Evidence-based data and rare cancers: The need for a new methodological approach in research and investigation

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.

Geographical and spatial disparities in the incidence and survival of rare cancers in Australia

Rare cancers collectively account for around a quarter of cancer diagnoses and deaths. However, epidemiological studies are sparse. We describe spatial and geographical patterns in incidence and survival of rare cancers across Australia using a population-based cancer registry cohort of rare cancer cases diagnosed among Australians aged at least 15 years, 2007 to 2016. Rare cancers were defined using site- and histology-based categories from the European RARECARE study, as individual cancer types having crude annual incidence rates of less than 6/100 000. Incidence and survival patterns were modelled with generalised linear and Bayesian spatial Leroux models. Spatial heterogeneity was tested using the maximised excess events test. Rare cancers (n = 268 070) collectively comprised 22% of all invasive cancer diagnoses and accounted for 27% of all cancer-related deaths in Australia, 2007 to 2016 with an overall 5-year relative survival of around 53%. Males and those living in more remote or more disadvantaged areas had higher incidence but lower survival. There was substantial evidence for spatial variation in both incidence and survival for rare cancers between small geographical areas across Australia, with similar patterns so that those areas with higher incidence tended to have lower survival. Rare cancers are a substantial health burden in Australia. Our study has highlighted the need to better understand the higher burden of these cancers in rural and disadvantaged regions where the logistical challenges in their diagnosis, treatment and support are magnified.

One-Drop Serum Screening Test for Anal Cancer in Men via Infrared Attenuated Total Reflection Spectroscopy

Rare cancers are a challenge for clinical practice, the treatment experience at major centers to which rare cancers are referred is limited and are the most difficult to diagnose. Research to identify causes or develop prevention and early detection strategies is extremely challenging. Anal cancer is an example of a rare cancer, with the human papillomavirus (HPV) infection being the most important risk factor associated. In the early stages, anal cancer does not exhibit evident symptoms. This disease is diagnosed by means of anoscopy, which diagnoses some cases of early cancer; nevertheless, sensitivity of this test ranges between 47 and 89%. Therefore, the development of new, effective, and evidence-based screening methodologies for the early detection of rare cancers is of great relevance. In this study, the potential of ATR-FTIR spectroscopy has been explored as a sensitive, nondestructive, and inexpensive analytical method for developing disease screening platforms in serum. Spectral differences were found in the regions of 1700-1100 and 1700-1400 cm^-1 between the control group and the anal cancer group related to the presence of proteins and nucleic acids. The chemometric analysis presented differences in the spectral fingerprints for both spectral regions with a high sensitivity ranging from 95.2 to 99.9% and a specificity ranging from 99.2 to 100%. This is the first step that we report for a methodology that is fast, nondestructive, and easy to perform, and the high sensitivity and specificity of the method are the basis for extensive research studies to implement these technologies in the clinical field.

A framework for fibrolamellar carcinoma research and clinical trials

Fibrolamellar carcinoma (FLC), a rare, lethal hepatic cancer, occurs primarily in adolescents and young adults. Unlike hepatocellular carcinoma, FLC has no known association with viral, metabolic or chemical agents that cause cirrhosis. Currently, surgical resection is the only treatment demonstrated to achieve cure, and no standard of care exists for systemic therapy. Progress in FLC research illuminates a transition from an obscure cancer to one for which an interactive community seems poised to uncover fundamental mechanisms and initiate translation towards novel therapies. In this Roadmap, we review advances since the seminal discovery in 2014 that nearly all FLC tumours express a signature oncogene (DNAJB1-PRKACA) encoding a fusion protein (DNAJ-PKAc) in which the J-domain of a heat shock protein 40 (HSP40) co-chaperone replaces an amino-terminal segment of the catalytic subunit of the cyclic AMP-dependent protein kinase (PKA). Important gains include increased understanding of oncogenic pathways driven by DNAJ-PKAc; identification of potential therapeutic targets; development of research models; elucidation of immune mechanisms with potential for the development of immunotherapies; and completion of the first multicentre clinical trials of targeted therapy for FLC. In each of these key areas we propose a Roadmap for future progress.

Neuroblastoma in Spain: Linking the national clinical database and epidemiological registries - A study by the Joint Action on Rare Cancers

PURPOSE

Linkage between clinical databases and population-based cancer registries may serve to evaluate European Reference Networks' (ERNs) activity, by monitoring the proportion of patients benefiting from these and their impact on survival at a population level. To test this, a study targeting neuroblastoma (Nb) was conducted in Spain by the European Joint Action on Rare Cancers.

MATERIAL AND METHODS

Subjects: Nb cases, incident 1999-2017, aged < 15 years. Linkage included: Spanish Neuroblastoma Clinical Database (NbCDB) (1217 cases); Spanish Registry of Childhood Tumours (RETI) (1514 cases); and 10 regional population-based registries (RPBCRs) which cover 33% of the childhood population (332 cases). Linkage was semiautomatic. We estimated completeness, incidence, contribution, deficit, and 5-year survival in the databases and specific subsets.

RESULTS

National completeness estimates for RETI and NbCDB were 91% and 72% respectively, using the Spanish RPBCRs on International Incidence of Childhood Cancer (https://iicc.iarc.fr/) as reference. RPBCRs' specific contribution was 1.6%. Linkage required manual crossover in 54% of the semiautomatic matches. Five-year survival was 74% (0-14 years) and 90% (0-18 months).

CONCLUSIONS

All three databases were incomplete as regards Spain as a whole and should therefore be combined to achieve full childhood cancer registration. A unique personal patient identifier could facilitate such linkage. Most children have access to Nb clinical trials. Consolidated interconnections between the national registry and clinical registries (including ERNs and paediatric oncology clinical groups) should be established to evaluate outcomes.

Descriptive epidemiological study of rare, less common and common cancers in Western Australia

Background

There are no epidemiological studies describing rare cancers in Western Australia (WA). We aimed to fill this gap by estimating the incidence and five-year survival of rare, less common and common cancers in WA, based on definitions for rarity used by the Australian Institute of Health and Welfare and cancer groupings from the project on Surveillance of Rare Cancers in Europe (RARECARE). This research will enable policy- and decision-makers to better understand the size and nature of the public health problem presented by rare cancers in WA. It is anticipated that this study will inform improved health service design and delivery for all WA cancer patients, but particularly those with rare and less common cancers.

Methods

We estimated incidence and five-year survival rates of rare, less common and common cancers in WA using data sourced from the WA Cancer Registry for the 2013–2017 period. Cancers were defined as rare (< 6), less common (6–12), or common (> 12) based on their crude incidence rate per 100,000 people per year.

Results

Rare cancers make up 21.5% of all cancer diagnoses in WA, with a significantly poorer five-year survival of 58.2% (95% confidence interval (CI) 57.3–59.1%), compared to patients diagnosed with a common cancer, whose five-year survival was 87.8% (95% CI 87.3–88.3%). Survival for less common cancers was significantly poorer than both rare and common cancers, at 48.1% (95% CI 47.3–49.0%). Together, rare and less common cancers represent 48.4% of all cancer diagnoses in WA.

Conclusions

While rare cancers are individually scarce, collectively over one in five cancer patients in WA are diagnosed with a rare cancer. These patients experience significantly worse prognoses compared to patients with common cancers.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-021-08501-4.

Prognostic significance of histopathological response to preoperative chemotherapy in unilateral Wilms' tumor: An analysis of 899 patients treated on the SIOP WT 2001 protocol in the UK-CCLG and GPOH studies

In the SIOP Wilms' tumor (WT) studies, preoperative chemotherapy is used as primary treatment, and tumors are classified thereafter by pathologists. Completely necrotic WTs (CN-WTs) are classified as low-risk tumors. The aim of the study was to evaluate whether a subset of regressive type WTs (RT-WTs) (67%-99% chemotherapy-induced changes [CIC]) showing an exceptionally good response to preoperative chemotherapy had comparably excellent survivals as CN-WTs, and to establish a cut-off point of CIC that could define this subset. The study included 2117 patients with unilateral, nonanaplastic WTs from the UK-CCLG and GPOH-WT studies (2001-2020) treated according to the SIOP-WT-2001 protocol. There were 126 patients with CN-WTs and 773 with RT-WTs, stages I-IV. RT-WTs were subdivided into subtotally necrotic WTs (>95% CIC) (STN-WT96-99) (124 patients) and the remaining of RT-WT (RR-WT67-95) (649 patients). The 5-year event-free survival (EFS) and overall survival (OS) for CN-WTs were 95.3% (±2.1% SE) and 97.3% (±1.5% SE), and for RT-WTs 85.7% (±1.14% SE, P < .01) and 95.2% (±0.01% SE, P = .59), respectively. CN-WT and STN-WT96-99 groups showed significantly better EFS than RR-WT67-95 (P = .003 and P = .02, respectively), which remained significantly superior when adjusted for age, local stage and metastasis at diagnosis, in multivariate analysis, whereas OS were superimposable (97.3 ± 1.5% SE for CN-WT; 97.8 ± 1.5% SE for STN-WT96-99; 94.7 ± 1.0% SE for RR-WT67-95). Patients with STN-WT96-99 share the same excellent EFS and OS as patients with CN-WTs, and although this was achieved by more treatment for patients with STN-WT96-99 than for patients with CN-WT, reduction in postoperative treatment of these patients may be justified.

"It's Always Been a Second Class Cancer": An Exploration of the Experiences and Journeys of Bereaved Family Carers of People with Sarcoma

Sarcomas are a group of rare and aggressive cancers, which develop in bones and connective tissue throughout the body. Sarcomas account for only 1-2% of all cancers worldwide; however, mortality rates for sarcoma are high with approximately two in four sarcoma patients dying following a diagnosis. Delays in diagnosis, poor management of symptoms, patients' high symptom loads and high carer burden are all associated with carer distress, which may lead to complications after bereavement. The experience of having a family member referred for palliative care is also distressing for carers, with the realisation that their family member is dying. This study aimed to explore the experiences of bereaved family carers of people diagnosed with sarcoma. A qualitative descriptive design using a social constructionist framework was adopted. Interviews were conducted with sixteen participants, and thematic analysis was used to identify patterns in the data. Four overarching themes emerged: beginning the journey; moving through treatment; transitioning to palliative care; and experiencing bereavement. The narratives were coherent and potent, and people reflected on their journeys. Interventions and supports for bereaved carers could include opportunities for counselling to support reflections, supports for developing a narrative such as writing therapy, and preparation for the death of the family member.

The Importance of Cancer Registry Linkage for Studying Rare Cancers in Prospective Cohorts

Large prospective cohort studies may offer an opportunity to study the etiology and natural history of rare cancers. Cancer diagnoses in observational cohort studies are often self-reported. Little information exists on the validity of self-reported cancer diagnosis, especially rare cancers, in Canada. This study evaluated the validity of self-reported cancer diagnosis in Alberta's Tomorrow Project (ATP), a provincial cohort in Canada. ATP data were linked to the Alberta Cancer Registry (ACR). The first instance of self-reported cancer in a follow-up survey was compared to the first cancer diagnosis in the ACR after enrollment. The sensitivity and positive predictive value (PPV) were estimated for the reporting of cancer status, reporting of common or rare cancer, and reporting of site-specific cancer. Logistic regression analysis explored factors associated with false positive, false negative, and incorrect cancer site reporting. In the 30,843 ATP participants who consented to registry linkage, there were 810 primary cancer diagnoses in the ACR and 959 self-reports of first cancer post-enrollment, for a cancer status sensitivity of 92.1% (95% CI: 90.0-93.9) and PPV of 77.8% (95% CI: 75.0-80.4). Compared to common cancers, rare cancers had a lower sensitivity (62.8% vs. 89.6%) and PPV (35.8% vs. 84.5%). Participants with a rare cancer were more likely to report an incorrect site than those with a common cancer. Rare cancers were less likely to be captured by active follow-up than common cancers. While rare cancer research may be feasible in large cohort studies, registry linkage is necessary to capture rare cancer diagnoses completely and accurately.

Clinical and Translational Research Challenges in Neuroendocrine Tumours

Neuroendocrine tumours (NETs) represent a range of neoplasms that may arise from any (neuro)endocrine cell situated in any part of the human body. As any other rare diseases, NETs face several difficulties in relation to research. This review will describe some of the main challenges and proposed solutions faced by researchers with expertise in rare malignancies. Some of the most common challenges in clinical and translational research are enumerated in this review, covering aspects from clinical, translational and basic research. NETs being a heterogeneous group of diseases and a limited sample size of clinical and translational research projects are the main challenges. Challenges with NETs lay over the disparities between healthcare models to tackle rare diseases. NETs add an extra layer of complexity due to a numerous group of different entities. Prospective real-world data trials are an opportunity for rare cancers with the revolution of electronic health technologies. This review explores potential solutions to these challenges that could be useful not only to the NET community but also to other rare tumours researchers.

Accuracy of pathologic diagnosis for thymic epithelial tumors: a brief report from an Italian reference Center

Objectives - Rare tumors are diagnostic challenges for pathologists. Consultation or referral to Centers with expertise is crucial for the right diagnosis. This is particularly true for Thymic Epithelial Tumors (TETs), whose treatment strategies vary according to histological subgroup. We aimed at evaluating the accuracy of TET pathologic characterization in an Italian reference Center. Materials and methods - All the cases with diagnosis or suspicion of TETs, which underwent a pathological second opinion at Istituto Nazionale dei Tumori (INT), Milan, between 2015 and 2019 were retrospectively reviewed. All cases had been pathologically characterized through immunohistochemistry (IHC). Descriptive statistics were used for qualitative variables. Concordance was estimated through Cohen's kappa (k). Results - Out of 278 cases of TETs diagnosed in INT, 72 were referred to INT for a pathologic revision. The INT revision changed the diagnosis in 41 cases (56.9%), with a potential therapeutic shift in 32 (44.4%). In particular, 20 cases of thymoma were reviewed as a different subtype of thymoma (19/20) or lymphoma (1/20); nine cases of thymic carcinoma were reviewed as thymoma. On the other hand, three cases of lung carcinoma were reviewed as thymic carcinoma (2/3) or thymoma (1); eight cases of carcinoma Not Otherwise Specified were reviewed as thymic carcinoma; one case of lymphoma was reviewed as thymoma. Concordance between pathologists was moderate for thymoma (74.7%, k 0.447), inferior for thymic carcinoma (60.5%, k 0.139). Conclusion - A significant proportion of cases referred to INT for a presumptive TET received a different characterization. A potential shift in therapeutic indication was not rare. This underlines the importance for TETs to get a second pathological diagnosis by an expert pathologist and supports the need for networks on rare cancers.

Use case driven evaluation of open databases for pediatric cancer research

BACKGROUND

A plethora of Web resources are available offering information on clinical, pre-clinical, genomic and theoretical aspects of cancer, including not only the comprehensive cancer projects as ICGC and TCGA, but also less-known and more specialized projects on pediatric diseases such as PCGP. However, in case of data on childhood cancer there is very little information openly available. Several web-based resources and tools offer general biomedical data which are not purpose-built, for neither pediatric nor cancer analysis. Additionally, many Web resources on cancer focus on incidence data and statistical social characteristics as well as self-regulating communities.

METHODS

We summarize those resources which are open and are considered to support scientific fundamental research, while we address our comparison to 11 identified pediatric cancer-specific resources (5 tools, 6 databases). The evaluation consists of 5 use cases on the example of brain tumor research and covers user-defined search scenarios as well as data mining tasks, also examining interactive visual analysis features.

RESULTS

Web resources differ in terms of information quantity and presentation. Pedican lists an abundance of entries with few selection features. PeCan and PedcBioPortal include visual analysis tools while the latter integrates published and new consortia-based data. UCSC Xena Browser offers an in-depth analysis of genomic data. ICGC data portal provides various features for data analysis and an option to submit own data. Its focus lies on adult Pan-Cancer projects. Pediatric Pan-Cancer datasets are being integrated into PeCan and PedcBioPortal. Comparing information on prominent mutations within glioma discloses well-known, unknown, possible, as well as inapplicable biomarkers. This summary further emphasizes the varying data allocation. Tested tools show advantages and disadvantages, depending on the respective use case scenario, providing inhomogeneous data quantity and information specifics.

CONCLUSIONS

Web resources on specific pediatric cancers are less abundant and less-known compared to those offering adult cancer research data. Meanwhile, current efforts of ongoing pediatric data collection and Pan-Cancer projects indicate future opportunities for childhood cancer research, that is greatly needed for both fundamental as well as clinical research.