Convergence of advances in genomics, team science, and repositories as drivers of progress in psychiatric genomics

Biological Psychiatry

Volumn 77, Issue 1, 2015, Pages 6-14

  Lehner, Thomas ^a   Senthil, Geetha ^a   Addington, Anjené M ^a  

^a NATIONAL INSTITUTE OF MENTAL HEALTH   (United States)

Author keywords

Biosamples; Data Sharing; dbGaP; NIMH Repository and Genomics Resource; Psychiatric Genomics; Team Science

Indexed keywords

CLINICAL DATA REPOSITORY; GENE MAPPING; GENETIC ASSOCIATION; GENOMICS; HEALTH CARE POLICY; HUMAN; HUMAN GENOME; MENTAL DISEASE; PRIORITY JOURNAL; REVIEW; SCIENCE; TECHNOLOGY; COOPERATION; GENETIC DATABASE; PROCEDURES; PSYCHIATRY; TRENDS;

BIOLOGICAL PSYCHIATRY; COOPERATIVE BEHAVIOR; DATABASES, GENETIC; GENOMICS; HUMANS;

EID: 84920669681     PISSN: 00063223     EISSN: 18732402     Source Type: Journal    
DOI: 10.1016/j.biopsych.2014.01.003     Document Type: Review

References (68)

1. A Catalog of Published Genome-Wide Association Studies. Available at: http://www.genome.gov/gwastudies/. Accessed January 28, 2014.
2. P.F. Sullivan, M.J. Daly, and M. O'Donovan Genetic architectures of psychiatric disorders: The emerging picture and its implications Nat Rev Genet 13 2012 537 551
3. NIMH Repository and Genomics Resource. Available at: https://www.nimhgenetics.org/. Accessed January 28, 2014.
4. Database of Genotypes and Phenotypes. Available at: http://www.ncbi.nlm.nih.gov/gap. Accessed January 28, 2014.
5. Summary of principles agreed at the International Strategy Meeting on Human Genome Sequencing, Bermuda, 25-28 February 1996. Available at http://www.ornl.gov/sci/techresources/Human-Genome/research/bermuda.shtml. Accessed January 28, 2014.
6. Policy for Sharing of Data Obtained in NIH Supported or Conducted Genome-Wide Association Studies (GWAS). Available at: http://grants.nih.gov/grants/guide/notice-files/NOT-OD-07-088.html. Accessed January 28, 2014.
7. Final NIH Statement on Sharing Research Data. Available at: http://grants.nih.gov/grants/guide/notice-files/NOT-OD-03-032.html. Accessed January 28, 2014.
8. T. Strachan, and A.P. Read Human Molecular Genetics 3 3rd ed. 2004 Garland Press London; New York
9. J. Ott Analysis of Human Genetic Linkage 3rd ed 1999 The Johns Hopkins University Press Baltimore, MD
10. F.S. Collins Positional cloning moves from perditional to traditional Nat Genet 9 1995 347 350
11. E.P. Consortium, B.E. Bernstein, E. Birney, I. Dunham, E.D. Green, and C. Gunter An integrated encyclopedia of DNA elements in the human genome Nature 489 2012 57 74
12. C. Genomes Project, G.R. Abecasis, A. Auton, L.D. Brooks, M.A. DePristo, and R.M. Durbin An integrated map of genetic variation from 1,092 human genomes Nature 491 2012 56 65
13. C. International HapMap, D.M. Altshuler, R.A. Gibbs, L. Peltonen, D.M. Altshuler, and R.A. Gibbs Integrating common and rare genetic variation in diverse human populations Nature 467 2010 52 58
14. International Human Genome Sequencing C Finishing the euchromatic sequence of the human genome Nature 431 2004 931 945
15. E.S. Lander, L.M. Linton, B. Birren, C. Nusbaum, M.C. Zody, and J. Baldwin Initial sequencing and analysis of the human genome Nature 409 2001 860 921
16. J.C. Venter, M.D. Adams, E.W. Myers, P.W. Li, R.J. Mural, and G.G. Sutton The sequence of the human genome Science 291 2001 1304 1351
17. A. McKenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, and A. Kernytsky The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data Genome Res 20 2010 1297 1303
18. S. Purcell, B. Neale, K. Todd-Brown, L. Thomas, M.A. Ferreira, and D. Bender PLINK: A tool set for whole-genome association and population-based linkage analyses Am J Hum Genet 81 2007 559 575
19. N.A. Rosenberg, L. Huang, E.M. Jewett, Z.A. Szpiech, I. Jankovic, and M. Boehnke Genome-wide association studies in diverse populations Nat Rev Genet 11 2010 356 366
20. Limited Competition for Data Deposition and Analyses of Genome Wide Association Studies of Mental Disorders (R01). Available at: http://grants.nih.gov/grants/guide/rfa-files/RFA-MH-08-120.html. Accessed January 28, 2014.
21. Recovery Act Limited Competition for NIH Grants: Research and Research Infrastructure "Grand Opportunities" (RC2) (RFA-OD-09-004). Available at: http://nimh.nih.gov/recovery/recovery-act-grand-opportunities-grants-nimh-areas.shtml. Accessed January 28, 2014.
22. Limited Competition: Genomic Risk and Resilience in 22q11 Deletion Syndrome: A Window into the Genetic Architecture of Mental Disorders (Collaborative R01). Available at: http://grants.nih.gov/grants/guide/rfa-files/RFA-MH-13-120.html. Accessed January 28, 2014.
23. Unveiling the Genome: Genetic Architecture of Severe Mental Disorders Revealed (Collaborative U01). Available at: http://grants.nih.gov/grants/guide/pa-files/PAR-13-241.html. Accessed January 28, 2014.
24. GCCC Psychiatric, S. Cichon, N. Craddock, M. Daly, S.V. Faraone, and P.V. Gejman Genomewide association studies: History, rationale, and prospects for psychiatric disorders Am J Psychiatry 166 2009 540 556
25. GCSC Psychiatric A framework for interpreting genome-wide association studies of psychiatric disorders Mol Psychiatry 14 2009 10 17
26. P.F. Sullivan The psychiatric GWAS consortium: Big science comes to psychiatry Neuron 68 2010 182 186
27. C Cross-Disorder Group of the Psychiatric Genomics, S.H. Lee, S Ripke, BM Neale, S.V. Faraone, and S.M. Purcell Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs Nat Genet 45 2013 984 994
28. S. Ripke, C. O'Dushlaine, K. Chambert, J.L. Moran, A.K. Kahler, and S. Akterin Genome-wide association analysis identifies 13 new risk loci for schizophrenia Nat Genet 45 2013 1150 1159
29. J.D. Buxbaum, M.J. Daly, B. Devlin, T. Lehner, K. Roeder, and M.W. State The autism sequencing consortium: Large-scale, high-throughput sequencing in autism spectrum disorders Neuron 76 2012 1052 1056
30. B.M. Neale, Y. Kou, L. Liu, A. Ma'ayan, K.E. Samocha, and A. Sabo Patterns and rates of exonic de novo mutations in autism spectrum disorders Nature 485 2012 242 245
31. B.J. O'Roak, L. Vives, S. Girirajan, E. Karakoc, N. Krumm, and B.P. Coe Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations Nature 485 2012 246 250
32. S.J. Sanders, M.T. Murtha, A.R. Gupta, J.D. Murdoch, M.J. Raubeson, and A.J. Willsey De novo mutations revealed by whole-exome sequencing are strongly associated with autism Nature 485 2012 237 241
33. T.S. Stroup, J.P. McEvoy, M.S. Swartz, M.J. Byerly, I.D. Glick, and J.M. Canive The National Institute of Mental Health Clinical Antipsychotic Trials of Intervention Effectiveness (CATIE) project: Schizophrenia trial design and protocol development Schizophr Bull 29 2003 15 31
34. A.J. Rush, M. Fava, S.R. Wisniewski, P.W. Lavori, M.H. Trivedi, and H.A. Sackeim Sequenced treatment alternatives to relieve depression (STAR∗D): Rationale and design Control Clin Trials 25 2004 119 142
35. J.L. Stein, S.E. Medland, A.A. Vasquez, D.P. Hibar, R.E. Senstad, and A.M. Winkler Identification of common variants associated with human hippocampal and intracranial volumes Nat Genet 44 2012 552 561
36. S.O. Moldin NIMH Human Genetics Initiative: 2003 update Am J Psychiatry 160 2003 621 622
37. S. Steinberg, S. de Jong, M. Mattheisen, J. Costas, D. Demontis, and S. Jamain Common variant at 16p11.2 conferring risk of psychosis Mol Psychiatry 19 2014 108 114
38. E.T. Lim, S. Raychaudhuri, S.J. Sanders, C. Stevens, A. Sabo, and D.G. MacArthur Rare complete knockouts in humans: Population distribution and significant role in autism spectrum disorders Neuron 77 2013 235 242
39. A.E. Timms, M.O. Dorschner, J. Wechsler, K.Y. Choi, R. Kirkwood, and S. Girirajan Support for the N-methyl-D-aspartate receptor hypofunction hypothesis of schizophrenia from exome sequencing in multiplex families JAMA Psychiatry 70 2013 582 590
40. G.C.R. Group, T.A. Manolio, L.L. Rodriguez, L. Brooks, G. Abecasis, and P Collaborative Association Study of New models of collaboration in genome-wide association studies: the Genetic Association Information Network Nat Genet 39 2007 1045 1051
41. Genetics and Mental Disorders. Available at: http://wwwapps.nimh.nih.gov/ecb/archives/nimhgenetics.pdf. Accessed January 28, 2014.
42. E.M. Ramos, C. Din-Lovinescu, E.B. Bookman, L.J. McNeil, C.C. Baker, and G. Godynskiy A mechanism for controlled access to GWAS data: Experience of the GAIN Data Access Committee Am J Hum Genet 92 2013 479 488
43. C. International Schizophrenia, S.M. Purcell, N.R. Wray, J.L. Stone, P.M. Visscher, and M.C. O'Donovan Common polygenic variation contributes to risk of schizophrenia and bipolar disorder Nature 460 2009 748 752
44. J. Shi, D.F. Levinson, J. Duan, A.R. Sanders, Y. Zheng, and I. Pe'er Common variants on chromosome 6p22.1 are associated with schizophrenia Nature 460 2009 753 757
45. H. Stefansson, R.A. Ophoff, S. Steinberg, O.A. Andreassen, S. Cichon, and D. Rujescu Common variants conferring risk of schizophrenia Nature 460 2009 744 747
46. P.I. de Bakker, N.P. Burtt, R.R. Graham, C. Guiducci, R. Yelensky, and J.A. Drake Transferability of tag SNPs in genetic association studies in multiple populations Nat Genet 38 2006 1298 1303
47. N. Risch, and K. Merikangas The future of genetic studies of complex human diseases Science 273 1996 1516 1517
48. P.R. Burton, A.L. Hansell, I. Fortier, T.A. Manolio, M.J. Khoury, and J. Little Size matters: just how big is BIG?: Quantifying realistic sample size requirements for human genome epidemiology Int J Epidemiol 38 2009 263 273
49. A. Kiezun, K. Garimella, R. Do, N.O. Stitziel, B.M. Neale, and P.J. McLaren Exome sequencing and the genetic basis of complex traits Nat Genet 44 2012 623 630
50. E.E. Schadt Molecular networks as sensors and drivers of common human diseases Nature 461 2009 218 223
51. S. Gulsuner, T. Walsh, A.C. Watts, M.K. Lee, A.M. Thornton, and S. Casadei Spatial and temporal mapping of de novo mutations in schizophrenia to a fetal prefrontal cortical network Cell 154 2013 518 529
52. N.N. Parikshak, R. Luo, A. Zhang, H. Won, J.K. Lowe, and V. Chandran Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism Cell 155 2013 1008 1021
53. A.J. Willsey, S.J. Sanders, M. Li, S. Dong, A.T. Tebbenkamp, and R.A. Muhle Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism Cell 155 2013 997 1007
54. Z.P. Pang, N. Yang, T. Vierbuchen, A. Ostermeier, D.R. Fuentes, and T.Q. Yang Induction of human neuronal cells by defined transcription factors Nature 476 2011 220 223
55. M.A. Lancaster, M. Renner, C.A. Martin, D. Wenzel, L.S. Bicknell, and M.E. Hurles Cerebral organoids model human brain development and microcephaly Nature 501 2013 373 379
56. L. Cong, F.A. Ran, D. Cox, S. Lin, R. Barretto, and N. Habib Multiplex genome engineering using CRISPR/Cas systems Science 339 2013 819 823
57. D.G. Wang, J.B. Fan, C.J. Siao, A. Berno, P. Young, and R. Sapolsky Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome Science 280 1998 1077 1082
58. C. International HapMap The International HapMap Project Nature 426 2003 789 796
59. D.R. Bentley, S. Balasubramanian, H.P. Swerdlow, G.P. Smith, J. Milton, and C.G. Brown Accurate whole human genome sequencing using reversible terminator chemistry Nature 456 2008 53 59
60. J.D. Watson The human genome project: Past, present, and future Science 248 1990 44 49
61. J. Sebat, B. Lakshmi, D. Malhotra, J. Troge, C. Lese-Martin, and T. Walsh Strong association of de novo copy number mutations with autism Science 316 2007 445 449
62. T. Walsh, J.M. McClellan, S.E. McCarthy, A.M. Addington, S.B. Pierce, and G.M. Cooper Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia Science 320 2008 539 543
63. M.A. Ferreira, M.C. O'Donovan, Y.A. Meng, I.R. Jones, D.M. Ruderfer, and L. Jones Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder Nat Genet 40 2008 1056 1058
64. C. Cross-Disorder Group of the Psychiatric Genomics, J.W. Smoller, N. Craddock, K. Kendler, P.H. Lee, and B.M. Neale Identification of risk loci with shared effects on five major psychiatric disorders: A genome-wide analysis Lancet 381 2013 1371 1379
65. SPIRES. Available at: http://era.nih.gov/nih-and-grantor-agencies/other/spires.cfm. Accessed January 28, 2014.
66. 2) Tool. Indiana University and SciTech Strategies Available at 2009 http://sci2.cns.iu.edu. Accessed January 28, 2014
67. Scopus database. Available at: http://www.scopus.com/search/form.url. Accessed January 28, 2014.
68. Journal Citation Reports at ISI Web of knowledge. Available at: http://thomsonreuters.com/journal-citation-reports/. Accessed January 28, 2014.