1. UCLA Precision Health and Genomic Medicine Changing the Future of Healthcare
Dan Geschwind, MD, PhD
Director, Institute for Precision Health
Senior Associate Dean and
Associate Vice Chancellor, Precision Health
David Geffen School of Medicine
UCLA Data Day
May 9, 2019

2. UCLA IPH Signature Initiatives
Clara Lajonchere, PhD

3. SNP Genotyping (Illumina GSA) High Performance Computing
UCLA ATLAS Project
Vision: Create a powerful and robust cloud-based clinical and multi-omic data resource from a diverse sample of 150,000 patients across the health system for cutting-edge translational research
Universal Consent (recruitment)
Central Biobanking (sample collection/storage)
SNP Genotyping (Illumina GSA)
High Performance Computing
(clinical & genetic data integration)
ATLAS 150k

4. ATLAS IS CONSENTING PATIENTS ACROSS UCLA HEALTH (21 Locations)
Westwood Locations
Santa Monica
Ronald Reagan Medical Center - Surgical Procedures (PTU)
Ronald Regan Medical Center – Admissions
Cardiothoracic Surgery Inpatient Unit (Bedside)
Medicine and Surgery Inpatient Unit (Bedside)
Medical Procedure Unit (MPU)
Clinical Laboratories
100 Medical Plaza, Suite 245
200 Medical Plaza, Suite 145
Cardiology Clinics
100 Medical Plaza, Suite 630 West
100 Medical Plaza, Suite 630 East
Center for Inflammatory Bowel Disease (GI Clinic)
Neurology Outpatient Clinic
SM Hospital Admissions
SM Hospital GI Clinic
SM Pre-op
Oncology Inpatient Unit
Merle Norman (Medical/Surgical) Inpatient Unit
SM Medical Office Building – Surgery Center Admissions
Radiology
Clinical Lab Draw Station (BURL)
Burbank
Santa Clarita

6. DEMOGRAPHICS ATLAS patients appear to be sicker than the average
Count on 5/6/19 
Total number of unique patient records in Epic
                     5,234,304
Total number of unique active patients
                     2,512,552
Number of annual Inpatient visits
                          56,284
Number of annual Ambulatory visits
                     3,132,514
Number of annual Emergency visits
                        104,423
Number of Patients with a diabetes DX (E10, E11, 250)
                        116,722
Number of Patients with a heart failure DX (I50, 428)
                          44,462
Total number of ATLAS Patients (opt-in)
                          26,867
                          10,055
                        376,897
                            7,707
                            4,747
                            2,278
ATLAS patients appear to be sicker than the average
“healthy” patient

7. ATLAS Genomic Data Resources
V1 4/26/19 (CTD)

8. Parallel Genomic Data Repositories
PLINK
Very compact compression
Designed for genetic association applications
Access: Linux command line; Jupyter notebook (Python)
I2B2
Repository of clinical data from CareConnect
Cohort finding based on clinical and genetic attributes
Access: Graphical User Interface
Genomics DB
.vcf files stored as sparse arrays
Comprehensive genomic data store
Access: Zeppelin notebook (Scala)

9. Retrieve Genotype Data from (x) Samples at (y) Genomic Locations (J
Retrieve Genotype Data from (x) Samples at (y) Genomic Locations (J. Wang)
Zeppelin paragraphs with Scala code
Cut/paste sample IDs & SNP IDs into boxes
Query
Map SNPs to genomic coordinates
Get genotype data

10. Genomics DB: I2b2 Variant View Plug-In
If we wanted to get the reference and alternate allele counts at rs16942 for patients who consented to share their genetic data, and have been diagnosed with malignant neoplasms of the breast. The Total Allele Counts report will allow us to answer this query.

11. Is this result normal for someone like me?
Insights from big data
- Define new normal range for blood test based on personalized features
Is this result normal for someone like me?
GENOMICS
eranhalperingenomics.com

12. Ancestry adjusted normal ranges
Work by Noah Zaitlen’s group (UCLA, Neurology)
African American patients are 3 times more
likely to exceed upper threshold
Eran Halperin

13. Performance of mortality prediction
Eran Halperin PhD

14. Summary ATLAS is running in many clinics and labs
We are working to expand under-represented minority populations
We will have about 30,000 patients genotyped within 3 months and hope to attain 50,000 people this year.
These clinical and genetic datasets are available and can be linked to the EHR (manually, via honest broker, we will automate later this year).