Medical data mining Linking diseases, drugs, and adverse reactions Lars Juhl Jensen.

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Presentation transcript:

Medical data mining Linking diseases, drugs, and adverse reactions Lars Juhl Jensen

unstructured data

structured data

Jensen et al., Nature Reviews Genetics, 2012

individual hospitals

central registries

opt-out

opt-in

Danish registries

civil registration system

CPR number

established in 1968

Jensen et al., Nature Reviews Genetics, 2012

national discharge registry

14 years

6.2 million patients

45 million admissions

68 million records

119 million diagnosis

ICD-10

Jensen et al., Nature Reviews Genetics, 2012

reimbursement

not research

diagnosis trajectories

naïve approach

comorbidity

Jensen et al., Nature Reviews Genetics, 2012

confounding factors

“known knowns”

gender

age

type of hospital encounter

Jensen et al., submitted, 2013 FemaleMale In-patient Out-patient Emergency room

“known unknowns”

smoking

diet

“unknown unknowns”

reporting biases

disease clustering

temporal correlation

Jensen et al., submitted, 2013

diagnosis trajectories

Jensen et al., submitted, 2013

epilepsy

Jensen et al., submitted, 2013

gout

Jensen et al., submitted, 2013

electronic health records

structured data

Jensen et al., Nature Reviews Genetics, 2012

unstructured data

free text

Danish

busy doctors

psychiatric patients

delusions

text mining

named entity recognition

custom dictionaries

diseases

drugs

adverse drug events

expansion rules

orthographic variation

typos

“negative modifiers”

negations

family members

detailed disease profiles

Roque et al., PLOS Computational Biology, Assigned codes Text mined codes

comorbidity

Roque et al., PLOS Computational Biology, 2011

patient stratification

Roque et al., PLOS Computational Biology, 2011

cluster characterization

Roque et al., PLOS Computational Biology, 2011

adverse drug reactions

structured data

medication

clinical narrative

possible ADRs

semi-structured data

SPC Summary of Product Characteristics

drug indications

known ADRs

temporal correlation

link drugs to ADRs

complex filtering

Eriksson et al., submitted, 2013

new ADRs

Eriksson et al., submitted, 2013 Drug substanceADEp-value ChlordiazepoxideNystagmus4.0e-8 SimvastatinPersonality changes8.4e-8 DipyridamoleVisual impairment4.4e-4 CitalopramPsychosis8.8e-4 BendroflumethiazideApoplexy8.5e-3

ADR frequencies

Eriksson et al., submitted, 2013

heavily medicated

Eriksson et al., submitted, 2013

ADR dose dependency

Eriksson et al., submitted, 2013

ADR similarity

Eriksson et al., submitted, 2013

drug repurposing

Campillos, Kuhn et al., Science, 2008

Disease trajectories Anders Bøck Jensen Tudor Oprea Pope Moseley Søren Brunak Adverse drug reactions Robert Eriksson Thomas Werge Søren Brunak EHR text mining Peter Bjødstrup Jensen Robert Eriksson Henriette Schmock Francisco S. Roque Anders Juul Marlene Dalgaard Massimo Andreatta Sune Frankild Eva Roitmann Thomas Hansen Karen Søeby Søren Bredkjær Thomas Werge Søren Brunak Acknowledgments

Thank you!