an integrated genomic pathology curriculum: development, design, and pilot implementation
DESCRIPTION
An Integrated Genomic Pathology Curriculum: Development, Design, and Pilot Implementation. John Pfeifer, MD, PhD Tina Lockwood, PhD, DABCC. Historical training in molecular pathology AP Residency. Molecular diagnostics: 3 weeks. Cytogenetics, microarray, NGS: 3 weeks. - PowerPoint PPT PresentationTRANSCRIPT
An Integrated Genomic Pathology Curriculum: Development, Design, and Pilot
Implementation
John Pfeifer, MD, PhDTina Lockwood, PhD, DABCC
Historical training in molecular pathologyAP Residency
Molecular diagnostics:
3 weeks
Cytogenetics, microarray,
NGS: 3 weeks
Historical training in molecular pathology CP Residency
Molecular diagnostics:
2 weeks
Cytogenetics: 2 weeks
HLA:1 week
Informatics (added 2009):
2 weeks
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
Genomics curriculum implemented 2011-2012
Molecular Diagnostics
Statistics
Informatics I
Cytogenetics
Informatics II, NGS
Tissue Banking
HLA
Molecular Diagnostics
Cytogenetics
AP CP
NGS
Current CP structure
Molecu
lar
Statisti
cs
Informati
cs I
Cytoge
netics
NGS, Inform
atics
II
Tissue ban
king
HLA0%
5%
10%
15%
20%
25%
30%
35% 4 weeks
1 week 1 week
2 weeks 2 weeks
1 week 1 week
Variable learning styles
(Yale residents’ ranking of teaching modalities)
Rinder HM and Smith BR, Clinics in Lab Med. 2007;27:257-266
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
Hands-on experience is essential
• Review test procedures– Observation
• Hands-on experience– Extract nucleic acids– PCR– Restriction enzyme digest– Gel electrophoresis– Interpret results
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
Assessment varies for each rotation
• Service-based rotations assess whether trainees can interpret patient results
• Non-service rotations assign readings with trainee-led discussion
Revise rotations based on evaluations
Develop curriculum
Rotation modules
Assess their learning
Gather resident feedback
Week 1: Informatics & NGS
Formal instruction
Pre-analytic
Technologies
Informatics pipeline
Clinical sequence analysis tools
Regulatory
Computational training
Public databases
Integrative Genomics
Viewer/IGV
Clinical Genomicist Workstation
Shadow labtechnologists
Consensus sign out
Week 2: Interpreting clinical NGS
Paper discussion
Preview cases
PracticumTeaching Case(s)
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
Week 3: Interpreting clinical NGS
PracticumClinical Case(s)
patient care– Preview sequencing results– Retrieve relevant patient history– Draft a preliminary report– Present at consensus conference
American Journal of Clinical Pathology 2010; 133: 832-834, Supplemental
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
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
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
Acknowledgements
Molecular Diagnostics-Jacqueline Payton
Statistics-Josh Swamidass
Cytogenetics-Shashi Kulkarni, Cathy Cottrell, Hussam Al-KatebInformatics II/ NGS-Mark Watson, Rakesh Nagarajan, Eric Duncavage
Tissue Banking-Sandra McDonald
HLA-Jerry Morris
Informatics -Rakesh Nagarajan
Tina Lockwood!