We obtained a data set (diagnoses by date) from the UW Medicine (the University of Washington Health System) enterprise data warehouse (EDW). The EDW includes patient data from over 4.5 million patients spanning ~25 years, and representing various clinical sites across the UW Medicine system including University of Washington Medical Center, Harborview Medical Center, and Northwest Hospital and Medical Center.
“Injury and poisoning” is a category of clinical affliction that includes any traumatic injury or poisoning and is coded as E-codes (E000-E999) or 800-999 codes using the ICD-9-CM diagnosis coding standard or S00-T99 or V00-Y99 codes using the ICD-10-CM coding standard, as defined in the CDC’s guidelines for traumatic injury and poisoning.[23,24] From the EDW, we selected records of all visits between January 1, 1994 and May 2, 2017 for patients who were over the age of 18 as of May 2, 2017 and where, for each visit, at least one ICD-9-CM code or ICD-10-CM code in the “Injury and poisoning” category was recorded. For each patient record, we collected patient visit information which included de-identified patient ID, diagnosis coding method (ICD-9-CM or ICD-10-CM), visit number identifier, admission date and time, diagnosis codes (ICD-9-CM or ICD-10-CM), and diagnosis code description. These data represent just over 3,000,000 unique trauma-related visits to the UW medical system made by over 650,000 unique individuals.
UW Medicine adopted the ICD-10-CM billing code system in mid-2015. In order to ensure we had consistent data throughout, we mapped ICD-10-CM codes to their ICD-9-CM equivalents, using the Center for Medicare and Medicaid Services (CMS) General Equivalence Mappings. Since ICD-10-CM has more detailed coding descriptions than ICD-9-CM, there is a potential for data loss when converting from ICD-10-CM to ICD-9-CM. While this may be an issue in some studies, we were more interested in the high level view of UW’s patient population, and this data loss was not a major concern for this study. We used a custom tool, DxCodeHandler (https://github.com/UWMooneyLab/DxCodeHandler), to handle code conversion, ICD hierarchy traversal, and diagnosis code manipulation (Additional File 1).
Obtaining Count Data
Per our selection criteria, each patient visit included one or more ICD-9-CM or ICD-10-CM billing codes representing the billing information for the patient visit. We attributed all codes appearing in a visit to the day that visit occurred such that each day was considered a collection of independent code counts. We also included all higher level categories in the ICD hierarchy along with the low level codes. For example, a day that had the code E880.0 (Accidental Fall on or from Escalator) would also have E880 (Accidental Fall from Stairs or Steps), E880-E888 (Accidental Falls), and E000-E999 (External Causes of Injury or Poisoning) counted on that day. This incorporation of multiple category levels was necessary because some real world events enrich different classes of injury such as large classes of injury (e.g. 800-829, Fractures), mid-level classes of injury (e.g. 989, Toxic Effect of Non-medicinal Substances), or specific injury types (e.g. 854.06, Intracranial injury with loss of consciousness).
Binomial Test and Hypothesis Testing
For each diagnosis code, both billable and parent codes, we tested the null hypothesis that the prevalence of each diagnosis code, when calculated against all trauma visits, was consistent across time. We tested this hypothesis using a binomial test, where we tested whether a diagnosis code is more or less prevalent in a given time period when compared to the expected prevalence if the null hypothesis were true. If a code-time period pair had a p-value less than the Bonferroni cutoff, we said that the code is enriched for that tested time period. We used an ɑ=0.01 when calculating the Bonferroni cut off for each experiment. We ran this test for every code that appears more than 10 times in our dataset for all four seasons and for all 365 (non-leap year) days. For each code-time period pair, we generated a score by calculating the -log(p-value) from the binomial test.
Enrichment of Seasons
To find seasonal statistical enrichment of ICD-9-CM billing codes we summed daily counts of each of the 4,582 poisoning and injury billing codes within each season. We defined Winter as December - February, Spring as March - May, Summer as June - August, and Autumn as September - November. For each season/code pair, we performed a binomial test, treating the sum of all codes in that season as the trials, and the count of the code in question for that season as the successes. The expected rate of appearance for each code in question was established by calculating its proportion of all trauma visits across all seasons and years. Thus, the p-value from this test is interpretable as the probability that these many codes or more would be seen in a given season under the null hypothesis that codes are evenly distributed across the year. We used a Bonferroni correction at n = 18,328 (4 x 4582). We also filtered out codes that appeared less than 10 times over the course of the 24-year period.
Enrichment of Dates
We used an analogous method to detect code enrichments for days of the year. Again, we computed the sum of codes occurring on each of the 365 (non-leap-day) days of the year. For each code/day pair, we performed a binomial test using the total number of codes used on that day as the number of trials, and the number of times the specific code of interest was used as the number of successes. The expected rate was derived from the baseline rate of appearance for the code of interest per day across the entire year when compared to the total number of trauma visits on that given day. We calculated a Bonferroni cutoff at n = 1,672,430 (4582 x 365). We counted codes as enriched if the p-value was less that the Bonferroni correction and the daily rate of the code was greater than the baseline expected rate of the code (we did not look at depletions). We also filtered out codes that appeared less than 10 times over the course of the 24 year dataset period.
We received an IRB non-human subjects research designation from the University of Washington Human Subjects Research Division to construct a dataset derived from all patient diagnoses from the EDW over the age of 18. (IRB number: STUDY00000669) Data was extracted by an honest broker, the UW Medicine Research IT data services team, and no patient identifiers were available to the research team.