Surveillance of Peripheral Arterial Disease Cases Using Natural Language Processing of Clinical Notes
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1 Surveillance of Peripheral Arterial Disease Cases Using Natural Language Processing of Clinical Notes Naveed Afzal, Sunghwan Sohn, Christopher G. Scott, Hongfang Liu, Iftikhar J. Kullo, Adelaide M. Arruda-Olson 2017 MFMER slide-1
2 Peripheral arterial disease (PAD) Affects 8.5 million in US, 200 million worldwide Associated with high risk of mortality and morbidity Under-diagnosed and undertreated Lack of awareness of PAD-associated risks for adverse cardiovascular outcomes Diagnosed by ankle-brachial index (ABI) test but this method remains underutilized Kullo & Rooke: NEJM, 2016; Hirsch et al: JAMA, 2001; Gerhard-Herman et al: J Am Coll Cardiol, MFMER slide-2
3 Background Manual methods for disease surveillance are costly, time-consuming and inconsistent Automated surveillance of clinical notes from EHRs may effectively identify PAD cases Use NLP to extract PAD related information from narrative clinical notes 2017 MFMER slide-3
4 Objectives To develop and validate a PAD surveillance system using NLP for detection of PAD symptoms from narrative clinical notes 2017 MFMER slide-4
5 PAD diagnosis based on ABI test Reports were in PDF format and were not part of clinical notes PAD cases ABI 0.90 rest or postexercise 20% decrease ABI after exercise High ABI >1.40 = poorly compressible arteries Controls Normal ABI results Date of ABI testing = index date Kullo & Rooke: NEJM, MFMER slide-5
6 EHR System NLP Algorithm Documents, patient IDS, dates Sentence Detection Tokenization Concept Identification ABI (Gold Standard) Concept features and rules System output Assertion Patient Classification Evaluation 2017 MFMER slide-6
7 PAD-NLP Algorithm Expert clinician manually reviewed clinical notes 20 patients with PAD 20 patients without PAD Created list of PAD-related keywords for NLP algorithm prototype List of keywords refined by manual review of charts by a board certified cardiologist Afzal et al: J Vasc Surg, MFMER slide-7
8 Examples of keywords for confirmation of PAD Right lower extremity critical limb ischemia. She has history of peripheral vascular disease She has been followed in the Wound Care Center this year for ulcerations to the toes of her right foot Ultrasound shows severe right lower extremity atherosclerotic disease, beginning at the level of the right common femoral artery Noninvasive lower extremity arterial study demonstrated indeterminate ankle-brachial indices due to poorly compressible vessels bilaterally His past medical history is also significant for peripheral arterial occlusive disease with aorto-bifemoral bypass, Peripheral vascular disease Critical limb ischemia right lower extremity LLE ischemia Noncritical infrapopliteal level lower extremity arterial occlusive disease bilaterally Lower extremity atherosclerosis obliterans Severe lower extremity arterial occlusive disease Examples of keywords for exclusion of PAD There is no evidence of critical limb ischemia No evidence of PAD Vascular lab - normal lower extremity arterial study No evidence of arterial occlusive disease 2017 MFMER slide-8
9 Keywords - NLP algorithm Confirmation - Disease Location lower extremities/extremity; lower limbs/limb; Leg /legs; Iliac/femoral/tibial/popliteal artery/ arteries; Distal/ infrarenal /abdominal aorta/aorto (bi)iliac/ aorto (bi)iliac/aorto(bi)-iliac; aorto- (bi)femoral; foot, toe, toes, shin; plantar, heel, ankle, interdigital; below/above knee, Claudication /calf pain; Ischemic ulcer/ulcers; ASO/Arteriosclerosis obliterans/ arterial sclerosis obliterans/ atherosclerotic disease; PAD/ Peripheral arterial disease/peripheral vascular disease / Peripheral arterial occlusive disease Confirmation - Diagnosis Arterial occlusive disease/occlusion/occluded; Stenosis; non compressible vessels (NCV), noncompressible arteries (NCA), poorly compressible vessels (PCV), stiff vessels/ arteries ischemia; positive ABI/ankle brachial index/ vascular labs/ extremities study /arterial studies; revascularization/recanalization/bypass/angioplasty/pta/stenting/stent/graft/endarterectomy/ endarterectomies; thrombectomy/thrombosis/thromboembolectomy/embolectomy/ embolectomies Exclusion Family history of, Upper extremities/upper extremity; Arm/arms, hand(s); Brachial artery, axillary artery, radial artery, ulnar artery; carotid, innominate artery, subclavian artery; mesenteric artery; celiac artery; AAA, abdominal aortic aneurysm/abd aortic aneurysm; renal arteries/artery; coronaries, coronary arteries/ artery /cerebrovascular-disease /arteries/artery; Amputation; traumatic/trauma; sarcoma/osteoma; pseudoclaudication/pseudoclaudicatory pain; diabetic foot, hammer toe/ toes; vascular calcification; varicose veins 2017 MFMER slide-9
10 PAD-NLP Algorithm Rules PAD One disease location keyword + one diagnostic keyword within two sentences 1) No PAD criteria Non-PAD 2) One exclusion keyword 2017 MFMER slide-10
11 Included Note Types Note Sections Service Groups Consult Impression / Report / Plan Primary Care Subsequent Visit Diagnosis Hospital Internal Medicine Patient Progress Principal/primary Diagnosis General Medicine Supervisory Secondary Diagnoses Family Medicine Limited Exam Past Medical/Surgical History Critical Care Specialty Evaluation Ongoing Care Urgent Care Multisystem Evaluation Immunizations Cardiology Injection Key Findings / Test Results Vascular Educational Visit Pre-Procedure Information Pulmonary Hospital Service Transfer Post-Procedure Information Oncology Vital Signs Nephrology Current Medications Neurology Revision History Pathology Special Instructions Gastroenterology Advance Directives Vascular Wound Care Discharge Activity Vascular Surgery Final Pathology Diagnosis Cardiac Surgery 2017 MFMER slide-11
12 Excluded Note Types Note Sections Service Groups Miscellaneous Chief Complaint Orthopedic Test- Oriented Miscellaneous History of Present Illness Podiatry Dismissal Summary Family History Endocrinology Therapy System Reviews Emergency Medicine Emergency Medicine Hospital Admission Note Visit Anticipated Problems and Interventions Allergy Hospital Admission Note Informed Consent Dermatology Emergency Medicine Visit Patient Education Sports Medicine Physical Examination Spine Center Work Rehabilitation Plastic Surgery Nursing Home Social Services Addiction Afzal et al: J Vasc Surg, MFMER slide-12
13 1569 patients 806 cases 763 controls Average age: 71 years 44% women 90% white REP PAD Cohort ABI test date 21-day MFMER slide-13
14 2017 MFMER slide-14
15 Performance of PAD-NLP algorithm vs. gold standard (ABI) PPV 0.93 Sensitivity 0.70 NPV 0.80 Specificity MFMER slide-15
16 Temporality of PAD-NLP Algorithm Compared temporal association between PAD- NLP algorithm inception date (date on which NLP algorithm classified patient as PAD) with gold standard index date for each PAD patient For true positive cases, difference between NLP algorithm inception date and gold standard index date was measured in days 2017 MFMER slide-16
17 Temporality of PAD-NLP Algorithm Before gold standard index date 329 cases (41%) At gold standard index date 93 cases (12%) After gold standard index date but within 21 day-window 141 cases (18%) 2017 MFMER slide-17
18 Temporality of PAD-NLP Algorithm Number of patients true positives < to to to to to to 20 Number of days from ABI test 2017 MFMER slide-18
19 Discussion PAD-NLP algorithm identified PAD cases from clinical notes with high PPV Prior to ABI test date in 41% of the cases from the community Delay in establishing PAD diagnosis despite presence of PAD symptoms 2017 MFMER slide-19
20 Study Limitations Data were retrieved from a single academic medical center Results may not be generalized to other practice settings 2017 MFMER slide-20
21 Clinical Implications Accurate and timely detection of actual or possible PAD will: Remind clinicians to order ABI testing confirming diagnosis of PAD Implement risk modification strategies in PAD patients PAD-NLP algorithm may be incorporated to clinical CDS to identify PAD patients Future studies will evaluate impact of CDS system on outcomes in PAD patients 2017 MFMER slide-21
22 Conclusions PAD-NLP surveillance algorithm enabled early identification of PAD with high PPV This may promote diagnosis earlier in the course of PAD 2017 MFMER slide-22
23 Acknowledgements Grants NHLBI: K01HL NHGRI: HG04599 and HG NIA: R01AG NIGMS: R01GM102283A MFMER slide-23
24 Questions? 2017 MFMER slide-24
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