1. Making Sense of Uncertainty

2. Step 1 Whole Genome Sequencing: Exploring the human genome
3 billion DNA letters
~22,000 genes
(genes only make up1% of overall genome)

3. when might whole genome sequencing be used?

4. get to know your patient

5. find all the differences, all 1,000,000+ of them
Step 2
Identifying Variation:
Comparison with the “reference” sequence
find all the differences, all 1,000,000+ of them

6. Step 3 Understanding Variation:
Filtering for likely disease causing variants
computer programs
people

7. get to know your variant(s)

8. Step 3 Making the Claim: Assigning a variant a score1
Benign (not disease causing) 2
Likely benign 3
Variant of Uncertain Significance 4
Likely pathogenic 5
Pathogenic (disease causing)
Most DNA changes have little or no impact
Scores based on research, and multiple types of evidence
Subjective, based on human interpretation

9. Your Turn…
You will be given a case study (patient and reason for testing) and a variant to analyze
This variant is the “top hit”: most likely candidate after computerized filtering
Analyze each piece of evidence individually
Does it support the variant being pathogenic? benign? uncertain?
Put it all together and make a final call about your variant
Would you call your variant pathogenic? benign? uncertain?
Why?

10. Wrap Up What did you “call” your variant? Did you make a diagnosis?
Why or why not?
Would you advocate for returning the variant to a physician and patient?
Why or why not?

11. vs Determine Next Steps: Will the variant be returned to the patient?
Primary result:
related to symptoms, reason for testing
Secondary result:
not related to symptoms or reason for testing vs
Who decides what gets returned? Should you return variants of uncertain significance? Should patient age play a role in decision making? Other considerations?

12. Real World Example Continuing the Search:
Reanalysis with new knowledge
Case Study: 5 year old female with moderate developmental delay
Whole genome sequencing identified de novo (new) mutation in the DDX3X gene
DNA sequence does not change much over time, however our knowledge and interpretation of the DNA sequence does

13. Real World Example Continuing the Search:
Reanalysis with new knowledge
Paper published linking DDX3X mutations to developmental delay in females
April 2015
Feb 2015 1
Benign (not disease causing) 2
Likely benign 3
Variant of Uncertain Significance 4
Likely pathogenic 5
Pathogenic (disease causing)
nonsense mutation, G>T
never been seen before in databases
gene not associated with any disease or syndrome
DNA sequence does not change much over time, however our knowledge and interpretation of the DNA sequence does

14. Acknowledgements Kelly East, MS, CGC Genetic Counselor
Clinical Applications Lead
HudsonAlpha Educational Outreach
Madelene Loftin
Educator Professional Dev’t Lead
HudsonAlpha Educational Outreach
The GREAT workshop and associated materials are made possible through support from the State of Alabama.