Skip to main content

Genomic Pathology: Training for New Technology

  • Chapter
  • First Online:
Book cover Genomic Applications in Pathology
  • 2145 Accesses

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 239.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. National Human Genome Research Institute. The human genome project completion: Frequently asked questions. 2010. http://www.genome.gov/11006943. Accessed 5 Feb 2013.

  2. Roychowdhury S, Iyer MK, Robinson DR, et al. Personalized oncology through integrative high-throughput sequencing: a pilot study. Sci Transl Med. 2011;3:111ra121.

    Article  PubMed  PubMed Central  Google Scholar 

  3. Jones SJM, Laskin J, Li YY, et al. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol. 2010;11:R82.

    Article  PubMed  PubMed Central  Google Scholar 

  4. Welch JS, Westervelt P, Ding L, et al. Use of whole-genome sequencing to diagnose a cryptic fusion oncogene. JAMA. 2011;305:1577–84.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  5. Azim HA Jr, Michiels S, Zagouri F, et al. Utility of prognostic genomic tests in breast cancer practice: the IMPAKT 2012 Working Group Consensus Statement. Ann Oncol. 2013. [epub ahead of print].

    Google Scholar 

  6. Alexander EK, Kennedy GC, Baloch ZW, et al. Preoperative diagnosis of benign thyroid nodules with indeterminate cytology. N Engl J Med. 2012;367:705–15.

    Article  PubMed  CAS  Google Scholar 

  7. Nardi V, Sadow PM, Juric D, et al. Detection of novel actionable genetic changes in salivary duct carcinoma helps direct patient treatment. Clin Cancer Res. 2013;19:480–90.

    Article  PubMed  CAS  Google Scholar 

  8. Worthey EA, Mayer AN, Syverson GD, et al. Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet Med. 2011;13:255–62.

    Article  PubMed  Google Scholar 

  9. Heinzen EL, Swoboda KJ, Hitomi Y, et al. De novo mutations in ATP1A3 cause alternating hemiplegia of childhood. Nat Genet. 2012;44:1030–4.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  10. Counsyl Web site. https://www.counsyl.com. Accessed 5 Feb 2013.

  11. Sequenom Web site. http://www.sequenomcmm.com/Home/Health-Care-Professionals/Trisomy-21. Accessed 5 Feb 2013.

  12. Wapner RJ, Martin CL, Levy B, et al. Chromosomal microarray versus karyotyping for prenatal diagnosis. N Engl J Med. 2012;367:2175–84.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  13. Reddy UM, Page GP, Saade GR, et al. Karyotype versus microarray testing for genetic abnormalities after stillbirth. N Engl J Med. 2012;367:2185–93.

    Article  PubMed  CAS  Google Scholar 

  14. Denomme GA, Johnson ST, Pietz BC. Mass-scale red cell genotyping of blood donors. Transf Apher Sci. 2011;44:93–9.

    Article  Google Scholar 

  15. Ashley EA, Butte AJ, Wheeler MT, et al. Clinical assessment incorporating a personal genome. Lancet. 2010;375:1525–35.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  16. Chen R, Mias GI, Li-Pook-Than J, et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell. 2012;148:1293–307.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  17. Bio-IT World Staff. German teams, BGI and Life Technologies identify deadly European E. Coli strain. 2011.http://www.bio-itworld.com/news/06/02/2011/German-teams-BGI-Life-Technologies-Identify-E-coli-strain.html. Accessed 5 Feb 2012.

  18. Gardy JL, Johnston JC, Ho Sui SJ, et al. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med. 2011;364:730–9.

    Article  PubMed  CAS  Google Scholar 

  19. Giardiello FM, Brensinger JD, Petersen GM, et al. The use and interpretation of commercial APC gene testing for familial adenomatous polyposis. N Engl J Med. 1997;336:823–7.

    Article  PubMed  CAS  Google Scholar 

  20. ARUP Laboratories. Value of genetic counselors in the laboratory. 2011.http://www.aruplab.com/files/resources/genetics/White-paper-1-value-of-GCs-in-lab.pdf. Accessed 5 Feb 2013.

  21. Klitzman R, Chung W, Marder K, et al. Attitudes and practices among internists concerning genetic testing. J Genet Couns. 2013;22:90–100.

    Article  PubMed  PubMed Central  Google Scholar 

  22. Laedtke AL, O’Neill SM, Rubinstein WS, et al. Family physicians’ awareness and knowledge of the Genetic Information Non-Discrimination Act (GINA). J Genet Couns. 2012;21:345–52.

    Article  PubMed  Google Scholar 

  23. Bell MA, Wales PS, Torbeck LJ, et al. The current status of medical genetics instruction in U.S. and Canadian medical schools. Acad Med. 2007;82:441–5.

    Article  PubMed  Google Scholar 

  24. Telner D, Carroll JC, Talbot Y. Genetics education in medical school: a qualitative study exploring educational experiences and needs. Med Teach. 2008;30:192–8.

    Article  PubMed  Google Scholar 

  25. Guttmacher AE, Porteous ME, McInerney JD. Educating health-care professionals about genetics and genomics. Nat Rev Genet. 2007;8:151–7.

    Article  PubMed  CAS  Google Scholar 

  26. Salari K. The dawning era of personalized medicine exposes a gap in medical education. PLoS Med. 2009;6(8):e1000138.

    Article  PubMed  PubMed Central  Google Scholar 

  27. Nelson EA, McGuire AL. The need for medical education reform: genomics and the changing nature of health information. Genome Med. 2010;2(3):18.

    Article  PubMed  PubMed Central  Google Scholar 

  28. Feero WG, Green ED. Genomics education for health care professionals in the 21st century. JAMA. 2011;306(9):989–90.

    Article  PubMed  CAS  Google Scholar 

  29. 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;86:925–7.

    Article  PubMed  Google Scholar 

  30. Dhar SU, Alford RL, Nelson EA, et al. Enhancing exposure to genetics and genomics through an innovative medical school curriculum. Genet Med. 2012;14:163–7.

    Article  PubMed  Google Scholar 

  31. Walt DR, Kuhlik A, Epstein SK, et al. Lessons learned from the introduction of personalized genotyping into a medical school curriculum. Genet Med. 2011;13:63–6.

    Article  PubMed  Google Scholar 

  32. Wiener CM, Thomas PA, Goodspeed E, et al. “Genes to society”—the logic and process of the new curriculum for the Johns Hopkins University School of Medicine. Acad Med. 2010;85:498–506.

    Article  PubMed  Google Scholar 

  33. Skirton H, Lewis C, Kent A, et al. Genetic education and the challenge of genomic medicine: development of core competences to support preparation of health professionals in Europe. Eur J Hum Genet. 2010;18:972–7.

    Article  PubMed  PubMed Central  Google Scholar 

  34. Patay BA, Topol EJ. The unmet need of education in genomic medicine. Am J Med. 2012;125:5–6.

    Article  PubMed  Google Scholar 

  35. Goetz L, Bethel K, Topol EJ. Rebooting cancer tissue handling in the sequencing era: toward routine use of frozen tumor tissue. JAMA. 2013;309:37–8.

    Article  PubMed  CAS  Google Scholar 

  36. MacArthur D. Sample swaps at 23andMe: a cautionary tale. 2010. http://scienceblogs.com/geneticfuture/2010/06/sample_swaps_at_23andme_a_caut.php. Accessed 5 Feb 2013.

  37. Pearson TA, Manolio TA. How to interpret a genome-wide association study. JAMA. 2008;299:1335–44.

    Article  PubMed  CAS  Google Scholar 

  38. Ng PC, Murray SS, Levy S, Venter JC. An agenda for personalized medicine. Nature. 2009;461:724–6.

    Article  PubMed  CAS  Google Scholar 

  39. Smith BR, Wells A, Alexander CB, et al. Curriculum content and evaluation of resident competency in clinical pathology (laboratory medicine): a proposal. Am J Clin Pathol. 2006;125(Suppl):S3–37.

    PubMed  Google Scholar 

  40. Kohane IS, Masys DR, Altman RB. The incidentalome: a threat to genomic medicine. JAMA. 2006;296:212–5.

    Article  PubMed  CAS  Google Scholar 

  41. ICPI. Career opportunities in pathology. http://www.pathologytraining.org/trainees/documents/recruit.ppt. Accessed 5 February 2013.

  42. Tonellato PJ, Crawford JM, Boguski MS, et al. 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;135:668–72.

    Article  PubMed  Google Scholar 

  43. Ross JS. Next-generation pathology. Am J Clin Pathol. 2011;135:663–5.

    Article  PubMed  Google Scholar 

  44. ACGME. Hospital based accreditation: pathology. 2008. http://www.acgme.org/acgmeweb/tabid/142/ProgramandInstitutionalGuidelines/Hospital-BasedAccreditation/Pathology.aspx. Accessed 5 Feb 2013.

  45. Kern DE, Thomas PA, Howard DM, et al. Curriculum development for medical education: a six step approach. Baltimore: The Johns Hopkins University Press; 1998.

    Google Scholar 

  46. Elliott R, Jacobs WC. Multiple sclerosis. 2010.http://genomicmedicineinitiative.org/wp-content/uploads/2010/03/Multiple-Sclerosis.pdf. Accessed 5 Feb 2013.

  47. Knowles MS, Holton III EF, Swanson RA. The adult learner 6th edition. Burlington: Elsevier; 2005.

    Google Scholar 

  48. Callier SL. Swabbing students: should universities be allowed to facilitate educational DNA testing? Am J Bioeth. 2012;12:32–40.

    Article  PubMed  PubMed Central  Google Scholar 

  49. Grenzen JR, Krasowski MD. Resident training in clinical chemistry. Clin Lab Med. 2007;27:343–58.

    Article  Google Scholar 

  50. Haspel RL, Arnaout R, Briere L, et al. A curriculum in genomics and personalized medicine for pathology residents. Am J Clin Pathol. 2010; 133(6): online supplement. http://ajcp.ascpjournals.org/site/misc/pdf/Haspel_online.pdf Accessed 5 Feb 2013.

  51. Haspel RL, Arnaout R, Briere L, et al. A call to action: training pathology residents in genomics and personalized medicine. Am J Clin Pathol. 2010;133:832–4.

    Article  PubMed  Google Scholar 

  52. BIDMC Department of Pathology. Genomic medicine initiative. 2010. genomicmedicineinitiative.org. Accessed 5 Feb 2013.

    Google Scholar 

  53. Schrijver I, Natkunam Y, Galli S, et al. Integration of genomic medicine into pathology residency training: the Stanford Open Curriculum. J Mol Diagn. 2013;15:141–8.

    Article  PubMed  Google Scholar 

  54. Stanford University Faculty. Stanford open curriculum in genomic medicine. 2012.http://www.youtube.com/playlist?list=PLfTljtR5bxMcTg8hgQp9sA4YQwicpSAQv. Accessed 5 Feb 2013.

  55. Haspel RL, Atkinson JB, Barr FG, et al. TRIG on track: educating pathology residents in genomic medicine. Pers Med. 2012;9:287–93.

    Article  Google Scholar 

  56. The TRIG Working Group. Lecture materials from the Training Residents in Genomics (TRIG) Working Group. 2012. http://www.pathologytraining.org/trig_lecture.htm. Accessed 5 Feb 2013.

  57. TRIG Working Group Website. 2013. ascp.org/TRIG. Accessed 8 June 2013.

    Google Scholar 

  58. Haspel RL. How can we teach genomic medicine to pathology professionals? Crit Values. 2013;6:19.

    Google Scholar 

  59. Haspel RL. NCHPEG Member news: Free genomic medicine PowerPoint lectures now available. 2012. http://www.nchpeg.org/index.php?option=com_content&view=article&id=400:nchpeg-member-news-free-genomic-medicine-powerpoint-lectures-now-available-from-the-intersociety-council-for-pathology-information-&catid=92:in-practice-fall-2012&Itemid=271. Accessed 5 Feb 2013.

  60. Rinder HM, Grimes MM, Wagner J, et al. Senior pathology resident in-service examination (RISE) scores correlate with outcomes of the American Board of Pathology (ABP) certifying examinations. Am J Clin Pathol. 2011;136:499–506.

    Article  PubMed  Google Scholar 

  61. Talbert ML, Dunn ST, Hunt J, et al. Competency-based education for the molecular genetic pathology fellow: a report of the association for molecular pathology training and education committee. J Mol Diagn. 2009;11:497–507.

    Article  PubMed  PubMed Central  Google Scholar 

  62. ACGME. The next accreditation system. http://www.acgme-nas.org/index.html. Accessed 5 Feb 2013.

Download references

Acknowledgement

This work was supported by the National Institutes of Health (1R25CA168544-01).

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer Science+Business Media New York

About this chapter

Cite this chapter

Haspel, R.L. (2015). Genomic Pathology: Training for New Technology. In: Netto, G., Schrijver, I. (eds) Genomic Applications in Pathology. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-0727-4_7

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-0727-4_7

  • Published:

  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-4939-0726-7

  • Online ISBN: 978-1-4939-0727-4

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics