Impact of biobanks on research outcomes in rare diseases: a systematic review

Synthetic datasets for open software development in rare disease research

BACKGROUND

Globally, researchers are working on projects aiming to enhance the availability of data for rare disease research. While data sharing remains critical, developing suitable methods is challenging due to the specific sensitivity and uniqueness of rare disease data. This creates a dilemma, as there is a lack of both methods and necessary data to create appropriate approaches initially. This work contributes to bridging this gap by providing synthetic datasets that can form the foundation for such developments.

METHODS

Using a hierarchical data generation approach parameterised with publicly available statistics, we generated datasets reflecting a random sample of rare disease patients from the United States (US) population. General demographics were obtained from the US Census Bureau, while information on disease prevalence, initial diagnosis, survival rates as well as race and sex ratios were obtained from the information provided by the US Centers for Disease Control and Prevention as well as the scientific literature. The software, which we have named SynthMD, was implemented in Python as open source using libraries such as Faker for generating individual data points.

RESULTS

We generated three datasets focusing on three specific rare diseases with broad impact on US citizens, as well as differences in affected genders and racial groups: Sickle Cell Disease, Cystic Fibrosis, and Duchenne Muscular Dystrophy. We present the statistics used to generate the datasets and study the statistical properties of output data. The datasets, as well as the code used to generate them, are available as Open Data and Open Source Software.

CONCLUSION

The results of our work can serve as a starting point for researchers and developers working on methods and platforms that aim to improve the availability of rare disease data. Potential applications include using the datasets for testing purposes during the implementation of information systems or tailored privacy-enhancing technologies.

Scoping review of the recommendations and guidance for improving the quality of rare disease registries

BACKGROUND

Rare disease registries (RDRs) are valuable tools for improving clinical care and advancing research. However, they often vary qualitatively, structurally, and operationally in ways that can determine their potential utility as a source of evidence to support decision-making regarding the approval and funding of new treatments for rare diseases.

OBJECTIVES

The goal of this research project was to review the literature on rare disease registries and identify best practices to improve the quality of RDRs.

METHODS

In this scoping review, we searched MEDLINE and EMBASE as well as the websites of regulatory bodies and health technology assessment agencies from 2010 to April 2023 for literature offering guidance or recommendations to ensure, improve, or maintain quality RDRs.

RESULTS

The search yielded 1,175 unique references, of which 64 met the inclusion criteria. The characteristics of RDRs deemed to be relevant to their quality align with three main domains and several sub-domains considered to be best practices for quality RDRs: (1) governance (registry purpose and description; governance structure; stakeholder engagement; sustainability; ethics/legal/privacy; data governance; documentation; and training and support); (2) data (standardized disease classification; common data elements; data dictionary; data collection; data quality and assurance; and data analysis and reporting); and (3) information technology (IT) infrastructure (physical and virtual infrastructure; and software infrastructure guided by FAIR principles (Findability; Accessibility; Interoperability; and Reusability).

CONCLUSIONS

Although RDRs face numerous challenges due to their small and dispersed populations, RDRs can generate quality data to support healthcare decision-making through the use of standards and principles on strong governance, quality data practices, and IT infrastructure.

Standards for clinical trials for treating TB

BACKGROUND: The value, speed of completion and robustness of the evidence generated by TB treatment trials could be improved by implementing standards for best practice.METHODS: A global panel of experts participated in a Delphi process, using a 7-point Likert scale to score and revise draft standards until consensus was reached.RESULTS: Eleven standards were defined: Standard 1, high quality data on TB regimens are essential to inform clinical and programmatic management; Standard 2, the research questions addressed by TB trials should be relevant to affected communities, who should be included in all trial stages; Standard 3, trials should make every effort to be as inclusive as possible; Standard 4, the most efficient trial designs should be considered to improve the evidence base as quickly and cost effectively as possible, without compromising quality; Standard 5, trial governance should be in line with accepted good clinical practice; Standard 6, trials should investigate and report strategies that promote optimal engagement in care; Standard 7, where possible, TB trials should include pharmacokinetic and pharmacodynamic components; Standard 8, outcomes should include frequency of disease recurrence and post-treatment sequelae; Standard 9, TB trials should aim to harmonise key outcomes and data structures across studies; Standard 10, TB trials should include biobanking; Standard 11, treatment trials should invest in capacity strengthening of local trial and TB programme staff.CONCLUSION: These standards should improve the efficiency and effectiveness of evidence generation, as well as the translation of research into policy and practice.

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.

A Rapid Review on the Value of Biobanks Containing Genetic Information

OBJECTIVES

Increasing access to health data through biobanks containing genetic information has the potential to expand the knowledge base and thereby improve screening, diagnosis, and treatment options for many diseases. Nevertheless, although privacy concerns and risks surrounding genetic data sharing are well documented, direct evidence in favor of the hypothesized benefits of data integration is scarce, which complicates decision making in this area. Therefore, the objective of this study is to summarize the available evidence on the research and clinical impacts of biobanks containing genetic information, so as to better understand how to quantify the value of expanding genomic data access.

METHODS

Using a rapid review methodology, we performed a search of MEDLINE/PubMed and Embase databases; and websites of biobanks and genomic initiatives published from 2010 to 2022. We classified findings into 11 indicators including outputs (a direct product of the biobank activities) and outcomes (changes in scientific and clinical capacity).

RESULTS

Of 8479 abstracts and 101 gray literature sources were reviewed, 96 records were included. Although most records did not report key indicators systematically, the available evidence concentrated on research indicators such as publications and gene-disorder association discoveries (63% of studies), followed by research infrastructure (26%), and clinical indicators (11%) such as supporting the diagnosis of individual patients.

CONCLUSIONS

Existing evidence on the benefits of biobanks is skewed toward easily quantifiable research outputs. Measuring a comprehensive set of outputs and outcomes inspired by value frameworks is necessary to generate better evidence on the benefits of genomic data sharing.

Worldwide sources of data in haematology: Importance of clinician-biostatistician collaboration

The field of haematology has benefitted greatly from registry-based observational research. Medical and technical advances, changes in regulations and events such as the global pandemic is changing the landscape for registries. This review describes features of high-quality registries, statistical approaches and study design needed, an overview of worldwide hematologic registries, and how registries are evolving and expanding. The importance of collaborations between biostatisticians and haematologists in designing and conducting registry-related research is highlighted.

Emerging roles and opportunities for rare disease patient advocacy groups

Background

Patient advocacy groups (PAGs) serve a vital role for rare disease patients and families by providing educational resources, support, and a sense of community. Motivated by patient need, PAGs are increasingly at the forefront of policy, research, and drug development for their disease of interest.

Objectives

The study explored the current landscape of PAGs in order to guide new and existing PAGs on available resources and challenges to research engagement. We aim to inform industry, advocates, and healthcare personnel about PAG achievements and ways they are increasingly involved in research.

Design

We chose PAGs from the Rare Diseases Clinical Research Network (RDCRN) Coalition for Patient Advocacy Groups (CPAG) listserv and the National Organization for Rare Disorders (NORD) 'Find a patient organization'.

Methods

We surveyed eligible PAG leaders about the demographics, goals, and research activities of their organization. For analysis, PAGs were bucketed by size, age, prevalence of disease, and budget. Data were de-identified for cross-tabulation and multinomial logistic regression analysis with R.

Results

Research engagement was an extremely important goal for most PAGs (81%), though ultra-rare disease and high-budget PAGs were most likely to cite it as the top priority. In total, 79% reported research engagement in some capacity, including registries, translational research, and clinical trials. 'Ultra-rare' PAGs were less likely than 'rare' PAGs to have an ongoing clinical trial.

Conclusion

While PAGs of varying sizes, budgets, and maturity levels reported an interest in research, limited funding and lack of disease awareness continue to create barriers to achieving their goals. While support tools exist to make research more accessible, often their utility depends on the funding, sustainability, maturity of the PAG itself, and the level of investment of collaborators. Despite the availability of current support systems, there are challenges related to both the start-up and sustainability of patient-centric research efforts.

Sharing is caring: a call for a new era of rare disease research and development

Scientific advances in the understanding of the genetics and mechanisms of many rare diseases with previously unknown etiologies are inspiring optimism in the patient, clinical, and research communities and there is hope that disease-specific treatments are on the way. However, the rare disease community has reached a critical point in which its increasingly fragmented structure and operating models are threatening its ability to harness the full potential of advancing genomic and computational technologies. Changes are therefore needed to overcome these issues plaguing many rare diseases while also supporting economically viable therapy development. In "Data silos are undermining drug development and failing rare disease patients (Orphanet Journal of Rare Disease, Apr 2021)," we outlined many of the broad issues underpinning the increasingly fragmented and siloed nature of the rare disease space, as well as how the issues encountered by this community are representative of biomedical research more generally. Here, we propose several initiatives for key stakeholders - including regulators, private and public foundations, and research institutions - to reorient the rare disease ecosystem and its incentives in a way that we believe would cultivate and accelerate innovation. Specifically, we propose supporting non-proprietary patient registries, greater data standardization, global regulatory harmonization, and new business models that encourage data sharing and research collaboration as the default mode. Leadership needs to be integrated across sectors to drive meaningful change between patients, industry, sponsors, and academic medical centers. To transform the research and development landscape and unlock its vast healthcare, economic, and scientific potential for rare disease patients, a new model is ultimately the goal for all.

Stakeholders' views on drug development: the congenital disorders of glycosylation community perspective

BACKGROUND

Congenital disorders of glycosylation (CDG) are a large family of rare genetic diseases for which therapies are virtually nonexistent. However, CDG therapeutic research has been expanding, thanks to the continuous efforts of the CDG medical/scientific and patient communities. Hence, CDG drug development is a popular research topic. The main aim of this study was to understand current and steer future CDG drug development and approval by collecting and analysing the views and experiences of the CDG community, encompassing professionals and families. An electronic (e-)survey was developed and distributed to achieve this goal.

RESULTS

A total of 128 respondents (46 CDG professionals and 82 family members), mainly from Europe and the USA, participated in this study. Most professionals (95.0%) were relatively familiar with drug development and approval processes, while CDG families revealed low familiarity levels, with 8.5% admitting to never having heard about drug development. However, both stakeholder groups agreed that patients and families make significant contributions to drug development and approval. Regarding their perceptions of and experiences with specific drug development and approval tools, namely biobanks, disease models, patient registries, natural history studies (NHS) and clinical trials (CT), the CDG community stakeholders described low use and participation, as well as variable familiarity. Additionally, CDG professionals and families shared conflicting views about CT patient engagement and related information sharing. Families reported lower levels of involvement in CT design (25.0% declared ever being involved) and information (60.0% stated having been informed) compared to professionals (60.0% and 85.7%, respectively). These contrasting perceptions were further extended to their insights and experiences with patient-centric research. Finally, the CDG community (67.4% of professionals and 54.0% of families) reported a positive vision of artificial intelligence (AI) as a drug development tool. Nevertheless, despite the high AI awareness among CDG families (76.8%), professionals described limited AI use in their research (23.9%).

CONCLUSIONS

This community-centric study sheds new light on CDG drug development and approval. It identifies educational, communication and research gaps and opportunities for CDG professionals and families that could improve and accelerate CDG therapy development.

Development of an International Database for a Rare Genetic Disorder: The MECP2 Duplication Database (MDBase)

The natural history of MECP2 duplication syndrome (MDS), a rare X-linked neurodevelopmental disorder with an estimated birth prevalence of 1/150,000 live births, is poorly understood due to a lack of clinical data collected for research. Such information is critical to the understanding of disease progression, therapeutic endpoints and outcome measures for clinical trials, as well as the development of therapies and orphan products. This clinical information can be systematically collected from caregivers through data collation efforts—yet, no such database has existed for MDS before now. Here, in this methodological study, we document the development, launch and management of the international MECP2 Duplication Database (MDBase). The MDBase consists of an extensive family questionnaire that collects information on general medical history, system-specific health problems, medication and hospitalisation records, developmental milestones and function, and quality of life (for individuals with MDS, and their caregivers). Launched in 2020, in its first two years of operation the MDBase has collected clinical data from 154 individuals from 26 countries—the largest sample size to date. The success of this methodology for the establishment and operation of the MDBase may provide insight and aid in the development of databases for other rare neurodevelopmental disorders.

Biobank as a key component of supporting research in phthisiology and infectious diseases

Conducting fundamental and clinical research in the field of tuberculosis is an important step towards reducing related morbidity and mortality, but access to a sufficient number of high-quality samples required for research is an unsolved problem in Russia. This review is devoted to biobanking as a key component of modern research in personalized medicine, as well as to the status and prospects for developing this area in phthisiology and infectious diseases combined with tuberculosis.

An Integrated clinical pathway for diagnosis, treatment and care of rare diseases: model, operating procedures, and results of the project TRANSLATE-NAMSE funded by the German Federal Joint Committee

BACKGROUND

Diagnosis, treatment, and care of patients with rare diseases require multidisciplinary cooperation between medical and paramedical specialities and with patients and families. Innovative genetic diagnostics, whole exome and whole genome sequencing (WES, WGS) has enlarged the diagnostic toolkit but also increased the complexity of the endeavour. Structured multidisciplinary clinical pathways (CPW) can guide diagnosis, treatment, and care of patients with rare diseases, link scientific evidence to clinical practice and optimise clinical outcomes whilst maximising clinical efficiency.

RESULTS

In contrast to the common approach of appending disease-specific CPWs to disease-specific guidelines, we suggest a generic CPW manoeuvring the patient along the way of finding the correct diagnosis by applying the best diagnostic strategy into an appropriate system of treatment and care. Available guidelines can be integrated into the generic CPW in the course of its application. The approach also applies to situations where a diagnosis remains unsolved. The backbone of the generic CPW is a set of multidisciplinary structured case conferences projecting and evaluating diagnostic and/or therapeutic steps, enforcing to integrate best scientific evidence with clinical experience. The generic CPW is stated as a flowchart and a checklist which can be used to record and document parsimoniously the structure, process and results of a patient's pathway, but also as a data model for research. It was applied in a multicentre setting with 587 cases each with a presumptive diagnosis of a rare disease. In 369 cases (62.8%) a diagnosis could be confirmed, and multidisciplinary treatment and/or care was initiated. The median process time from first contact until confirmation of diagnosis by WES was 109 days and much shorter than diagnostic delays reported in the literature. Application of the CPW is illustrated by two case reports.

CONCLUSIONS

Our model is a tool to change the diagnostic odyssey into an organised and trackable route. It can also be used to inform patients and families about the stages of their individual route, to update health care providers only partially involved or attending specialised treatment and care, like the patient's or family's primary physician, and finally to train novices in the field.

Boston biorepository, recruitment and integrative network (BBRAIN): A resource for the Gulf War Illness scientific community

AIMS

Gulf War Illness (GWI), a chronic debilitating disorder characterized by fatigue, joint pain, cognitive, gastrointestinal, respiratory, and skin problems, is currently diagnosed by self-reported symptoms. The Boston Biorepository, Recruitment, and Integrative Network (BBRAIN) is the collaborative effort of expert Gulf War Illness (GWI) researchers who are creating objective diagnostic and pathobiological markers and recommend common data elements for GWI research.

MAIN METHODS

BBRAIN is recruiting 300 GWI cases and 200 GW veteran controls for the prospective study. Key data and biological samples from prior GWI studies are being merged and combined into retrospective datasets. They will be made available for data mining by the BBRAIN network and the GWI research community. Prospective questionnaire data include general health and chronic symptoms, demographics, measures of pain, fatigue, medical conditions, deployment and exposure histories. Available repository biospecimens include blood, plasma, serum, saliva, stool, urine, human induced pluripotent stem cells and cerebrospinal fluid.

KEY FINDINGS

To date, multiple datasets have been merged and combined from 15 participating study sites. These data and samples have been collated and an online request form for repository requests as well as recommended common data elements have been created. Data and biospecimen sample requests are reviewed by the BBRAIN steering committee members for approval as they are received.

SIGNIFICANCE

The BBRAIN repository network serves as a much needed resource for GWI researchers to utilize for identification and validation of objective diagnostic and pathobiological markers of the illness.

The IDeaS initiative: pilot study to assess the impact of rare diseases on patients and healthcare systems

Background

Rare diseases (RD) are a diverse collection of more than 7–10,000 different disorders, most of which affect a small number of people per disease. Because of their rarity and fragmentation of patients across thousands of different disorders, the medical needs of RD patients are not well recognized or quantified in healthcare systems (HCS).

Methodology

We performed a pilot IDeaS study, where we attempted to quantify the number of RD patients and the direct medical costs of 14 representative RD within 4 different HCS databases and performed a preliminary analysis of the diagnostic journey for selected RD patients.

Results

The overall findings were notable for: (1) RD patients are difficult to quantify in HCS using ICD coding search criteria, which likely results in under-counting and under-estimation of their true impact to HCS; (2) per patient direct medical costs of RD are high, estimated to be around three–fivefold higher than age-matched controls; and (3) preliminary evidence shows that diagnostic journeys are likely prolonged in many patients, and may result in progressive, irreversible, and costly complications of their disease

Conclusions

The results of this small pilot suggest that RD have high medical burdens to patients and HCS, and collectively represent a major impact to the public health. Machine-learning strategies applied to HCS databases and medical records using sentinel disease and patient characteristics may hold promise for faster and more accurate diagnosis for many RD patients and should be explored to help address the high unmet medical needs of RD patients.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13023-021-02061-3.

Horizon Scanning: Teaching Genomics and Personalized Medicine in the Digital Age

Digital transformation is currently impacting not only health care but also education curricula for medicine and life sciences. The COVID-19 pandemic has accelerated the deployment of digital technologies such as the Internet of Things and artificial intelligence in diverse fields of biomedicine. Genomics and related fields of inquiry such as pharmacogenomics and personalized medicine have been making important progress over the past decades. However, the genomics knowledge of health care professionals and other stakeholders in society is not commensurate with the current state of progress in these scientific fields. The rise of digital health offers unprecedented opportunities both for health care professionals and the general public to expand their genomics literacy and education. This expert review offers an analysis of the bottlenecks that affect and issues that need to be addressed to catalyze genomics and personalized medicine education in the digital era. In addition, we summarize and critically discuss the various educational and awareness opportunities that presently exist to catalyze the delivery of genomics knowledge in ways closely attuned to the emerging field of digital health.

Pregnancy cohorts and biobanking in sub-Saharan Africa: a systematic review

Background

Technological advances and high throughput biological assays can facilitate discovery science in biobanks from population cohorts, including pregnant women. Biological pathways associated with health outcomes differ depending on geography, and high-income country data may not generalise to low-resource settings. We conducted a systematic review to identify prospective pregnancy cohorts in sub-Saharan Africa (SSA) that include biobanked samples with potential to enhance discovery science opportunity.

Methods

Inclusion criteria were prospective data collection during pregnancy, with associated biobanking in SSA. Data sources included: scientific databases (with comprehensive search terms), grey literature, hand searching applicable reference lists and expert input. Results were screened in a three-stage process based on title, abstract and full text by two independent reviewers. The review is registered on PROSPERO (CRD42019147483).

Results

Fourteen SSA studies met the inclusion criteria from database searches (n=8), reference list searches (n=2) and expert input (n=4). Three studies have ongoing data collection. The most represented countries were South Africa and Mozambique (Southern Africa) (n=3), Benin (Western Africa) (n=4) and Tanzania (Eastern Africa) (n=4); including an estimated 31 763 women. Samples commonly collected were blood, cord blood and placenta. Seven studies collected neonatal samples. Common clinical outcomes included maternal and perinatal mortality, malaria and preterm birth.

Conclusions

Increasingly numerous pregnancy cohorts in SSA that include biobanking are generating a uniquely valuable resource for collaborative discovery science, and improved understanding of the high regional risks of maternal, fetal and neonatal morbidity and mortality. Future studies should align protocols and consider their added value and distinct contributions.

Vignettes to Illustrate the Value of Tumor Biobanks in Cancer Research in Canada

Background: Tumor biobanks are a common research infrastructure. As a collection of biospecimens and annotated data collected to support a multitude of research projects, biobanks facilitate access to materials that are the critical fuel for the generation of data in up to 40% of cancer research publications. However, quantifying how to measure biobanks' impact and their value on the field of cancer research discoveries and findings, has not been well elucidated. Methods: We have used a qualitative case study approach to illustrate the impact of tumor biobanks. We assessed the impact of three research studies published between 2010 and 2012 that required easily accessible "classic" biobanks. Each study utilized preassembled collections of tumor biospecimens with associated patient outcomes data at the outset of the research project. We compared the resulting journal impact factor, altmetric and field-weighted citation impact factor scores for each article to a set of six "benchmark" articles that represent cancer research and treatment discoveries from the same time period and two sentinel scientific discovery articles. Results: We developed a value model using a literature search and design-thinking methodologies to illustrate the contributions of these "classic" model biobanks to these research studies. Assessment of the three example articles supported by biobanks demonstrates that the output can have impact that is comparable to the impact of a set of benchmark articles describing milestones in the field of cancer research and cancer care. Conclusions: These case studies illustrate the value of the sustained investment of funds, planning, time, and effort on the part of the biobanks before the conduct of the research study to be able to ultimately support high-value research. The "value" model will enable further discussion around impact and may be useful in better delineating qualitative metrics of biobank value in the future.

The landscape of biobanks in Poland-characteristics of Polish biobanking units at the beginning of BBMRI.pl organization

Background

Biobanking is an area of scientific activity that is growing in strength and importance. The variety of collections combining biological samples and medical scientific information makes biobanking an indispensable tool in the development of modern medicine. In 2016, Poland, a country with one of the largest populations in Europe, joined the Biobanking and BioMolecular resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC) to facilitate access to quality-defined human disease-relevant biological resources. This push led to the development of the Polish Biobanking Network. The purpose of this paper is to present the current state of biobanks in Poland in the context of their location, nature and resources.

Methods

To obtain information about and overall characteristics of Polish entities dealing with biobanking biological material, the dedicated Information Survey was designed. The survey was prepared in an electronic form and consisted of 53 questions—both open and closed, single and multiple choice—with some questions depending on each other. Sixty-five Polish biobanks/biorepositories participated in the survey.

Results

Polish biobanks are mostly affiliated with research entities (universities—42% and research institutes—30%). The data collected indicate that a considerable number of Polish biobanks are specialized (33 units), in contrast to population-based biobanks (8 units). These biobanks are mostly focused on collecting samples from oncological (23 biobanks) and rare diseases (12 biobanks). In general, great diversity was found in the material collected. Scientists working in Polish biobanks are very open to scientific cooperation (declared by 60% of units) and sharing their collections with the international scientific environment. In terms of quality issues, most biobanks declared that their quality management system was in the process of implementation (45%) or had already been implemented (23%).

Conclusions

Although biobanking in Poland is still in its infancy, the results of this study seem promising and may be valuable to the wider biobanking research community. The distribution of biobanks throughout the Polish territory, their connection with scientific and clinical units, and their involvement in research on rare diseases may contribute to an increase in the number of multicenter studies.

An Overview of Benefits and Challenges of Rare Disease Biobanking in Africa, Focusing on South Africa

The North-West University's Centre for Human Metabolomics (CHM) is in the process of establishing the first rare disease (RD) biobank in South Africa and Africa. The CHM Biobank's main focus is on the collection of samples and information for rare congenital disorders. Approximately 72% of all RDs have a genetic origin, of which 70% have an exclusive pediatric onset. The need for such a biobank was identified by the CHM diagnostic laboratory. Feedback toward this initiative was overwhelmingly positive at the first stakeholder meeting in August 2019. However, gaining support from the public sector and recruiting of participants have proven to be challenging. Problems experienced to date include lack of support from government and clinicians; lack of knowledge on RDs (patients and clinicians); public health care focus not directed toward RDs; patients not returning for follow-up visits; and unwillingness to participate due to fear of exploitation. The CHM Biobank's vision and goals are aligned to address a national and international research need: it will provide a valuable resource for scientists to improve what is known about these diseases; to better understand the natural history and pathophysiology; to optimize diagnostic methods; and to potentially develop treatments. The genetic variability of the South African population provides added value to the RD biobank. This review provides a brief overview of the literature on the challenges and benefits of an RD biobank and how this relates to low- and middle-income countries (LMIC) like South Africa. The aim of the review is to draw attention to the potential benefits of such an undertaking and to create awareness, at both local and global level, toward some of the unique collective considerations that an RD biobank in LMIC (also unique South African challenges) faces on an operational, collaborate, and sustainability level.

Cost-effectiveness analysis of using the TBX6-associated congenital scoliosis risk score (TACScore) in genetic diagnosis of congenital scoliosis

Background

We previously reported a novel clinically distinguishable subtype of congenital scoliosis (CS), namely, TBX6-associated congenital scoliosis (TACS). We further developed the TBX6-associated CS risk score (TACScore), a multivariate phenotype-based model to predict TACS according to the patient’s clinical manifestations. In this study, we aimed to evaluate whether using the TACScore as a screening method prior to performing whole-exome sequencing (WES) is more cost-effective than using WES as the first-line genetic test for CS.

Methods

We retrospectively collected the molecular data of 416 CS patients in the Deciphering disorders Involving Scoliosis and COmorbidities (DISCO) study. A decision tree was constructed to estimate the cost and the diagnostic time required for the two alternative strategies (TACScore versus WES). Bootstrapping simulations and sensitivity analyses were performed to examine the distributions and robustness of the estimates. The economic evaluation considered both the health care payer and the personal budget perspectives.

Results

From the health care payer perspective, the strategy of using the TACScore as the primary screening method resulted in an average cost of $1074.2 (95%CI: $1044.8 to $1103.5) and an average diagnostic duration of 38.7d (95%CI: 37.8d to 39.6d) to obtain a molecular diagnosis for each patient. In contrast, the corresponding values were $1169.6 (95%CI: $1166.9 to $1172.2) and 41.4d (95%CI: 41.1d to 41.7d) taking WES as the first-line test (P < 0.001). From the personal budget perspective, patients who were predicted to be positive by the TACScore received a result with an average cost of $715.1 (95%CI: $594.5 to $835.7) and an average diagnostic duration of 30.4d (95%CI: 26.3d to 34.6d). Comparatively, the strategy of WES as the first-line test was estimated to have significantly longer diagnostic time with an average of 44.0d (95%CI: 43.2d to 44.9d), and more expensive with an average of $1193.4 (95%CI: $1185.5 to $1201.3) (P < 0.001). In 100% of the bootstrapping simulations, the TACScore strategy was significantly less costly and more time-saving than WES. The sensitivity analyses revealed that the TACScore strategy remained cost-effective even when the cost per WES decreased to $8.8.

Conclusions

This retrospective study provides clinicians with economic evidence to integrate the TACScore into clinical practice. The TACScore can be considered a cost-effective tool when it serves as a screening test prior to performing WES.

Rare disease data stewardship in Canada

The Canadian Genomics Partnership for Rare Diseases, spearheaded by Genome Canada, will integrate genome-wide sequencing to rare disease clinical care in Canada. Centralized and tiered models of data stewardship are proposed to ensure that the data generated can be shared for secondary clinical, research, and quality assurance purposes in compliance with ethics and law. The principal ethico-legal obligations of clinicians, researchers, and institutions are synthesized. Governance infrastructures such as registered access platforms, data access compliance offices, and Beacon systems are proposed as potential organizational and technical foundations of responsible rare disease data sharing. The appropriate delegation of responsibilities, the transparent communication of rights and duties, and the integration of data privacy safeguards into infrastructure design are proposed as the cornerstones of rare disease data stewardship.

In search of an evidence-based strategy for quality assessment of human tissue samples: report of the tissue Biospecimen Research Working Group of the Spanish Biobank Network

The purpose of the present work is to underline the importance of obtaining a standardized procedure to ensure and evaluate both clinical and research usability of human tissue samples. The study, which was carried out by the Biospecimen Science Working Group of the Spanish Biobank Network, is based on a general overview of the current situation about quality assurance in human tissue biospecimens. It was conducted an exhaustive review of the analytical techniques used to evaluate the quality of human tissue samples over the past 30 years, as well as their reference values if they were published, and classified them according to the biomolecules evaluated: (i) DNA, (ii) RNA, and (iii) soluble or/and fixed proteins for immunochemistry. More than 130 publications released between 1989 and 2019 were analysed, most of them reporting results focused on the analysis of tumour and biopsy samples. A quality assessment proposal with an algorithm has been developed for both frozen tissue samples and formalin-fixed paraffin-embedded (FFPE) samples, according to the expected quality of sample based on the available pre-analytical information and the experience of the participants in the Working Group. The high heterogeneity of human tissue samples and the wide number of pre-analytic factors associated to quality of samples makes it very difficult to harmonize the quality criteria. However, the proposed method to assess human tissue sample integrity and antigenicity will not only help to evaluate whether stored human tissue samples fit for the purpose of biomarker development, but will also allow to perform further studies, such as assessing the impact of different pre-analytical factors on very well characterized samples or evaluating the readjustment of tissue sample collection, processing and storing procedures. By ensuring the quality of the samples used on research, the reproducibility of scientific results will be guaranteed.

Oesophageal atresia

Oesophageal atresia (EA) is a congenital abnormality of the oesophagus that is caused by incomplete embryonic compartmentalization of the foregut. EA commonly occurs with a tracheo-oesophageal fistula (TEF). Associated birth defects or anomalies, such as VACTERL association, trisomy 18 or 21 and CHARGE syndrome, occur in the majority of patients born with EA. Although several studies have revealed signalling pathways and genes potentially involved in the development of EA, our understanding of the pathophysiology of EA lags behind the improvements in surgical and clinical care of patients born with this anomaly. EA is treated surgically to restore the oesophageal interruption and, if present, ligate and divide the TEF. Survival is now ~90% in those born with EA with severe associated anomalies and even higher in those born with EA alone. Despite these achievements, long-term gastrointestinal and respiratory complications and comorbidities in patients born with EA are common and lead to decreased quality of life. Oesophageal motility disorders are probably ubiquitous in patients after undergoing EA repair and often underlie these complications and comorbidities. The implementation of several new diagnostic and screening tools in clinical care, including high-resolution impedance manometry, pH-multichannel intraluminal impedance testing and disease-specific quality of life questionnaires now provide better insight into these problems and may contribute to better long-term outcomes in the future.