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Genetic test (upstream) Clinician orders test/services for patient, collects sample Sample preparation and sequencing Core processing (Mapping, Variation Calling) Special processing (Annotation, Filtering, Interpretation) + (downstream) Clinician discusses outcome with patient NGS-based Genetic Test (end-to-end product)
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Joint work with many colleagues at FDA
precision.fda.gov | [email protected] | @precisionFDA
Taha A. Kass-Hout, MD, MSFDA Chief Health Informatics OfficerDirector, FDA’s Office of Health Informatics
David Litwack, PhDPolicy AdvisorFDA’s Center for Devices and Radiological Health
Elaine R. JohansonDeputy, FDA Chief Health Informatics OfficerDeputy Director, FDA’s Office of Health Informatics
Genetic test
(upstream)
Clinician orders test/services for patient,
collects sample
Sample preparation
and sequencing
Core processing(Mapping,
Variation Calling)
Special processing(Annotation, Filtering, Interpretation)
+
(downstream)
Clinician discusses outcomewith patient
NGS-based Genetic Test (end-to-end product)
Initial Focus
Genotype
Location 9: C → G mutation...
File with variants (VCF)
" You are at risk for X outcome. "
Report
Predicted Outcome
Analytical Benchmark Clinical Benchmark
Initial Focus – Analytic Benchmarking
•Assess reproducibility of a test
•Assess accuracy using reference samples
•Assess agreement with other methods
•Assess test performance on synthetic data
Features
Private or community areas
Data
Apps
Comparisons
Notes
https://github.com/FDA
>930 members from >450 organizations
precision.fda.gov
Thank You!
precision.fda.gov | [email protected] | @precisionFDA
Backup Slides
precision.fda.gov | [email protected] | @precisionFDA
… AGCATCGATGCAGAAGATTACAAGACGATCCGCTC …
DNA
Gene
We are all unique
… AGCATCGATGCAGAAGATTACAACATAAAAAGATTACACGCGATCCGCTC …
… AGCATCGATGCATAAGATTACAAGATAAAAAGATTACACGCGATCCGCTC …
… AGCATCGATGCATAAGATTACAACATAAAAAGATTACATGCGATCCGCTC …
… AGCATCGCTGCAGAAGATTACAACATAAAAAGATTACATGCGATCCGCTC …
reference
David
Taha
Elaine
The Internet Cloud
Community Assurance
Add new Feature (Discussion)
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