Coding practice in national and regional kidney biopsy registries

Design and methodology of the PRIMETIME 1 cohort study: PRecIsion MEdicine based on kidney TIssue Molecular interrogation in diabetic nEphropathy

Background

Clinical features of diabetic kidney disease alone cannot differentiate between the histopathology that defines diabetic nephropathy (DN) and non-diabetic nephropathy (NDN). A kidney biopsy is necessary to make the definitive diagnosis of DN. However, there is no consensus on when to perform a kidney biopsy in individuals with diabetes and kidney disease. Furthermore, the implications of NDN versus DN for management, morbidity and kidney prognosis are unclear. To address the gap in knowledge, we aimed to create a national retrospective cohort of people with diabetes and a performed kidney biopsy.

Methods

Adults diagnosed with diabetes in Denmark between 1996 and 2020 who had a kidney biopsy performed were included. The cohort was established by linking a nationwide diabetes registry with the Danish Pathology Registry. Data from 11 national registries and databases were compiled. The type of kidney disease was classified using a three-step analysis of Systematized Nomenclature of Medicine codes reported in relation to the histopathological examinations of kidney tissue. The final cohort and classification of kidney disease was as follows: out of 485 989 individuals with diabetes 2586 were included, 2259 of whom had type 2 diabetes. We were able to classify 599 (26.5%) with DN, 703 (31.1%) with NDN and 165 (7.3%) with mixed disease in individuals with type 2 diabetes. In individuals with type 1 diabetes, 132 (40.4%) had DN, 73 (22.3%) NDN and 39 (11.9%) mixed disease. The remaining could not be classified or had normal histology. The overall median (Q1-Q3) follow-up time was 3.8 (1.6-7.2) years.

Conclusions

This cohort is a novel platform based on high-quality registry data for important longitudinal studies of the impact of kidney disease diagnosis on prognosis. With regular updates of data from the Danish registries, the presented follow-up will increase over time and is only limited by emigration or death.

The Development of a Comprehensive Clinicopathologic Registry for Glomerular Diseases Using Natural Language Processing

Background

Glomerulonephritis (GN) represents a common cause of chronic kidney disease, and treatment to slow or prevent progression of GN is associated with significant morbidity. Large patient registries have improved the understanding of risk stratification, treatment selection, and definitions of treatment response in GN, but can be resource-intensive, with incomplete patient capture.

Objective

To describe the creation of a comprehensive clinicopathologic registry for all patients undergoing kidney biopsy in Manitoba, using natural language processing software for data extraction from pathology reports, as well as to describe cohort characteristics and outcomes.

Design

Retrospective population-based cohort study.

Setting

Tertiary care center in the province of Manitoba.

Patients

All patients undergoing a kidney biopsy in the province of Manitoba from 2002 to 2019.

Measurements

Descriptive statistics are presented for the most common glomerular diseases, along with outcomes of kidney failure and mortality for the individual diseases.

Methods

Data from native kidney biopsy reports from January 2002 to December 2019 were extracted into a structured database using a natural language processing algorithm employing regular expressions. The pathology database was then linked with population-level clinical, laboratory, and medication data, creating a comprehensive clinicopathologic registry. Kaplan-Meier curves and Cox models were constructed to assess the relationship between type of GN and outcomes of kidney failure and mortality.

Results

Of 2421 available biopsies, 2103 individuals were linked to administrative data, of which 1292 had a common glomerular disease. The incidence of yearly biopsies increased almost 3-fold over the study period. Among common glomerular diseases, immunoglobulin A (IgA) nephropathy was the most common (28.6%), whereas infection-related GN had the highest proportions of kidney failure (70.3%) and all-cause mortality (42.3%). Predictors of kidney failure included urine albumin-to-creatinine ratio at the time of biopsy (adjusted hazard ratio [HR] = 1.43, 95% confidence interval [CI] = 1.24-1.65), whereas predictors of mortality included age at the time of biopsy (adjusted HR = 1.05, 95% CI = 1.04-1.06) and infection-related GN (adjusted HR = 1.85, 95% CI = 1.14-2.99, compared with the reference category of IgA nephropathy).

Limitations

Retrospective, single-center study with a relatively small number of biopsies.

Conclusions

Creation of a comprehensive glomerular diseases registry is feasible and can be facilitated through the use of novel data extraction methods. This registry will facilitate further epidemiological research in GN.

The Cleveland Clinic Kidney Biopsy Epidemiological Project

BACKGROUND

The kidney biopsy is the gold standard for diagnosing glomerular diseases. Large-scale, epidemiologic studies describing the prevalence of kidney diseases are lacking, especially in the United States. We aimed to determine the spectrum of biopsy-proven kidney disease across the Cleveland Clinic enterprise.

METHODS

We identified all patients with a native kidney biopsy performed or reviewed at the Cleveland Clinic from January 2015 to September 2021. Retrospective chart review was performed to obtain clinical and demographic characteristics. Results were stratified by age, sex, race, and location to determine epidemiologic trends.

RESULTS

Of >9600 patients, we excluded transplant and donor biopsies and unavailable records, and included 4128 patients with native kidney biopsy data. The median age was 60 years, with 46% female patients. Self-reported racial demographics included 73% White, 22% Black, 3% multiracial, and 2% Asian background, with 5% Hispanic. Common diagnoses were: FSGS (n=633, 15%), diabetic kidney disease (DKD) (n=602, 15%), IgA nephropathy (n=319, 8%), lupus nephritis (LN) (n=289, 7%), pauci-immune glomerulonephritis (n=275, 7%), membranous nephropathy (n=211, 5%), and amyloidosis (n=110, 3%). There were 3322 patients in Ohio, with 361 patients in Florida. Using multivariate analysis, those aged >70 years were more likely to have FSGS, whereas those <45 years were more likely to have IgA nephropathy or LN. Males were more likely to have FSGS or IgAN, and less likely to have LN. Black patients were more likely to have FSGS, DKD, or LN. Hispanic patients were more likely to have DKD. Finally, patients in Florida were more likely to have LN. There was no change in the disease spectrum before and during the COVID-19 pandemic.

CONCLUSION

Our study catalogs the spectrum of biopsy-proven kidney disease across the Cleveland Clinic enterprise. This lays the foundation for glomerular disease clinical trials, and highlights the need for a standardized national kidney biopsy registry to bolster glomerular and kidney disease research in the United States.

Epidemiology and clinicopathological characteristics of native kidney disease in children in Flanders, Belgium

BACKGROUND

The Flemish Collaborative Glomerulonephritis Group (FCGG) registry is a population-based kidney biopsy registry that has been including all native kidney biopsies performed in children in Flanders (Belgium), since 2017.

METHODS

From 2017 to 2020, 148 pediatric (< 18 years) native kidney biopsies were included. Each biopsy received a histopathological and final nephrological diagnosis, and concordance between both was assessed. Disease chronicity, summarized by the Mayo Clinic Chronicity Score, was determined on 122 biopsies with > 5 glomeruli.

RESULTS

Kidney biopsy rate was high (29.0 biopsies per million children per year), median age was 10.0 years (IQR 5.8-14.7), and boys predominated (56.1% males). A total of 140 biopsies (94.6%) showed a representative pathology result. Glomerular disease was most prevalent, with IgA nephropathy/IgA vasculitis (43 biopsies, 29.1%) and minimal change disease (MCD) (29 biopsies, 19.6%) being the overall most frequent diagnoses. In general, diagnostic concordance was high (80.7%). In Alport syndrome and focal segmental glomerulosclerosis (FSGS), concordance was lower, as the nephrological diagnosis was often determined by results of genetic analysis. Nephrotic syndrome was the most frequent indication for kidney biopsy (31.8%) and was mainly caused by MCD and FSGS. The degree of disease chronicity on kidney biopsies was generally low, although 27.3% of biopsies with a diagnosis of FSGS showed moderate-to-severe chronic damage.

CONCLUSIONS

The presented epidemiological findings validate data from previous European registry studies and may inspire kidney biopsy registries worldwide to implement novel features such as clinicopathological concordance and chronicity grading. A higher resolution version of the Graphical abstract is available as Supplementary information.

Epidemiology of native kidney disease in Flanders: results from the FCGG kidney biopsy registry

Background

The Flemish Collaborative Glomerulonephritis Group (FCGG) registry is the first population-based native kidney biopsy registry in Flanders, Belgium. In this first analysis, we report on patient demographics, frequency distribution and incidence rate of biopsied kidney disease in adults in Flanders.

Methods

From January 2017 to December 2019, a total of 2054 adult first native kidney biopsies were included. A ‘double diagnostic coding’ strategy was used, in which every biopsy sample received a histopathological and final clinical diagnosis. Frequency distribution and incidence rate of both diagnoses were reported and compared with other European registries.

Results

The median age at biopsy was 61.1 years (interquartile range, 46.1–71.7); male patients were more prevalent (62.1%) and biopsy incidence rate was 129.3 per million persons per year. Immunoglobulin A nephropathy was the most frequently diagnosed kidney disease (355 biopsies, 17.3% of total) with a similar frequency as in previously published European registries. The frequency of tubulointerstitial nephritis (220 biopsies, 10.7%) and diabetic kidney disease (154 biopsies, 7.5%) was remarkably higher, which may be attributed to changes in disease incidence as well as biopsy practices. Discordances between histopathological and final clinical diagnoses were noted and indicate areas for improvement in diagnostic coding systems.

Conclusions

The FCGG registry, with its ‘double diagnostic coding’ strategy, provides useful population-based epidemiological data on a large Western European population and allows subgroup selection for future research.

Systematic reporting of medical kidney biopsies

The medical kidney biopsy has an important added value in patient care in nephrology. In order to facilitate communication between the pathologist and the nephrologist and optimize patient care, both the content and form of the medical kidney biopsy report matter. With some exceptions, current guidelines in nephropathology focus on content rather than form and, not surprisingly, medical kidney biopsy reports mostly consist of unformatted and often lengthy free text. In contrast, in oncology, a more systematic reporting called synoptic reporting has become the dominant method. Synoptic formats enable complete, concise and clear reports that comply with agreed upon standards. In this review we discuss the possibilities of systematic reporting in nephropathology (including synoptic reporting). Furthermore, we explore applications of electronic formats with structured data and usage of international terminologies or coding systems. The benefits include the timely collection of high-quality data for benchmarking between centres as well as for epidemiologic and other research studies. Based on these developments, a scenario for future medical kidney biopsy reporting is drafted.