Whole genome sequencing as a diagnostic test: Challenges and opportunities

Clinical Chemistry

Volumn 60, Issue 5, 2014, Pages 724-733

  Chrystoja, Caitlin C ^a,b   Diamandis, Eleftherios P ^a,b,c  

^a UNIVERSITY OF TORONTO   (Canada)

^b MOUNT SINAI HOSPITAL   (Canada)

^c UNIVERSITY HEALTH NETWORK   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; CLINICAL MEDICINE; CLINICAL PRACTICE; CONFIDENTIALITY; DIAGNOSTIC TEST; EMOTIONAL STRESS; ETHICS; FOLLOW UP; GENE SEQUENCE; GENETIC DISORDER; GENETIC VARIABILITY; GENOME ANALYSIS; HEALTH; HUMAN; PATENT; QUALITY CONTROL; REVIEW; STANDARDIZATION;

COSTS AND COST ANALYSIS; DISEASE; GENETIC PREDISPOSITION TO DISEASE; GENETIC TESTING; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; QUALITY CONTROL;

EID: 84899585223     PISSN: 00099147     EISSN: 15308561     Source Type: Journal    
DOI: 10.1373/clinchem.2013.209213     Document Type: Review

References (74)

1. Pasche B, Absher D. Whole-genome sequencing: a step closer to personalized medicine. JAMA 2011;305:1596-7.
2. Diamandis EP. Next-generation sequencing: a new revolution in molecular diagnostics? Clin Chem 2009;55:2088-92.
3. Voelkerding KV, Dames SA, Durtschi JD. Nextgeneration sequencing: from basic research to diagnostics. Clin Chem 2009;55:641-58.
4. Bloss CS, Darst BF, Topol EJ, Schork NJ. Directto-consumer personalized genomic testing. Hum Mol Genet 2011;20:R132-41.
5. Bellcross CA, Page PZ, Meaney-Delman D. Directto-consumer personal genome testing and cancer risk prediction. Cancer J 2012;18:293-302.
6. Diamandis M, White NM, Yousef GM. Personalized medicine: marking a new epoch in cancer patient management. Mol Cancer Res 2010;8:1175-87.
7. Worthey EA, Mayer AN, Syverson GD, Helbling D, Bonacci BB, Decker B, et al. Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet Med 2011;13:255-62.
8. Choi M, Scholl UI, Ji W, Liu T, Tikhonova IR, Zumbo P, et al. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci USA 2009;106:19096-101.
9. Welch JS, Westervelt P, Ding L, Larson DE, Klco JM, Kulkarni S, et al. Use of whole-genome sequencing to diagnose a cryptic fusion oncogene. JAMA 2011;305:1577-84.
10. Jones SJ, Laskin J, Li YY, Griffith OL, An J, Bilenky M, et al. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol 2010;11:R82.
11. Bick D, Dimmock D. Whole exome and whole genome sequencing. Curr Opin Pediatr 2011;23:594-600.
12. Drmanac R. Medicine. The ultimate genetic test. Science 2012;336:1110-2.
13. Pelak K, Shianna KV, Ge D, Maia JM, Zhu M, Smith JP, et al. The characterization of twenty sequenced human genomes. PLoS Genet 2010;6:e1001111.
14. 1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, et al. A map of human genome variation from population-scale sequencing. Nature 2010;467:1061-73.
15. MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, et al. A systematic survey of loss-of-function variants in human protein-coding genes. Science 2012;335:823-8.
16. Zhao S, Prenger K, Smith L, Messina T, Fan H, Jaeger E, Stephens S. Rainbow: a tool for largescale whole-genome sequencing data analysis using cloud computing. BMC Genomics 2013;14:425.
17. Ormond KE, Wheeler MT, Hudgins L, Klein TE, Butte AJ, Altman RB, et al. Challenges in the clinical application of whole-genome sequencing. Lancet 2010;375:1749-51.
18. Prevention Genetics. Clinical DNA testing price list. http://preventiongenetics.com/files/4613/8333/9106/PricelistByDisease-10-15-13. pdf (Accessed March 2013).
19. SEQanswers. Software list. http://seqanswers.com/wiki/Software/list (Accessed March 2013).
20. Gargis AS, Kalman L, Berry MW, Bick DP, Dimmock DP, Hambuch T, et al. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat Biotechnol 2012;30:1033-6.
21. Kedes L, Campany G. The new date, new format, new goals and new sponsor of the Archon Genomics X PRIZE competition. Nat Genet 2011;43:1055-8.
22. Peters BA, Kermani BG, Sparks AB, Alferov O, Hong P, Alexeev A, et al. Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature 2012;487:190-5.
23. Sebastiani P, Solovieff N, Puca A, Hartley SW, Melista E, Andersen S, et al. Retraction. Science 2011;333:404.
24. Sebastiani P, Solovieff N, Puca A, Hartley SW, Melista E, Andersen S, et al. Genetic signatures of exceptional longevity in humans. Science 2010;2010.
25. Nothnagel M, Herrmann A, Wolf A, Schreiber S, Platzer M, Siebert R, et al. Technology-specific error signatures in the 1000 Genomes Project data. Hum Genet 2011;130:505-16.
26. Moore B, Hu H, Singleton M, De La Vega FM, Reese MG, Yandell M. Global analysis of diseaserelated DNA sequence variation in 10 healthy individuals: implications for whole genome-based clinical diagnostics. Genet Med 2011;13:210-7.
27. Rieber N, Zapatka M, Lasitschka B, Jones D, Northcott P, Hutter B, et al. Coverage bias and sensitivity of variant calling for four wholegenome sequencing technologies. PLoS One 2013;8:e66621.
28. Ledergerber C, Dessimoz C. Base-calling for nextgeneration sequencing platforms. Brief Bioinform 2011;12:489-97.
29. Huang X, Madan A. CAP3: a DNA sequence assembly program. Genome Res 1999;9:868-77.
30. Hatem A, Bozdaǧ D, Toland AE, Çatalyürekü V. Benchmarking short sequence mapping tools. BMC Bioinformatics 2013;14:184.
31. Loman NJ, Constantinidou C, Chan JZ, Halachev M, Sergeant M, Penn CW, et al. High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol 2012;10:599-606.
32. Pang AW, MacDonald JR, Pinto D, Wei J, Rafiq MA, Conrad DF, et al. Towards a comprehensive structural variation map of an individual human genome. Genome Biol 2010;11:R52.
33. Michaelson JJ, Sebat J. forestSV: structural variant discovery through statistical learning. Nat Methods 2012;9:819-21.
34. Roach JC, Glusman G, Hubley R, Montsaroff SZ, Holloway AK, Mauldin DE, et al. Chromosomal haplotypes by genetic phasing of human families. Am J Hum Genet 2011;89:382-97.
35. Ayuso C, Millán JM, Mancheño M, Dal-Ré R. Informed consent for whole-genome sequencing studies in the clinical setting. Proposed recommendations on essential content and process. Eur J Hum Genet 2013;21:1054-9.
36. Facio FM, Eidem H, Fisher T, Brooks S, Linn A, Kaphingst KA, et al. Intentions to receive individual results from whole-genome sequencing among participants in the ClinSeq study. Eur J Hum Genet 2013;21:261-5.
37. Ball MP, Thakuria JV, Zaranek AW, Clegg T, Rosenbaum AM, Wu X, et al. A public resource facilitating clinical use of genomes. Proc Natl Acad USA 2012;109:11920-7.
38. Green RC, Berg JS, Grody WW, Kalia SS, Korf BR, Martin CL, et al. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med 2013;15:565-74.
39. Wolf SM, Annas GJ, Elias S. Point-counterpoint. Patient autonomy and incidental findings in clinical genomics. Science 2013;340:1049-50.
40. McGuire AL, Joffe S, Koenig BA, Biesecker BB, McCullough LB, Blumenthal-Barby JS, et al. Pointcounterpoint. Ethics and genomic incidental findings. Science 2013;340:1047-8.
41. Hicks S, Wheeler DA, Plon SE, Kimmel M. Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed. Hum Mutat 2011;32:661-8.
42. Fowler DM, Araya CL, Fleishman SJ, Kellogg EH, Stephany JJ, Baker D, Fields S. High-resolution mapping of protein sequence-function relationships. Nat Methods 2010;7:741-6.
43. Hietpas RT, Jensen JD, Bolon DN. Experimental illumination of a fitness landscape. Proc Natl Acad Sci USA 2011;108:7896-901.
44. Sunyaev SR. Inferring causality and functional significance of human coding DNA variants. Hum Mol Genet 2012;21:R10-7.
45. Jones B. Genomics: personal genome project. Nat Rev Genet 2012;13:599.
46. Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, et al. The Genomes OnLine Database (GOLD) v. 4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2012;40:D571-9.
47. Tennessen JA, Bigham AW, O'Connor TD, Fu W, Kenny EE, Gravel S, et al. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 2012;337:64-9.
48. Walt DR, Kuhlik A, Epstein SK, Demmer LA, Knight M, Chelmow D, et al. Lessons learned from the introduction of personalized genotyping into a medical school curriculum. Genet Med 2011;13:63-6.
49. Rietschel M, Mattheisen M, Degenhardt F; Genetic Risk and Outcome in Psychosis (GROUP Investigators), Mühleisen TW, Kirsch P, et al. Association between genetic variation in a region on chromosome 11 and schizophrenia in large samples from Europe. Mol Psychiatry 2012;17:906-17.
50. Schosser A, Butler AW, Ising M, Perroud N, Uher R, Ng MY, et al. Genomewide association scan of suicidal thoughts and behaviour in major depression. PLoS One 2011;6:e20690.
51. Wellcome Trust Case Control Consortium. Genome-wide association study of 14, 000 cases of seven common diseases and 3, 000 shared controls. Nature 2007;447:661-78.
52. abc News. School shooter's DNA to be studied. http://news.yahoo.com/ school-shooters-dnastudied-214930321-abc-news-topstories.html (Accessed March 2013).
53. No easy answer. Nature 2013;493:133.
54. Presidential Commission for the Study of Bioethical Issues. Privacy and progress in whole genome sequencing. http://bioethics.gov/cms/node/764 (Accessed March 2013).
55. Zehnbauer B. Direct-to-consumer genetics testing-fair comparisons? Clin Chem 2011;57:369-71.
56. Imai K, Kricka LJ, Fortina P. Concordance study of 3 direct-to-consumer genetic-testing services. Clin Chem 2011;57:518-21.
57. Roberts NJ, Vogelstein JT, Parmigiani G, Kinzler KW, Vogelstein B, Velculescu VE. The predictive capacity of personal genome sequencing. Sci Transl Med 2012;4:133ra58.
58. Goh V, Helbling D, Biank V, Jarzembowski J, Dimmock D. Next-generation sequencing facilitates the diagnosis in a child with twinkle mutations causing cholestatic liver failure. J Pediatr Gastroenterol Nutr 2012;54:291-4.
59. Mendel's Pod. Father/scientist finds gene responsible for daughter's unknown syndrome: Hugh Rienhoff talks personal genomics. http://www.mendelspod. com/podcast/father-scientist-findsgene-responsible-for-daughters- unknownsyndrome-hugh-rienhoff-talks-personal-genomics (Accessed March 2013).
60. U. S. Food and Drug Administration. Table of pharmacogenomic biomarkers in drug labeling. http://www.fda.gov/Drugs/ScienceResearch/ResearchAreas/ Pharmacogenetics/ucm083378.htm (Accessed March 2014).
61. Gullapalli RR, Desai KV, Santana-Santos L, Kant JA, Becich MJ. Next generation sequencing in clinical medicine: challenges and lessons for pathology and biomedical informatics. J Pathol Inform 2012;3:40.
62. Ashley EA, Butte AJ, Wheeler MT, Chen R, Klein TE, Dewey FE, et al. Clinical assessment incorporating a personal genome. Lancet 2010;375:1525-35.
63. Bainbridge MN, Wiszniewski W, Murdock DR, Friedman J, Gonzaga-Jauregui C, Newsham I, et al. Whole-genome sequencing for optimized patient management. Sci Transl Med 2011;3:87re3.
64. Amberger J, Bocchini CA, Scott AF, Hamosh A. McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res 2009;37:D793-6.
65. Bell CJ, Dinwiddie DL, Miller NA, Hateley SL, Ganusova EE, Mudge J, et al. Carrier testing for severe childhood recessive diseases by nextgeneration sequencing. Sci Transl Med 2011;3:65ra4.
66. Fan HC, Gu W, Wang J, Blumenfeld YJ, El-Sayed YY, Quake SR. Non-invasive prenatal measurement of the fetal genome. Nature 2012;487 320-4.
67. Palomaki GE, Kloza EM, Lambert-Messerlian GM, Haddow JE, Neveux LM, Ehrich M, et al. DNA sequencing of maternal plasma to detect Down syndrome: an international clinical validation study. Genet Med 2011;13:913-20.
68. Talkowski ME, Ordulu Z, Pillalamarri V, Benson CB, Blumenthal I, Connolly S, et al. Clinical diagnosis by whole-genome sequencing of a prenatal sample. N Engl J Med 2012;367:2226-32
69. Saunders CJ, Miller NA, Soden SE, Dinwiddie DL, Noll A, Alnadi NA, et al. Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units. Sci Transl Med 2012;4:154ra135.
70. Kesselheim AS, Cook-Deegan RM, Winickoff DE, Mello MM. Gene patenting-the Supreme Court finally speaks. N Engl J Med 2013;369:869-75.
71. Association for Molecular Pathology v. United States Patent and Trademark office and Myriad Genetics, Inc., 689 F. 3d 1303 Fed. Cir. (2012).
72. New York Times. 2 Competitors sued by genetics company for patent infringement. http://www.nytimes.com/2013/07/11/business/2-competitors-suedby- genetics-company-for-patent-infringement.html?-r=0 (Accessed July 2013).
73. Mayo Collaborative Services v. Prometheus Laboratories, Inc., 566 U. S., 132 S. Ct. 1289 (2012).
74. The University of Texas at Austin. Illumina's historical list prices. https://wikis.utexas.edu/display/GSAF/Illumina's+historical+list+prices (Accessed August 2013).