Identification of medically actionable secondary findings in the 1000 genomes

PLoS ONE

Volumn 10, Issue 9, 2015, Pages

  Olfson, Emily ^a   Cottrell, Catherine E ^a   Davidson, Nicholas O ^a   Gurnett, Christina A ^a   Heusel, Jonathan W ^a   Stitziel, Nathan O ^a   Chen, Li Shiun ^a   Hartz, Sarah ^a   Nagarajan, Rakesh ^a,b   Saccone, Nancy L ^a   Bierut, Laura J ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Pierian DX   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

1000 GENOMES PROJECT; AFRICAN; ANCESTRY GROUP; ARTICLE; ASIAN; CANCER SUSCEPTIBILITY; EUROPE; FAMILIAL HYPERCHOLESTEROLEMIA; FOLLOW UP; GENE SEQUENCE; GENETIC VARIABILITY; GENOMICS; HEART DISEASE; HUMAN; HUMAN GENOME; PATHOGENICITY; WESTERN HEMISPHERE; GENETIC DATABASE; GENETIC PREDISPOSITION; GENETIC SCREENING; GENETIC VARIATION; MUTATION; PROCEDURES;

DATABASES, GENETIC; GENETIC PREDISPOSITION TO DISEASE; GENETIC TESTING; GENETIC VARIATION; GENOME, HUMAN; GENOMICS; HUMANS; MUTATION;

EID: 84947461294     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0135193     Document Type: Article

References (61)

1. ANTICIPATE and COMMUNICATE Ethical Management of Incidental and Secondary Findings in the Clinical, Research, and Direct-to-Consumer Contexts. Presidental Commision for the Study of Bioethical Issues. 2013. Available: http://bioethics.gov/sites/default/files/FINALAnticipateCommunicate- PCSBI-0.pdf.
2. Vernooij MW, Ikram MA, Tanghe HL, Vincent AJ, Hofman A, Krestin GP, et al. Incidental findings on brain MRI in the general population. N Engl J Med. 2007; 357(18):1821-1828. PMID: 17978290
3. Wolf SM, Lawrenz FP, Nelson CA, Kahn JP, Cho MK, Clayton EW, et al. Managing incidental findings in human subjects research: analysis and recommendations.J Law Med Ethics. 2008; 36(2):219-248, 211. doi: 10.1111/j.1748-720X.2008.00266.x PMID: 18547191
4. Kohane IS, Masys DR, Altman RB. The incidentalome: a threat to genomic medicine. JAMA. 2006; 296 (2):212-215. PMID: 16835427
5. Wolf SM. The past, present, and future of the debate over return of research results and incidental findings. Genet Med. 2012; 14(4):355-357. doi: 10.1038/gim.2012.26 PMID: 22481182
6. 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(7): 565-574. doi: 10.1038/gim.2013.73 PMID: 23788249
7. American College of Medical Genetics and Genomics. Incidental findings in clinical genomics: a clarification. Genet Med. 2013; 15(8):664-666. doi: 10.1038/gim.2013.82 PMID: 23828017
8. Wolf SM, Annas GJ, Elias S. Point-counterpoint. Patient autonomy and incidental findings in clinical genomics. Science. 2013; 340(6136):1049-1050. doi: 10.1126/science.1239119 PMID: 23686341
9. Ross L, Rothstein MA, Clayton E. Mandatory extended searches in all genome sequencing: "incidental findings, " patient autonomy, and shared decision making. JAMA. 2013; 310(4):367-368. doi: 10.1001/ jama.2013.41700 PMID: 23917281
10. Klitzman R, Appelbaum PS, Chung W. Return of secondary genomic findings vs patient autonomy: Implications for medical care. JAMA. 2013; 310(4):369-370. doi: 10.1001/jama.2013.41709 PMID: 23917282
11. Green RC, Lupski JR, Biesecker LG. Reporting genomic sequencing results to ordering clinicians: Incidental, but not exceptional. JAMA. 2013; 310(4):365-366. doi: 10.1001/jama.2013.41703 PMID: 23917280
12. McGuire AL, Joffe S, Koenig BA, Biesecker BB, McCullough LB, Blumenthal-Barby JS, et al. Pointcounterpoint. Ethics and genomic incidental findings. Science. 2013; 340(6136):1047-1048. doi: 10. 1126/science.1240156 PMID: 23686340
13. Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, et al. An integrated map of genetic variation from 1, 092 human genomes. Nature. 2012; 491(7422):56-65. doi: 10.1038/ nature11632 PMID: 23128226
14. Berg JS, Adams M, Nassar N, Bizon C, Lee K, Schmitt CP, et al. An informatics approach to analyzing the incidentalome. Genet Med. 2013; 15(1):36-44. doi: 10.1038/gim.2012.112 PMID: 22995991
15. Stenson PD, Ball EV, Howells K, Phillips AD, Mort M, Cooper DN. The Human Gene Mutation Database: providing a comprehensive central mutation database for molecular diagnostics and personalized genomics. Hum Genomics. 2009; 4(2):69-72. PMID: 20038494
16. Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014; 42: D980-985. doi: 10.1093/nar/gkt1113 PMID: 24234437
17. OMIM (Online Mendelian inheritance in man) Baltimore: Johns Hopkins University, Certer for Medical Genetics. 2012. Available: http://omim.org/.
18. Fokkema IF, den Dunnen JT, Taschner PE. LOVD: easy creation of a locus-specific sequence variation database using an LSDB-in-a-box approach. Hum Mutat. 2005; 26(2):63-68. PMID: 15977173
19. Beroud C, Collod-Beroud G, Boileau C, Soussi T, Junien C. UMD (Universal mutation database): a generic software to build and analyze locus-specific databases. Hum Mutat. 2000; 15(1):86-94. PMID: 10612827
20. Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP) Seattle, WA. 2014. Available: http://evs.gs.washington.edu/EVS/.
21. Dorschner MO, Amendola LM, Turner EH, Robertson PD, Shirts BH, Gallego CJ, et al. Actionable, pathogenic incidental findings in 1, 000 participants' exomes. Am J Hum Genet. 2013; 93(4):631-640. doi: 10.1016/j.ajhg.2013.08.006 PMID: 24055113
22. Easton DF, Deffenbaugh AM, Pruss D, Frye C, Wenstrup RJ, Allen-Brady K, et al. A systematic genetic assessment of 1, 433 sequence variants of unknown clinical significance in the BRCA1 and BRCA2 breast cancer-predisposition genes. Am J Hum Genet. 2007; 81(5):873-883. PMID: 17924331
23. Ng D, Johnston JJ, Teer JK, Singh LN, Peller LC, Wynter JS, et al. Interpreting Secondary Cardiac Disease Variants in an Exome Cohort. Circ Cardiovasc Genet. 2013; 6(4):337-346. doi: 10.1161/ CIRCGENETICS.113.000039 PMID: 23861362
24. Szabo C, Masiello A, Ryan JF, Brody LC. The breast cancer information core: database design, structure, and scope. Hum Mutat. 2000; 16(2):123-131. PMID: 10923033
25. Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009; 4(7):1073-81. doi: 10.1038/nprot.2009.86 PMID: 19561590
26. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010; 7(4):248-249. doi: 10.1038/ nmeth0410-248 PMID: 20354512
27. Gonzalez-Perez A, Lopez-Bigas N. Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. Am J Hum Genet. 2011; 88(4):440-449. doi: 10.1016/j.ajhg.2011.03.004 PMID: 21457909
28. Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, et al. ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007. Genet Med. 2008; 10(4):294-300. doi: 10.1097/GIM.0b013e31816b5cae PMID: 18414213
29. Plon SE, Eccles DM, Easton D, Foulkes WD, Genuardi M, Greenblatt MS, et al. Sequence variant classification and reporting: recommendations for improving the interpretation of cancer susceptibility genetic test results. Hum Mutat. 2008; 29(11):1282-1291. doi: 10.1002/humu.20880 PMID: 18951446
30. Kuznetsov SG, Liu P, Sharan SK. Mouse embryonic stem cell-based functional assay to evaluate mutations in BRCA2. Nat Med. 2008; 14(8):875-881. doi: 10.1038/nm.1719 PMID: 18607349
31. Malkin D, Jolly KW, Barbier N, Look AT, Friend SH, Gebhardt MC, et al. Germline mutations of the p53 tumor-suppressor gene in children and young adults with second malignant neoplasms. N Engl J Med. 1992; 326(20):1309-1315. PMID: 1565144
32. Fagin JA, Matsuo K, Karmakar A, Chen DL, Tang SH, Koeffler HP. High prevalence of mutations of the p53 gene in poorly differentiated human thyroid carcinomas. J Clin Invest. 1993; 91(1):179-184. PMID: 8423216
33. Astuti D, Latif F, Dallol A, Dahia PL, Douglas F, George E, et al. Gene mutations in the succinate dehydrogenase subunit SDHB cause susceptibility to familial pheochromocytoma and to familial paraganglioma. Am J Hum Genet. 2001; 69(1):49-54. PMID: 11404820
34. Bauce B, Rampazzo A, Basso C, Bagattin A, Daliento L, Tiso N, et al. Screening for ryanodine receptor type 2 mutations in families with effort-induced polymorphic ventricular arrhythmias and sudden death: early diagnosis of asymptomatic carriers. J Am Coll Cardiol. 2002; 40(2):341-349. PMID: 12106942
35. Cox MG, van der Zwaag PA, van der Werf C, van der Smagt JJ, Noorman M, Bhuiyan ZA, et al. Arrhythmogenic right ventricular dysplasia/cardiomyopathy: pathogenic desmosome mutations in indexpatients predict outcome of family screening: Dutch arrhythmogenic right ventricular dysplasia/cardiomyopathy genotype-phenotype follow-up study. Circulation. 2011; 123(23):2690-2700. doi: 10.1161/ CIRCULATIONAHA.110.988287 PMID: 21606396
36. Piippo K, Laitinen P, Swan H, Toivonen L, Viitasalo M, Pasternack M, et al. Homozygosity for a HERG potassium channel mutation causes a severe form of long QT syndrome: identification of an apparent founder mutation in the Finns. J Am Coll Cardiol. 2000; 35(7):1919-1925. PMID: 10841244
37. Hobbs HH, Brown MS, Goldstein JL. Molecular genetics of the LDL receptor gene in familial hypercholesterolemia. Hum Mutat. 1992; 1(6):445-466. PMID: 1301956
38. Garcia-Garcia AB, Ivorra C, Martinez-Hervas S, Blesa S, Fuentes MJ, Puig O, et al. Reduced penetrance of autosomal dominant hypercholesterolemia in a high percentage of families: importance of genetic testing in the entire family. Atherosclerosis. 2011; 218(2):423-430. doi: 10.1016/j. atherosclerosis.2011.07.106 PMID: 21868016
39. Petrucelli N, Daly MB, Feldman GL. BRCA1 and BRCA2 Hereditary Breast and Ovarian Cancer. In: Pagon RA, Bird TD, Dolan CR, Stephens K, Adam MP, editors. GeneReviews. Seattle WA: University of Washington, Seattle; 1993.
40. Schneider K, Zelley K, Nichols KE, Garber J. Li-Fraumeni Syndrome. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong CT, et al., editors. GeneReviews(R). Seattle WA: University of Washington, Seattle; 1993.
41. Kirmani S, Young WF. Hereditary Paraganglioma-Pheochromocytoma Syndromes. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong CT, et al., editors. GeneReviews(R). Seattle WA: University of Washington, Seattle; 1993.
42. Loeys BL, Dietz HC. Loeys-Dietz Syndrome. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong CT, et al., editors. GeneReviews(R). Seattle WA: University of Washington, Seattle; 1993.
43. McNally E, MacLeod H, Dellefave-Castillo L. Arrhythmogenic Right Ventricular Dysplasia/Cardiomyopathy. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong CT, et al., editors. GeneReviews (R). Seattle WA: University of Washington, Seattle; 1993.
44. Sen-Chowdhry S, Syrris P, McKenna WJ. Genetics of right ventricular cardiomyopathy. J Am Coll Cardiol. 2005; 16(8):927-935.
45. Napolitano C, Priori SG, Bloise R. Catecholaminergic Polymorphic Ventricular Tachycardia. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong CT, et al., editors. GeneReviews(R). Seattle WA: University of Washington, Seattle; 1993.
46. Schwartz PJ, Stramba-Badiale M, Crotti L, Pedrazzini M, Besana A, Bosi G, et al. Prevalence of the congenital long-QT syndrome. Circulation. 2009; 120(18):1761-1767. doi: 10.1161/ CIRCULATIONAHA.109.863209 PMID: 19841298
47. Alders M, Mannens M. Romano-Ward Syndrome. In: Pagon RA, Bird TD, Dolan CR, Stephens K, Adam MP, editors. GeneReviews. Seattle WA: University of Washington, Seattle; 1993.
48. Youngblom E, Knowles JW. Familial Hypercholesterolemia. In: Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong CT, et al., editors. GeneReviews(R). Seattle WA: University of Washington, Seattle; 1993.
49. Versmissen J, Oosterveer DM, Yazdanpanah M, Defesche JC, Basart DC, Liem AH, et al. Efficacy of statins in familial hypercholesterolaemia: a long term cohort study. BMJ. 2008; 337:a2423. doi: 10. 1136/bmj.a2423 PMID: 19001495
50. Neil A, Cooper J, Betteridge J, Capps N, McDowell I, Durrington P, et al. Reductions in all-cause, cancer, and coronary mortality in statin-treated patients with heterozygous familial hypercholesterolaemia: a prospective registry study. Eur Heart J. 2008; 29(21):2625-2633. doi: 10.1093/eurheartj/ehn422 PMID: 18840879
51. Amendola LM, Dorschner MO, Robertson PD, Salama JS, Hart R, Shirts BH, et al. Actionable exomic incidental findings in 6503 participants: challenges of variant classification. Genome Res. 2015; 25 (3):305-315. doi: 10.1101/gr.183483.114 PMID: 25637381
52. 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(6070):823-828. doi: 10.1126/science.1215040 PMID: 22344438
53. Xue Y, Chen Y, Ayub Q, Huang N, Ball EV, Mort M, et al. Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing. Am J Hum Genet. 2012; 91(6):1022-1032. doi: 10.1016/j.ajhg.2012.10.015 PMID: 23217326
54. Cassa CA, Tong MY, Jordan DM. Large numbers of genetic variants considered to be pathogenic are common in asymptomatic individuals. Hum Mutat. 2013; 34(9):1216-1220. doi: 10.1002/humu.22375 PMID: 23818451
55. Daneshjou R, Zappala Z, Kukurba K, Boyle SM, Ormond KE, Klein TE, et al. PATH-SCAN: a reporting tool for identifying clinically actionable variants. Pac Symp Biocomput. 2014:229-240.
56. Johnston JJ, Rubinstein WS, Facio FM, Ng D, Singh LN, Teer JK, et al. Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes. Am J Hum Genet. 2012; 91(1):97-108. doi: 10.1016/j.ajhg.2012.05.021 PMID: 22703879
57. McEwen JE. Ethical considerations for investigators proposing samples for inclusion in the 1000 Genomes Project. 2012. Available: http://www.1000genomes.org/sites/1000genomes.org/files/docs/ Informed%20Consent%20Background%20Document.pdf.
58. Collins FS, Varmus H. A new initiative on precision medicine. N Engl J Med. 2015; 372(9):793-795. doi: 10.1056/NEJMp1500523 PMID: 25635347
59. Bollinger JM, Scott J, Dvoskin R, Kaufman D. Public preferences regarding the return of individual genetic research results: findings from a qualitative focus group study. Genet Med. 2012; 14(4):451-457. doi: 10.1038/gim.2011.66 PMID: 22402755
60. Murphy J, Scott J, Kaufman D, Geller G, LeRoy L, Hudson K. Public expectations for return of results from large-cohort genetic research. Am J Bioeth. 2008; 8(11):36-43. doi: 10.1080/ 15265160802513093 PMID: 19061108
61. Baker M. One-stop shop for disease genes. Nature. 2012; 491(7423):171. doi: 10.1038/491171a PMID: 23135443