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!