1. Dewey et al. Presented By: Natasha Granneman & Christina Tran
Distribution and clinical impact of functional variants in 50,726 whole-exome sequences from the DiscovEHR Study
Dewey et al.
Presented By: Natasha Granneman & Christina Tran

2. Background What is Precision Medicine?
Considers a person’s environment, lifestyle, and genes when looking for course treatment
Theoretically, treatment should be catered to one person
Goals of Precision Medicine
Expand cancer treatments
Use a cohort study to learn more about health and disease
According to the NIH, the precision medicine initiative is an approach for treatment and prevention of diseases that puts a person’s lifestyle, environment, lifestyle, and genes into consideration
It is often referred to as personalized medicine bc theoretically, this approach should create treatments catered to a person
While it was an idea that had existed for years now, it was endorsed by obama in 2015 as an initiative
Two mains goals, one was short term and one was long term

3. Background

4. Background
In 2014, DiscovEHR initiative started by Regeneron Genetics Center and Geisinger Health Systems (GHS)
Cohort in this study came from consenting GHS patients who gave blood and DNA samples as well as clinical phenotypes and records
50, 726 participants
87 clinical examinations, 658 lab tests, and 7 procedures per participant
(had records that went back about 14 years: 87 clinical examinations, 658 lab tests, and procedures per participant)

5. Goals of DiscovEHR
Find genes that affect a large number of diseases and similar traits between them
Use these factors to uncover new scientific knowledge
Possible drug targets
Analyzing genetic variants to scale the use of precision medicine
Analyze by identifying, returning, and experimentally acting on actionable genetic variants to test their significance and function

6. Method Genome wide array genotyping via Omni Express exome platform
Sequenced coding regions of 18,852 genes in 50, 726 participants using Illumina Sequencing
20x read depth at > 85% of targeted bases in 96% of samples
Average of 80% mean read depth in targeted bases
Microarrays that can process thousands of samples quickly and effectively
Identify mutations and structural variants
Did this before sequencing, probably before sequencing
Sequencing gives more info

7. Bead MicroArray Technology
Higher throughput and more consistent reproducibility than typical microarray
Designed to capture SNPs and functional exonic content
-The array includes over 273,000 functional exonic markers, delivering coverage of putative functional exonic variants selected from over 12,000 individual exome and whole genome sequences.

8. Exome Capture Targeted Sequencing
Hybrid capture= probes specific to exon sequences (NimbleGen)
-captures fragments are then bound to streptavidin conjugated beads and non-specific DNA fragments washed away
-> Multiplexed samples and sequenced with Illumina
qPCR quantification because you need to normalize barcoded samples and load the precise amount of DNA into each flow cell

9. Method Once sequenced, uploaded to DNAnexus to analyze
Aligned the sequences from Illumina to a reference
GRCh37.p13
DNAnexus is basically a computer that analyzes the sequences for differences
Computer programs showed which changes from reference (reference shouldn’t have any pLOFs)

10. Method Used various computer programs to: Loss of functions variants
Align exomes to the reference
Loss of functions variants
Zygosity
Build pedigrees
Compared exome sequences to phenotypes derived from electronic health records
Lipid levels
Clinically actionable genetic variants
Heterozygosity, homozygosity, autozygosity

11. A nonsense mutation (encodes stops), loss of a start or stop
Mutations at locations where spicing should occur
Single base pair Insertions or deletions that caused frameshift mutations

12. Results
Found previously unidentified associations between pLOFs in various genes and phenotypes from EHR
4.2 million SNV’s and indels (176,000 predicted LOFs)
76 clinically actionable genes
3.5% of participants had possible pathogenic variants
Clinically actionable= diseases with a known monogenic cause (BRCA1/2, hypercholesterolemia, etc.)
3.5% of people found to have pathogenic or likely pathogenic variants in these genes that meet criteria for clinical action
EHR showed that 35% of these people had no history associated with the disease

13. PCSK9 was the most significant finding Normally degrades LDL receptor
blood LDL levels increase
pLOF in gene results in lower LDL levels
Similar to drugs that target the gene (alirocumab and evolocumab)
Validation of the drug target
APOC3- phase 2 clinical trials for lipid modification
APOB- mipomersen

14. Table shows premature stop variants divided into three more common and three rare
See that more are olfactory (since a lot of these aren’t as detrimental, it makes sense that a lot are mutated)
More common to get a recessive mutation than a dominant one (can carry this and not carry the phenotype)

15. Conclusion from Study
There needs to be large scale sequencing used in health care system
Allow us to fill gaps in our knowledge regarding role of genetic variation in health, disease, genomics, and medical care
Represents a “powerful platform” for human genetics research
DiscovEHR is merely a “blueprint” for precision medicine and target gene discovery

16. Need to expand because when you have a purified selection, you see that variants are at low freq
But we need large populations to find rare variants with large effects on clinical traits

17. Limitations Costly for general public
Pedigree studies showed that majority of population were related or family members
Possible inbred
Data sample was from a small area that was predominantly white
Not representative
Participants were old and ill patients
Most patients hard hypercholesterolemia and cardiac problems

18. Our Conclusions
Precision medicine using this is a great initiative, but might be too big to accomplish
Doubtful that this can be used to treat more terminal diseases such as cancer
Saw no links to cardiac illnesses in sample even though cardiac illnesses were in the majority
Big pharm companies might not find precision medicine as profitable as it costs too much per person

19. References/Additional Reading
Dewey, F.E, et al. Distribution and clinical impact of functional variants in 50,726 whole- exome sequences from the DiscovEHR Study. Science, 354: 1549.
Additional Reading
Precision Medicine – Personalized, Problematic, and Promising
A New Initiative on Precision Medicine