Top

Published in:

01-08-2014 | Next Generation Genetic Counseling

A Genetic Counselor’s Guide to Using Next-Generation Sequencing in Clinical Practice

Authors: Flavia M. Facio, Kristy Lee, Julianne M. O’Daniel

Published in: Journal of Genetic Counseling | Issue 4/2014

Abstract

Advances in next-generation sequencing (NGS) and rapid reductions in cost have increased the use of such technologies in research and clinical practice. However, many barriers exist to translating NGS for routine clinical use, including issues related to the interpretation of results, and the potential to find results that are secondary or incidental to the specific application of NGS. Nonetheless, NGS has become sufficiently affordable to be offered by several clinical laboratories, and increasingly it is becoming an attractive and viable option for clinicians and patients. This article reviews current NGS technologies, highlighting the information genetic counselors need to know to make informed-decisions about utilizing NGS in the clinic, and underscoring the impact of this new testing modality on the practice of genetic counseling.

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.CrossRef

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.CrossRef

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.CrossRef

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.CrossRef

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.CrossRef

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.CrossRef

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.CrossRef

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.CrossRef

Green, E. D., & Guyer, M. S. (2011). Charting a course for genomic medicine from base pairs to bedside. Nature, 470(7333), 204–213.CrossRef

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.CrossRef

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.CrossRef

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. CrossRef

Johnson, S. (2010). Where good ideas come from. New York: Riverhead Books.

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.CrossRef

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.CrossRef

Kohane, I. S., Masys, D. R., & Altman, R. B. (2006). The incidentalome: a threat to genomice medicine. JAMA, 296(2), 212–215.CrossRef

Korf, B. R., & Rehm, H. L. (2013). New approaches to molecular diangosis. JAMA, 309(14), 1511–1521.CrossRef

Ku, C. S., Cooper, D. N., & Roukos, D. H. (2013a). Clinical relevance of cancer genome sequencing. World Journal of Gastroenterology, 19(13), 2011–2018.CrossRef

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.CrossRef

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.CrossRef

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.CrossRef

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.CrossRef

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.CrossRef

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.CrossRef

Pasche, B., & Absher, D. (2011). Whole-genome sequencing: a step closer to personalized medicine. JAMA, 305(15), 1596–1597.CrossRef

Rehm, H. (2013). Disease-targeted sequencing: a cornestone in the clinic. Nature Reviews Genetics, 14(4), 295–300.CrossRef

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.CrossRef

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.CrossRef

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.CrossRef

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.CrossRef

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.CrossRef

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.CrossRef

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.CrossRef

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.CrossRef

Title: A Genetic Counselor’s Guide to Using Next-Generation Sequencing in Clinical Practice
Authors: Flavia M. Facio
Kristy Lee
Julianne M. O’Daniel
Publication date: 01-08-2014
Publisher: Springer US
Published in: Journal of Genetic Counseling / Issue 4/2014
Print ISSN: 1059-7700
Electronic ISSN: 1573-3599
DOI: https://doi.org/10.1007/s10897-013-9662-7

At a glance: The ONWARDS insulin icodec trials

Springer Medicine

A Genetic Counselor’s Guide to Using Next-Generation Sequencing in Clinical Practice

Abstract

At a glance: The ONWARDS insulin icodec trials

Springer Medicine

Abstract

Please log in to get access to this content

Other articles of this Issue 4/2014

Views of Genetics Health Professionals on the Return of Genomic Results

Teaching Genomic Counseling: Preparing the Genetic Counseling Workforce for the Genomic Era

Stakeholders’ Opinions on the Implementation of Pediatric Whole Exome Sequencing: Implications for Informed Consent

An Assessment of Time Involved in Pre-test Case Review and Counseling for a Whole Genome Sequencing Clinical Research Program

Genetic Testing of Children for Predisposition to Mood Disorders: Anticipating the Clinical Issues

Next Generation Sequencing is the Impetus for the Next Generation of Laboratory-Based Genetic Counselors