| Literature DB >> 30225406 |
Sudhi G Upadhyaya1, Dennis H Murphree1, Che G Ngufor1, Alison M Knight2, Daniel J Cronk3, Robert R Cima4,5, Timothy B Curry2,6, Jyotishman Pathak1, Rickey E Carter1, Daryl J Kor2.
Abstract
OBJECTIVE: To develop and validate a phenotyping algorithm for the identification of patients with type 1 and type 2 diabetes mellitus (DM) preoperatively using routinely available clinical data from electronic health records. PATIENTS AND METHODS: We used first-order logic rules (if-then-else rules) to imply the presence or absence of DM types 1 and 2. The "if" clause of each rule is a conjunction of logical and, or predicates that provides evidence toward or against the presence of DM. The rule includes International Classification of Diseases, Ninth Revision, Clinical Modification diagnostic codes, outpatient prescription information, laboratory values, and positive annotation of DM in patients' clinical notes. This study was conducted from March 2, 2015, through February 10, 2016. The performance of our rule-based approach and similar approaches proposed by other institutions was evaluated with a reference standard created by an expert reviewer and implemented for routine clinical care at an academic medical center.Entities:
Keywords: CCW, Chronic Condition Data Warehouse; DDC, Durham Diabetes Coalition; DM, diabetes mellitus; EHR, electronic health record; HbA1c of NYC, Hemoglobin A1c of New York City; HbA1c, hemoglobin A1c; ICD-9-CM, International Classification of Diseases, Ninth Revision, Clinical Modification; MICS, Mayo Integrated Clinical Systems; NLP, natural language processing; SUPREME-DM, Surveillance, Prevention, and Management of Diabetes Mellitus; T1DM, type 1 diabetes mellitus; T2DM, type 2 diabetes mellitus; eMERGE, Electronic Medical Records and Genomics
Year: 2017 PMID: 30225406 PMCID: PMC6135013 DOI: 10.1016/j.mayocpiqo.2017.04.005
Source DB: PubMed Journal: Mayo Clin Proc Innov Qual Outcomes ISSN: 2542-4548
Figure 1Overview of simple first-order rules–based DM phenotyping model. DM = diabetes mellitus; EHR = electronic health record; ICD-9-CM = International Classification of Diseases, Ninth Revision, Clinical Modification.
Accuracy of Mayo Clinic Proposed Method Compared With Preexisting Methods Proposed by Other Authors
| Measure | Mayo Clinic proposed | CCW | DDC | SUPREME-DM | eMERGE | HbA1c of NYC | Harvard Medical School | Mayo Clinic manual |
|---|---|---|---|---|---|---|---|---|
| Sensitivity | 0.99 (0.90-0.99) | 0.67 (0.63-0.70) | 0.92 (0.90-0.94) | 0.64 (0.60-0.68) | 0.55 (0.51-0.58) | 0.48 (0.44-0.52) | 0.93 (0.91-0.95) | 0.84 (0.82-0.87) |
| Specificity | 0.99 (0.99-1.00) | 1.00 (0.99-1.00) | 0.94 (0.94-0.95) | 0.97 (0.96-0.97) | 1.00 (0.99-1.00) | 0.99 (0.99-0.99) | 0.88 (0.87-0.89) | 0.98 (0.98-0.99) |
| Positive predictive value | 0.99 (0.99-0.99) | 0.94 (0.93-0.94) | 0.98 (0.98-0.98) | 0.93 (0.92-0.94) | 0.91 (0.91-0.92) | 0.90 (0.88-0.90) | 0.98 (0.98-0.99) | 0.97 (0.96-0.97) |
| Negative predictive value | 0.99 (0.99-1.00) | 1.00 (0.98-1.00) | 0.78 (0.75-0.80) | 0.81 (0.77-0.84) | 1.00 (0.98-1.00) | 0.94 (0.91-0.96) | 0.61 (0.58-0.64) | 0.92 (0.90-0.94) |
| Accuracy | 0.99 (0.99-0.99) | 0.94 (0.93-0.95) | 0.94 (0.93-0.95) | 0.91 (0.90-0.92) | 0.92 (0.91-0.93) | 0.90 (0.89-0.93) | 0.89 (0.88-0.90) | 0.96 (0.95-0.97) |
| McNemar χ2 test (sensitivity) | NA | 223.00 | 43.31 | 239.00 | 305.00 | 348.01 | 39.09 | 97.15 |
| NA | <.01 | <.01 | <.01 | <.01 | <.01 | <.01 | <.01 | |
| McNemar χ2 test (specificity) | NA | 1.00 | 176.02 | 98.04 | 1.00 | 16.20 | 398.01 | 41.09 |
| NA | .32 | <.01 | <.01 | .32 | <.01 | <.01 | <.01 | |
| Total patients identified, n | 684 | 460 | 815 | 543 | 377 | 350 | 1043 | 626 |
CCW = Chronic Condition Data Warehouse; DDC = Durham Diabetes Coalition; eMERGE = Electronic Medical Records and Genomics Network; HbA1c of NYC = Hemoglobin A1c of New York City; NA = not applicable; SUPREME-DM, Surveillance = Prevention, and Management of Diabetes Mellitus.
Patients’ Characteristics at Baseline and Predisposing Factors for DMa,b
| Characteristic | All patients, (N=4208) | Patients with DM present (n=684) | Patients with DM absent (n=3524) |
|---|---|---|---|
| Age (y) | |||
| <18 | 501 (11.91) | 12 (1.75) | 489 (13.88) |
| 18-21 | 83 (1.97) | 1 (0.15) | 82 (2.33) |
| 22-29 | 201 (4.77) | 10 (1.46) | 191 (5.42) |
| 30-39 | 337 (8.00) | 29 (4.24) | 308 (8.74) |
| 40-49 | 455 (10.81) | 94 (13.17) | 361 (10.24) |
| 50-65 | 1256 (29.84) | 284 (41.52) | 972 (27.58) |
| 66-80 | 1129 (26.82) | 230 (33.63) | 899 (25.51) |
| >80 | 246 (5.84) | 24 (3.51) | 222 (6.30) |
| BMI | |||
| Underweight | 378 (8.98) | 5 (0.73) | 373 (10.58) |
| Normal | 1105 (26.26) | 63 (9.21) | 1042 (29.57) |
| Overweight | 1199 (28.49) | 176 (25.73) | 1023 (29.03) |
| Obese | 1489 (35.38) | 439 (64.18) | 1050 (29.80) |
| Unavailable | 37 (0.88) | 1 (0.15) | 36 (1.02) |
| Sex | |||
| Female | 2152 (51.14) | 298 (43.57) | 1854 (52.61) |
| Male | 2056 (48.86) | 386 (56.43) | 1670 (47.39) |
| Race | |||
| American Indian/American Native | 25 (0.59) | 14 (2.14) | 11 (0.31) |
| Non-Hispanic white | 3848 (91.44) | 615 (90.05) | 3233 (91.73) |
| African American | 66 (1.57) | 12 (1.68) | 54 (1.53) |
| African | 11 (0.26) | 1 (0.15) | 10 (0.28) |
| Asian | 67 (1.59) | 9 (1.23) | 58 (1.65) |
| Native Hawaiian/Pacific Islander | 5 (0.12) | 1 (0.15) | 4 (0.11) |
| Other | 186 (4.42) | 32 (4.59) | 154 (4.37) |
BMI = body mass index; DM = diabetes mellitus.
Values are n (%).
Figure 2Aggregate summary of cases identified by ICD-9-CM codes, medications, abnormal laboratory values, and searches of free-text patient notes. DM = diabetes mellitus; ICD-9-CM = International Classification of Diseases, Ninth Revision, Clinical Modification.
Figure 3Cases identified by various, nonmutually exclusive combinations of ICD-9-CM codes, medications, abnormal laboratory values, and DM keywords within free-text patient notes. DM = diabetes mellitus; ICD-9-CM = International Classification of Diseases, Ninth Revision, Clinical Modification.
Overview of Differences Among Other Preexisting Methods Proposed by Other Authors
| Existing diabetes mellitus phenotype | Reference | Data elements used | Notes | |||
|---|---|---|---|---|---|---|
| Lab | Medications | Patient notes | ||||
| CCW | Chronic Condition Data Warehouse | x | Only | |||
| DDC | Spratt et al | x | x | x | ≥2 abnormal lab values, not more than 1 y apart | |
| SUPREME-DM | Desai et al | x | x | x | ≥2 abnormal lab values or | |
| eMERGE | Kho et al | x | x | x | Mainly designed to identify patients with T2DM and must satisfy ≥2 criteria | |
| HbA1c NYC | Chamany et al | x | Only HbA1c | |||
| Harvard Medical School | Klompas et al | x | x | x | Only abnormal lab value with no metformin requirement | |
CCW = Chronic Conditions Data Warehouse; DDC = Durham Diabetes Coalition; eMERGE = Electronic Medical Records and Genomics Network; HbA1c = hemoglobin A1c; HbA1c NYC = HbA1c of New York City; ICD-9 = International Classification of Diseases, Ninth Edition; lab = laboratory; SUPREME-DC = Surveillance, Prevention and Management of Diabetes Mellitus; T2DM = type 2 diabetes mellitus.