medical data mining
TRANSCRIPT
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Medical data mining
Lars Juhl Jensen
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unstructured data
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structured data
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Jensen et al., Nature Reviews Genetics, 2012
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individual hospitals
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central registries
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opt-out
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opt-in
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Danish registries
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civil registration system
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CPR number
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established in 1968
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Jensen et al., Nature Reviews Genetics, 2012
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national discharge registry
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14 years
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6.2 million patients
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45 million admissions
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68 million records
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119 million diagnosis
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ICD-10
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Jensen et al., Nature Reviews Genetics, 2012
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reimbursement
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not research
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diagnosis trajectories
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naïve approach
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comorbidity
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Jensen et al., Nature Reviews Genetics, 2012
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confounding factors
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“known knowns”
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gender
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age
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type of hospital encounter
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Jensen et al., submitted, 2013
Female MaleIn
-pati
ent
Out-
pati
ent
Em
erg
ency
room
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“known unknowns”
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smoking
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diet
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“unknown unknowns”
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reporting biases
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disease clustering
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temporal correlation
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Jensen et al., submitted, 2013
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diagnosis trajectories
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Jensen et al., submitted, 2013
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epilepsy
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Jensen et al., submitted, 2013
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gout
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Jensen et al., submitted, 2013
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electronic health records
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structured data
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Jensen et al., Nature Reviews Genetics, 2012
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unstructured data
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free text
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Danish
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busy doctors
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psychiatric patients
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delusions
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text mining
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computer
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as smart as a dog
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teach it specific tricks
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named entity recognition
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custom dictionaries
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diseases
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drugs
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adverse drug events
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expansion rules
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orthographic variation
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typos
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“negative modifiers”
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negations
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family members
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detailed disease profiles
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Roque et al., PLOS Computational Biology, 2011
3262638254947
Assigned codes
Text mined codes
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comorbidity
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Roque et al., PLOS Computational Biology, 2011
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patient stratification
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Roque et al., PLOS Computational Biology, 2011
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cluster characterization
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Roque et al., PLOS Computational Biology, 2011
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adverse drug reactions
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structured data
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medication
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clinical narrative
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possible ADRs
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semi-structured data
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SPCSummary of Product Characteristics
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drug indications
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known ADRs
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temporal correlation
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link drugs to ADRs
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complex filtering
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Eriksson et al., submitted, 2013
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new ADRs
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Eriksson et al., submitted, 2013
Drug substance ADE p-value
Chlordiazepoxide Nystagmus 4.0e-8
Simvastatin Personality changes
8.4e-8
Dipyridamole Visual impairment
4.4e-4
Citalopram Psychosis 8.8e-4
Bendroflumethiazide
Apoplexy 8.5e-3
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ADR frequencies
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Eriksson et al., submitted, 2013
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heavily medicated
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Eriksson et al., submitted, 2013
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ADR dose dependency
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Eriksson et al., submitted, 2013
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ADR similarity
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Eriksson et al., submitted, 2013
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drug repurposing
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Campillos, Kuhn et al., Science, 2008
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AcknowledgmentsDisease trajectoriesAnders Bøck JensenTudor OpreaPope MoseleySøren Brunak
Adverse drug reactionsRobert ErikssonThomas WergeSøren Brunak
EHR text mining
Peter Bjødstrup Jensen
Robert ErikssonHenriette SchmockFrancisco S. Roque
Anders JuulMarlene Dalgaard
Massimo AndreattaSune FrankildEva Roitmann
Thomas HansenKaren Søeby
Søren BredkjærThomas Werge
Søren Brunak
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Thank you!