Pancreatic cancer symptom trajectories from Danish registry data and free text in electronic health records
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
- Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Denmark
- Copenhagen University Hospital, Rigshospitalet, Blegdamsvej, Denmark
Figures
Figure 1 with 1 supplement
Comparison of pancreatic cancer symptoms in the Danish National Patient Registry (NPR) and electronic health records (EHRs).
(A) Symptoms before the pancreatic cancer diagnosis identified in NPR (NNPR = 24), by text mining of clinical notes from EHRs (Nnotes = 16) or in both data sources (Nboth = 57). (B) The top 10 most …
Figure 1—figure supplement 1
Comparing symptoms found from text mining, registry (NPR) and established well-known symptoms of pancreatic cancer.
Type 2 diabetes/new-onset diabetes was not included in the well-known symptoms list (Supplementary file 1a), since this is coded as a disease in the ICD-10 chapter. This comparison only covers the …
Figure 2 with 2 supplements
The most frequent text-mined symptoms from the clinical notes 5 years prior to pancreatic cancer diagnosis.
The most common and significant (p<0.05) symptoms in the text-mined clinical notes are shown with survival information and time to pancreatic cancer diagnosis (Supplementary file 3). The symptoms …
Figure 2—figure supplement 1
The most frequent registry-based symptoms from the NPR prior to pancreatic cancer diagnosis.
Significant symptoms are filtered so only those prior to a pancreatic cancer diagnosis with a RR>1 and p-value<0.05. Outlier dots has been removed to safeguard patient-sensitive information.
Figure 2—figure supplement 2
Staging information for pancreatic cancer patients.
(A) Pancreatic cancer cases with at least one clinical note 5 years prior to the cancer diagnosis. (B) Pancreatic cancer patients without any clinical notes 5 years prior to the cancer diagnosis. …
Figure 3 with 2 supplements
Symptom trajectories before and after pancreatic cancer diagnosis.
(A) The registry symptom trajectories consist of significant disease pairs with a Relative Risk (RR) >1 (Supplementary file 1d). Each trajectory has a minimum of 100 patients. (B) Symptom …
Figure 3—figure supplement 1
Registry-based trajectories with both symptoms and diseases.
Significant length 3 and length 4 trajectories for the registry-based analysis using the 18,523 pancreatic cancer cases from the Danish National Patient Registry. The diseases and chapters are from …
Figure 3—figure supplement 2
Survival of patients in significant trajectories.
(A) Survival in months for patients in the registry-based disease trajectories for both length 3 and 4 (N=10,542). (B) Survival in months for patients in the text-mined symptom trajectories (N=311). …
Figure 4
The text mining pipeline.
A dictionary was generated with symptoms and expanded with word endings to capture multiple forms of the same symptom. Afterwards, the dictionary and the corpus (clinical notes) were tokenized to …
Tables
Table 1
Data set and patient characteristics.
| General cohort information | The National Patient Registry (NPR) | Electronic Health Records (EHRs) |
|---|---|---|
| Data set timeline | 1994–2018 | 2006–2016 |
| N pancreatic cancer patients | 23,592 | 3078 |
| N controls | 6.9 million | 30,780 |
| Pancreatic cancer cohort information | ||
| Female | 9328 (50.4%) | 1506 (48.9%) |
| Male | 9195 (49.6%) | 1572 (51.1%) |
| Mean age at diagnosis (female/male) | 73/69 | 72/70 |
| Age distributions (years) | ||
| <40 | 139 (0.8%) | 16 (0.52%) |
| 40–50 | 733 (4.0%) | 107 (3.48%) |
| 50–60 | 2523 (13.6%) | 352 (11.4%) |
| 60–70 | 5288 (28.5%) | 941 (30.6%) |
| 70–80 | 6017 (32.5%) | 1037 (33.7%) |
| >80 | 3821 (20.6%) | 625 (20.3%) |
