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

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

Background

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)

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

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

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.

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

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)

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

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

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

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

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)

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

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

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

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

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. https://www.illumina.com/techniques/sequencing.html https://www.nih.gov/research-training/allofus-research-program Additional Reading Precision Medicine – Personalized, Problematic, and Promising http://www.nejm.org/doi/full/10.1056/NEJMsb1503104 A New Initiative on Precision Medicine https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5101938/