Definition of a SNOMED CT pathology subset and microglossary, based on 1.17 million biological samples from the Catalan Pathology Registry.

SNOMED CT terminology is not backed by standard norms of encoding among pathologists. The vast number of concepts ordered in hierarchies and axes, together with the lack of rules of use, complicates the functionality of SNOMED CT for coding, extracting, and analyzing the data. Defining subgroups of SNOMED CT by discipline could increase its functionality. The challenge lies in how to choose the concepts to be included in a subset from a total of over 300,000. Besides, SNOMED CT does not cover daily need, as the clinical reality is dynamic and changing. To adapt SNOMED CT to needs in a flexible way, the possibility exists to create extensions. In Catalonia, most pathology departments have been migrating from SNOMED II to SNOMED CT in a bid to advance the development of the Catalan Pathology Registry, which was created in 2014 as a repository for all the pathological diagnoses. This article explains the methodology used to: (a) identify the clinico-pathological entities and the molecular diagnostic procedures not included in SNOMED CT; (b) define the theoretical subset and microglossary of pathology; (c) describe the SNOMED CT concepts used by pathologists of 1.17 million samples of the Catalan Pathology Registry; and (d) adapt the theoretical subset and the microglossary according to the actual use of SNOMED CT. Of the 328,365 concepts available for coding the diagnoses (326,732 in SNOMED CT and 1576 in Catalan extension), only 2% have been used. Combining two axes of SNOMED CT, body structure and clinical findings, has enabled coding most of the morphologies.

Estimation of lung cancer diagnosis and treatment costs based on a patient-level analysis in Catalonia (Spain).

BACKGROUND: Assessing of the costs of treating disease is necessary to demonstrate cost-effectiveness and to estimate the budget impact of new interventions and therapeutic innovations. However, there are few comprehensive studies on resource use and costs associated with lung cancer patients in clinical practice in Spain or internationally. The aim of this paper was to assess the hospital cost associated with lung cancer diagnosis and treatment by histology, type of cost and stage at diagnosis in the Spanish National Health Service. METHODS: A retrospective, descriptive analysis on resource use and a direct medical cost analysis were performed. Resource utilisation data were collected by means of patient files from nine teaching hospitals. From a hospital budget impact perspective, the aggregate and mean costs per patient were calculated over the first three years following diagnosis or up to death. Both aggregate and mean costs per patient were analysed by histology, stage at diagnosis and cost type. RESULTS: A total of 232 cases of lung cancer were analysed, of which 74.1% corresponded to non-small cell lung cancer (NSCLC) and 11.2% to small cell lung cancer (SCLC); 14.7% had no cytohistologic confirmation. The mean cost per patient in NSCLC ranged from 13,218 Euros in Stage III to 16,120 Euros in Stage II. The main cost components were chemotherapy (29.5%) and surgery (22.8%). Advanced disease stages were associated with a decrease in the relative weight of surgical and inpatient care costs but an increase in chemotherapy costs. In SCLC patients, the mean cost per patient was 15,418 Euros for limited disease and 12,482 Euros for extensive disease. The main cost components were chemotherapy (36.1%) and other inpatient costs (28.7%). In both groups, the Kruskall-Wallis test did not show statistically significant differences in mean cost per patient between stages. CONCLUSIONS: This study provides the costs of lung cancer treatment based on patient file reviews, with chemotherapy and surgery accounting for the major components of costs. This cost analysis is a baseline study that will provide a useful source of information for future studies on cost-effectiveness and on the budget impact of different therapeutic innovations in Spain.

REGSTATTOOLS: freeware statistical tools for the analysis of disease population databases used in health and social studies.

BACKGROUND: The repertoire of statistical methods dealing with the descriptive analysis of the burden of a disease has been expanded and implemented in statistical software packages during the last years. The purpose of this paper is to present a web-based tool, REGSTATTOOLShttp://regstattools.net intended to provide analysis for the burden of cancer, or other group of disease registry data. Three software applications are included in REGSTATTOOLS: SART (analysis of disease's rates and its time trends), RiskDiff (analysis of percent changes in the rates due to demographic factors and risk of developing or dying from a disease) and WAERS (relative survival analysis). RESULTS: We show a real-data application through the assessment of the burden of tobacco-related cancer incidence in two Spanish regions in the period 1995-2004. Making use of SART we show that lung cancer is the most common cancer among those cancers, with rising trends in incidence among women. We compared 2000-2004 data with that of 1995-1999 to assess percent changes in the number of cases as well as relative survival using RiskDiff and WAERS, respectively. We show that the net change increase in lung cancer cases among women was mainly attributable to an increased risk of developing lung cancer, whereas in men it is attributable to the increase in population size. Among men, lung cancer relative survival was higher in 2000-2004 than in 1995-1999, whereas it was similar among women when these time periods were compared. CONCLUSIONS: Unlike other similar applications, REGSTATTOOLS does not require local software installation and it is simple to use, fast and easy to interpret. It is a set of web-based statistical tools intended for automated calculation of population indicators that any professional in health or social sciences may require.

A Population-Based Cross-Sectional Study of Paediatric Coeliac Disease in Catalonia Showed a Downward Trend in Prevalence Compared to the Previous Decade.

(1) Background: Previous studies showed an increased prevalence and incidence of coeliac disease (CD) over time. The objective is to ascertain whether the CD prevalence in Catalonia (a region of Southern Europe) among children aged 1-5 is as high as previously found in 2004-2009; (2) Methods: From 2013 to 2019, 3659 subjects aged 1-5 years were recruited following the previously used methodology. Factors with a potential impact on CD prevalence were investigated; (3) Results: In 2013-2019, 43/3659 subjects had positive serology, giving a standardised seroprevalence of 12.55/1000 (95% CI: 8.92; 17.40), compared to 23.62 (13.21; 39.40) in 2004-2007. The biopsy-proven crude prevalence was 7.92/1000 (95% CI: 5.50; 11.30), and the crude prevalence based on ESPGHAN criteria was 8.74/1000 (95% CI: 6.20-12.30). In contrast to 2004-2009, we did not find differences in the seroprevalence rates between 1 and 2 years vs. 3 and 4 years of age (age percentage of change -7.0 (-29.5; 22.8) vs. -45.3 (-67.5; -8.0)). Rotavirus vaccination was the most remarkable potential protective factor (48% vs. 9% in 2004-2009; p < 0.0001), but not the time of gluten introduction. (4) Conclusion: The present study did not confirm a worldwide CD prevalence increase and emphasizes the need to perform prevalence studies over time using the same methodology in the same geographical areas.

How cancer registries can detect neoplasms in pathology laboratories that code with SNOMED CT terminology? An actual, simple and flexible solution.

BACKGROUND: Pathology laboratories are one of the main information sources for cancer registries and have traditionally been coded with SNOMED; some of them are migrating to SNOMED CT (SCT). Cancer registries encode topography and morphology of neoplasms by the International Classification of Diseases for Oncology (ICD-O). ICD-O updates morphology with WHO Classification of Tumors (Blue-Books). Morphological codes of the ICD-O, Blue-Books and SNOMED (former SNOMEDID) have always coincided. In 2017, SCT removed the SNOMEDID. OBJECTIVES: to define neoplastic and topographic subsets in SCT and map them to ICD-O-3.1/Blue-Books; reduce the original number of SCT concepts; correctly identify neoplasms in the laboratories in accordance with international cancer registry rules. METHODOLOGY: SCT neoplastic concepts were identified by manual revision and SCT resources ("is a", "Associated morphology" relationships; Simple Map Reference Set). Topographic concepts were extracted from the body structure hierarchy of SCT. Both subsets were mapped to ICD-O-3.1/Blue-Books, afterwards. Updating algorithms were designed to automate and update each subset with every SCT release. The process of neoplasms identification was validated in a sample of 5212 specimens with 7378 records from 8 Catalan hospitals. RESULTS: The number of concepts in neoplastic and topographic subsets (16,448 and 32,278) was reduced after the mapping to ICD-O-3.1/Blue-Books (2115 and 330, respectively). Neoplastic subset classified the specimens correctly in the 98.6% of the specimens. CONCLUSIONS: This article presents a flexible tool to exhaustively identify neoplasms in pathology laboratories that code with SCT, following international PBCRs standards and in line with the pathologists, oncologists and epidemiologists' needs.

[Relative survival computation. Comparison of methods for estimating expected survival]. / Cálculo de la supervivencia relativa. Comparación de métodos de estimación de la supervivencia esperada.

Relative survival is the most commonly used method to determine survival in patients diagnosed with cancer. This method takes into account estimation of expected survival in cancer patients based on the observed mortality in the geographical area to which they belong. The most frequently used methods for estimation of expected survival are the Ederer (I and II) and Hakulinen methods. Survival tables for the geographical areas stratified by age and calendar year are required for these calculations. The present article presents an example of how to perform these estimations and how to choose the most appropriate method for the type of analysis to be performed. This article shows that if the follow-up of the cohort is less than 10 years, any of these methods should give similar results. However, the Hakulinen method is preferred, since it accounts for heterogeneity due to potential withdrawals.

A prospective study of outcomes of emergency and elective surgeries for complicated colonic cancer.

BACKGROUND: Although a significantly decreased long-term survival has been observed in patients undergoing surgery for complicated colorectal tumors compared with uncomplicated ones, the role of radical oncologic surgery on emergency colonic cancer is not defined clearly. The aim of this study was to analyze the efficacy of a curative emergency surgery in terms of tumor recurrence and cancer-related survival compared with elective colonic surgery. METHODS: Between January 1996 and December 1998, all patients with colonic cancer deemed to have undergone a curative resection were considered for inclusion in this prospective study. Patients were classified into 2 groups: group 1, after emergency surgery for complicated colonic cancer, and group 2, patients undergoing elective surgery. The main end points were cancer-related survival and the probability of being free from recurrence at 3 years. RESULTS: Of the 266 patients included in the study, 59 patients (22.2%) were in group 1 and 207 patients (77.8%) were in group 2. Postoperative mortality was higher in group 1 (P=.0004). After patients were stratified by the tumor node metastasis system, differences between the groups with respect to overall survival of stage II tumors (P=.0728), the probability of being free from recurrence (P=.0827), and cancer-related survival (P=.1071) of stage III cancers did not reach statistical significance. Differences were observed for the overall survival in stage III tumors (P=.0007), and for the probability of being free from recurrence (P=.0011) and cancer-related survival (P=.0029) in stage II cancers. When patients with elective stage II tumors presenting 1 or more negative prognostic factor were compared with emergency patients affected by a stage II colonic cancer, no differences were observed. CONCLUSION: Curative surgeries for complicated colonic cancer are acceptable in emergency conditions. Cancer-related survival and recurrence in patients with complicated colonic cancers may approach that of elective surgery if a surgical treatment with radical oncologic criteria is performed.

[Survival and recurrence in the multidisciplinary approach of colorectal cancer]. / Supervivencia y recidiva en el tratamiento multidisciplinario del carcinoma colorrectal.

BACKGROUND AND OBJECTIVE: Colorectal cancer is one of the most frequent causes of death in the general population. Our aim was to analyze our experience in the multidisciplinary approach of colorectal carcinoma during a three year period. PATIENTS AND METHOD: Between January 1996 and December 1998, we studied prospectively 807 patients with colorectal cancer. The epidemiology, treatment and outcome(recurrence and survival) were analyzed. The minimum follow-up was 3 years. RESULTS: There were 598 colon (65.5%) and 279 rectal (34.5%) tumors in all the series. Surgical treatment was elective in 84% and urgent in 16%, and was considered radical in 598 cases (74.1%). Chemotherapy or radiotherapy was administered in 49.6% and 18.3% patients, respectively. The overall 3-year survival was as follows: stage I 97.5%, stage II 90.6%, stage III 75.2%, and stage IV 12.6%. The 3-year free-disease survival was as follows: in colon cancer 97.8% for stage I, 87.3% for stage II, and 71.4% for stage III; and in rectal cancer 96.8% for stage I, 85.1% for stage II, and 75.4% for stage III. During the follow-up 124 patients (20.7%) developed recurrence: local (2.8%), systemic (15.9%) or both (2%). The three-year survival in operated patients with liver metastases was 61.9%. CONCLUSIONS: We have observed adequate survival and recurrence rates which are the result are of systematic protocols established by a multidisciplinary team.

Trends in the surgical procedures of women with incident breast cancer in Catalonia, Spain, over a 7-year period (2005-2011).

BACKGROUND: Breast cancer (BC) is the most frequent cancer in women, accounting for 28% of all tumors among women in Catalonia (Spain). Mastectomy has been replaced over time by breast-conserving surgery (BCS) although not as rapidly as might be expected. The aim of this study was to assess the evolution of surgical procedures in incident BC cases in Catalonia between 2005 and 2011, and to analyze variations based on patient and hospital characteristics. METHODS: We processed data from the Catalonian Health Service's Acute Hospital Discharge database (HDD) using ASEDAT software (Analysis, Selection and Extraction of Tumor Data) to identify all invasive BC incident cases according to the codes 174.0-174.9 of the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) that were attended for the one-year periods in 2005, 2008 and 2011. Patients were classified according to surgical procedures (BCS vs mastectomy, and immediate vs delayed reconstruction), and results were compared among periods according to age, stage, comorbidity and hospital level. RESULTS: BC surgical procedures were performed in more than 80% of patients. Surgical cases showed a significant increasing trend in the proportion of women aged 50-69 years, more advanced disease stages, higher comorbidity and they were attended in hospitals of less complexity level throughout the study period. Similar pattern was found for patients treated with BCS, which increased significantly from 67.9% in 2005 to 74.0% in 2011.Simple lymph node removal increased significantly (from 48.8% to 71.4% and from 63.6% to 67.8% for 2005 and 2011 in conservative and radical surgery, respectively). A slightly increase in the proportion of mastectomized young women (from 28% in 2005 to 34% in 2011) was detected, due to multiple factors. About 22% of women underwent post-mastectomy breast reconstruction, this being mostly immediate. CONCLUSIONS: The use of HDD linked to the ASEDAT allowed us to evaluate BC surgical treatment in Catalonia. A consolidating increasing trend of BCS was observed in women aged 50-69 years, which corresponds with the pattern in most European countries. Among the mastectomized patients, immediate breast reconstructions have risen significantly over the period 2005-2011.

[Statistical Analysis of Rates and Trends (SART): a web-based tool for statistical calculation of population indicators]. / SART (Statistical Analysis of Rates and Trends): herramienta vía web para el cálculo estadístico de indicadores poblacionales.

We propose a web-based tool (SART: http://regstattools.net/sart.html) that automates calculations to obtain various population indicators that can be used for the control of diseases or health events. SART has four modules: a) a descriptive module that allows calculation of the number of cases and their percentage, the crude rate, the adjusted rate, the truncated rate and the cumulative rate; b) the estimated annual percentage change of rates; c) calculation of expected cases; and d) the standardized incidence of mortality ratio. SART requests a base file and input parameters from the user before processing the data. The data and the results obtained are processed and then sent by email to the user. The results are provided by sex and for each of the study variables (diseases, ethnic groups, geographic areas...) introduced into the base file.

Monitoring the decreasing trend of testicular cancer mortality in Spain during 2005-2019 through a Bayesian approach.

PURPOSE: To assess time trends of testicular cancer (TC) mortality in Spain for period 1985-2019 for age groups 15-74 years old through a Bayesian age-period-cohort (APC) analysis. METHODS: A Bayesian age-drift model has been fitted to describe trends. Projections for 2005-2019 have been calculated by means of an autoregressive APC model. Prior precision for these parameters has been selected through evaluation of an adaptive precision parameter and 95% credible intervals (95% CRI) have been obtained for each model parameter. RESULTS: A decrease of -2.41% (95% CRI: -3.65%; -1.13%) per year has been found for TC mortality rates in age groups 15-74 during 1985-2004, whereas mortality showed a lower annual decrease when data was restricted to age groups 15-54 (-1.18%; 95% CRI: -2.60%; -0.31%). During 2005-2019 is expected a decrease of TC mortality of 2.30% per year for men younger than 35, whereas a leveling off for TC mortality rates is expected for men older than 35. CONCLUSIONS: A Bayesian approach should be recommended to describe and project time trends for those diseases with low number of cases. Through this model it has been assessed that management of TC and advances in therapy led to decreasing trend of TC mortality during the period 1985-2004, whereas a leveling off for these trends can be considered during 2005-2019 among men older than 35.

Colorectal cancer mortality in Spain: trends and projections for 1985-2019.

BACKGROUND AND AIM: To describe colorectal cancer (CRC) mortality trends during 1985-2004 and to estimate CRC mortality projections for the period 2005-2019 in Spain. MATERIAL AND METHODS: A Bayesian age-period-cohort analysis has been carried out to investigate the effect of the age, period, and birth cohort on CRC mortality in Spain. Mortality projections until 2019 were based on the age-period-cohort model. RESULTS: During 1985-1994, CRC mortality increased in both sexes (3.9% yearly in men and 1.5% in women). After 1995, CRC mortality increased in men (1.6%) and leveled off in women (-0.6%). Colon cancer mortality increased for the whole period in men, this increase being lower in the second decade (1985-1994: 5.0%; 1995-2004: 1.8%). In women, colon cancer mortality increased in the first decade (2.8%) and leveled off during the second decade (-0.1%). Rectal cancer mortality increased in men (1.2%) and decreased in women (-1.1%) during the whole study period. Projections showed an increase in the number of CRC deaths in men older than 60 years and a level off in women. CONCLUSION: Although mass screening for CRC in Spain has not been available, the favorable recent changes in CRC mortality trends observed after 1995 could be related to progress in diagnosis and treatment. The projected number of deaths could be used as reference scenario for assessing future impact of new treatments as well as the potential impact of future population-based screening when introduced.

WAERS: an application for Web-assisted estimation of relative survival.

Net cancer survival estimation is usually performed by computing relative survival (RS), which is defined as the ratio between observed and expected survival rates. The mortality of a reference population is required in order to compute the expected survival rate, which can be performed using a variety of statistical packages. A new Web interface to compute RS, called WAERS, has been developed by the Catalan Institute of Oncology. The reference population is first selected, and then the RS of a cohort is computed. A remote server is used for this purpose. A mock example serves to illustrate the use of the tool with a hypothetical cohort, for which RS is estimated based on three different reference populations (a province of Spain, an autonomous community (Region), and the entire Spanish population). At present, only mortality tables for different areas of Spain are available. Future improvements of this application will include mortality tables of Latin American and European Union countries, and stratified (control variable) analysis. This application can be also useful for cohort mortality studies and for registries of several diseases.

Imaging techniques contribute to increased surgical rescue of relapse in the follow-up of colorectal cancer.

PURPOSE: This study analyzes the results of a follow-up policy in colorectal cancer at our institution and evaluates the possible benefit provided by each test performed. PATIENTS AND METHODS: Six hundred nineteen patients who had radical surgery and adjuvant treatment for colorectal cancer were followed up with a protocol that included carcinoembryonic antigen testing and clinical examination every three months for the first two years, every four months in the third year, and every six months in the fourth and fifth years. Chest X-ray and colonoscopy were performed yearly for five years and abdominal ultrasound was done every six months for the first three years and yearly afterward. Abdominopelvic computerized tomography was performed yearly for the first two years in cases with rectal cancer. If relapse was detected, all operable cases underwent surgery if possible. RESULTS: Between 1993 and 1999, 619 patients were followed-up. Mean follow-up was 66.9 months. Two hundred eight relapses were detected, 83.6 percent in the first three years and 73 (35.1 percent) underwent surgical resection. Carcinoembryonic antigen testing detected 44.2 percent of recurrences and 31.9 percent of them were operated on. Imaging techniques detected a lower percentage of recurrences (18.7 percent) but were more often resectable: 52 percent and 60 percent of the recurrences detected by computerized tomography and chest X-ray, respectively, underwent surgery. Median overall survival of patients with resected relapse was 62 months, significantly higher than those who were not operable (12.4 months). CONCLUSION: Imaging techniques in the surveillance of resected colorectal cancer contribute to early detection of relapse with a high proportion of operable metastatic disease.

Tumor thymidylate synthase 1494del6 genotype as a prognostic factor in colorectal cancer patients receiving fluorouracil-based adjuvant treatment.

PURPOSE: The purpose of this study was to analyze the value of germline and tumor thymidylate synthase (TS) genotyping as a prognostic marker in a series of colorectal cancer patients receiving adjuvant fluorouracil (FU) -based treatment. PATIENTS AND METHODS: One hundred twenty-nine colorectal cancer patients homogeneously treated with FU plus levamisole or leucovorin in the adjuvant setting were included. TS enhancer region, 3R G > C single nucleotide polymorphism (SNP), and TS 1494del6 polymorphisms were assessed in both fresh-frozen normal mucosa and tumor. Mutational analyses of TS and allelic imbalances were studied in all primary tumors and in 18 additional metachronic metastases. TS protein immunostaining was assessed in an expanded series of 214 tumors. Multivariate Cox models were adjusted for stage, differentiation, and location. RESULTS: Tumor genotyping (frequency of allelic loss, 26%) showed that the 3R/3R genotype was associated with a better outcome (hazard ratio [HR] = 0.38; 95% CI, 0.16 to 0.93; P = .020 for the recessive model). 3R G > C SNP genotyping did not add prognostic information. Tumor TS 1494del6 allele (frequency of allelic loss, 36%) was protective (for each allele with the deletion, based on an additive model, HR = 0.42; 95% CI, 0.22 to 0.82; P = .0034). Both polymorphisms were in strong linkage disequilibrium (D' = 0.71, P < .001), and the 3R/-6 base pair (bp) haplotype showed a significant overall survival benefit compared with the most prevalent haplotype 2R/+6bp (HR = 0.42; 95% CI, 0.20 to 0.85; P = .017). No TS point mutation was detected in primary tumors or metastases. TS protein immunostaining was not associated with survival or any of the genotypes analyzed. CONCLUSION: Tumor TS 1494del6 genotype may be a prognostic factor in FU-based adjuvant treatment of colorectal cancer patients.