1. John Pfeifer, MD, PhD Tina Lockwood, PhD, DABCC
An Integrated Genomic Pathology Curriculum: Development, Design, and Pilot Implementation
John Pfeifer, MD, PhD
Tina Lockwood, PhD, DABCC

2. Historical training in molecular pathology AP Residency
Molecular diagnostics:
3 weeks
Cytogenetics, microarray, NGS:

3. Historical training in molecular pathology CP Residency
Molecular diagnostics:
2 weeks
Cytogenetics:
HLA:
1 week
Informatics (added 2009):

4. Goals of education Align content with contemporary practice
Train residents to critically evaluate data
Combine didactic and experiential learning
Integrate the curriculum
Analytical
Informatics
Interpretation

5. Genomics curriculum implemented 2011-2012AP CP
Molecular Diagnostics
Statistics
Informatics I
Cytogenetics
Informatics II, NGS
Tissue Banking
HLA
Molecular Diagnostics
Cytogenetics
NGS

6. Current CP structure 4 weeks 2 weeks 2 weeks 1 week 1 week 1 week
The current rotation emphasizes molecular diagnostics, as highlighted by the amount of time residents spend in my lab. The order is intentional with a flow from single-gene tests to massively parallel sequencing. Statistics and Informatics I introduce fundamental concepts and applications that are used in the modules. Occasionally tissue banking or HLA must be moved for scheduling.

7. Variable learning styles
(Yale residents’ ranking of teaching modalities)
Rinder HM and Smith BR, Clinics in Lab Med. 2007;27:

8. Modules incorporate “doing”
Fundamental premise that learning wet and dry components is crucial
Present concepts through didactics or interactive discussion
Reinforce with experiential learning
Laboratories: perform assays
Informatics: computational exercises

9. Hands-on experience is essential
Review test procedures
Observation
Hands-on experience
Extract nucleic acids
PCR
Restriction enzyme digest
Gel electrophoresis
Interpret results

10. Rotation is tailored to each trainee: MDL rotation
Perform a clinical project
Validate new reagents
Quality improvement
Design and validation of a new assay
Sign out participation
Preview results
Generate a preliminary report
Fragile X testing

11. Assessment varies for each rotation
Service-based rotations assess whether trainees can interpret patient results
Non-service rotations assign readings with trainee-led discussion

12. Revise rotations based on evaluations
Develop curriculum
Rotation modules
Assess their learning
Gather resident feedback

13. Week 1: Informatics & NGS
Formal instruction
Computational training
Public databases
Integrative Genomics Viewer/IGV
Clinical Genomicist Workstation
Shadow lab
technologists
Pre-analytic
Technologies
Informatics pipeline
Consensus
sign out
Clinical sequence analysis tools
Regulatory

14. Week 2: Interpreting clinical NGS
Paper
discussion
Preview
cases
Practicum
Teaching Case(s)

15. Practicum experience Assigned a de-identified patient sequencing case
Assess whether SNVs are polymorphisms
Incorporate public databases
Determine if variants have any clinical significance
Must critically evaluate literature
Goal: create a clinical report with references

16. Week 3: Interpreting clinical NGS
Practicum
Clinical Case(s)

17. patient care Preview sequencing results
Retrieve relevant patient history
Draft a preliminary report
Present at consensus conference

18. American Journal of Clinical Pathology 2010; 133: 832-834, Supplemental

19. Recognized Weakness: Didactics
Takes a lot of time to develop lectures, so faculty are not excited to do it
Repeating the same lecture three times a year is not interesting, so faculty are not excited to do it
Faculty expertise is lacking in some areas
Content requires constant updating
The solution is obvious: utilize resources developed by other stakeholders

20. Lecture series proposed: Training Residents In Genomics/TRIG
Lecture I: Genomic Pathology: An Introduction 
Lecture II: Genomic Methods
Lecture III: Interpreting Genomic Information for Clinical Care 
Lecture IV: Genomic Medicine: Communicating with the Patient 

21. Other key challenges
Develop objective metrics to measure success of training
Design clinically relevant statistics and informatics exercises
Develop and implement effective web-based resources

22. Acknowledgements Tina Lockwood!
Molecular Diagnostics-Jacqueline Payton
Statistics-Josh Swamidass
Informatics -Rakesh Nagarajan
Cytogenetics-Shashi Kulkarni, Cathy Cottrell, Hussam Al-Kateb
Informatics II/ NGS-Mark Watson, Rakesh Nagarajan, Eric Duncavage
Tissue Banking-Sandra McDonald
HLA-Jerry Morris