A genetic counselor's guide to using next-generation sequencing in clinical practice

Journal of Genetic Counseling

Volumn 23, Issue 4, 2014, Pages 455-462

  Facio, Flavia M ^a   Lee, Kristy ^b   O'Daniel, Julianne M ^b  

^a Department of Genetics University of North Carolina at Chapel Hill ^*  (United States)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

Genetic counseling; Next generation sequencing; Whole exome sequencing; Whole genome sequencing

Indexed keywords

GENETIC COUNSELING; HUMAN; PROCEDURES; SEQUENCE ANALYSIS;

GENETIC COUNSELING; HUMANS; SEQUENCE ANALYSIS;

EID: 84904260560     PISSN: 10597700     EISSN: 15733599     Source Type: Journal    
DOI: 10.1007/s10897-013-9662-7     Document Type: Article

References (34)

1. Abdul-Karim, R.; Berkman, B. E.; Wendler, D.; Rid, A.; Khan, J.; Badgett, T.; et al. (2013). Disclosure of incidental findings from next-generation sequencing in pediatric genomic research. Pediatrics, 131(3), 564-571.
2. Ashley, E. A.; Butte, A. J.; Wheeler, M. T.; Chen, R.; Klein, T. E.; Dewey, F. E.; et al. (2010). Clinical assessment incorporating a personal genome. Lancet, 375(9725), 1525-1535.
3. Bainbridge, M. N.; Wiszniewski, W.; Murdock, D. R.; Friedman, J.; Gonzaga-Jauregui, C.; Newsham, I.; et al. (2011). Whole-genome sequencing for optimized patient management. Science Translational Medicine, 3(87), re3.
4. Bamshad, M. J.; Ng, S. B.; Bigham, A. W.; Tabor, H. K.; Emond, M. J.; Nickerson, D. A.; et al. (2011). Exome sequencing as a tool for Mendelian disease gene discovery. Nature Reviews Genetics, 12(11), 745-755.
5. Biesecker, L. G. (2012). Opportunities and challenges for the integration of massively parallel genomic sequencing into clinical practice: lessons from the ClinSeq project. Genetics in Medicine, 14(4), 393-398.
6. Biesecker, L. G.; Mullikin, J. C.; Facio, F. M.; Turner, C.; Cherukuri, P. F.; Blakesley, R. W.; et al. (2009). The ClinSeq Project: piloting large-scale genome sequencing for research in genomic medicine. Genome Research, 19(9), 1665-1674.
7. Choi, M.; Scholl, U. I.; Ji, W.; Liu, T.; Tikhonova, I. R.; Zumbo, P.; et al. (2009). Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proceedings of the National Academy of Sciences of the United States of America, 106(45), 19096-19101.
8. Facio, F. M.; Brooks, S.; Loewenstein, J.; Green, S.; Biesecker, L. G.; Biesecker, B. B. (2011). Motivators for participation in a whole-genome sequencing study: implications for translational genomics research. European Journal of Human Genetics, 19(12), 1213-1217.
9. Green, E. D.; Guyer, M. S. (2011). Charting a course for genomic medicine from base pairs to bedside. Nature, 470(7333), 204-213.
10. Green, R. C.; Berg, J. S.; Grody, W. W.; Kalia, S. S.; Korf, B. R.; Martin, C. L.; et al. (2013). ACMG recommendations for reporting incidental findings in clinical exome and genome sequencing. Genetics in Medicine, 15(7), 565-74.
11. Hudson, T. J.; Anderson, W.; Artez, A.; Barker, A. D.; Bell, C.; Bernabe, R. R.; et al. (2010). International network of cancer genome projects. Nature, 464(7291), 993-998.
12. Jamal, S. M.; Yu, J. H.; Chong, J. X.; Dent, K. M.; Conta, J. H.; Tabor, H.; et al. (2013). Practices and policies of clinical exome sequencing providers: analysis and implications. American Journal of Medical Genetics Part A, 161A(5), 935-950.
13. Johnson, S. (2010). Where good ideas come from. New York: Riverhead Books.
14. Johnston, J. J.; Rubinstein, W. S.; Facio, F. M.; Ng, D.; Singh, L. N.; Teer, J. K.; et al. (2012). Secondary variants in individuals undergoing exome sequencing: screening of 572 individuals identifies high-penetrance mutations in cancer-susceptibility genes. American Journal of Human Genetics, 91(1), 97-108.
15. Kaufman, D.; Murphy, J.; Scott, J.; Hudson, K. (2008). Subjects matter: a survey of public opinions about a large genetic cohort study. Genetics in Medicine, 10(11), 831-839.
16. Kohane, I. S.; Masys, D. R.; Altman, R. B. (2006). The incidentalome: a threat to genomice medicine. JAMA, 296(2), 212-215.
17. Korf, B. R.; Rehm, H. L. (2013). New approaches to molecular diangosis. JAMA, 309(14), 1511-1521.
18. Ku, C. S.; Cooper, D. N.; Roukos, D. H. (2013a). Clinical relevance of cancer genome sequencing. World Journal of Gastroenterology, 19(13), 2011-2018.
19. Ku, C. S.; Polychronakos, C.; Tan, E. K.; Naidoo, N.; Pawitan, Y.; Roukos, D. H.; et al. (2013b). A new paradigm emerges from the study of the novo mutations in the context of neurodevelopmental. Molecular Psychiatry, 18(2), 141-153.
20. Lindhurst, M. J.; Sapp, J. C.; Teer, J. K.; Johnston, J. J.; Finn, E. M.; Peters, K.; et al. (2011). A mosaic activating mutation in AKT1 associated with the Proteus syndrome. The New England Journal of Medicine, 365(7), 611-619.
21. Lupski, J. R.; Reid, J. G.; Gonzaga-Jauregui, C.; Rio Deiros, D.; Chen, D. C.; Nazareth, L.; et al. (2010). Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. The New England Journal of Medicine, 362(13), 1181-1191.
22. McGuire, A. L.; Joffe, S.; Koenig, B. A.; Biesecker, B. B.; McCullough, L. B.; Blumenthal-Barby, J. S.; et al. (2013). Point-counterpoint. Ethics and genomic incidental findings. Science, 340(6136), 1047-1048.
23. Murphy, J.; Scott, J.; Kaufman, D.; Geller, G.; LeRoy, L.; Hudson, K. (2009). Public perspectives on informed consent for biobanking. American Journal of Public Health, 99(12), 2128-2134.
24. Ng, S. B.; Turner, E. H.; Robertson, P. D.; Flygare, S. D.; Bigham, A. W.; Lee, C.; et al. (2009). Targeted capture and massively parallel sequencing of 12 human exomes. Nature, 461(7261), 272-276.
25. Pasche, B.; Absher, D. (2011). Whole-genome sequencing: a step closer to personalized medicine. JAMA, 305(15), 1596-1597.
26. Rehm, H. (2013). Disease-targeted sequencing: a cornestone in the clinic. Nature Reviews Genetics, 14(4), 295-300.
27. Richards, C. S.; Bale, S.; Bellissimo, D. B.; Das, S.; Grody, W. W.; Hedge, M. R.; et al. (2008). ACMG recommendations for standards for interpretation and reporting of sequence variations: revisions 2007. Genetics in Medicine, 10(4), 294-300.
28. Rios, J.; Stein, E.; Shendure, J.; Hobbs, H. H.; Cohen, J. C. (2010). Identification by whole-genome resequencing of gene defect responsible for severe hypercholesterolemia. Human Molecular Genetics, 19(22), 4313-4318.
29. Roach, J. C.; Glusman, G.; Smit, A. F.; Huff, C. D.; Hubley, R.; Shannon, P. T.; et al. (2010). Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science, 328(5878), 636-639.
30. Sloan, J. L.; Johnston, J. J.; Manoli, I.; Chandler, R. J.; Krause, C.; Carrillo-Carrasco, N.; et al. (2011). Exome sequencing identifies ACSF3 as a cause of combined malonic and methylmalonic aciduria. Nature Genetics, 43(9), 883-886.
31. Solomon, B. D.; Pineda-Alvarez, D. E.; Hadley, D. W.; Comparative Sequencing Program, N. I. S. C.; Teer, J. K.; Cherukuri, P. F.; et al. (2011). Personalized genomic medicine: lessons from the exome. Molecular Genetics and Metabolism, 104(1-2), 189-191.
32. Teer, J. K.; Green, E. D.; Mullikin, J. C.; Biesecker, L. G. (2012). VarSifter: visualizing and analyzing exome-scale sequence variation data on a desktop computer. Bioinformatics, 28(4), 599-600.
33. Tong, P.; Prendergast, J. G.; Lohan, A. J.; Farrington, S. M.; Cronin, S.; Friel, N.; et al. (2010). Sequencing and analysis of an Irish human genome. Genome Biology, 11(9), R91.
34. Worthey, E. A.; Mayer, A. N.; Syverson, G. D.; Helbling, D.; Bonacci, B. B.; Decker, B.; et al. (2011). Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genetics in Medicine, 13(3), 255-262.