ACMG (American College of Medical Genetics and Genomics) Board of Directors. 2012. Points to consider in the clinical application of genomic sequencing. Genetics in Medicine 14(8):759–761.
Bean, L. J., S. W. Tinker, C. da Silva, and M. R. Hegde. 2013. Free the data: One laboratory’s approach to knowledge-based genomic variant classification and preparation for emr integration of genomic data. Human Mutatation 34(9):1183–1188.
Berg, J. S., M. J. Khoury, and J. P. Evans. 2011. Deploying whole genome sequencing in clinical practice and public health: Meeting the challenge one bin at a time. Genetics in Medicine 13(6):499–504.
Berg, J. S., L. M. Amendola, C. Eng, E. Van Allen, S. W. Gray, N. Wagle, H. L. Rehm, E. T. DeChene, M. C. Dulik, F. M. Hisama, W. Burke, N. B. Spinner, L. Garraway, R. C. Green, S. Plon, J. P. Evans, G. P. Jarvik, and members of the CSER Actionability and Return of Results Working Group. 2013. Processes and preliminary outputs for identification of actionable genes as incidental findings in genomic sequence data in the clinical sequencing exploratory research consortium. Genetics in Medicine 15(11): 860–867.
Bombard, Y., M. Robson, and K. Offit. 2013. Revealing the incidentalome when targeting the tumor genome. Journal of the American Medical Association 310(8):795–796.
Callaway, E. 2013. Open-access genome project lands in UK. In Nature News Blog, November 7. http://blogs.nature.com/news/2013/11/open-access-genomeproject-lands-in-uk.html (accessed May 30, 2014).
Callaway, E. 2014. Global genomic data-sharing effort kicks off. Nature News: Q&A, March 6. http://www.nature.com/news/global-genomic-data-sharingeffort-kicks-off-1.14826 (accessed June 16, 2014).
Below are the first 10 and last 10 pages of uncorrected machine-read text (when available) of this chapter, followed by the top 30 algorithmically extracted key phrases from the chapter as a whole.
Intended to provide our own search engines and external engines with highly rich, chapter-representative searchable text on the opening pages of each chapter. Because it is UNCORRECTED material, please consider the following text as a useful but insufficient proxy for the authoritative book pages.
Do not use for reproduction, copying, pasting, or reading; exclusively for search engines.
OCR for page 67
References ACMG (American College of Medical Genetics and Genomics) Board of Directors. 2012. Points to consider in the clinical application of genomic sequencing. Genetics in Medicine 14(8):759–761. Bean, L. J., S. W. Tinker, C. da Silva, and M. R. Hegde. 2013. Free the data: One laboratory’s approach to knowledge-based genomic variant classification and preparation for emr integration of genomic data. Human Mutatation 34(9):1183–1188. Berg, J. S., M. J. Khoury, and J. P. Evans. 2011. Deploying whole genome sequencing in clinical practice and public health: Meeting the challenge one bin at a time. Genetics in Medicine 13(6):499–504. Berg, J. S., L. M. Amendola, C. Eng, E. Van Allen, S. W. Gray, N. Wagle, H. L. Rehm, E. T. DeChene, M. C. Dulik, F. M. Hisama, W. Burke, N. B. Spinner, L. Garraway, R. C. Green, S. Plon, J. P. Evans, G. P. Jarvik, and members of the CSER Actionability and Return of Results Working Group. 2013. Processes and preliminary outputs for identification of actionable genes as incidental findings in genomic sequence data in the clinical sequencing exploratory research consortium. Genetics in Medicine 15(11): 860–867. Bombard, Y., M. Robson, and K. Offit. 2013. Revealing the incidentalome when targeting the tumor genome. Journal of the American Medical Association 310(8):795–796. Callaway, E. 2013. Open-access genome project lands in UK. In Nature News Blog, November 7. http://blogs.nature.com/news/2013/11/open-access-genome- project-lands-in-uk.html (accessed May 30, 2014). Callaway, E. 2014. Global genomic data-sharing effort kicks off. Nature News: Q&A, March 6. http://www.nature.com/news/global-genomic-data-sharing- effort-kicks-off-1.14826 (accessed June 16, 2014). 67
OCR for page 67
68 GENOME SEQUENCE INFORMATION IN HEALTH CARE DECISIONS Cirino, A. L., and C. Ho. 2008. Hypertrophic cardiomyopathy overview. R. A. Pagon, M. P. Adam, H. H. Ardinger, et al. (eds.), GeneReviews. Seattle: University of Washington. http://www.ncbi.nlm.nih.gov/books/NBK1768 (accessed May 16, 2014). CMTP (Center for Medical Technology Policy). 2013. Evaluation of clinical validity and clinical utility of actionable molecular diagnostic tests in adult oncology. http://www.cmtpnet.org/docs/resources/MDX_EGD.pdf (accessed May 15, 2014). Collins, F. S. 2010. The language of life: DNA and the revolution in personalized medicine. New York: Harper. Committee on Bioethics, Committee on Genetics, and the American College of Medical Genetics and Genomics Social, Ethical, and Legal Issues Committee. 2013. Ethical and policy issues in genetic testing and screening of children. Pediatrics 131(3):620–622. Coste, B., G. Houge, M. F. Murray, N. Stitziel, M. Bandell, M. A. Giovanni, A. Philippakis, A. Hoischen, G. Riemer, U. Steen, V. M. Steen, J. Mathur, J. Cox, M. Lebo, H. Rehm, S. T. Weiss, J. N. Wood, R. L. Maas, S. R. Sunyaev, and A. Patapoutian. 2013. Gain-of-function mutations in the mechanically activated ion channel PIEZO2 cause a subtype of distal arthrogryposis. Proceedings of the National Academy of Sciences of the United States of America 110(12):4667–4672. Cruchaga, C., C. M. Karch, S. C. Jin, B. A. Benitez, Y. Cai, R. Guerreiro, O. Harari, J. Norton, J. Budde, S. Bertelsen, A. T. Jeng, B. Cooper, T. Skorupa, D. Carrell, D. Levitch, S. Hsu, J. Choi, M. Ryten, U. K. Brain Expression Consortium, J. Hardy, M. Ryten, D. Trabzuni, M. E. Weale, A. Ramasamy, C. Smith, C. Sassi, J. Bras, J. R. Gibbs, D. G. Hernandez M. K. Lupton, J. Powell, P. Forabosco, P. G. Ridge, C. D. Corcoran, J. T. Tschanz, M. C. Norton, R. G. Munger, C. Schmutz, M. Leary, F. Y. Demirci, M. N. Bamne, X. Wang, O. L. Lopez, M. Ganguli, C. Medway, J. Turton, J. Lord, A. Braae, I. Barber, K. Brown, Alzheimer’s Research Consortium U.K., P. Passmore, D. Craig, J. Johnston, B. McGuinness, S. Todd, R. Heun, H. Kolsch, P. G. Kehoe, N. M. Hooper, E. R. Vardy, D. M. Mann, S. Pickering-Brown, K. Brown, N. Kalsheker, J. Lowe, K. Morgan, A. David Smith, G. Wilcock, D. Warden, C. Holmes, P. Pastor, O. Lorenzo-Betancor, Z. Brkanac, E. Scott, E. Topol, K. Morgan, E. Rogaeva, A. B. Singleton, J. Hardy, M. I. Kamboh, P. St George-Hyslop, N. Cairns, J. C. Morris, J. S. Kauwe, and A. M. Goate. 2014. Rare coding variants in the phospholipase D3 gene confer risk for Alzheimer’s disease. Nature 505(7484):550–554. Dean, L. 2013. Warfarin therapy and the genotypes CYP2C9 and VKORC1. Medical Genetics Summaries. http://www.ncbi.nlm.nih.gov/books/NBK84174 (accessed April 29, 2014).
OCR for page 67
REFERENCES 69 EGAPP (Evaluation of Genomic Applications in Practice and Prevention). 2009. Recommendations from the EGAPP working group: Can tumor gene expression profiling improve outcomes in patients with breast cancer? Genetics in Medicine 11(1):66–73. EGAPP. 2010. Recommendations from the EGAPP working group: Genomic profiling to assess cardiovascular risk to improve cardiovascular health. Genetics in Medicine 12(12):839–843. EGAPP. 2014a. The EGAPP initiative: Lessons learned. Genetics in Medicine 16(3):217–224. EGAPP. 2014b. Recommendations from the EGAPP working group: Does PCA3 testing for the diagnosis and management of prostate cancer improve patient health outcomes? Genetics in Medicine 16(4):338–346. Enns, G. M., V. Shashi, M. Bainbridge, M. J. Gambello, F. R. Zahir, T. Bast, R. Crimian, K. Schoch, J. Platt, R. Cox, J. A. Bernstein, M. Scavina, R. S. Walter, A. Bibb, M. Jones, M. Hegde, B. H. Graham, A. C. Need, A. Oviedo, C. P. Schaaf, S. Boyle, A. J. Butte, R. Chen, M. J. Clark, R. Haraksingh, T. M. Cowan, P. He, S. Langlois, H. Y. Zoghbi, M. Snyder, R. A. Gibbs, H. H. Freeze, and D. B. Goldstein. 2014. Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum-associated degradation pathway. Genetics in Medicine, March 20. http://www.nature. com/gim/journal/vaop/ncurrent/full/gim201422a.html (accessed May 30, 2014). Garraway, L. A. 2013. Genomics-driven oncology: Framework for an emerging paradigm. Journal of Clinical Oncology 31(15):1806–1814. Green, R. C., J. S. Berg, W. W. Grody, S. S. Kalia, B. R. Korf, C. L. Martin, A. L. McGuire, R. L. Nussbaum, J. M. O’Daniel, K. E. Ormond, H. L. Rehm, M. S. Watson, M. S. Williams, and L. G. Biesecker. 2013. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genetics in Medicine 15(7):565–574. Hayden, E. C. 2014. Technology: The $1,000 genome. Nature 507(7492):294–295. Hickey, K. T., R. R. Sciacca, A. B. Biviano, W. Whang, J. M. Dizon, H. Garan, and W. K. Chung. 2014. The effect of cardiac genetic testing on psychological well-being and illness perceptions. Heart & Lung 43(2):127– 132. IOM (Institute of Medicine). 2011. Clinical practice guidelines we can trust. Washington, DC: The National Academies Press. IOM. 2014. Refining processes for the co-development of genome-based therapeutics and companion diagnostic tests: Workshop summary. Washington, DC: The National Academies Press. Kaye, J., E. A. Whitley, D. Lund, M. Morrison, H. Teare, and K. Melham. 2014. Dynamic consent: a patient interface for twenty-first century research networks. European Journal of Human Genetics. http://www.nature.com/ ejhg/journal/vaop/ncurrent/full/ejhg201471a.html (accessed June 25, 2014) doi: 10.1038/ejhg.2014.71.
OCR for page 67
70 GENOME SEQUENCE INFORMATION IN HEALTH CARE DECISIONS Kimmel, S. E., B. French, S. E. Kasner, J. A. Johnson, J. L. Anderson, B. F. Gage, Y. D. Rosenberg, C. S. Eby, R. A. Madigan, R. B. McBane, S. Z. Abdel- Rahman, S. M. Stevens, S. Yale, E. R. Mohler, M. C. Fang, V. Shah, R. B. Horenstein, N. A. Limdi, J. A. S. Muldowney, J. Gujral, P. Delafontaine, R. J. Desnick, T. L. Ortel, H. H. Billett, R. C. Pendleton, N. L. Geller, J. L. Halperin, S. Z. Goldhaber, M. D. Caldwell, R. M. Califf, and J. H. Ellenberg. 2013. A pharmacogenetic versus a clinical algorithm for warfarin dosing. New England Journal of Medicine 369(24):2283–2293. Kohane, I. S., D. R. Masys, and R. B. Altman. 2006. The incidentalome: A threat to genomic medicine. Journal of the American Medical Association 296(2):212–215. Landrum, M. J., J. M. Lee, G. R. Riley, W. Jang, W. S. Rubinstein, D. M. Church, and D. R. Maglott. 2014. ClinVar: Public archive of relationships among sequence variation and human phenotype. Nucleic Acids Research 42(Database issue):D980–D985. Lyman, G. H., S. Temin, S. B. Edge, L. A. Newman, R. R. Turner, D. L. Weaver, A. B. Benson, 3rd, L. D. Bosserman, H. J. Burstein, H. Cody, 3rd, J. Hayman, C. L. Perkins, D. A. Podoloff, and A. E. Giuliano. 2014. Sentinel lymph node biopsy for patients with early-stage breast cancer: American Society of Clinical Oncology clinical practice guideline update. Journal of Clinical Oncology 32(13):1365–1383. McCormack, R. T., J. Armstrong, and D. Leonard. 2014. Codevelopment of genome-based therapeutics and companion diagnostics: Insights from an Institute of Medicine roundtable. Journal of the American Medical Association 311(14):1395–1396. NIH (National Institutes of Health). 2013. New NIH-funded resource focuses on use of genomic variants in medical care. http://www.nih.gov/news/health/sep 2013/nhgri-25.htm (accessed April 16, 2014). Parsons, D. W., M. M. Chintagumpala, S. L. Berg, D. H. López-Terrada, R. Angshumoy, R. A. Kerstein, S. Scollon, S. G. Hilsenbeck, U. Ramamurthy, C. M. Eng, Y. Yang, R. A. Gibbs, D. A. Wheeler, R. L. Street, L. B. McCullough, A. L. McGuire, F. A. Monzon, and S. E. Plon. 2013. Implementation and evaluation of clinical exome sequencing in childhood cancer care: The BASIC3 study. Journal of Clinical Oncology 31(suppl; abstr 10023). Pellegrini, I., M. Rapti, J. M. Extra, A. Petri-Cal, T. Apostolidis, J. M. Ferrero, T. Bachelot, P. Viens, C. Julian-Reynier, and F. Bertucci. 2012. Tailored chemotherapy based on tumour gene expression analysis: Breast cancer patients’ misinterpretations and positive attitudes. European Journal of Cancer Care 21(2):242–250.
OCR for page 67
REFERENCES 71 Pirmohamed, M., G. Burnside, N. Eriksson, A. L. Jorgensen, C. H. Toh, T. Nicholson, P. Kesteven, C. Christersson, B. Wahlström, C. Stafberg, J. E. Zhang, J. B. Leathart, H. Kohnke, A. H. Maitland-van der Zee, P. R. Williamson, A. K. Daly, P. Avery, F. Kamali, and M. Wadelius. 2013. A randomized trial of genotype-guided dosing of warfarin. New England Journal of Medicine 369(24):2294–2303. Rehm, H. L. 2013. Disease-targeted sequencing: A cornerstone in the clinic. Nature Reviews Genetics 14(4):295–300. Robson, M. 2014. Multigene panel testing: Planning the next generation of research studies in clinical cancer genetics. Journal of Clinical Oncology published online on May 27, 2014; DOI:10.1200/JCO.2014.56.0474. http://jco.ascopubs.org/content/early/2014/05/20/JCO.2014.56.0474.long (acc- essed June 24, 2014). Ross, L. F., H. M. Saal, K. L. David, R. R. Anderson, American Academy of Pediatrics, and American College of Medical Genetics and Genomics. 2013. Technical report: Ethical and policy issues in genetic testing and screening of children. Genetics in Medicine 15(3):234–245. Roychowdhury, S., M. K. Iyer, D. R. Robinson, R. J. Lonigro, Y. M. Wu, X. Cao, S. Kalyana-Sundaram, L. Sam, O. A. Balbin, M. J. Quist, T. Barrette, J. Everett, J. Siddiqui, L. P. Kunju, N. Navone, J. C. Araujo, P. Troncoso, C. J. Logothetis, J. W. Innis, D. C. Smith, C. D. Lao, S. Y. Kim, J. S. Roberts, S. B. Gruber, K. J. Pienta, M. Talpaz, and A. M. Chinnaiyan. 2011. Personalized oncology through integrative high-throughput sequencing: A pilot study. Science Transational Medicine 3(111):111ra121. Stadler, Z. K., K. A. Schrader, J. Vijai, M. E. Robson, and K. Offit. 2014. Cancer genomics and inherited risk. Journal of Clinical Oncology 32(7):687–698. Stenson, P. D., E. V. Ball, M. Mort, A. D. Phillips, J. A. Shiel, N. S. Thomas, S. Abeysinghe, M. Krawczak, and D. N. Cooper. 2003. Human gene mutation database (HGMD): 2003 update. Human Mutation 21(6):577–581. Stenson, P. D., M. Mort, E. V. Ball, K. Shaw, A. Phillips, and D. N. Cooper. 2014. The human gene mutation database: Building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Human Genetics 133(1):1–9. Vassy, J. L., D. M. Lautenbach, H. M. McLaughlin, S. W. Kong, K. D. Christensen, J. Krier, I. S. Kohane, L. Z. Feuerman, J. Blumenthal-Barby, J. S. Roberts, L. S. Lehmann, C. Y. Ho, P. A. Ubel, C. A. Macrae, C. E. Seidman, M. F. Murray, A. L. McGuire, H. L. Rehm, R. C. Green, and the MedSeq Project. 2014. The MedSeq project: A randomized trial of integrating whole genome sequencing into clinical medicine. Trials 15(1):85.
OCR for page 67
72 GENOME SEQUENCE INFORMATION IN HEALTH CARE DECISIONS Verhoef, T. I., G. Ragia, A. de Boer, R. Barallon, G. Kolovou, V. Kolovou, S. Konstantinides, S. Le Cessie, E. Maltezos, F. J. M. van der Meer, W. K. Redekop, M. Remkes, F. R. Rosendaal, R. M. F. van Schie, A. Tavridou, D. Tziakas, M. Wadelius, V. G. Manolopoulos, and A. H. Maitland-van der Zee. 2013. A randomized trial of genotype-guided dosing of acenocoumarol and phenprocoumon. New England Journal of Medicine 369(24):2304– 2312. Wagle, N., M. F. Berger, M. J. Davis, B. Blumenstiel, M. Defelice, P. Pochanard, M. Ducar, P. Van Hummelen, L. E. Macconaill, W. C. Hahn, M. Meyerson, S. B. Gabriel, and L. A. Garraway. 2012. High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Cancer Discovery 2(1):82–93. Yang, Y., D. M. Muzny, J. G. Reid, M. N. Bainbridge, A. Willis, P. A. Ward, A. Braxton, J. Beuten, F. Xia, Z. Niu, M. Hardison, R. Person, M. R. Bekheirnia, M. S. Leduc, A. Kirby, P. Pham, J. Scull, M. Wang, Y. Ding, S. E. Plon, J. R. Lupski, A. L. Beaudet, R. A. Gibbs, and C. M. Eng. 2013. Clinical whole-exome sequencing for the diagnosis of Mendelian disorders. New England Journal of Medicine 369(16):1502–1511.