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From Bedside to Bench and Back. Isaac “ Zak ” Kohane, MD, PhD. First signal: 1 year after Celecoxib 8 months after Rofecoxib. Oral Hypoglycemic Agents. Without strong priors. Major Modes of E HR D riven G enomic R esearch (EDGR). EHR. EHR. EDGR Advantages. Timeliness

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from bedside to bench and back

From Bedside to Bench and Back

Isaac “Zak” Kohane, MD, PhD

slide2

First signal:

  • 1 year after Celecoxib
  • 8 months after Rofecoxib
edgr advantages
EDGR Advantages
  • Timeliness
  • Clinical Relevance
  • Underserved populations
  • Controls
  • Co-morbidity recognition (e.g. PheWAS)
accrual rates
Accrual Rates

Murphy et al Genome Research, 2009

costs
Costs

Murphy et al Genome Research, 2009

slide9

But it works…

Kurreeman, AJHG 2011

edgr challenges
EDGR Challenges
  • Consent (None/Opt-in/Opt-Out)
  • Cost of EHRs
  • Quality of EHR data
  • Lack of Family History codification
  • Lack of EHR standardization
  • Cultural gulf between clinical informatics and bioinformatics.
    • Translational Bioinformatics
application to a common pediatric disease
Application to a common pediatric disease
  • With an understudied epidemiology
slide17
2012

SHRINE conf 6/29

challenge efficiently reach large n for population studies
Challenge: Efficiently Reach LargeN for Population studies
  • High throughput genotyping
  • High throughput phenotyping
  • High throughput sample acquisition

DHHS Secretary’s Advisory Committee on Genetics, Health, and Society (SACGHS) argues for the health value of a 500,000 to 1M subject study. Estimated cost: $3,000,000,000

nlp and comedy is not pretty

SH: widow,lives alone,2 children,no tob/alcohol.

BRIEF RESUME OF HOSPITAL COURSE: 63 yo woman with COPD, 50 pack-yr tobacco (quit 3 wks ago), spinal stenosis, ...

SOCIAL HISTORY: Negative for tobacco, alcohol, and IV drug abuse.

HOSPITAL COURSE: ... It was recommended that she receive …We also added Lactinax, oral form of Lactobacillus acidophilus to attempt a repopulation of her gut.

SOCIAL HISTORY: The patient is a nonsmoker. No alcohol.

SOCIAL HISTORY: The patient is married with four grown daughters,uses tobacco, has wine with dinner.

SOCIAL HISTORY: The patient lives in rehab, married. Unclear smoking history

from the admission note…

Smoker

Non-Smoker

Past Smoker

???

Hard to pick

Hard to pick

NLP (and comedy) is not pretty
crimson core functions

Matched

Anonymous

ID

Richly annotated biospecimens

Mined Phenotypes

Clinical discard

Crimson: Core Functions
free and open source translational toolkit implementations

Project

Management

Natural

Language

Processing

Visual Term

Mapping

File

Repository

De -

Identification

Of data

Ontology

Management

Identity

Management

Annotating

Genomic

Data

Data

Repository

(CRC)

Workflow

Framework

Data Queries

Data

Visualization

Correlation

Analysis

Free and Open Source Translational Toolkit: Implementations