The impact of reporting incidental findings from exome and whole-genome sequencing: Predicted frequencies based on modeling

Genetics in Medicine

Volumn 17, Issue 3, 2015, Pages 197-204

  Ding, Lucy Enid ^a   Burnett, Leslie ^a,b,c   Chesher, Douglas ^a,b  

^a ROYAL NORTH SHORE HOSPITAL   (Australia)

^b UNIVERSITY OF SYDNEY   (Australia)

^c UNIVERSITY OF SYDNEY   (Australia)

Author keywords

incidental findings; massively parallel sequencing; result reporting; whole genome sequencing

Indexed keywords

ARTICLE; CLINICAL ARTICLE; COMPUTER MODEL; DIAGNOSTIC TEST ACCURACY STUDY; EXOME; GENE FREQUENCY; GENE SEQUENCE; HUMAN; INCIDENTAL FINDING; INHERITANCE; MATHEMATICAL MODEL; PREDICTION; PREVALENCE; SENSITIVITY AND SPECIFICITY; ALGORITHM; BIOLOGICAL MODEL; COMPUTER SIMULATION; DNA MICROARRAY; HUMAN GENOME; PROCEDURES; STATISTICAL MODEL;

ALGORITHMS; COMPUTER SIMULATION; EXOME; GENOME, HUMAN; HUMANS; INCIDENTAL FINDINGS; MODELS, GENETIC; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 84938513618     PISSN: 10983600     EISSN: 15300366     Source Type: Journal    
DOI: 10.1038/gim.2014.94     Document Type: Article

References (40)

1. Crawford G, Foulds N, Fenwick A, Hallowell N, Lucassen A. Genetic medicine and incidental findings: it is more complicated than deciding whether to disclose or not. Genet Med 2013;15:896-899.
2. Presidential Commission for the Study of Bioethical Issues. Anticipate and Communicate: Ethical Management of Incidental and Secondary Findings in the Clinical, Research, and Direct-to-Consumer Contexts. http://bioethics.gov/sites/default/files/FINALAnticipateCommunicate-PCSBI-0.pdf. 2013.
3. Green RC, Berg JS, Grody WW, et al.; American College of Medical Genetics and Genomics. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med 2013;15:565-574.
4. American College of Medical Genetics and Genomics. Incidental findings in clinical genomics: a clarification. Genet Med 2013;15:664-666.
5. American College of Medical Genetics and Genomics. ACMG Updates Recommendation on "Opt Out" for Genome Sequencing Return of Results. http://www.acmg.net/docs/Release-ACMGUpdatesRecommendations-final.pdf. Accessed 1 May 2014.
6. Xue Y, Chen Y, Ayub Q, et al.; 1000 Genomes Project Consortium. Deleteriousand disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing. Am J Hum Genet 2012;91:1022-1032.
7. 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.
8. 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.
9. Cassa CA, Tong MY, Jordan DM. Large numbers of genetic variants considered to be pathogenic are common in asymptomatic individuals. Hum Mutat 2013;34:1216-1220.
10. Thompson BA, Spurdle AB, Plazzer JP, et al. Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database. Nat Genet 2014;46:107-115.
11. Spiegel MR, Boxer RW. Schaum's Outline of Theory and Problems of Statistics SI (Metric) Edition. McGraw-Hill, New York, 1981.
12. Kohane IS, Hsing M, Kong SW. Taxonomizing, sizing, and overcoming the incidentalome. Genet Med 2012;14:399-404.
13. Krier JB, Green RC. Management of Incidental Findings in Clinical Genomic Sequencing. Wiley: Hoboken, NJ, 2001.
14. Ford D, Easton DF, Peto J. Estimates of the gene frequency of BRCA1 and its contribution to breast and ovarian cancer incidence. Am J Hum Genet 1995;57:1457-1462.
15. Antoniou AC, Pharoah PD, McMullan G, et al. A comprehensive model for familial breast cancer incorporating BRCA1, BRCA2 and other genes. Br J Cancer 2002;86:76-83.
16. Whittemore AS, Gong G, John EM, et al. Prevalence of BRCA1 mutation carriers among U.S. non-Hispanic Whites. Cancer Epidemiol Biomarkers Prev 2004;13:2078-2083.
17. Schneider K, Zelley K, Nichols KE, Garber J. Li-Fraumeni syndrome. In: Pagon RA, Adam MP, Ardinger HH, et al (eds.) GeneReviews. University of Washington: Seattle, WA, 2013.
18. McGarrity TJ, Amos CI, Frazier ML, Wei C. Peutz-Jeghers syndrome. In: Pagon RA, Adam MP, Ardinger HH, et al (eds.). GeneReviews. University of Washington: Seattle, WA, 2013.
19. Kohlmann W, Gruber SB. Lynch syndrome. In: Pagon RA, Adam MP, Ardinger HH, et al (eds.). GeneReviews. University of Washington: Seattle, WA, 2012.
20. Jasperson KW, Burt RW. APC-associated polyposis conditions. In: Pagon RA, Adam MP, Ardinger HH, et al (eds.). GeneReviews. University of Washington: Seattle, WA, 2011.
21. Brand R, Nielsen M, Lynch H, Infante E. MUTYH-associated polyposis. In: Pagon RA, Adam MP, Ardinger HH, et al (eds.). GeneReviews. University of Washington: Seattle, WA, 2012.
22. Frantzen C, Links TP, Giles RH. Von Hippel-Lindau disease. In: Pagon RA, Adam MP, Ardinger HH, et al (eds.). GeneReviews. University of Washington: Seattle, WA, 2012.
23. Giusti F, Marini F, Brandi ML. Multiple endocrine neoplasia type 1. In: Pagon RA, Adam MP, Ardinger HH, et al (eds.). GeneReviews. University of Washington: Seattle, WA, 2012.
24. Moline J, Eng C. Multiple endocrine neoplasia type 2. In: Pagon RA, Adam MP, Ardinger HH, et al (eds.). GeneReviews. University of Washington: Seattle, WA, 2013.
25. Eng C. PTEN hamartoma tumor syndrome (PHTS). In: Pagon RA, Adam MP, Ardinger HH, et al (eds.). GeneReviews. University of Washington: Seattle, WA, 2012.
26. Lohmann DR, Gallie BL. Retinoblastoma. In: Pagon RA, Adam MP, Ardinger HH, et al (eds.). GeneReviews. University of Washington: Seattle, WA, 2013.
27. Gimenez-Roqueplo P.A.-P. Hereditary pheochromocytoma-paraganglioma. http://www.orpha.net/consor/cgi-bin/OC-Exp.php?Lng=EN&Expert= 29072. Accessed 19 July 2014.
28. Northrup H, Koenig MK, Au KS. Tuberous sclerosis complex. In: Pagon RA, Adam MP, Ardinger HH, et al (eds.). GeneReviews. University of Washington: Seattle, WA, 2011.
29. Dome JS, Huff V. Wilms tumor overview. In: Pagon RA, Adam MP, Ardinger HH, et al (eds.). GeneReviews. University of Washington: Seattle, WA, 2013.
30. Evans DG. Neurofibromatosis 2. In: Pagon RA, Adam MP, Ardinger HH, et al (eds.). GeneReviews. University of Washington: Seattle, WA, 2011.
31. Pepin MG, Byers PH. Ehlers-Danlos syndrome type IV. In: Pagon RA, Adam MP, Ardinger HH, et al (eds.). GeneReviews. University of Washington: Seattle, WA, 2011.
32. Dietz HC. Marfan syndrome. In: Pagon RA, Adam MP, Ardinger HH, et al (eds.). GeneReviews. University of Washington: Seattle, WA, 2011.
33. Milewicz DM, Regalado E. Thoracic aortic aneurysms and aortic dissections. In: Pagon RA, Adam MP, Ardinger HH, et al (eds.). GeneReviews. University of Washington: Seattle, WA, 2012.
34. Clouse WD, Hallett JW Jr, Schaff HV, et al. Acute aortic dissection: populationbased incidence compared with degenerative aortic aneurysm rupture. Mayo Clin Proc 2004;79:176-180.
35. Cirino AL, Ho C. Familial hypertrophic cardiomyopathy overview. In: Pagon RA, Adam MP, Ardinger HH, et al (eds.). GeneReviews. University of Washington: Seattle, WA, 2014.
36. Napolitano C, Priori SG, Bloise R. Catecholaminergic polymorphic ventricular tachycardia. In: Pagon RA, Adam MP, Ardinger HH, et al (eds.). GeneReviews. University of Washington: Seattle, WA, 2013.
37. McNally E, MacLeod H, Dellefave-Castillo L. Arrhythmogenic right ventricular dysplasia/cardiomyopathy, autosomal dominant. In: Pagon RA, Adam MP, Ardinger HH, et al (eds.). GeneReviews. University of Washington: Seattle, WA, 2014.
38. Alders M, Mannens M. Romano-Ward syndrome. In: Pagon RA, Adam MP, Ardinger HH, et al (eds.). GeneReviews. University of Washington: Seattle, WA, 2012.
39. Rader DJ, Cohen J, Hobbs HH. Monogenic hypercholesterolemia: new insights in pathogenesis and treatment. J Clin Invest 2003;111:1795-1803.
40. Rosenberg H, Sambuughin N, Riazi S, Dirksen R. Malignant hyperthermia susceptibility. In: Pagon RA, Adam MP, Ardinger HH, et al (eds.). GeneReviews. University of Washington: Seattle, WA, 2013.