Recommendations for the integration of genomics into clinical practice

Genetics in Medicine

Volumn 18, Issue 11, 2016, Pages 1075-1084

  Bowdin, Sarah ^a   Gilbert, Adel ^a   Bedoukian, Emma ^b   Carew, Christopher ^a   Adam, Margaret P ^c   Belmont, John ^d   Bernhardt, Barbara ^e   Biesecker, Leslie ^f   Bjornsson, Hans T ^g   Blitzer, Miriam ^h   D'Alessandro, Lisa C A ^a   Deardorff, Matthew A ^b,i   Demmer, Laurie ^j   Elliott, Alison ^k   Feldman, Gerald L ^l   Glass, Ian A ^c   Herman, Gail ^m   Hindorff, Lucia ^f   Hisama, Fuki ^c   Hudgins, Louanne ⁿ   Innes, A Micheil ^o   Jackson, Laird ^p   Jarvik, Gail ^f   Kim, Raymond ^p   Korf, Bruce ^q   Ledbetter, David H ^r   Li, Mindy ⁱ   Liston, Eriskay ^p   Marshall, Christian ^a   Medne, Livija ^a,b   Meyn, M Stephen ^a,p   Monfared, Nasim ^p   Morton, Cynthia ^s   Mulvihill, John J ^t   Plon, Sharon E ^d   Rehm, Heidi ^s   Roberts, Amy ^u   Shuman, Cheryl ^a,p   Spinner, Nancy B ⁱ   Stavropoulos, D James ^a   Valverde, Kathleen ^v   Waggoner, Darrel J ^w   Wilkens, Alisha ^b   Cohn, Ronald D ^a,p   Krantz, Ian D ^b,i   more..

^a HOSPITAL FOR SICK CHILDREN   (Canada)

^b CHILDREN S HOSPITAL OF PHILADELPHIA   (United States)

^c UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^d BAYLOR COLLEGE OF MEDICINE   (United States)

^e HOSPITAL OF THE UNIVERSITY OF PENNSYLVANIA   (United States)

^f NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^g JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^h UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

ⁱ UNIVERSITY OF PENNSYLVANIA   (United States)

^j CAROLINAS MEDICAL CENTER   (United States)

^k UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^l WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^m OHIO STATE UNIVERSITY   (United States)

ⁿ STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^o UNIVERSITY OF CALGARY   (Canada)

^p DREXEL UNIVERSITY COLLEGE OF MEDICINE   (United States)

^q UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

^r GEISINGER HEALTH SYSTEM   (United States)

^s BRIGHAM AND WOMEN S HOSPITAL   (United States)

^t UNIVERSITY OF OKLAHOMA COLLEGE OF MEDICINE   (United States)

^u BOSTON CHILDREN S HOSPITAL   (United States)

^v ARCADIA UNIVERSITY   (United States)

^w UNIVERSITY OF CHICAGO   (United States)

more..

Author keywords

clinical genetics; genetics counseling; genomics; phenotyping; precision medicine

Indexed keywords

CLINICAL GENETICS; CLINICAL PRACTICE; EXOME; GENOME; GENOMICS; GOVERNMENT; HEALTH INSURANCE; HUMAN; INTEGRATION; PATIENT CARE; PATIENT EDUCATION; PATIENT SELECTION; PHENOTYPE; REVIEW; GENETIC COUNSELING; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN GENOME; MEDICAL GENETICS; TRENDS;

EXOME; GENETIC COUNSELING; GENETICS, MEDICAL; GENOME, HUMAN; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS;

EID: 84994165185     PISSN: 10983600     EISSN: 15300366     Source Type: Journal    
DOI: 10.1038/gim.2016.17     Document Type: Review

References (67)

1. Tjio JH, Levan A. The chromosome number of man. Hereditas 1956;42:1-6. http://onlinelibrary.wiley.com/doi/10.1111/j.1601-5223.1956.tb03010.x/abstract.
2. Lejeune J, Gautier M, Turpin R. [Study of somatic chromosomes from 9 mongoloid children]. C R Hebd Seances Acad Sci 1959;248:1721-1722.
3. Pinkel D, Gray JW, Trask B, van den Engh G, Fuscoe J, van Dekken H. Cytogenetic analysis by in situ hybridization with fluorescently labeled nucleic acid probes. Cold Spring Harb Symp Quant Biol 1986;51 Pt 1:151-157.
4. Kølvraa S, Koch J, Gregersen N, et al. Application of fluorescence in situ hybridization techniques in clinical genetics: use of two alphoid repeat probes detecting the centromeres of chromosomes 13 and 21 or chromosomes 14 and 22, respectively. Clin Genet 1991;39:278-286.
5. Magenis RE, Maslen CL, Smith L, Allen L, Sakai LY. Localization of the fibrillin (FBN) gene to chromosome 15, band q21.1. Genomics 1991;11:346-351.
6. Pinkel D, Segraves R, Sudar D, et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998;20:207-211.
7. Miller DT, Adam MP, Aradhya S, et al. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet 2010;86:749-764.
8. Ley TJ, Mardis ER, Ding L, et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 2008;456:66-72.
9. Ng SB, Buckingham KJ, Lee C, et al. Exome sequencing identifies the cause of a mendelian disorder. Nat Genet 2010;42:30-35.
10. Choi M, Scholl UI, Ji W, et al. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci USA 2009;106: 19096-19101.
11. Ng SB, Turner EH, Robertson PD, et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 2009;461:272-276.
12. Maher B. Exome sequencing takes centre stage in cancer profiling. Nature 2009;459:146-147.
13. Biesecker LG, Green RC. Diagnostic clinical genome and exome sequencing. N Engl J Med 2014;370:2418-2425.
14. Johnston JJ, Rubinstein WS, Facio FM, et al. Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies highpenetrance mutations in cancer-susceptibility genes. Am J Hum Genet 2012;91:97-108.
15. Dorschner MO, Amendola LM, Turner EH, et al.; National Heart, Lung, and Blood Institute Grand Opportunity Exome Sequencing Project. Actionable, pathogenic incidental findings in 1,000 participants' exomes. Am J Hum Genet 2013;93:631-640.
16. Tabor HK, Auer PL, Jamal SM, et al.; NHLBI Exome Sequencing Project. Pathogenic variants for Mendelian and complex traits in exomes of 6,517 European and African Americans: implications for the return of incidental results. Am J Hum Genet 2014;95:183-193.
17. Amendola LM, Dorschner MO, Robertson PD, et al. Actionable exomic incidental findings in 6503 participants: challenges of variant classification. Genome Res 2015;25:305-315.
18. Jurgens J, Ling H, Hetrick K, et al. Assessment of incidental findings in 232 whole-exome sequences from the Baylor-Hopkins Center for Mendelian Genomics. Genet Med 2015;17:782-788.
19. Biesecker LG. Incidental variants are critical for genomics. Am J Hum Genet 2013;92:648-651.
20. Bowdin S, Ray PN, Cohn RD, Meyn MS. The genome clinic: a multidisciplinary approach to assessing the opportunities and challenges of integrating genomic analysis into clinical care. Hum Mutat 2014;35:513-519.
21. Manolio TA, Chisholm RL, Ozenberger B, et al. Implementing genomic medicine in the clinic: the future is here. Genet Med 2013;15:258-267.
22. Atwal PS, Brennan ML, Cox R, et al. Clinical whole-exome sequencing: are we there yet? Genet Med 2014;16:717-719.
23. Points to consider in the clinical application of genomic sequencing. Genet Med 2012;14:759-761
24. Boycott K, Hartley T, Adam S, et al.; Canadian College of Medical Geneticists. The clinical application of genome-wide sequencing for monogenic diseases in Canada: Position Statement of the Canadian College of Medical Geneticists. J Med Genet 2015;52:431-437.
25. Shashi V, McConkie-Rosell A, Rosell B, et al. The utility of the traditional medical genetics diagnostic evaluation in the context of next-generation sequencing for undiagnosed genetic disorders. Genet Med 2014;16:176-182.
26. Gilissen C, Hehir-Kwa JY, Thung DT, et al. Genome sequencing identifies major causes of severe intellectual disability. Nature 2014;511:344-347.
27. Yuen RK, Thiruvahindrapuram B, Merico D, et al. Whole-genome sequencing of quartet families with autism spectrum disorder. Nat Med 2015;21:185-191.
28. Teeuw M, Waisfisz Q, Zwijnenburg PJ, et al. First steps in exploring prospective exome sequencing of consanguineous couples. Eur J Med Genet 2014;57: 613-616.
29. Deverka PA, Kaufman D, McGuire AL. Overcoming the reimbursement barriers for clinical sequencing. JAMA 2014;312:1857-1858.
30. Chakradhar S. Insurance companies are slow to cover next-generation sequencing. Nat Med 2015;21:204-205.
31. Vrijenhoek T, Kraaijeveld K, Elferink M, et al. Next-generation sequencing-based genome diagnostics across clinical genetics centers: implementation choices and their effects. Eur J Hum Genet 2015;23:1142-1150.
32. Scollon S, Bergstrom K, Kerstein RA, et al. Obtaining informed consent for clinical tumor and germline exome sequencing of newly diagnosed childhood cancer patients. Genome Med 2014;6:69.
33. Henderson GE, Wolf SM, Kuczynski KJ, et al. The challenge of informed consent and return of results in translational genomics: empirical analysis and recommendations. J Law Med Ethics 2014;42:344-355.
34. Bergner AL, Bollinger J, Raraigh KS, et al. Informed consent for exome sequencing research in families with genetic disease: the emerging issue of incidental findings. Am J Med Genet A 2014;164A:2745-2752.
35. Appelbaum PS, Parens E, Waldman CR, et al. Models of consent to return of incidental findings in genomic research. Hastings Cent Rep 2014;44:22-32.
36. Points to consider for informed consent for genome/exome sequencing. Genet Med 2013;15:748-749
37. Levenseller BL, Soucier DJ, Miller VA, Harris D, Conway L, Bernhardt BA. Stakeholders' opinions on the implementation of pediatric whole exome sequencing: implications for informed consent. J Genet Couns 2014;23:552-565.
38. Ayuso C, Millán JM, Mancheño M, Dal-Ré R. Informed consent for wholegenome sequencing studies in the clinical setting. Proposed recommendations on essential content and process. Eur J Hum Genet 2013;21:1054-1059.
39. Tabor HK, Stock J, Brazg T, et al. Informed consent for whole genome sequencing: a qualitative analysis of participant expectations and perceptions of risks, benefits, and harms. Am J Med Genet A 2012;158A:1310-1319.
40. National Coalition for Health Professional Education in Genetics. Core competencies in genetics for health professionals. 2007. http://www.nchpeg. org/index.php?option=com-content&view=article&id=237.
41. Hennekam RC, Allanson JE, Biesecker LG, Carey JC, Opitz JM, Vilain E. Elements of morphology: standard terminology for the external genitalia. Am J Med Genet A 2013;161A:1238-1263.
42. Carey JC. Editor's forward to special articles: elements of morphology. Am J Med Genet A 2013;161A:2710.
43. Biesecker LG, Carey JC. Implementing the elements of morphology in the American Journal of Medical Genetics. Am J Med Genet A 2011;155A:969-971.
44. Hennekam RC, Cormier-Daire V, Hall JG, Méhes K, Patton M, Stevenson RE. Elements of morphology: standard terminology for the nose and philtrum. Am J Med Genet A 2009;149A:61-76.
45. Hunter A, Frias JL, Gillessen-Kaesbach G, Hughes H, Jones KL, Wilson L. Elements of morphology: standard terminology for the ear. Am J Med Genet A 2009;149A:40-60.
46. Allanson JE, Cunniff C, Hoyme HE, McGaughran J, Muenke M, Neri G. Elements of morphology: standard terminology for the head and face. Am J Med Genet A 2009;149A:6-28.
47. Allanson JE, Biesecker LG, Carey JC, Hennekam RC. Elements of morphology: introduction. Am J Med Genet A 2009;149A:2-5.
48. Biesecker LG, Aase JM, Clericuzio C, Gurrieri F, Temple IK, Toriello H. Elements of morphology: standard terminology for the hands and feet. Am J Med Genet A 2009;149A:93-127.
49. Carey JC, Cohen MM Jr, Curry CJ, Devriendt K, Holmes LB, Verloes A. Elements of morphology: standard terminology for the lips, mouth, and oral region. Am J Med Genet A 2009;149A:77-92.
50. Robinson PN, Mundlos S. The human phenotype ontology. Clin Genet 2010;77:525-534.
51. Köhler S, Doelken SC, Mungall CJ, et al. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res 2014;42(Database issue):D966-D974.
52. Robinson PN, Köhler S, Bauer S, Seelow D, Horn D, Mundlos S. The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. Am J Hum Genet 2008;83:610-615.
53. Girdea M, Dumitriu S, Fiume M, et al. PhenoTips: patient phenotyping software for clinical and research use. Hum Mutat 2013;34:1057-1065.
54. Richards S, Aziz N, Bale S, et al.; ACMG Laboratory Quality Assurance Committee. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 2015;17:405-424.
55. Rehm HL, Bale SJ, Bayrak-Toydemir P, et al.; Working Group of the American College of Medical Genetics and Genomics Laboratory Quality Assurance Commitee. ACMG clinical laboratory standards for next-generation sequencing. Genet Med 2013;15:733-747.
56. Gargis AS, Kalman L, Berry MW, et al. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat Biotechnol 2012;30: 1033-1036.
57. Duzkale H, Shen J, McLaughlin H, et al. A systematic approach to assessing the clinical significance of genetic variants. Clin Genet 2013;84:453-463.
58. MacArthur DG, Manolio TA, Dimmock DP, et al. Guidelines for investigating causality of sequence variants in human disease. Nature 2014;508:469-476.
59. Rehm HL, Berg JS, Brooks LD, et al.; ClinGen. ClinGen-the Clinical Genome Resource. N Engl J Med 2015;372:2235-2242.
60. Jarvik GP, Amendola LM, Berg JS, et al.; eMERGE Act-ROR Committee and CERC Committee; CSER Act-ROR Working Group. Return of genomic results to research participants: the floor, the ceiling, and the choices in between. Am J Hum Genet 2014;94:818-826.
61. ACMG Board of Directors. ACMG policy statement: updated recommendations regarding analysis and reporting of secondary findings in clinical genome-scale sequencing. Genet Med 2015;17:68-69.
62. Korf BR, Ledbetter D, Murray MF. Report of the Banbury Summit Meeting on the evolving role of the medical geneticist, February 12-14, 2006. Genet Med 2008;10:502-507.
63. Kullo IJ, Jarvik GP, Manolio TA, Williams MS, Roden DM. Leveraging the electronic health record to implement genomic medicine. Genet Med 2013;15:270-271.
64. Manolio TA, Green ED. Leading the way to genomic medicine. Am J Med Genet C Semin Med Genet 2014;166C:1-7.
65. Burke W, Evans BJ, Jarvik GP. Return of results: ethical and legal distinctions between research and clinical care. Am J Med Genet C Semin Med Genet 2014;166C:105-111.
66. Jacob HJ, Abrams K, Bick DP, et al. Genomics in clinical practice: lessons from the front lines. Sci Transl Med 2013;5:194cm195.
67. Vassy JL, Lautenbach DM, McLaughlin HM, et al.; MedSeq Project. The MedSeq Project: a randomized trial of integrating whole genome sequencing into clinical medicine. Trials 2014;15:85.