the age of genomic medicine. Rotimi CN, Jorde LB, N Engl J Med 2010 363 1551 1558 10.1056/NEJMra0911564 20942671
7. H3Africa, Human Heredity and Health in Africa http://www.h3africa.org/
8. NIH News, First recipients of research grants to support genomic studies in Africa announced http://www.genome.gov/27550933
9. Informed consent in genomics and genetic research. McGuire AL, Beskow LM, Annu Rev Genomics Hum Genet 2010 11 361 381 10.1146/annurev-genom-082509-141711 20477535
10. US Department of Health and Human Services Policy for the Protection of Human Research Subjects Code of Federal Regulations, 45 CFR Part 46 http://www.hhs.gov/ohrp/humansubjects/guidance/45cfr46.html
11. H3Africa Funding, Informed Consent http://h3africa.org/informedConsent. cfm
12. The Belmont Report http://www.hhs.gov/ohrp/policy/belmont.html
13. Federal Policy for the Protection of Human Subjects ('Common Rule') http://www.hhs.gov/ohrp/humansubjects/commonrule/index.html 22194319
14. Data sharing in genomics-re-shaping scientific practice. Kaye J, Heeney C, Hawkins N, De Vries J, Boddington P, Nat Rev Genet 2009 10 331 335 10.1038/nrg2573 19308065
15. SF424 (R&R) Application Guide for NIH and Other PHS Agencies http://grants.nih.gov/grants/funding/424/SF424-RR-Guide-General-Adobe-VerB.pdf
16. Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays. Homer N, Szelinger S, Redman M, Duggan D, Tembe W, Muehling J, Pearson JV, Stephan DA, Nelson SF, Craig DW, PLoS Genet 2008 4 1000167 10.1371/journal.pgen.1000167 18769715
17. Assessing the privacy risks of data sharing in genomics. Heeney C, Hawkins N, De Vries J, Boddington P, Kaye J, Public Health Genomics 2011 14 17 25 10.1159/000294150 20339285
18. An evaluation of the current state of genomic data privacy protection technology and a roadmap for the future. Malin BA, J Am Med Inform Assoc 2005 12 28 34 15492030 (Pubitemid 40038620)
19. Ethics. Identifiability in genomic research. Lowrance WW, Collins FS, Science 2007 317 600 602 10.1126/science.1147699 17673640 (Pubitemid 47240914)
20. Inferential genotyping of Y chromosomes in Latter-Day Saints founders and comparison to Utah samples in the HapMap project. Gitschier J, Am J Hum Genet 2009 84 251 258 10.1016/j.ajhg.2009.01.018 19215731
21. Identifying Personal Genomes by Surname Inference. Gymrek M, McGuire AL, Golan D, Halperin E, Erlich Y, Science 2013 339 321 324 10.1126/science.1229566 23329047
22. dbGAP, Data Use Certification http://www.ncbi.nlm.nih.gov/projects/gap/ cgi-bin/about.html#duc
23. The European Genome-Phenome Archive, Data Access Agreements https://www.ebi.ac.uk/ega/data-access-agreement-daa-examples
24. The disclosure of diagnosis codes can breach research participants' privacy. Loukides G, Denny JC, Malin B, J Am Med Inform Assoc 2010 17 322 327 20442151
25. NHGRI Intramural Research Bioethics Core, Points to Consider in the Transition Toward Whole-Genome Sequencing in Human Subjects Research http://www.genome.gov/Pages/Research/Intramural/IRB/WES-WGS-Points-to-Consider. pdf
26. Informed consent for whole genome sequencing: a qualitative analysis of participant expectations and perceptions of risks, benefits, and harms. Tabor HK, Stock J, Brazg T, McMillin MJ, Dent KM, Yu J-H, Shendure J, Bamshad MJ, Am J Med Genet A 2012 158A 1310 1319 10.1002/ajmg.a.35328 22532433
27. Research ethics, Research practice and participant preferences: the growing gulf. Trinidad SB, Fullerton SM, Ludman EJ, Jarvik GP, Larson EB, Burke W, Science 2011 331 287 288 10.1126/science.1199000 21252333
28. Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes. Johnston JJ, Rubinstein WS, Facio FM, Ng D, Singh LN, Teer JK, Mullikin JC, Biesecker LG, Am J Hum Genet 2012 91 97 108 10.1016/j.ajhg.2012.05.021 22703879
29. Consent and population genomics: the creation of generic tools. Wallace S, Lazor S, Knoppers BM, IRB 2009 31 15 20 19873837
30. Public opinion about the importance of privacy in biobank research. Kaufman DJ, Murphy-Bollinger J, Scott J, Hudson KL, Am J Hum Genet 2009 85 643 654 10.1016/j.ajhg.2009.10.002 19878915
31. The International HapMap Project http://hapmap.ncbi.nlm.nih.gov/
32. A genome-wide association study identifies five Loci influencing facial morphology in Europeans. Liu F, Van der Lijn F, Schurmann C, Zhu G, Chakravarty MM, Hysi PG, Wollstein A, Lao O, De Bruijne M, Ikram MA, Van der Lugt A, Rivadeneira F, Uitterlinden AG, Hofman A, Niessen WJ, Homuth G, De Zubicaray G, McMahon KL, Thompson PM, Daboul A, Puls R, Hegenscheid K, Bevan L, Pausova Z, Medland SE, Montgomery GW, Wright MJ, Wicking C, Boehringer S, Spector TD, PLoS Genet 2012 8 1002932 10.1371/journal.pgen.1002932 23028347
33. The past, present, and future of the debate over return of research results and incidental findings. Wolf SM, Genet Med 2012 14 355 357 10.1038/gim.2012.26 22481182
34. The law of incidental findings in human subjects research: establishing researchers' duties. Wolf SM, Paradise J, Caga-anan C, J Law Med Ethics 2008 36 361 383 214 10.1111/j.1748-720X.2008.00281.x 18547206
35. Offering individual genetic research results: context matters. Beskow LM, Burke W, Sci Transl Med 2010 2 38 cm20
36. Ethical and practical guidelines for reporting genetic research results to study participants: updated guidelines from a National Heart, Lung, and Blood Institute working group. Fabsitz RR, McGuire A, Sharp RR, Puggal M, Beskow LM, Biesecker LG, Bookman E, Burke W, Burchard EG, Church G, Clayton EW, Eckfeldt JH, Fernandez CV, Fisher R, Fullerton SM, Gabriel S, Gachupin F, James C, Jarvik GP, Kittles R, Leib JR, O'Donnell C, O'Rourke PP, Rodriguez LL, Schully SD, Shuldiner AR, Sze RKF, Thakuria JV, Wolf SM, Burke GL, Circ Cardiovasc Genet 2010 3 574 580 10.1161/CIRCGENETICS.110.958827 21156933
37. IRB perspectives on the return of individual results from genomic research. Dressler LG, Smolek S, Ponsaran R, Markey JM, Starks H, Gerson N, Lewis S, Press N, Juengst E, Wiesner GL, Genet Med 2012 14 215 222 10.1038/gim.2011.10 22241094
38. There is nothing "incidental" about unrelated findings. Lyon GJ, Pers Med 2012 9 163 166 10.2217/pme.11.98
39. Feedback of individual genetic results to research participants: in favor of a qualified disclosure policy. Bredenoord AL, Onland-Moret NC, Van Delden JJM, Hum Mutat 2011 32 861 867 10.1002/humu.21518 21538687
40. Managing incidental findings and research results in genomic research involving biobanks and archived data sets. Wolf SM, Crock BN, Van Ness B, Lawrenz F, Kahn JP, Beskow LM, Cho MK, Christman MF, Green RC, Hall R, Illes J, Keane M, Knoppers BM, Koenig BA, Kohane IS, Leroy B, Maschke KJ, McGeveran W, Ossorio P, Parker LS, Petersen GM, Richardson HS, Scott JA, Terry SF, Wilfond BS, Wolf WA, Genet Med 2012 14 361 384 10.1038/gim.2012.23 22436882
41. Deploying whole genome sequencing in clinical practice and public health: Meeting the challenge one bin at a time. Berg JS, Khoury MJ, Evans JP, Genet Med 2011 13 499 504 10.1097/GIM.0b013e318220aaba 21558861
42. Incidental medical information in whole-exome sequencing. Solomon BD, Hadley DW, Pineda-Alvarez DE, Kamat A, Teer JK, Cherukuri PF, Hansen NF, Cruz P, Young AC, Berkman BE, Chandrasekharappa SC, Mullikin JC, Pediatrics 2012 129 1605 1611 10.1542/peds.2011-0080 22585771
43. The legal risks of returning results of genomics research. Clayton EW, McGuire AL, Genet Med 2012 14 473 477 10.1038/gim.2012.10 22323070
44. Medicine. Whole-genome sequencing: the new standard of care. Brunham LR, Hayden MR, Science 2012 336 1112 1113 10.1126/science.1220967 22654044
45. Consortium the 1000 GP: Deleterious- and Disease-Allele Prevalence in Healthy Individuals: Insights from Current Predictions, Mutation Databases, and Population-Scale Resequencing. Xue Y, Chen Y, Ayub Q, Huang N, Ball EV, Mort M, Phillips AD, Shaw K, Stenson PD, Cooper DN, Tyler-Smith C, Am J Hum Genet 2012 91 1022 1032 10.1016/j.ajhg.2012.10.015 23217326
46. My46 https://www.my46.org/
47. American College of Medical Genetics and Genomics http://www.acmg.net
48. Exploring concordance and discordance for return of incidental findings from clinical sequencing. Green RC, Berg JS, Berry GT, Biesecker LG, Dimmock DP, Evans JP, Grody WW, Hegde MR, Kalia S, Korf BR, Krantz I, McGuire AL, Miller DT, Murray MF, Nussbaum RL, Plon SE, Rehm HL, Jacob HJ, Genet Med 2012 14 405 410 10.1038/gim.2012.21 22422049
49. Community engagement and informed consent in the International HapMap project. Rotimi C, Leppert M, Matsuda I, Zeng C, Zhang H, Adebamowo C, Ajayi I, Aniagwu T, Dixon M, Fukushima Y, Macer D, Marshall P, Nkwodimmah C, Peiffer A, Royal C, Suda E, Zhao H, Wang VO, McEwen J, Community Genet 2007 10 186 198 10.1159/000101761 17575464 (Pubitemid 46944295)
50. NHGRI Issues in Genetics, Special Informed Consent Considerations http://www.genome.gov/27026636
51. Taking tissue seriously means taking communities seriously. Upshur REG, Lavery JV, Tindana PO, BMC Med Ethics 2007 8 11 10.1186/1472-6939-8-11 17963497
52. Reactions, beliefs and concerns associated with providing hair specimens for medical research among a South African sample: a qualitative approach. Coetzee B, Kagee A, Tomlinson M, Warnich L, Ikediobi O, Futur Virol 2012 7 1135 1142 10.2217/fvl.12.100
53. Ethical and practical challenges surrounding genetic and genomic research in developing countries. Nyika A, Acta Trop 2009 112 Suppl 1 21 31 19665983
54. Ethical issues in human genomics research in developing countries. De Vries J, Bull SJ, Doumbo O, Ibrahim M, Mercereau-Puijalon O, Kwiatkowski D, Parker M, BMC Med Ethics 2011 12 5 10.1186/1472-6939-12-5 21418562
55. Human subjects protections in community-engaged research: a research ethics framework. Ross LF, Loup A, Nelson RM, Botkin JR, Kost R, Smith GR Jr, Gehlert S, J Empir Res Hum Res Ethics 2010 5 5 17 10.1525/jer.2010.5.1.5 20235860
56. Grand challenges in global health: community engagement in research in developing countries. Tindana PO, Singh JA, Tracy CS, Upshur REG, Daar AS, Singer PA, Frohlich J, Lavery JV, PLoS Med 2007 4 273 10.1371/journal.pmed. 0040273 17850178 (Pubitemid 47503036)
57. South Africa: from species cradle to genomic applications. Hardy B-J, Séguin B, Ramesar R, Singer PA, Daar AS, Nat Rev Genet 2008 9 1 19 23 18802417
58. Mental health policy development in Africa. Gureje O, Alem A, Bull World Health Organ 2000 78 475 482 10885166 (Pubitemid 30367601)
59. The Stigma of Being HIV-Positive in Africa. Rankin WW, Brennan S, Schell E, Laviwa J, Rankin SH, PLoS Med 2005 2 247 10.1371/journal.pmed.0020247 16008508 (Pubitemid 46179233)
60. Person and community in African traditional thought. Menkiti IA, African philosophy: An introduction 1984 3
61. What is in a cause? Exploring the relationship between genetic cause and felt stigma. Sankar P, Cho MK, Wolpe PR, Schairer C, Genet Med 2006 8 33 42 10.1097/01.gim.0000195894.67756.8b 16418597
62. Impact of social stigma on the process of obtaining informed consent for genetic research on podoconiosis: a qualitative study. Tekola F, Bull S, Farsides B, Newport MJ, Adeyemo A, Rotimi CN, Davey G, BMC Med Ethics 2009 10 13 10.1186/1472-6939-10-13 19698115
63. Patient perspectives on group benefits and harms in genetic research. Goldenberg AJ, Hull SC, Wilfond BS, Sharp RR, Public Health Genomics 2011 14 135 142 10.1159/000317497 20938159
64. Investigating the potential for ethnic group harm in collaborative genomics research in Africa: is ethnic stigmatisation likely? De Vries J, Jallow M, Williams TN, Kwiatkowski D, Parker M, Fitzpatrick R, Soc Sci Med 2012 75 1400 1407 10.1016/j.socscimed.2012.05.020 22749442
65. "A Room of Our Own?"Legal Lacunae Regarding Genomic Sovereignty in South Africa. Slabbert M, Pepper M, Journal of Contemporary Roman-Dutch Law 2010 73 432
66. Ethnologue, Languages of the World http://www.ethnologue.com/
67. Regulation of biomedical research in Africa. Chima SC, BMJ 2006 332 848 851 10.1136/bmj.332.7545.848 16601051 (Pubitemid 44365628)
68. The structure and function of research ethics committees in Africa: a case study. Kass NE, Hyder AA, Ajuwon A, Appiah-Poku J, Barsdorf N, Elsayed DE, Mokhachane M, Mupenda B, Ndebele P, Ndossi G, Sikateyo B, Tangwa G, Tindana P, PLoS Med 2007 4 3 10.1371/journal.pmed.0040003 17253898 (Pubitemid 46191817)
69. Composition, training needs and independence of ethics review committees across Africa: are the gate-keepers rising to the emerging challenges? Nyika A, Kilama W, Chilengi R, Tangwa G, Tindana P, Ndebele P, Ikingura J, J Med Ethics 2009 35 189 193 10.1136/jme.2008.025189 19251972
70. The South African National Accreditation System http://www.sanas.co.za/
71. UCT's contribution to medical genetics in Africa-from the past into the future. Beighton P, Fieggen K, Wonkam A, Ramesar R, Greenberg J, S Afr Med J 2012 102 446 448 22668932
72. Southern African Society for Human Genetics (SASHG) http://www.sashg.org/
73. African American attitudes toward exome and whole genome sequencing (Program 148). Yu J, Crouch J, Jamal S, Tabor H, Bamshad M, San Francisco, CA: Presented at the 62nd Annual Meeting of The American Society of Human Genetics 2012
74. The 1000 genomes project, A deep catalog of human genetic variation http://www.1000genomes.org/
75. MalariaGEN, Genomic Epidemiology Network http://www.malariagen.net/
76. Hammond E, Mayet M, Genes From Africa: The Colonisation of Human DNA South Africa: African center for Biosafety 2009
77. Voluntary participation and informed consent to international genetic research. Marshall PA, Adebamowo CA, Adeyemo AA, Ogundiran TO, Vekich M, Strenski T, Zhou J, Prewitt TE, Cooper RS, Rotimi CN, Am J Public Health 2006 96 1989 1995 10.2105/AJPH.2005.076232 17018820 (Pubitemid 44655924)
78. Tailoring consent to context: designing an appropriate consent process for a biomedical study in a low income setting. Tekola F, Bull SJ, Farsides B, Newport MJ, Adeyemo A, Rotimi CN, Davey G, PLoS Negl Trop Dis 2009 3 482 10.1371/journal.pntd.0000482 19621067
79. Experiences with community engagement and informed consent in a genetic cohort study of severe childhood diseases in Kenya. Marsh VM, Kamuya DM, Mlamba AM, Williams TN, Molyneux SS, BMC Med Ethics 2010 11 13 10.1186/1472-6939-11-13 20633282
80. Complete Khoisan and Bantu genomes from southern Africa. Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, Muzny DM, Reid JG, Nazareth LV, Wang Q, Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall EA, Danko CG, Teo WS, Buboltz AM, Zhang Z, Ma Q, Oosthuysen A, Nature 2010 463 943 947 10.1038/nature08795 20164927
81. A global network for investigating the genomic epidemiology of malaria. MalariaGEN, Nature 2008 456 732 737 10.1038/nature07632 19079050
82. Ethical data release in genome-wide association studies in developing countries. Parker M, Bull SJ, De Vries J, Agbenyega T, Doumbo OK, Kwiatkowski DP, PLoS Med 2009 6 1000143 10.1371/journal.pmed.1000143 19956792
83. The right to privacy. Warren SD, Brandeis LD, Harv Law Rev 1890 4 193 220 10.2307/1321160
84. The Presidential Commission for the Study of Bioethical Issues, Privacy and Progress in Whole Genome Sequencing http://bioethics.gov/cms/node/764
85. Genetic information and testing in insurance and employment: technical, social and ethical issues. Godard B, Raeburn S, Pembrey M, Bobrow M, Farndon P, Aymé S, Eur J Hum Genet 2003 11 123 S142 14718940
86. Van Der Merwe D, Roos A, Pistorius T, Eiselen S, Information and Communication Technology Law Durban: LexisNexis 2008
87. Harmonizing US-EU Online Privacy Laws: Toward a US Comprehensive Regime for the Protection of Personal Data. Zaidi K, Mich. St. J. Int'l L 2003 12 169
88. European Commission, Overview on Binding Corporate rules http://ec.europa.eu/justice/data-protection/document/international-transfers/ binding-corporate-rules/index-en.htm
89. Forgó N, Kollek R, Arning M, Kreugel T, Petersen I, Ethical and Legal Requirements for Transnational Genetic Research Munich: C.H. Beck 1 2010
90. Seeking consent to genetic and genomic research in a rural Ghanaian setting: A qualitative study of the MalariaGEN experience. Tindana P, Bull S, Amenga-Etego L, De Vries J, Aborigo R, Koram K, Kwiatkowski D, Parker M, BMC Med Ethics 2012 13 15 10.1186/1472-6939-13-15 22747883
91. Genomic sovereignty and the African promise: mining the African genome for the benefit of Africa. De Vries J, Pepper M, J Med Ethics 2012 38 474 478 10.1136/medethics-2011-100448 22493187
92. Capacity-building in human genetics for developing countries: initiatives and perspectives in sub-Saharan Africa. Wonkam A, Muna W, Ramesar R, Rotimi CN, Newport MJ, Public Health Genomics 2010 13 492 494 21135570
93. The New York Times, Genes Now Tell Doctors Secrets They Can't Utter http://www.nytimes.com/2012/08/26/health/research/with-rise-of-gene-sequencing- ethical-puzzles.html?smid=pl-share&-r=0
94. iTunes, MyGenome by Illumina for iPad https://itunes.apple.com/us/app/ mygenome/id516405838?mt=8
95. Human Heredity and Health in Africa (H3Africa), Ethical, Legal, and Societal Issues (ELSI) Research Program (U01) http://grants.nih.gov/grants/ guide/rfa-files/RFA-RM-12-005.html
96. Ethical, legal and social issues in the context of the planning stages of the Southern African Human Genome Programme. De Vries J, Slabbert M, Pepper MS, Med Law 2012 31 119 152 22908741
97. EAGER-Africa, EAGER-Africa http://eager-africa.com/ea/
98. Whole-genome resequencing in pharmacogenomics: moving away from past disparities to globally representative applications. Drögemöller BI, Wright GEB, Niehaus DJH, Emsley RA, Warnich L, Pharmacogenomics 2011 12 1717 1728 10.2217/pgs.11.119 22118054