w14: analyzing large drug prescription datasets - principles, … · 03/11/2018 · systemic vs....
TRANSCRIPT
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Olivier Bodenreider, MD, PhD, NLMVojtech Huser, MD, PhD, NLMChristian Reich, MD, PhD, IQVIA
Analyzing Large Drug Prescription DatasetsPrinciples, Tools and Examples
AMIA 2018 – San Francisco, CAW14: Analyzing Large Drug Prescription Datasets - Principles, Tools and Examples
(sponsored by Pharmacoinformatics Working Group)November 3, 2018
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DisclosureOB, VH: No relationships with commercial interest
The views and opinions expressed do not necessarily state or reflect those of the U.S. Government, and they may not be used for advertising or product endorsement purposes.
CR: IQVIA has many clients in the pharmaceutical industry, whose products are the subject of this Tutorial. However, all products are intended to only be mentioned for the purposes of this Tutorial and without any recommendation or judgment of their use.
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Learning ObjectivesTo become familiar with large prescription datasets
To gain knowledge about tools available for analyzing prescription datasets
To gain knowledge about clinical data models, such as OMOP
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OverviewPart 1 – Resources and use cases (OB)
• Prescription datasets• RxNorm and NLM drug APIs; drug classification systems• Common use cases
Part 2 – Drug data processing in practice (VH)• Implementing use cases with RxMix and R
Part 3 – Experience with OHDSI (CR)• Clinical data models• Handling international drugs
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Olivier Bodenreider, MD, PhD, NLMVojtech Huser, MD, PhD, NLMChristian Reich, MD, PhD, IQVIA
Part 1 – Resources and use cases
AMIA 2018 – San Francisco, CAW14: Analyzing Large Drug Prescription Datasets - Principles, Tools and Examples
(sponsored by Pharmacoinformatics Working Group)November 3, 2018
![Page 6: W14: Analyzing Large Drug Prescription Datasets - Principles, … · 03/11/2018 · Systemic vs. topical drugs ... • Link to drug classification systems • E.g., NDC → clinical](https://reader036.vdocuments.site/reader036/viewer/2022062607/6053edccde130a20361fe94c/html5/thumbnails/6.jpg)
Part 1 overviewTypes of drug entities
• Drugs• Drug classes
Prescription datasets• Structure• Sources
Drug data processing• Mapping drugs to standards• Aggregating drugs (by ingredient, by class)
Resources for processing drug datasets• RxNorm• Drug classification systems• NLM drug APIs
Common use cases• Pharmaco-epidemiology• Assess exposure to drugs by ingredient or class• Identify potentially inappropriate medications
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@AMIAInformatics
@AMIAinformatics
Official Group of AMIA
@AMIAInformatics
#WhyInformatics
Types of drug entities
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Part 1 – Resources and use cases
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Types of drug entities (drugs I)Ingredient
• Azithromycin
Drug form• Ingredient + dose form
• Azithromycin Oral Tablet
Clinical drug (unit of prescription)• Ingredient + dose form + strength
• Azithromycin 250 MG Oral Tablet
Pack (packaging level)• Collection of clinical drugs (unit of dispensation)
• Z-PAK ({6 (Azithromycin 250 MG Oral Tablet [Zithromax]) })• Collection of clinical drugs (bulk)
• Manufacturer: Apotex Corp.; pack size: 500 in 1 BOTTLE
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Types of drug entities (drugs II)Generic vs. Brand
• G: Azithromycin 250 MG Oral Tablet• B: Zithromax 250 MG Oral Tablet
Single vs. multi-ingredient drug• S: Amoxicillin 250 MG Oral Capsule• M: Amoxicillin 250 MG / Clavulanate 125 MG Oral Tablet
Systemic vs. topical drugs• S: Azithromycin 250 MG Oral Tablet• T: Azithromycin 10 MG/ML Ophthalmic Solution
Base vs. salt/ester (as basis of strength substance)• B: Erythromycin 250 MG Oral Tablet• S: Erythromycin Ethylsuccinate 400 MG Oral Tablet
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Types of drug entities (drug classes)Atorvastatin
Therapeutic class• Anticholesteremic Agent
Chemical structure• n/a
Mechanism of action• HMG-CoA Reductase Inhibitor
Physiologic effect• Decreased Cholesterol Synthesis
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Types of drug entities (drug classes)
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@AMIAInformatics
@AMIAinformatics
Official Group of AMIA
@AMIAInformatics
#WhyInformatics
Prescription datasets
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Part 1 – Resources and use cases
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StructureTransactions captured at dispensation time (pharmacy)
• Pharmaceutical claims data sent to payers
Common elements• Prescription ID 999999• Patient identifier 123456• Date (prescription) 20161112• Product ID (NDC) 00071015623• Total quantity dispensed 30• Days supply 30• Cost data --• Drug name LIPITOR TAB 20MG• Strength 20• Generic name Atorvastatin• Prescriber ID 789
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Drug names are not
standardized
RequiredOptional
NDCs are not unique identifiers for clinical
drugs
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Product Name from Medicaid ClaimsProduct Name FrequencyCOUMADIN 270COUMADIN TAB 13COUMADIN TABLET 215JANTOVEN 130JANTOVEN TAB 24JANTOVEN TABLET 262WARFARIN 1,093WARFARIN TAB 763WARFARIN SODIUM 8,717WARFARIN SODIUM TA 95WARFARIN SODIUM TAB 516WARFARIN SODIUM TABL 587WARFARIN SODIUM TABLET 8,555
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Source: Dan Malone
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Product Identification: NDCsNational Drug Codes
• Product identification system• Three components
• Manufacturer• Product• Packaging
Introduced in 1972 by FDA
Only format permitted by NCPDP
Mandated by HIPAA regulations for drug transactions
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Source: Dan Malone
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NDC Elements: 3 segments
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XXXXX-XXXX-XX
Manufacturer Product Packaging
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NDC Forms
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XXXX-XXXX-XX (4-4-2)
XXXXX-XXX-XX (5-3-2)
XXXXX-XXXX-X (5-4-1)
0555-0831-02 (Teva Pharmaceuticals USA, Inc.; 100 in 1 BOTTLE)
Warfarin Sodium 1 MG Oral Tablet
21695-672-30 (Rebel Distributors Corp; 30 in 1 BOTTLE)
50090-1213-0 (A-S Medication Solutions; 30 in 1 BOTTLE)
→ 0XXXX XXXX XX
→ XXXXX 0XXX XX
→ XXXXX XXXX 0X
→ 00555083102
→ 21695067230
→ 50090121300
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NDC Characteristics11 Digit code (leading zero for 4-4-2 format)
Hyphens between segments are missing in claims transmission (Field 407 in NCPDP claim format)
NDC codes set by the manufacturer/labeler
High turnover compared to other drug IDs
Product codes are unique to manufacturer – not to the chemical entity
Package codes are unique to the manufacturer and product – there is no standardization for packaging codes
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Source: Dan Malone
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Source of prescription datasetsSurescripts transactions
Data from payers• Medicaid• Medicare Part D
Commercial health analytics companies• Truven (120M patients)• PharMetrics Plus (100M patients)• Ambulatory EMR (35M patients)• Open Claims (250M patients)
Reagan-Udall Foundation for the FDA• IMEDS Research Lab (temporarily suspended)
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@AMIAInformatics
@AMIAinformatics
Official Group of AMIA
@AMIAInformatics
#WhyInformatics
Drug data processing
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Part 1 – Resources and use cases
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Mapping and aggregationMapping to standard resources (e.g., RxNorm)
• Standard names and codes• Standard set of relations among drug entities• Link to drug classification systems• E.g., NDC → clinical drug
Aggregation• “roll up” to the appropriate level of granularity for analytics (use case-dependent)• E.g., branded drug → clinical drug → ingredient → drug class
Temporal aggregation• Aggregate individual prescriptions into longer spans (“drug eras” in OHDSI)
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0186-5040-31
Esomeprazole (A02BC05)Esomeprazole (283742)
Esomeprazole 40 MG Delayed Release Oral Capsule (606730)
Esomeprazole 40 MG Delayed Release Oral Capsule [Nexium] (606731)
00186504031
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@AMIAInformatics
@AMIAinformatics
Official Group of AMIA
@AMIAInformatics
#WhyInformatics
Resources for processing drug datasets – RxNorm
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Part 1 – Resources and use cases
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RxNormTerminology integration system
• Structured Product Labels, First DataBank, Micromedex, Multum, MeSH, SNOMED CT, MED-RT, ATC, …
Scope• Drug names and codes• Drugs available on the U.S. market
Developer: National Library of Medicine
Publicly available*
Monthly updates
Size: > 10k ingredients; 19k clinical drugs
Uses: e-prescription, information exchange, analytics
https://www.nlm.nih.gov/research/umls/rxnorm/
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Normalization Lexical levelName Code SourceWARFARIN (COUMADIN) NA 1MG TAB 4005203 VANDFwarfarin 1 mg oral tablet 3617 MMSLWARFARIN NA 1MG TAB,UD 4014039 VANDFWARFARIN NA 1MG TAB,UD [VA Product] N0000161787 NDFRTWARFARIN SODIUM 1 mg ORAL TABLET 14198 NDDFWARFARIN SODIUM 1 mg ORAL TABLET 60429-784 MTHSPLWarfarin Sodium 1 MG Oral Tablet 104045 MMXWARFARIN SODIUM 1 mg ORAL TABLET 63629-4017 MTHSPLWARFARIN SODIUM 1 mg ORAL TABLET [Warfarin Sodium] 53808-0985 MTHSPLWarfarin Sodium 1 MILLIGRAM In 1 TABLET ORAL TABLET 15330-100 MTHSPLWARFARIN SODIUM 1.09 MG ORAL TABLET 281572 MTHFDAWarfarin Sodium 1mg Oral tablet 933 GSWarfarin sodium 1mg tablet (product) 319733000 SNOMEDCT_USWarfarin Sodium Tab 1 MG 6749 MDDBWarfarin Sodium, 1 mg oral tablet 3617 MMSLWARFARIN SODIUM@1 mg@ORAL@TABLET 14198 NDDF[...]
Warfarin Sodium 1 MG Oral Tablet (855288)
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Normalized form
Ingredient
Dose form
Strength
Ingredient
IngredientStrength Dose form
Strength
1 MG
Ingredient
Warfarin Sodium
Dose form
Oral Tablet
Warfarin Sodium 1 MG (855287)
Warfarin Sodium 1 MG Oral Tablet (855288)
Warfarin Oral Tablet (374319)
Clinical drug componentClinical drug form
Clinical drug
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Relations among drug entities
Ingredient
C. Drug Comp. C. Drug Form
C. Drug
Brand Name
B. Drug Comp. B. Drug Form
B. Drug
B. PackG. Pack
Zithromax 250 MG Oral TabletAzithromycin 250 MG Oral Tablet
Z-PAK{6 (Azithromycin 250 MG Oral Tablet) } Pack
Azithromycin 250 MG Azithromycin Oral Tablet Azithromycin 250 MG[Zithromax]
Azithromycin Oral Tablet[Zithromax]
ZithromaxAzithromycin
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RxNav – RxNorm browser
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https://mor.nlm.nih.gov/RxNav/
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@AMIAInformatics
@AMIAinformatics
Official Group of AMIA
@AMIAInformatics
#WhyInformatics
Resources for processing drug datasets – Drug classification systems
29
Part 1 – Resources and use cases
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ATC/DDD IndexOrigin
• World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology (Norway)
Purpose• For drug utilization research / pharmaco-epidemiology
~1300 classes (1-4)Organization
• Drug classification on 4 levels• Anatomical• Therapeutic• Chemical
• Drugs (5th level)
http://www.whocc.no/atc_ddd_index/
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Established Pharmacologic Classes (EPCs)Origin
• Veterans Health Administration’s Medication Reference Terminology (MED-RT)• For use by the U.S. Food and Drug Administration (FDA)
Purpose• For drug classification in the Structured Product Labels
~600 classes
No hierarchical organization
Examples• Macrolide antibacterial (e.g., Azithromycin)
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Mechanism of action (MoA)Physiologic effect (PE)Chemical structure (Chem)
Origin• Veterans Administration’s Medication Reference Terminology (MED-RT)
Purpose• For drug classification in the Structured Product Labels• For drug classification at the VA
Number of classes• MoA: ~600; PE: ~1900; Chem: ~10,000
Hierarchical organization
Examples• MoA: HMG-CoA Reductase Inhibitor (e.g., atorvastatin)• PE: Decreased Blood Pressure (e.g., enalapril)• Chem: Penicillins (e.g., amoxicillin)
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VA ClassesOrigin
• Veterans Administration’s National Drug File
Purpose• For drug classification in the VA formulary
~500 classes
Shallow hierarchical organization (3 levels)
Examples• L1: ANTIMICROBIALS• L2: PENICILLINS AND BETA-LACTAM ANTIMICROBIALS• L3: QUINOLONES (e.g., Ofloxacin 200 MG Oral Tablet)
NB: links to clinical drugs rather than ingredients
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RxClass – Drug class browserhttps://mor.nlm.nih.gov/RxClass/
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@AMIAInformatics
@AMIAinformatics
Official Group of AMIA
@AMIAInformatics
#WhyInformatics
Resources for processing drug datasets – NLM drug APIs
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Part 1 – Resources and use cases
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NLM drug APIsExpose the content of RxNorm, RxTerms and MED-RT (and other resources)
• Logical structure, not storage format• Up-to-date information (monthly updates of RxNorm)• Additional features
• Normalized and approximate matching; spelling correction• Drug-drug interactions checking (from DrugBank)• Link to drug classes (from ATC, DailyMed, MeSH, MED-RT)• Archive of NDCs since 2007
• Optimized graph traversal (pre-computed)
For use in applications• Web services• SOAP, REST (XML, JSON)• Independent of any programming language
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API documentation and examples
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https://rxnav.nlm.nih.gov/
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0186-5040-31
Esomeprazole (A02BC05)Esomeprazole (283742)
Esomeprazole 40 MG Delayed Release Oral Capsule (606730)
Esomeprazole 40 MG Delayed Release Oral Capsule [Nexium] (606731)
00186504031rxnorm:findRxcuiById(
“NDC”, “0186-5040-31”, 0)→ 606731
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0186-5040-31
Esomeprazole (A02BC05)Esomeprazole (283742)
Esomeprazole 40 MG Delayed Release Oral Capsule (606730)
Esomeprazole 40 MG Delayed Release Oral Capsule [Nexium] (606731)
00186504031
rxnorm:getRelatedByType( “606731”, “IN”)
→ 283742
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0186-5040-31
Esomeprazole (A02BC05)Esomeprazole (283742)
Esomeprazole 40 MG Delayed Release Oral Capsule (606730)
Esomeprazole 40 MG Delayed Release Oral Capsule [Nexium] (606731)
00186504031
rxclass:getClassByRxNormDrugId( “283742”, “ATC”, “ALL”)→ A02BC, Proton pump
inhibitors
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0186-5040-31
Esomeprazole (A02BC05)Esomeprazole (283742)
Esomeprazole 40 MG Delayed Release Oral Capsule (606730)
Esomeprazole 40 MG Delayed Release Oral Capsule [Nexium] (606731)
00186504031
rxclass:getClassGraph( “A02BC”)→ A02B, DRUGS FOR PEPTIC ULCER AND GASTRO-
OESOPHAGEAL REFLUX DISEASE (GORD); A02, DRUGS FOR ACID RELATED DISORDERS;
A, ALIMENTARY TRACT AND METABOLISM
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RxMixGraphical interface to the drug APIs
• RxNorm, MED-RT, RxTerms, RxImage, Interactions, RxClass, MedEx, DailyMed
Handles interoperability between functions
Helps users compose complex queries• Find all the NDC codes for a given allergy class (e.g., barbiturates)
Supports batch execution
https://mor.nlm.nih.gov/RxMix/
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@AMIAInformatics
@AMIAinformatics
Official Group of AMIA
@AMIAInformatics
#WhyInformatics
Common use cases
43
Part 1 – Resources and use cases
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Common use casesPharmaco-epidemiology
• Assess exposure to drugs (by ingredient or class)• Assess prescribed daily dose
Identify potentially inappropriate medications• Elderly (Beers)• Pregnant women (Briggs)
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Use case #1
Pharmaco-epidemiology
[Bodenreider, AMIA, 2014]
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Prescribed vs. defined daily doseDataset
• Surescripts feed• All prescriptions to ER patients• For 3 months in 2011 in a Bethesda hospital
Reference for defined daily dose: ATC
Methods• RxNorm clinical drug → RxNorm ingredient ↔ ATC ingredient → ATC defined daily dose ↔ prescribed daily
dose • Restricted to systemic drugs (based on dose form)
Findings• Confirmed feasibility• 25% of the prescriptions exactly match the ATC DDD• 50% of the prescriptions within 66-150% of the ATC DDD• 75% of the prescriptions within 50-200% of the ATC DDD
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ATC/DDD Index
Surescripts
Amoxicillin 500 MG Oral Capsule(308191)
40 capsules 10 days
Methods Example
RxNorm
Amoxicillin 500 MG Oral Capsule(308191)
40 x 500 mg / 10 = 2
g
Amoxicillin (723)
Oral Capsule
amoxicillin(J01CA04)
O1 g
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Results Prescription classification
N=86,578
AtorvastatinSimvastatinLisinoprilMetoprolol
AmlodipineFurosemideAtenololHydrochlorothiazide
ZolpidemSertralineEscitalopramAlprazolamClonazepam
GabapentinQuetiapineOxycodoneFluoxetineDuloxetine
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PDD/DDD(log scale)
86.1% of the prescriptions are within 33%-300% of the ATC DDD3x
1/3
Deviation of the prescribed daily dose (PDD) in Surescriptsfrom the defined daily dose (DDD) in ATC
for 68,462 oral solid dose form prescriptions
10.4% < 33%of the ATC DDD
3.5% > 300%of the ATC DDD
2x
1/2
76.1% of the prescriptions are within 50%-200% of the ATC DDD1.5x 49.5% of the prescriptions are within 66%-150% of the ATC DDD
2/3
28.6% of the prescriptionsexactly match the ATC DDD
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Use case #2
Identifying potentially inappropriate medications for elderly patients
[Mundkur, AMIA, 2016]
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PIMs for elderly patientsDataset
• Medicare Part D• 1M beneficiaries ≥ 65• All prescriptions for one year (2009)
Reference list of PIMs: Beers list
Methods• NDC → RxNorm clinical drug → ingredient ↔ Beers• Restricted to systemic drugs (based on dose form)
Findings• 47% of all beneficiaries were prescribed at least 1 PIM• Top PIMs: zolpidem (6.3%), nitrofurantoin (4.5%)
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Methods Example
Medicare
Demographic data470,523 prescriptions55111047901
RxNorm
55111047901zolpidem
Oral Tablet
DFG filter
Oral Pill
Beers
zolpidemZolpidem tartrate 10 MG Oral Tablet (854873)
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Use case #3
Identifying potential risk in drug prescriptions during pregnancy
[Dhombres, AMIA, 2016]
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Potential risk during pregnancyDataset
• Large prescription dataset from private insurer (150M patients)• 3.7M pregnant women; 19M prescriptions (2003-2014)• OMOP common data model
Reference list for risk during pregnancy: Briggs textbook
Methods• RxNorm clinical drug → ingredient ↔ Briggs drug → fetal risk• Restricted to systemic drugs (based on dose form)
Findings• 41.2% compatible with pregnancy or probably compatible• 55.6% potential risk• 3.29% high risk or contraindicated
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Specific challengeObsolete identifiers
• NDC = drug + manufacturer + packaging information• ~250,000 active NDCs• ~300,000 obsolete NDCs in the past 10 years• ~220.000 “alien” NDCs (not curated by RxNorm)
• Obsolete NDCs• Removed from RxNorm (e-prescribing use case)• Needed for analytics (longitudinal datasets)
• RxNorm API provides access to obsolete NDCs• Mapping obsolete NDCs to active drugs
• rxnorm:getNDCStatus( ndc, startDate, endDate, option )
• List of all NDCs – active or obsolete – for a given drug• rxnorm:getAllHistoricalNDCs( rxcui, history )
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Other challengesReuse of identifiers
• NDCs (time-indexed)
Insufficient coverage in RxNorm• International drugs• Over-the-counter drugs
Granularity of knowledge• Ingredient-class vs. clinical drug-class
Heterogeneity of drug classification• Different use cases
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Impact assessment1B prescriptions from Medicare analyzed
• Over a 10-year period (2005-2014)
Vast majority of NDCs can be resolved with the RxNorm API functions• Minor issues
• Start/End date do not match prescription date• Ambiguous mapping (multiple RxCUIs; often clinically insignificant – generic vs. brand)
• <5% unmapped NDCs (mostly supplies; OTCs)
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Olivier Bodenreider, MD, PhD, NLMVojtech Huser, MD, PhD, NLMChristian Reich, MD, PhD, IQVIA
Part 2 – Drug data processing in practice
AMIA 2018 – San Francisco, CAW14: Analyzing Large Drug Prescription Datasets - Principles, Tools and Examples
(sponsored by Pharmacoinformatics Working Group)November 3, 2018
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Part 2 overviewDetailed look at the API
Try it yourself (Follow-along examples with RxMix)• and get help (if you hit a problem) • 5-10 min
R code examples
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Links
https://github.com/lhncbc/r-snippets-bmi/tree/master/rxnorm
https://github.com/mpancia/RxNormR (not used in this session)
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@AMIAInformatics
@AMIAinformatics
Official Group of AMIA
@AMIAInformatics
#WhyInformatics
Detailed look at the API
61
Part 2 – Drug data processing in practice
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API and RxMix web-toolhttps://rxnav.nlm.nih.gov/
https://mor.nlm.nih.gov/RxMix/
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0186-5040-31
Esomeprazole (A02BC05)Esomeprazole(283742)
Esomeprazole 40 MG Delayed Release Oral Capsule (606730)
Esomeprazole 40 MG Delayed Release Oral Capsule [Nexium] (606731)
00186504031
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Functionsrxnorm:findRxcuiById
• Parameters• id_string: NDC• AllSourcesFlag: 0
• Input: 00186504031 or 0186-5040-31• Output: 606731
rxnorm:getRelatedByType• Parameters:
• term_type: IN
• Input: 606731• Output: Esomeprazole 283742
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@AMIAInformatics
@AMIAinformatics
Official Group of AMIA
@AMIAInformatics
#WhyInformatics
Try it yourself (Follow-along examples with RxMix)
65
Part 2 – Drug data processing in practice
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RxMix
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Library of pre-built workflows
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Lyrica 150 MG Oral Capsule NCD: 00071101668
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Resolving NDC 00071101668 in RxNav
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Getting properties for NDC 00071101668
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Getting all other NDCs for Lyrica 150 MG Oral Capsule
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Getting all RxNorm entities related to Lyrica 150 MG Oral Capsule
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Selecting parameters
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Getting ATC classes for Lyrica 150 MG Oral Capsule
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Getting drug-drug interactions for Lyrica 150 MG Oral Capsule
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Nonsensical query returning no results
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Output options - JSON
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TXT output
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Saving your workflow
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@AMIAInformatics
@AMIAinformatics
Official Group of AMIA
@AMIAInformatics
#WhyInformatics
R code examples
80
Part 2 – Drug data processing in practice
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Olivier Bodenreider, MD, PhD, NLMVojtech Huser, MD, PhD, NLMChristian Reich, MD, PhD, IQVIA
Part 3 – Experience with OHDSI
AMIA 2018 – San Francisco, CAW14: Analyzing Large Drug Prescription Datasets - Principles, Tools and Examples
(sponsored by Pharmacoinformatics Working Group)November 3, 2018
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Part 3 overviewClinical data models
Handling international drugs
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@AMIAInformatics
@AMIAinformatics
Official Group of AMIA
@AMIAInformatics
#WhyInformatics
Clinical data models
89
Part 3 – Experience with OHDSI
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FDA Regulatory Action over Time
0
5
10
15
20
25
30
1960ies 1970ies 1980ies 1990ies 2000ies
Number of FDA-caused Withdrawals
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FDAAA calls for establishing Risk Identification and Analysis System
Risk Identification and Analysis System:
a systematic and reproducible process to efficiently generate evidence to support the characterization of the potential effects of medical products from across a network of disparate observational healthcare data sources
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OMOP Experiment 1 (2009-2010)OMOP Methods Library
Inceptioncohort
Case control
Logisticregression
Common Data Model
Drug
Outcome ACE Inhibito
rs
Amphoter
icin B
Antibiotic
s: ery
thromyc
ins,
sulfo
namide
s, tet
racyc
lines
Antiepil
eptics
:
carba
mazepin
e, phe
nytoi
n
Benzo
diazep
ines
Beta block
ers
Bisphos
phonate
s:
alend
ronate
Tricyc
lic an
tidep
ressa
nts
Typica
l antip
sychoti
cs
Warfarin
Angioedema Aplastic Anemia Acute Liver Injury Bleeding Hip Fracture Hospitalization Myocardial Infarction Mortality after MI Renal Failure GI Ulcer Hospitalization
• 10 data sources • Claims and EHRs• 200M+ lives
• 14 methods • Epidemiology designs • Statistical approaches
adapted for longitudinal data
• Open-source• Standards-based
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OMOP Experiment 2 (2011-2012)
Drug-outcome pairs
Positives NegativesTotal 165 234Myocardial Infarction 36 66Upper GI Bleed 24 67Acute Liver Injury 81 37Acute Renal Failure 24 64
Methods• Case-Control• New User Cohort• Disproportionality methods• ICTPD• LGPS• Self-Controlled Cohort• SCCS
Observational data4 claims databases
1 ambulatory EMR
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European OMOP Experiment
Aarhus
IPCIARS
HS
Pedianet
PHARMO Drug-outcome pairs
Positives NegativesTotal 165 234Myocardial Infarction 36 66Upper GI Bleed 24 67Acute Liver Injury 81 37Acute Renal Failure 24 64
Methods• Case-Control• New User Cohort• Disproportionality methods• ICTPD• LGPS• Self-Controlled Cohort• SCCS
Observational data
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Data Used in European ExperimentName Description Populati
onAarhus Danish national health registry, covering the Aarhus region.
Includes inhabitant registry, drug dispensations, hospital claims, lab values, and death registry.
2 M
ARS Italian record linkage system covering the Tuscany region, including inhabitant registry, drug dispensations, hospital claims, and death registry
4 M
Health-Search
Italian general practice database (no children) 1 M
IPCI Dutch general practice database 0.75 M
Pedianet Italian general practice pediatric database 0.14 M
PHARMO Dutch record linkage system. Includes inhabitant registry, drug dispensations, hospital claims, and lab values.
1.28 M
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OBSERVATIONAL MEDICALOUTCOMESPARTNERSHIP
Results
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• Heterogeneity in estimates due to choice of database
• Heterogeneity in estimates due to analysis choices
• Except little heterogeneity due to outcome definitions
• Good performance (AUC > 0.7) in distinguishing positive from
negative controls for optimal methods when stratifying by
outcome and restricting to powered test cases
• Self controlled methods perform best for all outcomes
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Observational Health Data Sciences and Informatics (OHDSI) Plans and Ambitions
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Letter SoupOMOP: ended in 2013 with Symposium
IMEDS: Program at Reagan-Udall Foundation of the FDA• Methodological research to inform Industry and Agency• Research Lab
OHDSI: Open Research Collaborative started by OMOP Pis and coordinated through Columbia University• Multiple stakeholders: academia, government, industry• Multiple geographies: US, Europe, Asia-Pacific• Multiple disciplines: Statistics, epidemiology, informatics, clinical sciences• Maintains OMOP CDM and Vocabularies
99
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OHDSI’s visionOHDSI collaborators access a network of 1 billion patients to generate
evidence about all aspects of healthcare. Patients and clinicians and other decision-makers around the world use OHDSI tools and evidence every day.
100
http://ohdsi.org
Join us on the journey
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OHDSI: a global community101
OHDSI Collaborators:• >220 researchers in academia,
industry and government• >21 countries
OHDSI Data Network:• >114 databases from 19 countries• 1.9 billion patients records (duplicates)
• ~222 million non-US patients
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A caricature of the patient journey
Conditions
Drugs
Procedures
Measurements
Person time
Dise
ase
Trea
tmen
t
Out
com
e
0Baseline time Follow-up time
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Questions asked across the patient journey
Conditions
Drugs
Procedures
Measurements
Person time
Dise
ase
Trea
tmen
t
Out
com
e
0Baseline time Follow-up time
Which treatment did patients choose after diagnosis?
Which patients chose which treatments?
How many patients experienced the outcome after treatment?
What is the probability I will experience the outcome?
Does treatment cause outcome?
Does one treatment cause the outcome more than an alternative?
What is the probability I will develop the disease?
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Classifying questions across the patient journeyClinical characterization: What happened to them?
• What treatment did they choose after diagnosis?• Which patients chose which treatments?• How many patients experienced the outcome after treatment?
Patient-level prediction: What will happen to me?• What is the probability that I will develop the disease?• What is the probability that I will experience the outcome?
Population-level effect estimation: What are the causal effects?• Does treatment cause outcome?• Does one treatment cause the outcome more than an alternative?
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OBSERVATIONAL MEDICALOUTCOMESPARTNERSHIP
OMOP Common Data Model
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Stan
dard
ized
clin
ical
dat
a
Person
Drug_exposure
Condition_occurrence
Procedure_occurrence
Visit_occurrence
Measurement
Procedure_cost
Drug_cost
Observation_period
Payer_plan_period
Provider
Care_siteLocation
Cohort
Death
Dose_era Condition_era
OMOP Common Data Model
Visit_cost
Device_exposure
Device_cost
Observation
Drug_era
Concept
Concept_relationship
Concept_ancestor
Vocabulary
Source_to_concept_map
Relationship
Concept_synonym
Drug_strength
Cohort_definitionNote
Standardized health system data
Standardized vocabulary
Standardized derived elementsFact_relationship
SpecimenCDM_source
Standardized meta-data
Standardized health econom
ics
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NDFRT
GPINDC EU Product
ATC
CPT4
Source codes
Drug products
Ingredients
Classifications
VA-Product
Drug Forms and Components
HCPCS
ETCFDB Ind
CIEL Gemscript
Genseqno
NDFRT Ind
MeSH Multum Oxmis Read
SPLVA Class CVX
NDFRT ATC ETCFDB IndNDFRT Ind SPLVA Class CVX
dm+d
RxNorm RxNorm Extension
SNOMED
SNOMED
Drugs
RxNorm RxNorm Extension
RxNorm RxNorm Extension
AMIS
DPD
BDPM
Drug Hierarchy
Standard Drug Vocabulary:
Drug Classes
Drug Codes
Procedure Drugs
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Simple Use CaseGive me all patients who take
Plavix 75 mg Tablets
108
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OMOP Vocabulary
Branded Drug
clopidogrel 75 MG Oral Tablet [Plavix]
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OMOP Vocabulary
Branded Drug
clopidogrel 75 MG Oral Tablet [Plavix]
Plavix
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OMOP Vocabulary
Clinical Drug
clopidogrel 75 MG Oral Tablet [Plavix]
clopidogrel 75 MG Oral Tablet
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OMOP Vocabulary
Drug Form
clopidogrel 75 MG Oral Tablet [Plavix]
clopidogrel 75 MG Oral Tablet
clopidogrel Tablet [Plavix]
clopidogrel Tablet
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OMOP Vocabulary
Drug Form
clopidogrel 75 MG Oral Tablet [Plavix]
clopidogrel 75 MG Oral Tablet
clopidogrel Tablet [Plavix]
clopidogrel Tablet Tablet
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OMOP Vocabulary Relationships
Drug Component
clopidogrel 75 MG Oral Tablet [Plavix]
clopidogrel 75 MG Oral Tablet
clopidogrel 75 MG [Plavix]
clopidogrel 75 MG
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OMOP Vocabulary Relationships
Drug Component
clopidogrel 75 MG Oral Tablet [Plavix]
clopidogrel 75 MG Oral Tablet
clopidogrel 75 MG [Plavix]
clopidogrel 75 MG
75 MG
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OMOP Vocabulary
clopidogrel
Ingredient
clopidogrel 75 MG Oral Tablet [Plavix]
clopidogrel 75 MG Oral Tablet
clopidogrel Tablet [Plavix]
clopidogrel Tablet clopidogrel 75 MG [Plavix]
clopidogrel 75 MG
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OMOP Vocabulary
clopidogrel
Ingredient
clopidogrel 75 MG Oral Tablet [Plavix]
clopidogrel 75 MG Oral Tablet
clopidogrel Tablet [Plavix]
clopidogrel Tablet clopidogrel 75 MG [Plavix]
clopidogrel 75 MG
RxNorm WWWWWWWWWWWWWWWWW
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OMOP Vocabulary
clopidogrel
Platelet aggregation inhibitors excl.
heparin
Platelet Aggregation Inhibitors -
Thienopyridines
Cerebral Thromboembolism
Prevention
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
Physiological Effect
clopidogrel 75 MG Oral Tablet [Plavix]
clopidogrel 75 MG Oral Tablet
clopidogrel Tablet [Plavix]
clopidogrel Tablet clopidogrel 75 MG [Plavix]
clopidogrel 75 MG
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
Platelet Aggregation
Alteration
ETC ATC SPLIndication
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OMOP Vocabulary
clopidogrel
Platelet aggregation inhibitors excl.
heparin
Platelet Aggregation Inhibitors -
Thienopyridines
Cerebral Thromboembolism
Prevention
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75 MG Oral Tablet [Plavix]
clopidogrel 75 MG Oral Tablet
clopidogrel Tablet [Plavix]
clopidogrel Tablet clopidogrel 75 MG [Plavix]
clopidogrel 75 MG
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
ANTITHROMBOTIC AGENTS
Platelet Aggregation Inhibitors &
Combinationsclopidogrel 75mg/1
ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
Platelet Aggregation
Alteration
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
Platelet Aggregation
Alteration
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OMOP Vocabulary
clopidogrel
Platelet aggregation inhibitors excl.
heparin
Platelet Aggregation Inhibitors -
Thienopyridines
Cerebral Thromboembolism
Prevention
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
ClopidogrelBisulfate
Tab 75 MG (Base Equiv)
clopidogrelbisulfate 75mg/1
ORAL TABLET,
FILM COATED [plavix]
CLOPIDOGREL 75 MG
Oral Enteric Coated Tablet
[PLAVIX]
Clopidogrel75mg
tablets
clopidogrel 75 MG Oral Tablet [Plavix]
clopidogrel 75 MG Oral Tablet
clopidogrel Tablet [Plavix]
clopidogrel Tablet clopidogrel 75 MG [Plavix]
clopidogrel 75 MG
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
ANTITHROMBOTIC AGENTS
Platelet Aggregation Inhibitors &
Combinationsclopidogrel 75mg/1
ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
Platelet Aggregation
Alteration
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
Platelet Aggregation
Alteration
clopidogrelbisulfate 75mg/1
ORAL TABLET,
FILM COATED [plavix]
clopidogrelbisulfate 75mg/1
ORAL TABLET,
FILM COATED [plavix]
clopidogrelbisulfate 75mg/1
ORAL TABLET,
FILM COATED [plavix]
BDPM France
GPI
NDC
SPL
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Concepts
clopidogrel
Platelet aggregation inhibitors excl.
heparin
Platelet Aggregation Inhibitors -
Thienopyridines
Cerebral Thromboembolism
Prevention
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
ClopidogrelBisulfate
Tab 75 MG (Base Equiv)
clopidogrelbisulfate 75mg/1
ORAL TABLET,
FILM COATED [plavix]
CLOPIDOGREL 75 MG
Oral Enteric Coated Tablet
[PLAVIX]
Clopidogrel75mg
tablets
clopidogrel 75 MG Oral Tablet [Plavix]
clopidogrel 75 MG Oral Tablet
clopidogrel Tablet [Plavix]
clopidogrel Tablet clopidogrel 75 MG [Plavix]
clopidogrel 75 MG
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
ANTITHROMBOTIC AGENTS
Platelet Aggregation Inhibitors &
Combinationsclopidogrel 75mg/1
ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
Platelet Aggregation
Alteration
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
Platelet Aggregation
Alteration
clopidogrelbisulfate 75mg/1
ORAL TABLET,
FILM COATED [plavix]
clopidogrelbisulfate 75mg/1
ORAL TABLET,
FILM COATED [plavix]
clopidogrelbisulfate 75mg/1
ORAL TABLET,
FILM COATED [plavix]
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Relationships
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Hierarchy
clopidogrel 75 MG Oral Tablet [Plavix]
clopidogrel 75 MG Oral Tablet
clopidogrel 75 MG
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
Platelet Aggregation
Alteration
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
Platelet Aggregation
Alteration
Concept Relationships
Concepts
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Hierarchy
clopidogrel 75 MG Oral Tablet [Plavix]
clopidogrel 75 MG Oral Tablet
clopidogrel 75 MG
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
Platelet Aggregation
Alteration
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
Platelet Aggregation
Alteration
Concept Relationships
Concepts
Ancestor
Descendant
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OMOP Vocabulary Common Data Model1. All content: concepts in concept table
2. Direct relationships between concepts listed in concept_relationship
3. Multi-step hierarchical relationships pre-processed in concept_ancestor
4. Local codes mapped to concepts trough source_to_concept_map
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CONCEPT –Single standardized Reference Table
Vocabulary ID
All vocabularies stacked up in one table
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All Content in CDM is Coded as ConceptsConcepts are referred to by concept_id
All details are in the CONCEPT table:
SELECT*
FROMconcept
WHEREconcept_id = 1322185
;
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Drugs by Ingredients3.Check Descendants (other drug products containing Warfarin and Dabigatran)
SELECT max_levels_of_separation, descendant.*
FROM concept_ancestor a, concept descendant
WHERE a.ancestor_concept_id = 1310149 /* Warfarin or 1322185 Clopidogrel*/
AND a.descendant_concept_id = descendant.concept_id
ORDER BY max_levels_of_separation;
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Members of out Drug ClassesCheck Ingredient Descendants of Drug Class Anticoagulants
SELECT max_levels_of_separation, descendant.*
FROM concept_ancestor a, concept descendant
WHERE a.ancestor_concept_id = 21600961 /* ATC Antithromboic Agent */
AND a.descendant_concept_id = descendant.concept_id
AND descendant.concept_class = 'Ingredient'
ORDER BY max_levels_of_separation;
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Fulfilling the Use Case
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Fulfilling Another Use Case
WHERE drug_concept_id IN (
SELECT descendant.concept_idFROM concept_ancestor a, concept descendant WHERE a.ancestor_concept_id = 21500803 /* ETC Anticoagulants */
AND a.descendant_concept_id = descendant.concept_id)
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@AMIAInformatics
@AMIAinformatics
Official Group of AMIA
@AMIAInformatics
#WhyInformatics
Handling international drugs (“RxNorm extension”)
133
Part 3 – Experience with OHDSI
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Germany: AMIS
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France
135
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Canada
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UK – dm+d
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Plavix Prepackaged Product
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OMOP Vocabulary
clopidogrel
Platelet aggregation inhibitors excl.
heparin
Platelet Aggregation Inhibitors -
Thienopyridines
Cerebral Thromboembolism
Prevention
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75 MG Oral Tablet [Plavix]
clopidogrel 75 MG Oral Tablet
clopidogrel Tablet [Plavix]
clopidogrel Tablet clopidogrel 75 MG [Plavix]
clopidogrel 75 MG
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
ANTITHROMBOTIC AGENTS
Platelet Aggregation Inhibitors &
Combinationsclopidogrel 75mg/1
ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
Platelet Aggregation
Alteration
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
clopidogrel 75mg/1 ORAL TABLET, FILM COATED
Platelet Aggregation
Alteration
clopidogrel 75 MG Oral Tablet [Plavix] Box of 28
by Sanofi Aventis
clopidogrel 75 MG Oral Tablet [Plavix]Box of 28
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@AMIAInformatics
@AMIAinformatics
Official Group of AMIA
@AMIAInformatics
#WhyInformatics
Resources
140
Part 3 – Experience with OHDSI
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RxNorm Extension Composition141
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Drug Forms Internationally142
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Resources1. Download
http://athena.ohdsi.org
2. Rebuild (not for the faint of heart)
https://github.com/OHDSI/Vocabulary-v5.0
3. Documentation (incomplete still)http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary
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Questions
AMIA 2018 – San Francisco, CAW14: Analyzing Large Drug Prescription Datasets - Principles, Tools and Examples
(sponsored by Pharmacoinformatics Working Group)November 3, 2018
Olivier Bodenreider, MD, PhD, [email protected]
Vojtech Huser, MD, PhD, [email protected]
Christian Reich, MD, PhD, [email protected]