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John Pfeifer, MD, PhD Tina Lockwood, PhD, DABCC

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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 2011-2012
AP 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


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