Patient-controlled encrypted genomic data: An approach to advance clinical genomics

BMC Medical Genomics

Volumn 5, Issue , 2012, Pages

  Trakadis, Yannis J ^a  

^a MONTREAL CHILDREN S HOSPITAL   (Canada)

Author keywords

Clinic; Encrypted; Exome; Genome; Genomic; I MPOS; I MPOSE; Integration; Sequencing

Indexed keywords

ACCESS TO INFORMATION; CLINICAL PRACTICE; COST EFFECTIVENESS ANALYSIS; GENE TECHNOLOGY; GENETIC DATABASE; GENETIC SCREENING; GENETIC VARIABILITY; GENOME ANALYSIS; HUMAN; MEDICAL DECISION MAKING; MEDICAL INFORMATICS; MEDICAL INFORMATION; OUTCOME ASSESSMENT; PATIENT ASSESSMENT; PHENOTYPE; PRACTICE GUIDELINE; PRIORITY JOURNAL; REVIEW; SEQUENCE ANALYSIS; TOTAL QUALITY MANAGEMENT;

COMPUTER SECURITY; DATA MINING; DISEASE; GENOMICS; HUMANS; MUTATION; PATIENTS; PHENOTYPE;

EID: 84866250442     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-5-31     Document Type: Review

References (93)

1. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P, Nazarenko I, Nilsen GB, Yeung G, Dahl F, Fernandez A, Staker B, Pant KP, Baccash J, Borcherding AP, Brownley A, Cedeno R, Chen L, Chernikoff D, et al. Science 2010 327 5961 78 81 10.1126/science.1181498 19892942
2. Genome sequencing: the third generation. Check Hayden E, Nature 2009 457 7231 768 769 10.1038/news.2009.86 19212365
3. Letting the genome out of the bottle-will we get our wish? Hunter DJ, Khoury MJ, Drazen JM, N Engl J Med 2008 358 2 105 107 10.1056/NEJMp0708162 18184955
4. Exome sequencing as a tool for Mendelian disease gene discovery. Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, Shendure J, Nat Rev Genet 2011 12 11 745 755 10.1038/nrg3031 21946919
5. Downsizing genomic medicine: approaching the ethical complexity of whole-genome sequencing by starting small. Sharp RR, Genet Med 2011 13 3 191 194 10.1097/GIM.0b013e31820f603f 21311340
6. Challenges in the clinical application of whole-genome sequencing. Ormond KE, Wheeler MT, Hudgins L, Klein TE, Butte AJ, Altman RB, Ashley EA, Greely HT, Lancet 2010 375 9727 1749 1751 10.1016/S0140-6736(10)60599-5 20434765
7. Generic consent for genetic screening. Elias S, Annas GJ, N Engl J Med 1994 330 22 1611 1613 10.1056/NEJM199406023302213 8177253
8. Research ethics and the challenge of whole-genome sequencing. McGuire AL, Caulfield T, Cho MK, Nat Rev Genet 2008 9 2 152 156 18087293
9. A map of human genome variation from population-scale sequencing. Nature 2010 467 7319 1061 1073 10.1038/nature09534 20981092
10. The limitations of risk factors as prognostic tools. Ware JH, N Engl J Med 2006 355 25 2615 2617 10.1056/NEJMp068249 17182986
11. When can a risk factor be used as a worthwhile screening test? Wald NJ, Hackshaw AK, Frost CD, BMJ 1999 319 7224 1562 1565 10.1136/bmj.319.7224.1562 10591726
12. Ethical implications of the use of whole genome methods in medical research. Kaye J, Boddington P, de Vries J, Hawkins N, Melham K, Eur J Hum Genet 2010 18 4 398 403 10.1038/ejhg.2009.191 19888293
13. The diploid genome sequence of an individual human. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, Lin Y, MacDonald JR, Pang AW, Shago M, Stockwell TB, Tsiamouri A, Bafna V, Bansal V, Kravitz SA, Busam DA, et al. PLoS Biol 2007 5 10 254 10.1371/journal.pbio.0050254 17803354
14. Educating health-care professionals about genetics and genomics. Guttmacher AE, Porteous ME, McInerney JD, Nat Rev Genet 2007 8 2 151 157 10.1038/nrg2007 17230201
15. Deficiency of knowledge of genetics and genetic tests among general practitioners, gynecologists, and pediatricians: a global problem. Baars MJ, Henneman L, Ten Kate LP, Genet Med 2005 7 9 605 610 10.1097/01.gim.0000182895. 28432.c7 16301861
16. Medicine. Kohane IS, Mandl KD, Taylor PL, Holm IA, Nigrin DJ, Kunkel LM, Reestablishing the researcher-patient compact. Science 2007 316 5826 836 837
17. Ethical issues raised by common copy number variants and single nucleotide polymorphisms of certain and uncertain significance in general medical practice. Beaudet AL, Genome Med 2010 2 7 42 10.1186/gm163 20642868
18. Cascade effects of medical technology. Deyo RA, Annu Rev Public Health 2002 23 23 44 10.1146/annurev.publhealth.23.092101.134534 11910053
19. An unwelcome side effect of direct-to-consumer personal genome testing: raiding the medical commons. McGuire AL, Burke W, JAMA 2008 300 22 2669 2671 10.1001/jama.2008.803 19066388
20. Personal genome sequencing: current approaches and challenges. Snyder M, Du J, Gerstein M, Genes Dev 2010 24 5 423 431 10.1101/gad.1864110 20194435
21. Intellectual property. Jensen K, Murray F, Enhanced: intellectual property landscape of the human genome. Science 2005 310 5746 239 240
22. Biomarkers Unbound-The Supreme Court's Ruling on Diagnostic-Test Patents. Kesselheim AS, Karlawish J, N Engl J Med 2012 366 25 2338 40 10.1056/NEJMp1204164 22621421
23. The fate and future of patents on human genes and genetic diagnostic methods. Huys I, Matthijs G, Van Overwalle G, Nat Rev Genet 2012 13 6 441 448 10.1038/nrg3255 22596320
24. Personalized genomic information: preparing for the future of genetic medicine. Guttmacher AE, McGuire AL, Ponder B, Stefansson K, Nat Rev Genet 2010 11 2 161 165 10.1038/nrg2735 20065954
25. ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007. Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE, Genet Med 2008 10 4 294 300 10.1097/GIM.0b013e31816b5cae 18414213
26. Do common in silico tools predict the clinical consequences of amino-acid substitutions in the CFTR gene? Dorfman R, Nalpathamkalam T, Taylor C, Gonska T, Keenan K, Yuan XW, Corey M, Tsui LC, Zielenski J, Durie P, Clin Genet 2010 77 5 464 473 10.1111/j.1399-0004.2009.01351.x 20059485
27. Performance of mutation pathogenicity prediction methods on missense variants. Thusberg J, Olatubosun A, Vihinen M, Hum Mutat 2011 32 4 358 368 10.1002/humu.21445 21412949
28. Exome sequencing identifies the cause of a mendelian disorder. Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon PT, Jabs EW, Nickerson DA, Shendure J, Bamshad MJ, Nat Genet 2010 42 1 30 35 10.1038/ng.499 19915526
29. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Ng SB, Bigham AW, Buckingham KJ, Hannibal MC, McMillin MJ, Gildersleeve HI, Beck AE, Tabor HK, Cooper GM, Mefford HC, Lee C, Turner EH, Smith JD, Rieder MJ, Yoshiura K, Matsumoto N, Ohta T, Niikawa N, Nickerson DA, Bamshad MJ, et al. Nat Genet 2010 42 9 790 793 10.1038/ng.646 20711175
30. De novo mutations of SETBP1 cause Schinzel-Giedion syndrome. Hoischen A, van Bon BW, Gilissen C, Arts P, van Lier B, Steehouwer M, de Vries P, de Reuver R, Wieskamp N, Mortier G, Devriendt K, Amorim MZ, Revencu N, Kidd A, Barbosa M, Turner A, Smith J, Oley C, Henderson A, Hayes IM, et al. Nat Genet 2010 42 6 483 485 10.1038/ng.581 20436468
31. Exome sequencing identifies WDR35 variants involved in Sensenbrenner syndrome. Gilissen C, Arts HH, Hoischen A, Spruijt L, Mans DA, Arts P, van Lier B, Steehouwer M, van Reeuwijk J, Kant SG, Roepman R, Knoers NV, Veltman JA, Brunner HG, Am J Hum Genet 2010 87 3 418 423 10.1016/j.ajhg.2010.08.004 20817137
32. Charting a course for genomic medicine from base pairs to bedside. Green ED, Guyer MS, Nature 2011 470 7333 204 213 10.1038/nature09764 21307933
33. Identification by whole-genome resequencing of gene defect responsible for severe hypercholesterolemia. Rios J, Stein E, Shendure J, Hobbs HH, Cohen JC, Hum Mol Genet 2010 19 22 4313 4318 10.1093/hmg/ddq352 20719861
34. Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. Lupski JR, Reid JG, Gonzaga-Jauregui C, Rio Deiros D, Chen DC, Nazareth L, Bainbridge M, Dinh H, Jing C, Wheeler DA, McGuire AL, Zhang F, Stankiewicz P, Halperin JJ, Yang C, Gehman C, Guo D, Irikat RK, Tom W, Fantin NJ, et al. N Engl J Med 2010 362 13) 1181 1191 20220177
35. From eugenics to patents: genetics, law, and human rights. Kevles DJ, Ann Hum Genet 2011 75 3 326 333 10.1111/j.1469-1809.2011.00648.x 21488849
36. The future of gene therapy. Cavazzana-Calvo M, Thrasher A, Mavilio F, Nature 2004 427 6977 779 781 10.1038/427779a 14985734
37. Medicine. McGuire AL, Cho MK, McGuire SE, Caulfield T, The future of personal genomics. Science 2007 317 5845 1687
38. Personalized medicine in the era of genomics. Burke W, Psaty BM, JAMA 2007 298 14 1682 1684 10.1001/jama.298.14.1682 17925520
39. Autosomal recessive Emery-Dreifuss muscular dystrophy caused by a novel mutation (R225Q) in the lamin A/C gene identified by exome sequencing. Jimenez-Escrig A, Gobernado I, Garcia-Villanueva M, Sanchez-Herranz A, Muscle Nerve 2012 45 4 605 610 10.1002/mus.22324 22431096
40. SVA: software for annotating and visualizing sequenced human genomes. Ge D, Ruzzo EK, Shianna KV, He M, Pelak K, Heinzen EL, Need AC, Cirulli ET, Maia JM, Dickson SP, et al. Bioinformatics 2011 27 14 1998 2000 10.1093/ bioinformatics/btr317 21624899
41. TDT-HET: a new transmission disequilibrium test that incorporates locus heterogeneity into the analysis of family-based association data. Londono D, Buyske S, Finch SJ, Sharma S, Wise CA, Gordon D, BMC Bioinforma 2012 13 13 10.1186/1471-2105-13-13
42. Family-based designs for genome-wide association studies. Ott J, Kamatani Y, Lathrop M, Nat Rev Genet 2011 12 7 465 474 10.1038/nrg2989 21629274
43. Family-based association studies for next-generation sequencing. Zhu Y, Xiong M, Am J Hum Genet 2012 90 6 1028 1045 10.1016/j.ajhg.2012.04.022 22682329
44. Two adaptive weighting methods to test for rare variant associations in family-based designs. Fang S, Sha Q, Zhang S, Genet Epidemiol 2012 36 5 499 507 10.1002/gepi.21646 22674630
45. Implementing a unified approach to family-based tests of association. Laird NM, Horvath S, Xu X, Genet Epidemiol 2000 19 Suppl 1 36 42 11055368
46. Database resources in metabolomics: an overview. Go EP, J Neuroimmune Pharmacol 2010 5 1 18 30 10.1007/s11481-009-9157-3 19418229
47. The human serum metabolome. Psychogios N, Hau DD, Peng J, Guo AC, Mandal R, Bouatra S, Sinelnikov I, Krishnamurthy R, Eisner R, Gautam B, et al. PLoS One 2011 6 2 16957 10.1371/journal.pone.0016957 21359215
48. Integration of bioinformatics resources for functional analysis of gene expression and proteomic data. Huang H, Hu ZZ, Arighi CN, Wu CH, Front Biosci 2007 12 5071 5088 10.2741/2449 17569631
49. Bell J, Bodmer D, Sistermans E, Ramsden SC, Practice guidelines for the interpretation and reporting of unclassified variants (UVs) in clinical molecular genetics Guidelines ratified by the UK CMGS (11th January, 2008) and the VGKL (22nd October, 2007), UK 2007 http://cmgsweb.shared.hosting.zen.co.uk/ BPGs/Best-practice-Guidelines.htm
50. ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007. Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE, Genet Med 2008 10 4 294 300 10.1097/GIM.0b013e31816b5cae 18414213
51. The Human Gene Mutation Database: 2008 update. Stenson PD, Mort M, Ball EV, Howells K, Phillips AD, Thomas NS, Cooper DN, Genome Med 2009 1 1 13 10.1186/gm13 19348700
52. The Diagnostic Mutation Database (DMuDB) http://www.ngrl.org.uk/ Manchester/projects/informatics/dmudb
53. MutaDATABASE: a centralized and standardized DNA variation database. Bale S, Devisscher M, Van Criekinge W, Rehm HL, Decouttere F, Nussbaum R, Dunnen JT, Willems P, Nat Biotechnol 2011 29 2 117 118 10.1038/nbt.1772 21301433
54. ClinVar http://www.ncbi.nlm.nih.gov/clinvar
55. Rehm H, Martin C, Bale S, Hegde M, Willems P, Miller D, Lyon E, Ferber M, Das S, Riggs E, Kaminsky E, Faucett W, Paschall J, Maglott D, Ostell J, Ledbetter D, Nussbaum R, ClinVar Community Group Centralizing the Deposition and Curation of Human Mutations [abstract] http://submissions.miracd.com/acmg/ ContentInfo.aspx?conID=2599
56. A new face and new challenges for Online Mendelian Inheritance in Man (OMIM(R)). Amberger J, Bocchini C, Hamosh A, Hum Mutat 2011 32 5 564 567 10.1002/humu.21466 21472891
57. GeneReviews™ http://www.ncbi.nlm.nih.gov/books/NBK1116/ 21324824
58. POSSUM Web http://www.possum.net.au/
59. The London Medical Databases http://www.lmdatabases.com/
60. The Human Phenotype Ontology http://www.human-phenotype-ontology.org
61. Crooks K, Berg J, Booker J, Evans J, Foreman K, Weck K, Separating the wheat from the chaff: A gene-based approach for prioritizing analysis of genetic variants in diagnostic whole-exome sequencing in NCGENES 2012 [abstract] http://submissions.miracd.com/acmg/ContentInfo.aspx?conID=2855
62. [Syndromic and diagnostic heterogeneity of schizophrenia]. Brazo P, Dollfus S, Encephale 1997 23 Spec No 2 20 24 9273303
63. Schizophrenia: disease, syndrome, or dimensions? Carpenter WT, Fam Process 2007 46 2 199 206 10.1111/j.1545-5300.2007.00204.x 17593885
64. The genetics of schizophrenia. Sullivan PF, PLoS Med 2005 2 7 212 10.1371/journal.pmed.0020212 16033310
65. Association analysis of 94 candidate genes and schizophrenia-related endophenotypes. Greenwood TA, Light GA, Swerdlow NR, Radant AD, Braff DL, PLoS One 2012 7 1 29630 10.1371/journal.pone.0029630 22253750
66. Concordance rates of insulin dependent diabetes mellitus: a population based study of young Danish twins. Kyvik KO, Green A, Beck-Nielsen H, BMJ 1995 311 7010 913 917 10.1136/bmj.311.7010.913 7580548
67. A framework for variation discovery and genotyping using next-generation DNA sequencing data. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, et al. Nat Genet 2011 43 5 491 498 10.1038/ng.806 21478889
68. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK, Nature 2010 464 7289 768 772 10.1038/nature08872 20220758
69. Transcriptome genetics using second generation sequencing in a Caucasian population. Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, Nisbett J, Guigo R, Dermitzakis ET, Nature 2010 464 7289 773 777 10.1038/nature08903 20220756
70. Stitching together multiple data dimensions reveals interacting metabolomic and transcriptomic networks that modulate cell regulation. Zhu J, Sova P, Xu Q, Dombek KM, Xu EY, Vu H, Tu Z, Brem RB, Bumgarner RE, Schadt EE, PLoS Biol 2012 10 4 1001301 10.1371/journal.pbio.1001301 22509135
71. Personal phenotypes to go with personal genomes. Snyder M, Weissman S, Gerstein M, Mol Syst Biol 2009 5 273 19455137
72. Epigenome mapping in normal and disease States. Maunakea AK, Chepelev I, Zhao K, Circ Res 2010 107 3 327 339 10.1161/CIRCRESAHA.110.222463 20689072
73. The KEGG database. Kanehisa M, Novartis Found Symp 2002 247 91 101 discussion 101-103, 119-128, 244-152 12539951
74. Epstein C, Erickson R, Wynshaw-Boris A, Inborn Errors of Development Oxford University Press, Oxford 2008
75. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, et al. Nucleic Acids Res 2010 38 Web Server issue) 214 220 20576703
76. Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. Raychaudhuri S, Plenge RM, Rossin EJ, Ng AC, Purcell SM, Sklar P, Scolnick EM, Xavier RJ, Altshuler D, Daly MJ, PLoS Genet 2009 5 6 1000534 10.1371/journal.pgen.1000534 19557189
77. Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk. Raychaudhuri S, Thomson BP, Remmers EF, Eyre S, Hinks A, Guiducci C, Catanese JJ, Xie G, Stahl EA, Chen R, et al. Nat Genet 2009 41 12 1313 1318 10.1038/ng.479 19898481
78. GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms. Jani SD, Argraves GL, Barth JL, Argraves WS, BMC Bioinforma 2010 11 166 10.1186/1471-2105-11-166
79. Protein interactome reveals converging molecular pathways among autism disorders. Sakai Y, Shaw CA, Dawson BC, Dugas DV, Al-Mohtaseb Z, Hill DE, Zoghbi HY, Sci Transl Med 2011 3(86 86ra49
80. Ma'ayan A: Network- and attribute-based classifiers can prioritize genes and pathways for autism spectrum disorders and intellectual disability. Kou Y, Betancur C, Xu H, Buxbaum JD, Am J Med Genet C Semin Med Genet 2012 160C 2 130 142 10.1002/ajmg.c.31330 22499558
81. Integration of metabolomics and transcriptomics data to aid biomarker discovery in type 2 diabetes. Connor SC, Hansen MK, Corner A, Smith RF, Ryan TE, Mol Biosyst 2010 6 5 909 921 10.1039/b914182k 20567778
82. A practical approach to detect unique metabolic patterns for personalized medicine. Johnson JM, Yu T, Strobel FH, Jones DP, Analyst 2010 135 11 2864 2870 10.1039/c0an00333f 20838665
83. Detecting gene-gene interactions that underlie human diseases. Cordell HJ, Nat Rev Genet 2009 10 6 392 404 19434077
84. A new strategy for linkage analysis under epistasis taking into account genetic heterogeneity. Bureau A, Merette C, Croteau J, Fournier A, Chagnon YC, Roy MA, Maziade M, Hum Hered 2009 68 4 231 242 10.1159/000228921 19622890
85. Epistasis among HLA-DRB1, HLA-DQA1, and HLA-DQB1 loci determines multiple sclerosis susceptibility. Lincoln MR, Ramagopalan SV, Chao MJ, Herrera BM, Deluca GC, Orton SM, Dyment DA, Sadovnick AD, Ebers GC, Proc Natl Acad Sci U S A 2009 106 18 7542 7547 19380721
86. Candidate gene association analysis for a quantitative trait, using parent-offspring trios. Gauderman WJ, Genet Epidemiol 2003 25 4 327 338 10.1002/gepi.10262 14639702
87. Gene-environment interactions in human diseases. Hunter DJ, Nat Rev Genet 2005 6 4 287 298 15803198
88. Gene-environment-wide association studies: emerging approaches. Thomas D, Nat Rev Genet 2010 11 4 259 272 10.1038/nrg2764 20212493
89. Nontraditional epidemiologic approaches in the analysis of gene-environment interaction: case-control studies with no controls! Khoury MJ, Flanders WD, Am J Epidemiol 1996 144 3 207 213 10.1093/oxfordjournals.aje. a008915 8686689
90. Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Worthey EA, Mayer AN, Syverson GD, Helbling D, Bonacci BB, Decker B, Serpe JM, Dasu T, Tschannen MR, Veith RL, Basehore MJ, Broeckel U, Tomita-Mitchell A, Arca MJ, Casper JT, Margolis DA, Bick DP, Hessner MJ, Routes JM, Verbsky JW, et al. Genet Med 2011 13 3 255 262 10.1097/GIM.0b013e3182088158 21173700
91. The genome gets personal-almost. Feero WG, Guttmacher AE, Collins FS, JAMA 2008 299 11 1351 1352 10.1001/jama.299.11.1351 18349096
92. Personalized medicine: are we there yet? Ikediobi ON, Pharmacogenomics J 2009 9 2 85 10.1038/tpj.2008.12 18794909
93. Principles and practice of mass screening for disease. Wilson JM, Jungner YG, Bol Oficina Sanit Panam 1968 65 4 281 393 4234760