Big data, open science and the brain: Lessons learned from genomics

Frontiers in Human Neuroscience

Volumn 8, Issue MAY, 2014, Pages

  Choudhury, Suparna ^a   Fishman, Jennifer R ^b   McGowan, Michelle L ^c   Juengst, Eric T ^d  

^a MCGILL UNIVERSITY   (Canada)

^b MCGILL UNIVERSITY   (Canada)

^c CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

Brain initiative; Data sharing; Human brain project; Human genome project; Neuroimaging; Open neuroscience; Open science

Indexed keywords

ACCESS TO INFORMATION; DATA SHARING; FUNCTIONAL MAGNETIC RESONANCE IMAGING; GENOMICS; HUMAN; HUMAN GENOME PROJECT; INFORMED CONSENT; MENTAL DISEASE; NEUROIMAGING; NEUROLOGIC DISEASE; NEUROSCIENCE; PRIVACY; RESEARCH ETHICS; RESEARCH SUBJECT; REVIEW;

EID: 84901309716     PISSN: None     EISSN: 16625161     Source Type: Journal    
DOI: 10.3389/fnhum.2014.00239     Document Type: Review

References (75)

1. Adelstein, J. S., Shehzad, Z., Mennes, M., DeYoung, C. G., Zuo, X.-N., Kelly, C., et al. (2011). Personality is reflected in the brain's intrinsic functional architecture. PLoS One 6:e27633. doi: 10.1371/journal.pone.0027633
2. Advisory Committee to the Director. (2013). Interim report: brain research through advancing innovative neurotechnologies: NIH. http://www.nih.gov/science/brain/
3. Biswal, B., Zerrin Yetkin, F., Haughton, V. M., and Hyde, J. S. (1995). Functional connectivity in the motor cortex of resting human brain using echo-planar MRI. Magn. Reson. Med. 34, 537-541. doi: 10.1002/mrm.1910340409
4. Blumenthal, D., Campbell, E. G., Gokhale, M., Yucel, R., Clarridge, B., Hilgartner, S., et al. (2006). Data withholding in genetics and the other life sciences: prevalences and predictors. Acad. Med. 81, 137-145. doi: 10.1097/00001888-200602000-00008
5. Brakewood, B., and Poldrack, R. A. (2013). The ethics of secondary data analysis: considering the application of belmont principles to the sharing of neuroimaging data. Neuroimage 82, 671-676. doi: 10.1016/j.neuroimage.2013.02.040
6. Brookshire, B. (2013). Ethical challenges facing new neuroscience technologies. Blog. Bioethics. Gov. http://blog.bioethics.gov/2013/08/20/ethical-challenges-facing-new-neuroscience-technologies/
7. Budin-Ljøsne, I., Isaeva, J., Knoppers, B. M., Tassé, A. M., Shen, H.-Y., McCarthy, M. I., et al. (2014). Data sharing in large research consortia: experiences and recommendations from ENGAGE. Eur. J. Hum. Genet. 22, 317-321. doi: 10.1038/ejhg.2013.131
8. Campbell, E. G., Clarridge, B. R., Gokhale, M., Birenbaum, L., Hilgartner, S., Holtzman, N. A., et al. (2002). Data withholding in academic genetics: evidence from a national survey. JAMA 287, 473-480. doi: 10.1001/jama.287.4.473
9. Carp, J. (2012). On the plurality of (methodological) worlds: estimating the analytic flexibility of fMRI experiments. Front. Neurosci. 6:149. doi: 10.3389/fnins.2012.00149
10. Choudhury, S., and Slaby, J. (2011). Critical Neuroscience: A Handbook of the Social and Cultural Contexts of Neuroscience. Chichester, UK: Wiley-Blackwell.
11. Clayton, E. W., Smith, M., Fullerton, S. M., Burke W., McCarty, C. A., Koenig, B. A., et al., and Consent and Community Consultation Working Group of the eMERGE Consortium. (2010). Confronting real time ethical, legal and social issues in the Electronic Medical Records and Genomics (eMERGE) Consortium. Genet. Med. 12, 616-620. doi: 10.1097/GIM.0b013e3181efdbd0
12. Cox, C. L., Uddin, L. Q., Di Martino, A., Castellanos, F. X., Milham, M. P., and Kelly, C. (2012). The balance between feeling and knowing: affective and cognitive empathy are reflected in the brain's intrinsic functional dynamics. Soc. Cogn. Affect. Neurosci. 7, 727-737. doi: 10.1093/scan/nsr051
13. Craig, D. W., Goor, R. M., Wang, Z., Paschall, J., Ostell, J., Feolo, M., et al. (2011). Assessing and managing risk when sharing aggregate genetic variant data. Nat. Rev. Genet. 12, 730-736. doi: 10.1038/nrg3067
14. Delorme, A., and Makeig, S. (2004). EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics including independent component analysis. J. Neurosci. Methods 134, 9-21. doi: 10.1016/j.jneumeth.2003.10.009
15. de Vries, J., and Pepper, M. (2012). Genomic sovereignty and the African promise: mining the African genome for the benefit of Africa. J. Med. Ethics 38, 474-478. doi: 10.1136/medethics-2011-100448
16. Di Martino, A., Ross, K., Uddin, L. Q., Sklar, A. B., Castellanos, F. X., and Milham, M. P. (2009). Functional brain correlates of social and nonsocial processes in autism spectrum disorders: an activation likelihood estimation meta-analysis. Biol. Psychiatry 65, 63-74. doi: 10.1016/j.biopsych.2008.09.022
17. Gardner, D., Akil, H., Ascoli, G., Bowden, D., Bug, W., Donohue, D., et al. (2008). The neuroscience information framework: a data and knowledge environment for neuroscience. Neuroinformatics 6, 149-160. doi: 10.1007/s12021-008-9024-z
18. Glover, G. H., Mueller, B. A., Turner, J. A., van Erp, T. G., Liu, T. T., Greve, D. N., et al. (2012). Function biomedical informatics research network recommendations for prospective multicenter functional MRI studies. J. Magn. Reson. Imaging 36, 39-54. doi: 10.1002/jmri.23572
19. Gorgolewski, K. J., Margulies, D. S., and Milham, M. P. (2013). Making data sharing count: a publication-based solution. Front. Neurosci. 7:9. doi: 10.3389/fnins.2013.00009
20. Gymrek, M., McGuire, A., Golan, D., Halperin, E., and Erlich, Y. (2013). Identifying personal genomes by surname inference. Science 339, 321-324. doi: 10.1126/science.1229566
21. Haga, S., and O'Daniel, J. (2011). Public perspectives regarding data-sharing practices in genomics research. Public Health Genomics 14, 319-324. doi: 10.1159/000324705
22. Hahn, T., Dresler, T., Ehlis, A.-C., Pyka, M., Dieler, A. C., Saathoff, C., et al. (2012). Randomness of resting-state brain oscillations encodes Gray's personality trait. Neuroimage 59, 1842-1845. doi: 10.1016/j.neuroimage.2011.08.042
23. Honigsbaum, M. (2013). Human brain project: Henry Markram plans to spend €1bn building a perfect model of the human brain. The Guardian. http://www.theguardian.com/science/2013/oct/15/human-brain-project-henry-markram
24. Illes, J., Moser, M. A., McCormick, J. B., Racine, E., Blakeslee, S., Caplan, A., et al. (2010). Neurotalk: improving the communication of neuroscience research. Nat. Rev. Neurosci. 11, 61-69. doi: 10.1038/nrn2773
25. Insel, T., and Lieberman, J. (2013). DSM-5 and RDoC: shared interests. NIMH Sci. News 1-2. http://www.nimh.nih.gov/news/science-news/2013/dsm-5-and-rdoc-shared-interests.shtml
26. International HapMap Consortium. (2003). The International HapMap project. Nature 426, 789-796. doi: 10.1038/nature02168
27. Jabbi, M., Keysers, C., Singer, T., and Stephan, K. E. (2009). Rebuttal of "Voodoo Correlations in Social Neuroscience" by Vul et al.-summary information for the press. http://www.edvul.com/extrapdf/voodoorebuttal.pdf
28. Jasny, B. R. (2013). Realities of data sharing using the genome wars as case study-an historical perspective and commentary. EPJ Data Sci. 2, 1-15. doi: 10.1140/epjds13
29. Jeffers, B. R. (2001). Human biological materials in research: ethical issues and the role of stewardship in minimizing research risks. ANS Adv. Nurs. Sci. 24, 32-46. doi: 10.1097/00012272-200112000-00005
30. Kaye, J. (2011). From single biobanks to international networks: developing e-governance. Hum. Genet. 130, 377-382. doi: 10.1007/s00439-011-1063-0
31. Kaye, J., Heeney, C., Hawkins, N., de Vries, J., and Boddington, P. (2009). Data sharing in genomics-re-shaping scientific practice. Nat. Rev. Genet. 10, 331-335. doi: 10.1038/nrg2573
32. Kelly, C., Biswal, B. B., Craddock, R. C., Castellanos, F. X., and Milham, M. P. (2012). Characterizing variation in the functional connectome: promise and pitfalls. Trends Cogn. Sci. 16, 181-188. doi: 10.1016/j.tics.2012.02.001
33. Kim, D. I., Manoach, D. S., Mathalon, D. H., Turner, J. A., Mannell, M., Brown, G. G., et al. (2009). Dysregulation of working memory and default-mode networks in schizophrenia using independent component analysis, an fBIRN and MCIC study. Hu. Brain Mapp. 30, 3795-3811. doi: 10.1002/hbm.20807
34. Kohane, I. S., and Altman, R. B. (2005). Health-information altruists-a potentiallly critical resource. N. Engl. J. Med. 353, 2074-2077. doi: 10.1056/nejmsb051220
35. Leonelli, S. (2014). Data interpretation in the digital age. Perspect. Sci. 397-417. doi: 10.1162/posc_a_00140
36. MacFarlane, B. (2008). Researching With Integrity: The Ethics of Academic Inquiry. New York: Routledge.
37. Manolio, T. A., Brooks, L. D., and Collins, F. S. (2008). A HapMap harvest of insights into the genetics of common disease. J. Clin. Invest. 118, 1590-1605. doi: 10.1172/JCI34772
38. Margulies, D. (2011). "The salmon of doubt: six months of methodological controversy within social neuroscience, " in Critical Neuroscience: A Handbook of the Social and Cultural Contexts of Neuroscience, eds S. Choudhury and J. Slaby (Chichester, UK: Wiley-Blackwell), 273-285.
39. McCarty, C. A., Chapman-Stone, D., Derfus, T., Giampietro, P. F., and Fost, N. (2008). Community consultation and communication for a population-based DNA biobank: the Marshfield clinic personalized medicine research project. Am. J. Med. Genet. A 146, 3026-3033. doi: 10.1002/ajmg.a.32559
40. McEwen, J. E., Boyer, J. T., and Sun, K. Y. (2013). Evolving approaches to the ethical management of genomic data. Trends Genet. 29, 375-382. doi: 10.1016/j.tig.2013.02.001
41. McGuire, A. L., Basford, M., Dressler, L. G., Fullerton, S. M., Koenig, B. A., Li, R., et al. (2011). Ethical and practical challenges of sharing data from genome-wide association studies: the eMERGE Consortium experience. Genome Res. 21, 1001-1007. doi: 10.1101/gr.120329.111
42. Milham, M. P. (2012). Open neuroscience solutions for the connectome-wide association era. Neuron 73, 214-218. doi: 10.1016/j.neuron.2011.11.004
43. Mitra, P. (2013). What's wrong with the brain activity map proposal. Scientific American. http://www.scientificamerican.com/article/whats-wrong-with-the-brain-activity-map-proposal/
44. Nanda, S., and Kowalczuk, M. K. (2014). Unpublished genomic data-how to share? BMC Genomics 15:5. doi: 10.1186/1471-2164-15-5
45. Nature Neuroscience. (2000). A debate over fMRI data sharing. Nat. Neurosci. 3, 845-846. doi: 10.1038/78728
46. Nature. (2000). Whose scans are they, anyway? Nature 406:443. doi: 10.1038/35020214
47. Nelkin, D., and Lindee, M. S. (2004). The DNA Mystique. AnnArbor: University of Michigan Press.
48. Oliver, J. M., Slashinski, M. J., Wang, T., Kelly, P. A., Hilsenbeck, S. G., and McGuire, A. L. (2012). Balancing the risks and benefits of genomic data sharing: genome research participants' perspectives. Public Health Genomics 15, 106-114. doi: 10.1159/000334718
49. Pickersgill, M. (2011). 'Promising' therapies: neuroscience, clinical practice, and the treatment of psychopathy. Sociol. Health Illn. 33, 448-464. doi: 10.1111/j.1467-9566.2010.01286.x
50. Poldrack, R. A., Barch, D. M., Mitchell, J., Wager, T., Wagner, A. D., Devlin, J. T., et al. (2013). Towards open sharing of task-based fMRI data: the OpenfMRI project. Front. Neuroinform. 7:12. doi: 10.3389/fninf.2013.00012
51. Poline, J.-B., Breeze, J. L., Ghosh, S., Gorgolewski, K., Halchenko, Y. O., Hanke, M., et al. (2012). Data sharing in neuroimaging research. Front. Neuroinform. 6:9. doi: 10.3389/fninf.2012.00009
52. Poline, J., and Poldrack, R. (2013). Introduction to the special issue: toward a new era of databasing and data sharing for neuroimaging. Neuroimage 82, 645-646. doi: 10.1016/j.neuroimage.2013.08.044
53. Potkin, S., Turner, J., Brown, G., McCarthy, G., Greve, D., Glover, G., et al. (2009). Working memory and DLPFC inefficiency in schizophrenia: the FBIRN study. Schizophr. Bull. 35, 19-31. doi: 10.1093/schbul/sbn162
54. Prainsack, B. (2014). "Understanding participation: the 'citizen science' of genetics, " in Genetics as Social Practice, eds B. Prainsack, G. Werner-Felmayer and S. Schicktanz (Farnham: Ashgate), 147-164.
55. President's Council of Advisors on Science and Technology. (2008). Priorities for Personalized Medicine. Washington, DC: Office of Science and Technology Policy.
56. Racine, E., Bar-Ilan, O., and Illes, J. (2005). fMRI in the public eye. Nat. Rev. Neurosci. 6, 159-164. doi: 10.1038/nrn1609
57. Racine, E., Waldman, S., Rosenberg, J., and Illes, J. (2010). Contemporary neuroscience in the media. Soc. Sci. Med. 71, 725-733. doi: 10.1016/j.socscimed.2010.05.017
58. Requarth, T. (2013). Bringing a virtual brain to life. The New York Times, D1. http://www.nytimes.com/2013/03/19/science/bringing-a-virtual-brain-to-life.html?pagewanted=all&_r=0
59. Robinson, J. O., Slashinski, M. J., Wang, T., Hilsenbeck, S. G., and McGuire, A. L. (2013). Participants' recall and understanding of genomic research and large-scale data sharing. J. Empir. Res. Hum. Res. Ethics 8, 42-52. doi: 10.1525/jer.2013.8.4.42
60. Rose, N., and Abi-Rached, J. (2013). Neuro: The New Brain Sciences and the Management of the Mind. Princeton, NJ: Princeton University Press.
61. Seung, S. (2012). Connectome: How the Brain'S Wiring Makes Us Who We Are. Boston: Houghton Mifflin Harcourt.
62. Shen, H. (2013). NIH serves up wide menu for US brain-mapping initiative. Nature. http://www.nature.com/news/nih-serves-up-wide-menu-for-us-brain-mapping-initiative-1.13745
63. Stein, D. (2013). Obama's brain map initiative needs a rethinking. LiveScience. http://www.livescience.com/28505-map-the-brain.html
64. Swanson, L. (2013). Embrace and shape the BRAIN initiative. Society for Neuroscience. http://www.sfn.org/news-and-calendar/news-and-calendar/news/spotlight/embrace-and-shape-the-brain-initiative
65. Tenopir, C., Allard, S., Douglass, K. L., Aydinoglu, A. U., Wu, L., Read, E., et al. (2011). Data sharing by scientists: practices and perceptions. PLoS One 6:e21101. doi: 10.1371/journal.pone.0021101
66. The Human Brain Project. (2012). A Report to the European Commission. Lausanne: The HBP-PS Consortium.
67. Van Horn, J. D., and Gazzaniga, M. S. (2013). Why share data? Lessons learned from the fMRIDC. Neuroimage 82, 677-682. doi: 10.1016/j.neuroimage.2012.11.010
68. Vidal, F., and Ortega, F. (2012). "Are there neural correlates of depression?, " in Critical Neuroscience: A Handbook of the Social and Cultural Contexts of Neuroscience, eds S. Choudhury and J. Slaby (Chichester, UK: Wiley-Blackwell), 345-366.
69. Visscher, K. M., and Weissman, D. H. (2011). Would the field of cognitive neuroscience be advanced by sharing functional MRI data? BMC Med. 9:34. doi: 10.1186/1741-7015-9-34
70. Vul, E., Harris, C., Winkielman, P., and Pashler, H. (2009). Puzzlingly high correlations in fMRI studies of emotion, personality, and social cognition. Perspect. Psychol. Sci. 4, 274-290. doi: 10.1111/j.1745-6924.2009.01126.x
71. Wei, L., Duan, X., Zheng, C., Wang, S., Gao, Q., Zhang, Z., et al. (2014). Specific frequency bands of amplitude low-frequency oscillation encodes personality. Hum. Brain Mapp. 35, 331-339. doi: 10.1002/hbm.22176
72. Williams, R. (2013). Anonymity under threat. The Scientist. http://www.the-scientist.com/?articles.view/articleNo/34006/title/Anonymity-Under-Threat/ (accessed 26, March 2014)
73. Winickoff, D. E., and Winickoff, R. N. (2003). The charitable trust as a model for genomic biobanks. N. Engl. J. Med. 349, 1180-1184. doi: 10.1056/nejmsb030036
74. Yassin, R., Lockhart, N., Gonzalez del Riego, M., Pitt, K., Thomas, J. W., Weiss, L., et al. (2010). Custodianship as an ethical framework for biospecimen-based research. Cancer Epidemiol. Biomarkers Prev. 19, 1012-1015. doi: 10.1158/1055-9965.EPI-10-0029
75. Zwerdling, D. (2013). Researchers Question Obama'S Motives for Brain Initiative. NPR: Morning Edition.