The pooling of manpower and resources through the establishment of European reference networks and rare disease patient registries is a necessary area of collaboration for rare renal disorders

The value of single biomarkers in the diagnosis of silicosis: A meta-analysis

This study aims to establish a scientific foundation for early detection and diagnosis of silicosis by conducting meta-analysis on the role of single biomarkers in independent diagnosis. The combined sensitivity (Sen), specificity (Spe), positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic score, and diagnostic odds ratio (DOR) were 0.84 (95% confidence interval (CI): 0.77-0.90), 0.83 (95% CI: 0.78-0.88), 5.08 (95% CI: 3.92-6.59), 0.19 (95% CI: 0.13-0.27), 3.31 (95% CI: 2.88-3.74) and 27.29 (95% CI: 17.77-41.91), respectively. The area under the curve (AUC) was 0.90 (95% CI: 0.88-0.93). The Fagan plot shows a positive posterior probability of 82% and a negative posterior probability of 15%. This study establishes an academic basis for the swift identification, mitigation, and control of silicosis through scientific approaches. The assessed biomarkers offer precision and dependability in silicosis diagnosis, opening novel paths for early detection and intervention, thereby mitigating the disease burden associated with silicosis.

Challenges in mapping European rare disease databases, relevant for ML-based screening technologies in terms of organizational, FAIR and legal principles: scoping review

Background

Given the increased availability of data sources such as hospital information systems, electronic health records, and health-related registries, a novel approach is required to develop artificial intelligence-based decision support that can assist clinicians in their diagnostic decision-making and shorten rare disease patients' diagnostic odyssey. The aim is to identify key challenges in the process of mapping European rare disease databases, relevant to ML-based screening technologies in terms of organizational, FAIR and legal principles.

Methods

A scoping review was conducted based on the PRISMA-ScR checklist. The primary article search was conducted in three electronic databases (MEDLINE/Pubmed, Scopus, and Web of Science) and a secondary search was performed in Google scholar and on the organizations' websites. Each step of this review was carried out independently by two researchers. A charting form for relevant study analysis was developed and used to categorize data and identify data items in three domains - organizational, FAIR and legal.

Results

At the end of the screening process, 73 studies were eligible for review based on inclusion and exclusion criteria with more than 60% (n = 46) of the research published in the last 5 years and originated only from EU/EEA countries. Over the ten-year period (2013-2022), there is a clear cycling trend in the publications, with a peak of challenges reporting every four years. Within this trend, the following dynamic was identified: except for 2016, organizational challenges dominated the articles published up to 2018; legal challenges were the most frequently discussed topic from 2018 to 2022. The following distribution of the data items by domains was observed - (1) organizational (n = 36): data accessibility and sharing (20.2%); long-term sustainability (18.2%); governance, planning and design (17.2%); lack of harmonization and standardization (17.2%); quality of data collection (16.2%); and privacy risks and small sample size (11.1%); (2) FAIR (n = 15): findable (17.9%); accessible sustainability (25.0%); interoperable (39.3%); and reusable (17.9%); and (3) legal (n = 33): data protection by all means (34.4%); data management and ownership (22.9%); research under GDPR and member state law (20.8%); trust and transparency (13.5%); and digitalization of health (8.3%). We observed a specific pattern repeated in all domains during the process of data charting and data item identification - in addition to the outlined challenges, good practices, guidelines, and recommendations were also discussed. The proportion of publications addressing only good practices, guidelines, and recommendations for overcoming challenges when mapping RD databases in at least one domain was calculated to be 47.9% (n = 35).

Conclusion

Despite the opportunities provided by innovation - automation, electronic health records, hospital-based information systems, biobanks, rare disease registries and European Reference Networks - the results of the current scoping review demonstrate a diversity of the challenges that must still be addressed, with immediate actions on ensuring better governance of rare disease registries, implementing FAIR principles, and enhancing the EU legal framework.

Kidney Failure in Bardet-Biedl Syndrome

The aim of this study was to explore kidney failure (KF) in Bardet–Biedl syndrome (BBS), focusing on high‐risk gene variants, demographics, and morbidity. We employed the Clinical Registry Investigating BBS (CRIBBS) to identify 44 (7.2%) individuals with KF out of 607 subjects. Molecularly confirmed BBS was identified in 37 KF subjects and 364 CRIBBS registrants. KF was concomitant with recessive causal variants in 12 genes, with BBS10 the most predominant causal gene (26.6%), while disease penetrance was highest in SDCCAG8 (100%). Two truncating variants were present in 67.6% of KF cases. KF incidence was increased in genes not belonging to the BBSome or chaperonin‐like genes (p < 0.001), including TTC21B, a new candidate BBS gene. Median age of KF was 12.5 years, with the vast majority of KF occurring by 30 years (86.3%). Females were disproportionately affected (77.3%). Diverse uropathies were identified, but were not more common in the KF group (p = 0.672). Kidney failure was evident in 11 of 15 (73.3%) deaths outside infancy. We conclude that KF poses a significant risk for premature morbidity in BBS. Risk factors for KF include female sex, truncating variants, and genes other than BBSome/chaperonin‐like genes highlighting the value of comprehensive genetic investigation.

Generalizable EHR-R-REDCap pipeline for a national multi-institutional rare tumor patient registry

Objective

To develop a clinical informatics pipeline designed to capture large-scale structured Electronic Health Record (EHR) data for a national patient registry.

Materials and Methods

The EHR-R-REDCap pipeline is implemented using R statistical software to remap and import structured EHR data into the Research Electronic Data Capture (REDCap)-based multi-institutional Merkel Cell Carcinoma (MCC) Patient Registry using an adaptable data dictionary.

Results

Clinical laboratory data were extracted from EPIC Clarity across several participating institutions. Laboratory values (Labs) were transformed, remapped, and imported into the MCC registry using the EHR labs abstraction (eLAB) pipeline. Forty-nine clinical tests encompassing 482 450 results were imported into the registry for 1109 enrolled MCC patients. Data-quality assessment revealed highly accurate, valid labs. Univariate modeling was performed for labs at baseline on overall survival (N = 176) using this clinical informatics pipeline.

Conclusion

We demonstrate feasibility of the facile eLAB workflow. EHR data are successfully transformed and bulk-loaded/imported into a REDCap-based national registry to execute real-world data analysis and interoperability.

Healthcare data collected during routine clinical care in patient electronic health records (EHRs) can be curated and organized into disease-focused registries. For example, the Merkel Cell Carcinoma Patient Registry is a multi-institutional national database that utilizes real-world health care data to inform best practices, improve patient outcomes, and test hypotheses that require large data samples. However, many challenges arise when capturing patient-level details/data from the health records especially when this data must be aggregated across multiple institutions. Here, we describe a pipeline that (1)pulls large-scale data from the EHRs, (2)wrangles and remaps the data in a format appropriate for the database using R statistical software, and (3)imports the data in bulk for thousands of patients at a time into Research Electronic Data Capture (REDCap), the electronic data capture system that houses the data. The EHR-R-REDCap pipeline can be utilized to capture many patient data features from the participating institutions. Here, we demonstrate eLAB, the EHR-R-REDCap pipeline utilized by our Merkel Cell Carcinoma Patient Registry to capture thousands of laboratory values from the EHR for thousands of patients. We provide source code, examples, and instructions for adaptability for other clinical research projects that aim to collect large-scale laboratory data from the EHR.

The Quality Evaluation of Rare Disease Registries-An Assessment of the Essential Features of a Disease Registry

Rare disease (RD) registries aim to promote data collection and sharing, and facilitate multidisciplinary collaboration with the overall aim of improving patient care. Recommendations relating to the minimum standards necessary to develop and maintain high quality registries are essential to ensure high quality data and sustainability of registries. The aim of this international study was to survey RD registry leaders to ascertain the level of consensus amongst the RD community regarding the quality criteria that should be considered essential features of a disease registry. Of 35 respondents representing 40 RD registries, over 95% indicated that essential quality criteria should include establishment of a good governance system (ethics approval, registry management team, standard operating protocol and long-term sustainability plan), data quality (personnel responsible for data entry and procedures for checking data quality) and construction of an IT infrastructure complying with Findable, Accessible, Interoperable and Reusable (FAIR) principles to maintain registries of high quality, with procedures for authorized user access, erasing personal data, data breach procedures and a web interface. Of the 22 registries that performed a self-assessment, over 80% stated that their registry had a leader, project management group, steering committee, active funding stream, website, and user access policies. This survey has acceptability amongst the RD community for the self-quality evaluation of RD registries with high levels of consensus for the proposed quality criteria.

CureGN Study Rationale, Design, and Methods: Establishing a Large Prospective Observational Study of Glomerular Disease

RATIONALE & OBJECTIVES

Glomerular diseases, including minimal change disease, focal segmental glomerulosclerosis, membranous nephropathy, and immunoglobulin A (IgA) nephropathy, share clinical presentations, yet result from multiple biological mechanisms. Challenges to identifying underlying mechanisms, biomarkers, and new therapies include the rarity of each diagnosis and slow progression, often requiring decades to measure the effectiveness of interventions to prevent end-stage kidney disease (ESKD) or death.

STUDY DESIGN

Multicenter prospective cohort study.

SETTING & PARTICIPANTS

Cure Glomerulonephropathy (CureGN) will enroll 2,400 children and adults with minimal change disease, focal segmental glomerulosclerosis, membranous nephropathy, or IgA nephropathy (including IgA vasculitis) and a first diagnostic kidney biopsy within 5 years. Patients with ESKD and those with secondary causes of glomerular disease are excluded.

EXPOSURES

Clinical data, including medical history, medications, family history, and patient-reported outcomes, are obtained, along with a digital archive of kidney biopsy images and blood and urine specimens at study visits aligned with clinical care 1 to 4 times per year.

OUTCOMES

Patients are followed up for changes in estimated glomerular filtration rate, disease activity, ESKD, and death and for nonrenal complications of disease and treatment, including infection, malignancy, cardiovascular, and thromboembolic events.

ANALYTICAL APPROACH

The study design supports multiple longitudinal analyses leveraging the diverse data domains of CureGN and its ancillary program. At 2,400 patients and an average of 2 years' initial follow-up, CureGN has 80% power to detect an HR of 1.4 to 1.9 for proteinuria remission and a mean difference of 2.1 to 3.0mL/min/1.73m² in estimated glomerular filtration rate per year.

LIMITATIONS

Current follow-up can only detect large differences in ESKD and death outcomes.

CONCLUSIONS

Study infrastructure will support a broad range of scientific approaches to identify mechanistically distinct subgroups, identify accurate biomarkers of disease activity and progression, delineate disease-specific treatment targets, and inform future therapeutic trials. CureGN is expected to be among the largest prospective studies of children and adults with glomerular disease, with a broad goal to lessen disease burden and improve outcomes.

Genomic medicine for kidney disease

Technologies such as next-generation sequencing and chromosomal microarray have advanced the understanding of the molecular pathogenesis of a variety of renal disorders. Genetic findings are increasingly used to inform the clinical management of many nephropathies, enabling targeted disease surveillance, choice of therapy, and family counselling. Genetic analysis has excellent diagnostic utility in paediatric nephrology, as illustrated by sequencing studies of patients with congenital anomalies of the kidney and urinary tract and steroid-resistant nephrotic syndrome. Although additional investigation is needed, pilot studies suggest that genetic testing can also provide similar diagnostic insight among adult patients. Reaching a genetic diagnosis first involves choosing the appropriate testing modality, as guided by the clinical presentation of the patient and the number of potential genes associated with the suspected nephropathy. Genome-wide sequencing increases diagnostic sensitivity relative to targeted panels, but holds the challenges of identifying causal variants in the vast amount of data generated and interpreting secondary findings. In order to realize the promise of genomic medicine for kidney disease, many technical, logistical, and ethical questions that accompany the implementation of genetic testing in nephrology must be addressed. The creation of evidence-based guidelines for the utilization and implementation of genetic testing in nephrology will help to translate genetic knowledge into improved clinical outcomes for patients with kidney disease.

Common Elements in Rare Kidney Diseases: Conclusions from a Kidney Disease: Improving Global Outcomes (KDIGO) Controversies Conference

Rare kidney diseases encompass at least 150 different conditions, most of which are inherited. Although individual rare kidney diseases raise specific issues, as a group these rare diseases can have overlapping challenges in diagnosis and treatment. These challenges include small numbers of affected patients, unidentified causes of disease, lack of biomarkers for monitoring disease progression, and need for complex care. To address common clinical and patient issues among rare kidney diseases, the KDIGO Controversies Conference entitled, Common Elements in Rare Kidney Diseases, brought together a panel of multidisciplinary clinical providers and patient advocates to address five central issues for rare kidney diseases. These issues encompassed diagnostic challenges, management of kidney functional decline and progression of chronic kidney disease, challenges in clinical study design, translation of advances in research to clinical care, and provision of practical and integrated patient support. Thus, by a process of consensus, guidance for addressing these challenges was developed and is presented here.

Renal transplantation in Bardet-Biedl Syndrome

BACKGROUND

Renal anomalies are common in patients with Bardet-Biedl syndrome (BBS), a renal cystic ciliopathy with multi-systemic features. Renal transplantation is indicated in cases of end-stage renal disease (ESRD), but transplant centers may be hesitant to perform the necessary transplant in light of the multitude of metabolic comorbidities these patients often face with the potential to complicate outcomes.

METHODS

Data from the Clinical Registry Investigating BBS (CRIBBS) were used to investigate renal transplant outcomes in the largest BBS cohort described to date.

RESULTS

Of the 206 patients enrolled in the CRIBBS, 21 children (10.2 %; 16 girls, 5 boys; median age 8.4 years) had been diagnosed with ESRD. Renal transplantation was performed in 18 of these individuals between 1982 and 2015, including repeat transplantation in some cases, for a total of 22 kidneys. Overall graft survival was 81.6 % at 1 year post-transplantation, 75.7 % at 5 years, 59 % at 10 years, and 49.2 % at 25 years. Patient survival was 94.4 % at 1 year post-transplantation, 87.2 % at 8 years, and 79.3 % at 25 years.

CONCLUSIONS

At a median follow-up time of 97 months, relatively few complications of renal transplantation were reported in the patients of this study. However, body mass index was significantly elevated in transplanted individuals compared to non-transplanted individuals participating in CRIBBS at the most recent follow-up. Although the frequency of obesity and other manifestations of the metabolic syndrome warrant meticulous management in this high-risk population, favorable long-term outcomes suggest that renal transplantation is a viable option for patients with BBS and ESRD.

The involvement of patient organisations in rare disease research: a mixed methods study in Australia

BACKGROUND

We report here selected findings from a mixed-methods study investigating the role of Australian rare disease patient organisations (RDPOs) in research. Despite there being many examples of RDPOs that have initiated and supported significant scientific advances, there is little information - and none at all in Australia - about RDPOs generally, and their research-related goals, activities, and experiences. This information is a pre-requisite for understanding what RDPOs bring to research and how their involvement could be strengthened.

METHODS

We reviewed 112 RDPO websites, conducted an online survey completed by 61 organisational leaders, and interviewed ten leaders and two key informants. Quantitative and qualitative data were analysed using basic descriptive statistics and content analysis, respectively.

RESULTS

Although most are small volunteer-based groups, more than 90% of the surveyed RDPOs had a goal to promote or support research on the diseases affecting their members. Nearly all (95 %) had undertaken at least one research-related activity - such as providing funding or other support to researchers - in the previous five years. However, RDPO leaders reported considerable challenges in meeting their research goals. Difficulties most frequently identified were insufficient RDPO resources, and a perceived lack of researchers interested in studying their diseases. Other concerns included inadequate RDPO expertise in governing research "investments", and difficulty engaging researchers in the organisation's knowledge and ideas. We discuss these perceived challenges in the light of two systemic issues: the proliferation of and lack of collaboration between RDPOs, and the lack of specific governmental policies and resources supporting rare disease research and patient advocacy in Australia.

CONCLUSION

This study provides unique information about the experiences of RDPOs generally, rather than experiences retrospectively reported by RDPOs associated with successful research. We describe RDPOs' valuable contributions to research, while also providing insights into the difficulties for small organisations trying to promote research. The study is relevant internationally because of what it tells us about RDPOs; however, we draw attention to specific opportunities in Australia to support RDPOs' involvement in research, for the benefit of current and future generations affected by rare diseases.

Review and comparison of clinical evidence submitted to support European Medicines Agency market authorization of orphan-designated oncological treatments

Background

Clinical trials for treatments indicated for orphan diseases may be limited due to the low prevalence of such diseases; this can result in implications for both regulatory and health economic perspectives. This study assessed the pivotal clinical evidence packages submitted to support applications for European Medicines Agency (EMA) marketing authorizations for treatments for orphan conditions, in relation to the size of the eligible patient population.

Methods

Approved treatments for EMA-designated orphan conditions (defined as life-threatening or chronically debilitating conditions that affect ≤5/10,000 people) were identified from the EMA web site. All treatments reviewed were included in anatomical therapeutic chemical (ATC) category L (antineoplastic and immunomodulating drugs): this category was selected because it is the largest ATC category, containing almost 50 % of all approved orphan-designated products. Treatments were reviewed if they had been approved within the past 7 years and had been evaluated in a controlled trial using at least one survival-based clinical endpoint. Treatments were compared in terms of patient-years (accumulated duration of follow-up), the number of patients in the pivotal trials and disease prevalence.

Results

As of 1 February 2014, 68 treatments had been approved for orphan-designated conditions, of which 30 belonged to ATC category L and 14 met all inclusion criteria. The number of patients in the pivotal trials ranged from 162 to 846 (median 485). In terms of patient-years, the longest duration of follow-up was seen in the pivotal trial of mifamurtide in osteosarcoma, which had 4068 patient-years; excluding this trial, follow-up ranged from 308 to 2906 patient-years (median 1796 years). Osteosarcoma had the second smallest eligible patient population (0.5/10,000 persons) of the reviewed treatments.

Conclusions

Clinical trials of orphan treatments are often limited by low patient numbers and inadequate follow-up. Pooling of expertise in single centres and the establishment of rare disease reference networks and patient registries may facilitate appropriate trial design for orphan-designated treatments. This analysis found that the pivotal clinical trial for mifamurtide in osteosarcoma had the largest number of patient-years of follow-up, despite a small eligible patient population, showing that it is possible to conduct studies with an adequate patient population size and duration of follow-up in patient-years, and a comparative design with clinical, survival-based, endpoints.