Soc Sci Med. 2023 Dec;338:116332. doi: 10.1016/j.socscimed.2023.116332. Epub 2023 Oct 17.

ABSTRACT

Patient organisations play an increasingly crucial role in the pharmaceutical sector, yet their impact on innovation remains unexplored. We estimate the impact of patient organisations on R&D activity in the context of rare diseases in Europe using a proprietary dataset that maps clinical trials from discovery to phase III across 29 countries, 1893 indications, and 30 years (1990-2019). By applying difference-in-differences and event study methodologies to a panel of 1,646,910 unique R&D observations, we find that country-indication pairs with at least one operating patient organisation have a higher rate of R&D activity compared to those without, with stronger effect in more prevalent rare diseases compared to ultra-rare conditions. We observe a lag in effects from patient organisation introduction, suggesting it takes approximately five years for these organisations to affect R&D activity. Overall, our work suggests that patient organisations play an important role in steering R&D efforts in rare diseases. Further research is needed to better understand mechanisms driving this effect and the potential impact of patient organisations on existing health inequities.

PMID:37866173 | DOI:10.1016/j.socscimed.2023.116332

Reumatol Clin (Engl Ed). 2023 Nov;19(9):527-529. doi: 10.1016/j.reumae.2023.10.001. Epub 2023 Oct 17.

ABSTRACT

Hajdu-Cheney syndrome or acro-dento-osteo-dysplasia syndrome is a rare disease characterized by band osteolysis of distal phalanges and facial dysmorphia, among other manifestations. We present the case of a 45-year-old male who consulted for mechanical joint pain of both hands, facial dysmorphism, cranio-facial alterations, and digital telescoping with acroosteolysis.

PMID:37858457 | DOI:10.1016/j.reumae.2023.10.001

Inn Med (Heidelb). 2023 Nov;64(11):1033-1040. doi: 10.1007/s00108-023-01599-7. Epub 2023 Oct 20.

ABSTRACT

BACKGROUND: Approximately 300 million people worldwide suffer from a rare disease. An optimal treatment requires a successful diagnosis. This takes a particularly long time, especially for rare diseases. Digital diagnosis support systems could be important aids in accelerating a successful diagnosis in the future.

OBJECTIVE: The current possibilities of digital diagnostic support systems in the diagnosis of rare diseases and questions that still need to be clarified are presented in relation to the parameters of ethics, economy and quality of life.

MATERIAL AND METHODS: Current research results of the authors were compiled and discussed in the context of the current literature. A case study is used to illustrate the potential of digital diagnostic support systems.

RESULTS: Digital diagnostic support systems and experts together can accelerate the successful diagnosis in patients with rare diseases. This could have a positive impact on patients' quality of life and lead to potential savings in direct and indirect costs in the healthcare system.

CONCLUSION: Ensuring data security, legal certainty and functionality in the use of digital diagnostic support systems is of great importance in order to create trust among experts and patients. Continuous further development of the systems by means of artificial intelligence (AI) could also enable patients to accelerate diagnosis in the future.

PMID:37861723 | DOI:10.1007/s00108-023-01599-7

Inn Med (Heidelb). 2023 Nov;64(11):1041-1043. doi: 10.1007/s00108-023-01616-9. Epub 2023 Oct 19.

NO ABSTRACT

PMID:37855883 | DOI:10.1007/s00108-023-01616-9

BMJ Open. 2023 Oct 18;13(10):e064811. doi: 10.1136/bmjopen-2022-064811.

ABSTRACT

OBJECTIVE: To evaluate the impacts of the 2017 adjustment of National Reimbursement Drug List (NRDL) on orphan drugs hospital procurement volumes and spending in China.

DESIGN: We used an interrupted time series design covering the period from 2016 to 2018 to analyse changes in hospital procurement volumes and spending of orphan drugs for which were included in the 2017 NRDL.

SETTING AND DATA: The study was conducted in China. Orphan drug procurement data of 789 public hospitals (594 tertiary hospitals and 195 secondary hospitals) were derived from the Chinese Medical Economic Information (CMEI).

OUTCOME MEASURES: Monthly orphan drugs hospital procurement volumes and spending.

RESULTS: Nine orphan drugs were included in the 2017 NRDL (seven were directly included, and two were included after price negotiation). Comparing to orphan drugs not included in the NRDL, hospital procurement volumes ([Formula: see text] =43 312, p<0.001) and spending ([Formula: see text] =6 48 927, p<0.001) of the nine included drugs showed significant upward trends after implementation of the 2017 NRDL adjustment.

CONCLUSIONS: Our results suggest that the 2017 adjustment of NRDL significantly changed the usage and spending on certain orphan drugs. The increase in orphan drug hospital procurement volumes should improve rare disease patients' access to these orphan drugs.

PMID:37852769 | DOI:10.1136/bmjopen-2022-064811

Orphanet J Rare Dis. 2023 Oct 17;18(1):328. doi: 10.1186/s13023-023-02907-y.

ABSTRACT

BACKGROUND: Progressive ataxias are rare and complex neurological disorders that represent a challenge for the clinicians to diagnose and manage them. This study explored the patient pathways of individuals attending specialist ataxia centres (SAC) compared with non-specialist settings. We investigated specifically how diagnosis was reached, the access to healthcare services, treatments, and care satisfaction. The focus of this study was on early intervention, coordination of treatment to understand the care provision in different countries.

METHODS: A patient survey was done in the UK, Germany and Italy to gather information about diagnosis and management of the ataxias in specialist (SAC) and non-specialist settings, utilisation of other primary and secondary health care services, and patients' satisfaction of received treatment.

RESULTS: Patients gave positive feedback about the role of SAC in understanding their condition, ways to manage their ataxia (p < 0.001; UK) and delivering care adapted to their needs (p < 0.001; UK), in coordinating referrals to other healthcare specialists, and in offering opportunities to take part in research studies. Similar barriers for patients were identified in accessing the SACs among the selected countries, UK, Germany, and Italy.

CONCLUSIONS: This study provides crucial information about the ataxia patients care pathways in three European countries. Overall, the results showed a trend in patients' satisfaction being better in SAC compared to non-SAC. The outcomes can be used now for policy recommendations on how to improve treatment and care for people with these very rare and complex neurological diseases across Europe.

PMID:37848998 | PMC:PMC10583310 | DOI:10.1186/s13023-023-02907-y

Orphanet J Rare Dis. 2023 Oct 17;18(1):327. doi: 10.1186/s13023-023-02935-8.

ABSTRACT

BACKGROUND: The purpose of this study was twofold: (i) To assess the parents' experiences and perception of participating in a "Parental Intervention Program for Preschool children with Rare Diseases" (PIPP-RDs). (ii) To evaluate which elements of the PIPP-RDs that the parents emphasized as important for improving their health literacy related to facilitating the transition of their children from kindergarten to school.

METHOD: A mixed methods evaluation study was conducted ten and eleven months post-intervention, integrating an online quantitative survey combined with individual semi-structured interviews. Twenty-two parents participated in individual interviews, of these 18 also responded to the online questionnaire survey.

RESULTS: All parents that participated in this study reported that the information conveyed at the program was of great value and utility, 88% reported significantly alleviated stress associated to their child`s school-start, 84% indicated had improved the school-home collaboration and 84% reported that it had encouraged them to establish contact with the school prior to school commencement. From the qualitative data five main themes emerged: (i) Competence and Knowledge Acquisition, (ii) Becoming more Prepared and Relaxed, (iii) Achieved Realistic Expectations, (iv) Enhanced Communication Skills, (v) Increased Health Literacy and Self-Efficacy. The evaluative findings suggest that this invention program has notably improved the parents' aptitude for school interaction, enhanced the adaptions according to children`s needs for accommodations, and has provided reassurance in the school-home collaboration. Parents also described increased self-confidence and self-efficacy in managing the school start for children with RDs.

CONCLUSION: The highly positive response of participating in PIPP-RDs may not only reflect the merits of the program`s content, but also underscore the significant needs for such support during the transition to school for parents of children with RDs. Comparable initiatives, oriented towards enhancing the health literacy and empowering the parents, are anticipated to yield similarly favourable results. We argue that intervention program amalgamate pertinent information, group discourse, and workshops on school-related issues, alongside opportunities for parents to meet other parents in similar situations.

PMID:37848938 | PMC:PMC10583464 | DOI:10.1186/s13023-023-02935-8

Clin Nucl Med. 2023 Dec 1;48(12):1102-1104. doi: 10.1097/RLU.0000000000004910. Epub 2023 Oct 16.

ABSTRACT

Thoracic SMARCA4-deficient undifferentiated tumor (SMARCA4-UT) is a rare malignant disease. We present the case of a 56-year-old woman with thoracic SMARCA4-UT presenting as a mediastinal mass who underwent 68 Ga-DOTA-FAPI-04 PET/CT imaging. Intense 68 Ga-DOTA-FAPI-04 uptake was observed in the primary tumor and lymph node metastases. After 7 cycles of immune checkpoint inhibitor plus chemotherapy, the patient underwent mediastinal mass resection, and postoperative pathology confirmed a complete pathologic response. This case may provide valuable insights into the diagnosis and monitoring of the treatment response of thoracic SMARCA4-UT.

PMID:37846457 | DOI:10.1097/RLU.0000000000004910

J Clin Endocrinol Metab. 2023 Oct 17:dgad610. doi: 10.1210/clinem/dgad610. Online ahead of print.

ABSTRACT

CONTEXT: Clinical endocrinology encompasses many diseases requiring long-term drug therapy. Prohibitive pricing of some endocrine drugs classified as essential by the World Health Organisation has created sub-optimal care of patients with endocrine disorders.

EVIDENCE ACQUISITION: This review is based on evidence obtained from several databases and search engines including PubMed, Google and Google Scholar, reference searches, manual searching for web pages of international regulatory bodies and the authors' experience from different healthcare settings.

EVIDENCE SYNTHESIS: After the expiry of a patent, generic versions with the opportunity for increased availability and a price reduction are expected. There are access barriers worldwide for many off-patent endocrine drugs. The high price is the main issue for several medicines including insulin, hydrocortisone, testosterone, and gonadotropins. This is contributed to by several factors including the market monopoly due to the lack of registered generics or suppliers limiting the benefit of competition and a complex supply chain. Additionally, the lack of some medicines had been concerning due to market factors such as the relatively small number of patients making it less attractive for the manufacturers. Commissioning of non-profit manufacturers and state manufacturing as well as strict price control measures could alleviate this situation.

CONCLUSIONS: Lack of availability and disproportionate price inflation affecting essential off-patent endocrine therapies is common due to several interrelated factors. Global collaboration among healthcare organisations with the support of policy-making bodies might be needed to mitigate this.

PMID:37846800 | DOI:10.1210/clinem/dgad610

Eur J Med Genet. 2023 Nov;66(11):104866. doi: 10.1016/j.ejmg.2023.104866. Epub 2023 Oct 13.

ABSTRACT

BACKGROUND: Hypophosphatasia (HPP) is a rare inherited disorder caused by pathogenic loss-of-function variants in the ALPL gene, encoding the tissue-nonspecific isoenzym of alkaline phosphatase (ALP; TNSALP). Low serum ALP is the biochemical hallmark of HPP, but it is unknown whether ALP levels can increase due to concurring liver disease, which may lead to a missed diagnose of HPP. We present a patient with genetically confirmed HPP, who showed a transient increase of serum ALP levels due to alcohol-induced hepatitis.

CLINICAL REPORT: A 71-year old man was seen at our Bone Center for surveillance of HPP. Serum ALP was always low (23 U/L; reference value: <115 U/L). During follow-up, his serum ALP increased (156 U/L, further rising to 204 U/L), with concomitantly elevated serum gamma-glutamyl transferase and transaminases, and a rise in bone specific ALP (18.7 μg/L; reference value: 5.7-32.9 μg/L). This was attributed to alcohol-induced hepatitis. After refraining from alcohol intake, both serum ALP and bone specific ALP levels returned to initial low levels (30 U/L and 4.3 μg/L respectively).

CONCLUSIONS: We demonstrated the history of a 71-year old patient with HPP, presenting during routine follow-up with an elevated serum ALP level up to 204 U/L due to alcohol-induced hepatitis. This case illustrates that the diagnosis of HPP can potentially be missed when ALP levels are normal or elevated due to a concomitant liver disease.

PMID:37839783 | DOI:10.1016/j.ejmg.2023.104866

Int J Environ Res Public Health. 2023 Sep 29;20(19):6863. doi: 10.3390/ijerph20196863.

ABSTRACT

The COVID-19 pandemic took a toll on everyone's lives, and patients with rare diseases (RDs) had to pay an even higher price. In this systematic review, we explored the impact of the COVID-19 pandemic on individuals with RDs from a psychological perspective. Using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we retrieved articles from the Google Scholar, Scopus, and PubMed databases focusing on 'COVID-19,' 'psychology,' and 'rare diseases.' Seventeen primary articles were identified (mainly from continental Europe). The results revealed the psychological effects of the pandemic on rare disease patients, including increased anxiety, stress, and depressive moods. This review also highlighted the increased vulnerability and reduced quality of life of rare disease patients during the pandemic, as well as the importance of telecare and psychological support as critical interventions for improving their well-being. There is an urgent need for multidisciplinary research and stronger healthcare systems to meet the unique challenges of rare disease patients, who represent 3.5-5.9% of the global population.

PMID:37835133 | PMC:PMC10573057 | DOI:10.3390/ijerph20196863

Orphanet J Rare Dis. 2023 Oct 13;18(1):324. doi: 10.1186/s13023-023-02947-4.

ABSTRACT

BACKGROUND: In the European Union, a disease is defined as rare when it affects fewer than 1 in 2000 people. Currently, there are up to 8000 described rare diseases (RDs), collectively affecting 30 million people in the European Union. In 2004 Tuscany region (Italy) established a Regional Network of hospital units to ensure highly specialised medical care in the field of RDs. Shortly after the Rare Diseases Registry of Tuscany (Registro Toscano Malattie Rare-RTMR) was implemented. Here we describe the analysis performed on RTMR data which has recently allowed to remap the Network based on European Reference Networks' model.

RESULTS: Data analysis was performed on 60,367 cases registered in RTMR, regarding 628 RDs. Two-hundred and fifteen active presidia have been evaluated. The assignment of each RD to the suitable European Reference Network has been made considering not only the number of registered cases, certifications and treatment plans for each Regional Presidium but also the competence in multidisciplinary management of the patient, from diagnosis to treatment. This evaluation has led to the establishment of twenty-one Regional Coordination Centres. They aggregate and coordinate Hospital Units which diagnose and treat one or a group of related RDs. In case of wide groups of RDs, Clinical Subnets are instituted. Updated statistics regarding RDs in Tuscany, list of RDs and Coordination Centres, as well as information about single Presidia are published and freely available on a designated webpage. Regional Decrees are regularly updated according to the network evolution.

CONCLUSIONS: The Rare Diseases Regional Network in Tuscany, based on the ERN model, has played a pivotal role in enhancing RD management and research. The remapping has led to a dynamic system, following not only scientific research but also the development of Presidia's expertise. By pooling resources and expertise, the network has improved the availability and accessibility of specialized care for patients with RDs. Collaborative efforts, data sharing, and standardized registries are crucial for advancing RD research, improving diagnosis and treatment, and ultimately enhancing the quality of life for individuals living with RDs.

PMID:37833795 | PMC:PMC10576286 | DOI:10.1186/s13023-023-02947-4

EBioMedicine. 2023 Oct 12;97:104829. doi: 10.1016/j.ebiom.2023.104829. Online ahead of print.

ABSTRACT

BACKGROUND: Malignant peripheral nerve sheath tumour (MPNST) is an aggressive orphan disease commonly affecting adolescents or young adults. Current knowledge of molecular tumour biology has been insufficient for development of rational treatment strategies. We aimed to discover molecular subtypes of potential clinical relevance.

METHODS: Fresh frozen samples of MPNSTs (n = 94) and benign neurofibromas (n = 28) from 115 patients in a European multicentre study were analysed by DNA copy number and/or transcriptomic profiling. Unsupervised transcriptomic subtyping was performed and the subtypes characterized for genomic aberrations, clinicopathological associations and patient survival.

FINDINGS: MPNSTs were classified into two transcriptomic subtypes defined primarily by immune signatures and proliferative processes. "Immune active" MPNSTs (44%) had sustained immune signals relative to neurofibromas, were more frequently low-grade (P = 0.01) and had favourable prognostic associations in a multivariable model of disease-specific survival with clinicopathological factors (hazard ratio 0.25, P = 0.003). "Immune deficient" MPNSTs were more aggressive and characterized by proliferative signatures, high genomic complexity, aberrant TP53 and PRC2 loss, as well as high relative expression of several potential actionable targets (EGFR, ERBB2, EZH2, KIF11, PLK1, RRM2). Integrated gene-wise analyses suggested a DNA copy number-basis for proliferative transcriptomic signatures in particular, and the tumour copy number burden further stratified the transcriptomic subtypes according to patient prognosis (P < 0.01).

INTERPRETATION: Approximately half of MPNSTs belong to an "immune deficient" transcriptomic subtype associated with an aggressive disease course, PRC2 loss and expression of several potential therapeutic targets, providing a rationale for molecularly-guided intervention trials.

FUNDING: Research grants from non-profit organizations, as stated in the Acknowledgements.

PMID:37837931 | DOI:10.1016/j.ebiom.2023.104829

J Neurodev Disord. 2023 Oct 13;15(1):33. doi: 10.1186/s11689-023-09502-z.

ABSTRACT

OBJECTIVE: Recent advances in the understanding of neurodevelopmental disorders such as Rett syndrome (RTT) have enabled the discovery of novel therapeutic approaches that require formal clinical evaluation of efficacy. Clinical trial success depends on outcome measures that assess clinical features that are most impactful for affected individuals. To determine the top concerns in RTT and RTT-related disorders we asked caregivers to list the top caregiver concerns to guide the development and selection of appropriate clinical trial outcome measures for these disorders.

METHODS: Caregivers of participants enrolled in the US Natural History Study of RTT and RTT-related disorders (n = 925) were asked to identify the top 3 concerning problems impacting the affected participant. We generated a weighted list of top caregiver concerns for each of the diagnostic categories and compared results between the disorders. Further, for classic RTT, caregiver concerns were analyzed by age, clinical severity, and common RTT-causing mutations in MECP2.

RESULTS: The top caregiver concerns for classic RTT were effective communication, seizures, walking/balance issues, lack of hand use, and constipation. The frequency of the top caregiver concerns for classic RTT varied by age, clinical severity, and specific mutations, consistent with known variation in the frequency of clinical features across these domains. Caregivers of participants with increased seizure severity often ranked seizures as the first concern, whereas caregivers of participants without active seizures often ranked hand use or communication as the top concern. Comparison across disorders found commonalities in the top caregiver concerns between classic RTT, atypical RTT, MECP2 duplication syndrome, CDKL5 deficiency disorder, and FOXG1 syndrome; however, distinct differences in caregiver concerns between these disorders are consistent with the relative prevalence and impact of specific clinical features.

CONCLUSION: The top caregiver concerns for individuals with RTT and RTT-related disorders reflect the impact of the primary clinical symptoms of these disorders. This work is critical in the development of meaningful therapies, as optimal therapy should address these concerns. Further, outcome measures to be utilized in clinical trials should assess these clinical issues identified as most concerning by caregivers.

PMID:37833681 | PMC:PMC10571464 | DOI:10.1186/s11689-023-09502-z

F1000Res. 2023 Nov 13;12:741. doi: 10.12688/f1000research.130388.1. eCollection 2023.

ABSTRACT

This article aims to synthesize the existing literature on the implementation of public policies to incentivize the development of treatments for rare diseases, (diseases with very low prevalence and therefore with low commercial interest) otherwise known as orphan drugs. The implementation of these incentives in the United States (US), Japan, and in the European Union (EU) seems to be related to a substantial increase in treatments for these diseases, and has influenced the way the pharmaceutical research & development (R&D) system operates beyond this policy area. Despite the success of the Orphan Drug model, the academic literature also highlights the negative implications that these public policies have on affordability and access to orphan drugs, as well as on the prioritization of certain disease rare areas over others. The synthesis focuses mostly on the United States' Orphan Drug Act (ODA) as a model for subsequent policies in other regions and countries. It starts with a historical overview of the creation of the term "rare diseases", continues with a summary of the evidence available on the US ODA's positive and negative impacts, and provides a summary of the different proposals to reform these incentives in light of the negative outcomes described. Finally, it describes some key aspects of the Japanese and European policies, as well as some of the challenges captured in the literature related to their impact in Low- and Middle-Income Countries (LMICs).

PMID:37822316 | PMC:PMC10562777 | DOI:10.12688/f1000research.130388.1

Orphanet J Rare Dis. 2023 Oct 12;18(1):321. doi: 10.1186/s13023-023-02943-8.

ABSTRACT

BACKGROUND: Generalized pairwise comparisons (GPC) can be used to assess the net benefit of new treatments for rare diseases. We show the potential of GPC through simulations based on data from a natural history study in mucopolysaccharidosis type IIIA (MPS IIIA).

METHODS: Using data from a historical series of untreated children with MPS IIIA aged 2 to 9 years at the time of enrolment and followed for 2 years, we performed simulations to assess the operating characteristics of GPC to detect potential (simulated) treatment effects on a multi-domain symptom assessment. Two approaches were used for GPC: one in which the various domains were prioritized, the other with all domains weighted equally. The net benefit was used as a measure of treatment effect. We used increasing thresholds of clinical relevance to reflect the magnitude of the desired treatment effects, relative to the standard deviation of the measurements in each domain.

RESULTS: GPC were shown to have adequate statistical power (80% or more), even with small sample sizes, to detect treatment effects considered to be clinically worthwhile on a symptom assessment covering five domains (expressive language, daily living skills, and gross-motor, sleep and pain). The prioritized approach generally led to higher power as compared with the non-prioritized approach.

CONCLUSIONS: GPC of prioritized outcomes is a statistically powerful as well as a patient-centric approach for the analysis of multi-domain scores in MPS IIIA and could be applied to other heterogeneous rare diseases.

PMID:37828533 | PMC:PMC10571482 | DOI:10.1186/s13023-023-02943-8

Front Public Health. 2023 Sep 26;11:1248260. doi: 10.3389/fpubh.2023.1248260. eCollection 2023.

ABSTRACT

BACKGROUND: Patients, families, the healthcare system, and society as a whole are all significantly impacted by rare diseases (RDs). According to various classifications, there are currently up to 9,000 different rare diseases that have been recognized, and new diseases are discovered every month. Although very few people are affected by each uncommon disease individually, millions of people are thought to be impacted globally when all these conditions are considered. Therefore, RDs represent an important public health concern. Although crucial for clinical care, early and correct diagnosis is still difficult to achieve in many nations, especially those with low and middle incomes. Consequently, a sizeable amount of the overall burden of RD is attributable to undiagnosed RD (URD). Existing barriers and policy aspects impacting the care of patients with RD and URD remain to be investigated.

METHODS: To identify unmet needs and opportunities for patients with URD, the Developing Nations Working Group of the Undiagnosed Diseases Network International (DNWG-UDNI) conducted a survey among its members, who were from 20 different nations. The survey used a mix of multiple choice and dedicated open questions covering a variety of topics. To explore reported needs and analyze them in relation to national healthcare economical aspects, publicly available data on (a) World Bank ranking; (b) Current health expenditure per capita; (c) GDP per capita; (d) Domestic general government health expenditure (% of GDP); and (e) Life expectancy at birth, total (years) were incorporated in our study.

RESULTS: This study provides an in-depth evaluation of the unmet needs for 20 countries: low-income (3), middle-income (10), and high-income (7). When analyzing reported unmet needs, almost all countries (N = 19) indicated that major barriers still exist when attempting to improve the care of patients with UR and/or URD; most countries report unmet needs related to the availability of specialized care and dedicated facilities. However, while the countries ranked as low income by the World Bank showed the highest prevalence of referred unmet needs across the different domains, no specific trend appeared when comparing the high, upper, and low-middle income nations. No overt trend was observed when separating countries by current health expenditure per capita, GDP per capita, domestic general government health expenditure (% of GDP) and life expectancy at birth, total (years). Conversely, both the GDP and domestic general government health expenditure for each country impacted the presence of ongoing research.

CONCLUSION: We found that policy characteristics varied greatly with the type of health system and country. No overall pattern in terms of referral for unmet needs when separating countries by main economic or health indicators were observed. Our findings highlight the importance of identifying actionable points (e.g., implemented orphan drug acts or registries where not available) in order to improve the care and diagnosis of RDs and URDs on a global scale.

PMID:37822540 | PMC:PMC10562568 | DOI:10.3389/fpubh.2023.1248260

Nat Commun. 2023 Oct 12;14(1):6403. doi: 10.1038/s41467-023-41980-6.

ABSTRACT

Rare Mendelian disorders pose a major diagnostic challenge and collectively affect 300-400 million patients worldwide. Many automated tools aim to uncover causal genes in patients with suspected genetic disorders, but evaluation of these tools is limited due to the lack of comprehensive benchmark datasets that include previously unpublished conditions. Here, we present a computational pipeline that simulates realistic clinical datasets to address this deficit. Our framework jointly simulates complex phenotypes and challenging candidate genes and produces patients with novel genetic conditions. We demonstrate the similarity of our simulated patients to real patients from the Undiagnosed Diseases Network and evaluate common gene prioritization methods on the simulated cohort. These prioritization methods recover known gene-disease associations but perform poorly on diagnosing patients with novel genetic disorders. Our publicly-available dataset and codebase can be utilized by medical genetics researchers to evaluate, compare, and improve tools that aid in the diagnostic process.

PMID:37828001 | PMC:PMC10570269 | DOI:10.1038/s41467-023-41980-6

Hum Gene Ther. 2023 Oct;34(19-20):980-981. doi: 10.1089/hum.2023.29248.rwh. Epub 2023 Oct 12.

NO ABSTRACT

PMID:37823804 | DOI:10.1089/hum.2023.29248.rwh

Database (Oxford). 2023 Oct 11;2023:baad066. doi: 10.1093/database/baad066.

ABSTRACT

In recent years, a huge amount of data on ncRNA interactions has been described in scientific papers and databases. Although considerable effort has been made to annotate the available knowledge in public repositories, there are still significant discrepancies in how different resources capture and interpret data on ncRNA functional and physical associations. In the present paper, we present a collection of microRNA-mRNA interactions annotated from the scientific literature following recognized standard criteria and focused on microRNAs, which regulate genes associated with rare diseases as a case study. The list of protein-coding genes with a known role in specific rare diseases was retrieved from the Genome England PanelApp, and associated microRNA-mRNA interactions were annotated in the IntAct database and compared with other datasets. RNAcentral identifiers were used for unambiguous, stable identification of ncRNAs. The information about the interaction was enhanced by a detailed description of the cell types and experimental conditions, providing a computer-interpretable summary of the published data, integrated with the huge amount of protein interactions already gathered in the database. Furthermore, for each interaction, the binding sites of the microRNA are precisely mapped on a well-defined mRNA transcript of the target gene. This information is crucial to conceive and design optimal microRNA mimics or inhibitors to interfere in vivo with a deregulated process. As these approaches become more feasible, high-quality, reliable networks of microRNA interactions are needed to help, for instance, in the selection of the best target to be inhibited and to predict potential secondary off-target effects. Database URL https://www.ebi.ac.uk/intact.

PMID:37819683 | PMC:PMC10566539 | DOI:10.1093/database/baad066