Advertisement

Genomic Pathology: Training for New Technology

  • Richard L. HaspelEmail author
Chapter

Abstract

Genomic testing is being incorporated into almost all areas of medicine. There is evidence, however, that many physicians do not understand single-gene testing, let alone genomic analysis. Pathologists, given their background in molecular diagnostics and experience directing clinical laboratories, must play a major role in translating genomic technology to patient care. This chapter reviews the significant progress that the pathology community has made in genomic medicine training.

Keywords

Genomics Education Team-based learning Flipped classroom Residency Pathology Graduate medical education Genetics Sequencing 

Notes

Acknowledgment

This work was supported by the National Institutes of Health (1R25CA168544).

Reference

  1. 1.
    National Human Genome Research Institute. The human genome project completion: Frequently asked questions. 2017. https://www.genome.gov/11006943.%20accessed%205%20feb%202013/. Accessed 6-1-2017.
  2. 2.
    Rangachari D, VanderLaan PA, Le X, Folch E, Kent MS, Gangadharan SP, et al. Experience with targeted next generation sequencing for the care of lung cancer: insights into promises and limitations of genomic oncology in day-to-day practice. Cancer Treat Commun. 2015;4:174–81.CrossRefGoogle Scholar
  3. 3.
    Jones SJ, Laskin J, Li YY, Griffith OL, An J, Bilenky M, et al. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol. 2010;11(8):R82.CrossRefGoogle Scholar
  4. 4.
    Welch JS, Westervelt P, Ding L, Larson DE, Klco JM, Kulkarni S, et al. Use of whole-genome sequencing to diagnose a cryptic fusion oncogene. JAMA. 2011;305(15):1577–84.CrossRefGoogle Scholar
  5. 5.
    Mody RJ, Wu YM, Lonigro RJ, Cao X, Roychowdhury S, Vats P, et al. Integrative clinical sequencing in the management of refractory or relapsed cancer in youth. JAMA. 2015;314(9):913–25.CrossRefGoogle Scholar
  6. 6.
    Stockley TL, Oza AM, Berman HK, Leighl NB, Knox JJ, Shepherd FA, et al. Molecular profiling of advanced solid tumors and patient outcomes with genotype-matched clinical trials: the Princess Margaret IMPACT/COMPACT trial. Genome Med. 2016;8(1):109.CrossRefGoogle Scholar
  7. 7.
    Kris MG, Johnson BE, Berry LD, Kwiatkowski DJ, Iafrate AJ, Wistuba II, et al. Using multiplexed assays of oncogenic drivers in lung cancers to select targeted drugs. JAMA. 2014;311(19):1998–2006.CrossRefGoogle Scholar
  8. 8.
    Azim HA Jr, Michiels S, Zagouri F, Delaloge S, Filipits M, Namer M, et al. Utility of prognostic genomic tests in breast cancer practice: the IMPAKT 2012 working group consensus statement. Ann Oncol. 2013;24(3):647–54.CrossRefGoogle Scholar
  9. 9.
    Zhang X. Value of molecular tests in cytologically indeterminate lesions of thyroid. Arch Pathol Lab Med. 2015;139(12):1484–90.CrossRefGoogle Scholar
  10. 10.
    Nardi V, Sadow PM, Juric D, Zhao D, Cosper AK, Bergethon K, et al. Detection of novel actionable genetic changes in salivary duct carcinoma helps direct patient treatment. Clin Cancer Res. 2013;19(2):480–90.CrossRefGoogle Scholar
  11. 11.
    Worthey EA, Mayer AN, Syverson GD, Helbling D, Bonacci BB, Decker B, et al. Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet Med. 2011;13(3):255–62.CrossRefGoogle Scholar
  12. 12.
    Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, et al. Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med. 2013;369(16):1502–11.CrossRefGoogle Scholar
  13. 13.
    Counsyl. Family Prep Screen. 2017. https://www.counsyl.com/services/family-prep-screen/2017. Accessed 6-2-2017.
  14. 14.
    Sequenom. MaterniT 21 Plus. 2017. https://www.sequenom.com/tests/reproductive-health/maternit21-plus. Accessed 6-2-2017.
  15. 15.
    St-Louis M. Molecular blood grouping of donors. Transfus Apher Sci. 2014;50(2):175–82.CrossRefGoogle Scholar
  16. 16.
    Bio-IT. German Teams, BGI and Life Technologies Identify Deadly European E.coli Strain. 2017. http://www.bio-itworld.com/news/06/02/2011/German-teams-BGI-Life-Technologies-Identify-E-coli-strain.html. Accessed 6-2-2017.
  17. 17.
    Gardy JL, Johnston JC, Ho Sui SJ, Cook VJ, Shah L, Brodkin E, et al. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med. 2011;364(8):730–9.CrossRefGoogle Scholar
  18. 18.
    Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, Yu G, et al. Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med. 2014;370(25):2408–17.CrossRefGoogle Scholar
  19. 19.
    Long SW, Williams D, Valson C, Cantu CC, Cernoch P, Musser JM, et al. A genomic day in the life of a clinical microbiology laboratory. J Clin Microbiol. 2013;51(4):1272–7.CrossRefGoogle Scholar
  20. 20.
    Giardiello FM, Brensinger JD, Petersen GM, Luce MC, Hylind LM, Bacon JA, et al. The use and interpretation of commercial APC gene testing for familial adenomatous polyposis. N Engl J Med. 1997;336(12):823–7.CrossRefGoogle Scholar
  21. 21.
    Kotzer KE, Riley JD, Conta JH, Anderson CM, Schahl KA, Goodenberger ML. Genetic testing utilization and the role of the laboratory genetic counselor. Clin Chim Acta. 2014;427:193–5.CrossRefGoogle Scholar
  22. 22.
    Miller CE, Krautscheid P, Baldwin EE, Tvrdik T, Openshaw AS, Hart K, et al. Genetic counselor review of genetic test orders in a reference laboratory reduces unnecessary testing. Am J Med Genet A. 2014;164A(5):1094–101.CrossRefGoogle Scholar
  23. 23.
    Klitzman R, Chung W, Marder K, Shanmugham A, Chin LJ, Stark M, et al. Attitudes and practices among internists concerning genetic testing. J Genet Couns. 2013;22(1):90–100.CrossRefGoogle Scholar
  24. 24.
    Salm M, Abbate K, Appelbaum P, Ottman R, Chung W, Marder K, et al. Use of genetic tests among neurologists and psychiatrists: knowledge, attitudes, behaviors, and needs for training. J Genet Couns. 2014;23(2):156–63.CrossRefGoogle Scholar
  25. 25.
    Laedtke AL, O'Neill SM, Rubinstein WS, Vogel KJ. Family physicians' awareness and knowledge of the genetic information non-discrimination act (GINA). J Genet Couns. 2012;21(2):345–52.CrossRefGoogle Scholar
  26. 26.
    Plunkett-Rondeau J, Hyland K, Dasgupta S. Training future physicians in the era of genomic medicine: trends in undergraduate medical genetics education. Genet Med. 2015;17(11):927–34.CrossRefGoogle Scholar
  27. 27.
    Korf BR, Berry AB, Limson M, Marian AJ, Murray MF, O'Rourke PP, et al. Framework for development of physician competencies in genomic medicine: report of the Competencies Working Group of the Inter-Society Coordinating Committee for Physician Education in Genomics. Genet Med. 2014;16(11):804–9.CrossRefGoogle Scholar
  28. 28.
    Feero WG, Green ED. Genomics education for health care professionals in the 21st century. JAMA. 2011;306(9):989–90.CrossRefGoogle Scholar
  29. 29.
    Demmer LA, Waggoner DJ. Professional medical education and genomics. Annu Rev Genomics Hum Genet. 2014;15:507–16.CrossRefGoogle Scholar
  30. 30.
    Slade I, Burton H. Preparing clinicians for genomic medicine. Postgrad Med J. 2016;92(1089):369–71.CrossRefGoogle Scholar
  31. 31.
    Wiener CM, Thomas PA, Goodspeed E, Valle D, Nichols DG. “Genes to society” – the logic and process of the new curriculum for the Johns Hopkins University School of Medicine. Acad Med. 2010;85(3):498–506.CrossRefGoogle Scholar
  32. 32.
    Salari K, Pizzo PA, Prober CG. Commentary: to genotype or not to genotype? Addressing the debate through the development of a genomics and personalized medicine curriculum. Acad Med. 2011;86(8):925–7.CrossRefGoogle Scholar
  33. 33.
    Dhar SU, Alford RL, Nelson EA, Potocki L. Enhancing exposure to genetics and genomics through an innovative medical school curriculum. Genet Med. 2012;14(1):163–7.CrossRefGoogle Scholar
  34. 34.
    Walt DR, Kuhlik A, Epstein SK, Demmer LA, Knight M, Chelmow D, et al. Lessons learned from the introduction of personalized genotyping into a medical school curriculum. Genet Med. 2011;13(1):63–6.CrossRefGoogle Scholar
  35. 35.
    Gerhard GS, Jin Q, Paynton BV, Popoff SN. The anatomy to genomics (ATG) start genetics medical school initiative: incorporating exome sequencing data from cadavers used for anatomy instruction into the first year curriculum. BMC Med Genet. 2016;9(1):62.Google Scholar
  36. 36.
    G2C2. G2C2 Genetics/Genomics Competency Center. 2017. http://genomicseducation.net/. Accessed 6-2-2017.
  37. 37.
    Hyland KM, Dasgupta S, Garber KB, Gold J-A, Toriello H, Weissbecker K, et al. APHMG Medical School Core Curriculum in Genetics. 2017. http://media.wix.com/ugd/3a7b87_7064376a9eb346cfa1b85bc2f137c48f.pdf. Accessed 6-2-2017.
  38. 38.
    Goetz L, Bethel K, Topol EJ. Rebooting cancer tissue handling in the sequencing era: toward routine use of frozen tumor tissue. JAMA. 2013;309(1):37–8.CrossRefGoogle Scholar
  39. 39.
    Dabbs DJ, Klein ME, Mohsin SK, Tubbs RR, Shuai Y, Bhargava R. High false-negative rate of HER2 quantitative reverse transcription polymerase chain reaction of the Oncotype DX test: an independent quality assurance study. J Clin Oncol. 2011;29(32):4279–85.CrossRefGoogle Scholar
  40. 40.
    Roychowdhury S, Iyer MK, Robinson DR, Lonigro RJ, Wu YM, Cao X, et al. Personalized oncology through integrative high-throughput sequencing: a pilot study. Sci Transl Med. 2011;3(111):111ra121.CrossRefGoogle Scholar
  41. 41.
    MacArthur D. Sample swaps at 23andMe: a cautionary tale. 2017. https://www.wired.com/2010/06/sample-swaps-at-23andme-a-cautionary-tale/6-7-2010. Accessed 6-2-2017.
  42. 42.
    Ng PC, Murray SS, Levy S, Venter JC. An agenda for personalized medicine. Nature. 2009;461(7265):724–6.CrossRefGoogle Scholar
  43. 43.
    Mathias PC, Conta JH, Konnick EQ, Sternen DL, Stasi SM, Cole BL, et al. Preventing genetic testing order errors with a laboratory utilization management program. Am J Clin Pathol. 2016;146(2):221–6.CrossRefGoogle Scholar
  44. 44.
    Cuzick J, Dowsett M, Pineda S, Wale C, Salter J, Quinn E, et al. Prognostic value of a combined estrogen receptor, progesterone receptor, Ki-67, and human epidermal growth factor receptor 2 immunohistochemical score and comparison with the Genomic Health recurrence score in early breast cancer. J Clin Oncol. 2011;29(32):4273–8.CrossRefGoogle Scholar
  45. 45.
    Morain S, Greene MF, Mello MM. A new era in noninvasive prenatal testing. N Engl J Med. 2013;369(6):499–501.CrossRefGoogle Scholar
  46. 46.
    Bianchi DW, Parker RL, Wentworth J, Madankumar R, Saffer C, Das AF, et al. DNA sequencing versus standard prenatal aneuploidy screening. N Engl J Med. 2014;370(9):799–808.CrossRefGoogle Scholar
  47. 47.
    Norton ME, Jacobsson B, Swamy GK, Laurent LC, Ranzini AC, Brar H, et al. Cell-free DNA analysis for noninvasive examination of trisomy. N Engl J Med. 2015;372(17):1589–97.CrossRefGoogle Scholar
  48. 48.
    Kohane IS, Masys DR, Altman RB. The incidentalome: a threat to genomic medicine. JAMA. 2006;296(2):212–5.CrossRefGoogle Scholar
  49. 49.
    Vassy JL, Korf BR, Green RC. How to know when physicians are ready for genomic medicine. Sci Transl Med. 2015;7(287):287fs19.CrossRefGoogle Scholar
  50. 50.
    National Society of Genetic Counselors. 2017. Who are genetic counselors? http://www.nsgc.org/page/whoaregcs. Accessed 6-12-2017.
  51. 51.
    Intersociety Council for Pathology Information. Career Opportunities in Pathology. 2017. http://www.pathologytraining.org/trainees/documents/recruit.ppt. Accessed 6-02-2017.
  52. 52.
    Tonellato PJ, Crawford JM, Boguski MS, Saffitz JE. A national agenda for the future of pathology in personalized medicine: report of the proceedings of a meeting at the Banbury Conference Center on genome-era pathology, precision diagnostics, and preemptive care: a stakeholder summit. Am J Clin Pathol. 2011;135(5):668–72.CrossRefGoogle Scholar
  53. 53.
    Ross JS. Next-generation pathology. Am J Clin Pathol. 2011;135(5):663–5.CrossRefGoogle Scholar
  54. 54.
    Accreditation Council for Graduate Medical Education. ACGME Program Requirements for Graduate Medical Education in Anatomic Pathology and Clinical Pathology. 2017. https://www.acgme.org/Portals/0/PFAssets/ProgramRequirements/300_pathology_2016.pdf. Accessed 6-2-2017.
  55. 55.
    Accrediation Council for Graduate Medical Education, American Board of Pathology. The Pathology Milestone Project. 2017. http://www.acgme.org/Portals/0/PDFs/Milestones/PathologyMilestones.pdf. Accessed 6-2-2017.
  56. 56.
    Aisner DL, Berry A, Dawson DB, Hayden RT, Joseph L, Hill CE. A suggested molecular pathology curriculum for residents: a report of the association for molecular pathology. J Mol Diagn. 2016;18(2):153–62.CrossRefGoogle Scholar
  57. 57.
    Laudadio J, McNeal JL, Boyd SD, Le LP, Lockwood C, McCloskey CB, et al. Design of a Genomics Curriculum: competencies for practicing pathologists. Arch Pathol Lab Med. 2015;139(7):894–900.CrossRefGoogle Scholar
  58. 58.
    Haspel RL, Arnaout R, Briere L, Kantarci S, Marchand K, Tonellato P, et al. A call to action: training pathology residents in genomics and personalized medicine. Am J Clin Pathol. 2010;133(6):832–4.CrossRefGoogle Scholar
  59. 59.
    Kern DE, Thomas PA, Hughes MT. Curriculum development for medical education: a six-step approach. 2nd ed. Baltimore, MD: The Johns Hopkins University Press; 2009.Google Scholar
  60. 60.
    Haspel RL, Olsen RJ, Berry A, Hill CE, Pfeifer JD, Schrijver I, et al. Progress and potential: training in genomic pathology. Arch Pathol Lab Med. 2014;138(4):498–504.CrossRefGoogle Scholar
  61. 61.
    Knowles MS, Holton EF, Swanson RA. The Adult Learner. Elsevier, Burlington, MA. 6th ed; 2005.Google Scholar
  62. 62.
    Callier SL. Swabbing students: should universities be allowed to facilitate educational DNA testing? Am J Bioeth. 2012;12(4):32–40.CrossRefGoogle Scholar
  63. 63.
    Genzen JR, Krasowski MD. Resident training in clinical chemistry. Clin Lab Med. 2007;27(2):343–58.CrossRefGoogle Scholar
  64. 64.
    Schrijver I, Natkunam Y, Galli S, Boyd SD. Integration of genomic medicine into pathology residency training: the Stanford open curriculum. J Mol Diagn. 2013;15(2):141–8.CrossRefGoogle Scholar
  65. 65.
    Haspel RL, Atkinson JB, Barr FG, Kaul KL, Leonard DGB, O'Daniel J, et al. TRIG on TRACK: educating pathology residents in genomic medicine. Pers Med. 2012;9:287–93.CrossRefGoogle Scholar
  66. 66.
    Training Residents in Genomics (TRIG) Working Group. Training Residents in Genomics (TRIG) Website. 2017. http://pathologylearning.org/trig. Accessed 6-2-2017.
  67. 67.
    Parmelee D, Michaelsen LK, Cook S, Hudes PD. Team-based learning: a practical guide: AMEE guide no. 65. Med Teach. 2012;34(5):e275–87.CrossRefGoogle Scholar
  68. 68.
    Haspel RL, Ali AM, Huang GC. Using a team-based learning approach at National Meetings to teach residents genomic pathology. J Grad Med Educ. 2016;8(1):80–4.CrossRefGoogle Scholar
  69. 69.
    Rinder HM, Grimes MM, Wagner J, Bennett BD. Senior pathology resident in-service examination scores correlate with outcomes of the American Board of Pathology certifying examinations. Am J Clin Pathol. 2011;136(4):499–506.CrossRefGoogle Scholar
  70. 70.
    Haspel RL, Rinder HM, Frank KM, Wagner J, Ali AM, Fisher PB, et al. The current state of resident training in genomic pathology: a comprehensive analysis using the resident in-service examination. Am J Clin Pathol. 2014;142(4):445–51.CrossRefGoogle Scholar
  71. 71.
    American Board of Pathology. Taking an examination: Primary examinations. 2017. http://www.abpath.org/index.php/taking-an-examination/primary-certificate-requirements. Accessed 10-13-2017.
  72. 72.
    Musunuru K, Haspel RL. Improving genomic literacy among cardiovascular practitioners via a flipped-classroom workshop at a National Meeting. Circ Cardiovasc Genet. 2016;9(3):287–90.CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of PathologyBeth Israel Deaconess Medical Center and Harvard Medical SchoolBostonUSA

Personalised recommendations