Stud Health Technol Inform. 2024 Aug 22;316:1442-1446. doi: 10.3233/SHTI240683.

ABSTRACT

Secondary use of data for research purposes is especially important in rare diseases (RD), since, per definition, data are sparse. The European Joint Programme on Rare Diseases (EJP RD) aims at developing an RD infrastructure which supports the secondary use of data. Significant amounts of RD data are a) distributed and b) available only in pseudonymised format. Privacy-Preserving Record Linkage (PPRL) concerns the linking of such distributed datasets without disclosing the participant's identities. We present a concept for linking a PPRL Service to the EJP RD Virtual Platform (VP). Level 1 (resource discovery) connection is provided by running an FDP within the PPRL Service. On Level 2 (data discoverability), the PPRL Service can represent both, an individual and a catalog endpoint. Our solution can count patients in PPRL-supporting resources, count duplicates only once, and count only patients registered to multiple resources. Currently, we are preparing the deployment within the EJP RD VP.

PMID:39176652 | DOI:10.3233/SHTI240683

Stud Health Technol Inform. 2024 Aug 22;316:1418-1419. doi: 10.3233/SHTI240677.

ABSTRACT

Rare neuromuscular diseases (NMDs) encompass various disorders of the nervous system and skeletal muscles, and present intricate challenges in diagnosis, treatment, and research due to their low prevalence and often diverse multisystemic manifestations. Leveraging collected patient data for secondary use and analysis holds promise for advancing medical understanding in this field. However, a certain level of data quality is a prerequisite for the methods that can be used to analyze data. The heterogeneous nature of NMDs poses a significant obstacle to the creation of standardized documentation, as there are still many challenges to accurate diagnosis and many discrepancies in the diagnostic process between different countries. This paper proposes the development of an information model tailored to NMDs, aiming to augment visibility, address deficiencies in documentation, and facilitate comprehensive analysis and research endeavors. By providing a structured framework, this model seeks to propel advancements in understanding and managing NMD, ultimately benefiting patients and healthcare providers worldwide.

PMID:39176646 | DOI:10.3233/SHTI240677

Stud Health Technol Inform. 2024 Aug 22;316:1396-1400. doi: 10.3233/SHTI240672.

ABSTRACT

This paper explores key success factors for the development and implementation of a Common Data Model (CDM) for Rare Diseases (RDs) focusing on the European context. Several challenges hinder RD care and research in diagnosis, treatment, and research, including data fragmentation, lack of standardisation, and Interoperability (IOP) issues within healthcare information systems. We identify key issues and recommendations for an RD-CDM, drawing on international guidelines and existing infrastructure, to address organisational, consensus, interoperability, usage, and secondary use challenges. Based on these, we analyse the importance of balancing the scope and IOP of a CDM to cater to the unique requirements of RDs while ensuring effective data exchange and usage across systems. In conclusion, a well-designed RD-CDM can bridge gaps in RD care and research, enhance patient care and facilitate international collaborations.

PMID:39176641 | DOI:10.3233/SHTI240672

Stud Health Technol Inform. 2024 Aug 22;316:1785-1789. doi: 10.3233/SHTI240777.

ABSTRACT

Rare diseases pose significant challenges due to their heterogeneity and lack of knowledge. This study develops a comprehensive pipeline interoperable with a document-oriented clinical data warehouse, integrating cohort characterization, patient clustering and interpretation. Leveraging NLP, semantic similarity, machine learning and visualization, the pipeline enables the identification of prevalent phenotype patterns and patient stratification. To enhance interpretability, discriminant phenotypes characterizing each cluster are provided. Users can visually test hypotheses by marking patients exhibiting specific keywords in the EHR like genes, drugs and procedures. Implemented through a web interface, the pipeline enables clinicians to navigate through different modules, discover intricate patterns and generate interpretable insights that may advance rare diseases understanding, guide decision-making, and ultimately improve patient outcomes.

PMID:39176563 | DOI:10.3233/SHTI240777

Zh Nevrol Psikhiatr Im S S Korsakova. 2024;124(7. Vyp. 2):33-36. doi: 10.17116/jnevro202412407233.

ABSTRACT

Rare demyelinating diseases are a group of diseases whose pathogenesis is based on the process of demyelination. This group of diseases includes acute multiple encephalomyelitis (ADEM), opticoneuromyelitis spectrum diseases (NMOSD) and anti-myelin-oligodendrocyte glycoprotein-associated diseases (MOG-antibodies-associated diseases - MOGAD). Recently, new biological drugs for pathogenetic therapy have been developed, which have shown their effectiveness and good tolerability in comparison with therapy with first- and second-line drugs. Aim of the study - analysis of modern possibilities of pathogenetic treatment of patients with ADEM, seronegative and seropositive patients with NMOSD. The analysis was carried out on the basis of English-language publications in PubMed published over the past five years. This review summarizes current ideas about the possibilities of pathogenetic treatment of rare diseases. The advantages of using ravulizumab over other representatives of a new biological therapy associated with the use of monoclonal antibodies are shown. The analyzed data allow us to conclude that there is a significant development of pathogenetic treatment options for ZSONM. However, the effectiveness of new therapeutic biological drugs is still limited due to the lack of a large amount of clinical data to confirm, which creates the need to continue analyzing the experience of their use.

PMID:39175237 | DOI:10.17116/jnevro202412407233

Neurology. 2024 Sep 24;103(6):e209743. doi: 10.1212/WNL.0000000000209743. Epub 2024 Aug 22.

ABSTRACT

Progress in genetic diagnosis and orphan drug legislation has opened doors to new therapies in rare neurogenetic diseases (RNDs). Innovative therapies such as gene therapy can improve patients' quality of life but come with academic, regulatory, and financial challenges. Registries can play a pivotal role in generating evidence to tackle these, but their development requires multidisciplinary knowledge and expertise. This study aims to develop a practical framework for creating and implementing patient registries addressing common challenges and maximizing their impact on care, research, drug development, and regulatory decision making with a focus on RNDs. A comprehensive 3-step literature and qualitative research approach was used to develop the framework. A qualitative systematic literature review was conducted, extracting guidance and practices leading to the draft framework. Subsequently, we interviewed representatives of 5 established international RND registries to add learnings from hands-on experiences to the framework. Expert input on the draft framework was sought in digital multistakeholder focus groups to refine the framework. The literature search; interviews with 5 registries; and focus groups with patient representatives (n = 4), clinicians (n = 6), regulators, health technology assessment (HTA) bodies and payers (n = 7), industry representatives (n = 7), and data/information technology (IT) specialists (n = 5) informed development of the framework. It covers the interests of different stakeholders, purposes for data utilization, data aspects, IT infrastructure, governance, and financing of rare disease registries. Key principles include that data should be rapidly accessible, independent, and trustworthy. Governance should involve multiple stakeholders. In addition, data should be highly descriptive, machine-readable, and accessible through a shared infrastructure and not spread over multiple isolated repositories. Sustainable and independent financing of registries is deemed important but remains challenging because of a lack of widely supported funding models. The proposed framework will guide stakeholders in establishing or improving rare disease registries that fulfill requirements of academics and patients as well as regulators, HTA bodies, and commercial parties. There is a need for more clarity regarding quality requirements for registries in regulatory and HTA context. In addition, independent financing models for registries should be developed, as well as well-defined policies on technical uniformity in health data.

PMID:39173102 | DOI:10.1212/WNL.0000000000209743

N Engl J Med. 2024 Aug 22;391(8):770-772. doi: 10.1056/NEJMc2407971.

NO ABSTRACT

PMID:39167815 | DOI:10.1056/NEJMc2407971

J Bone Miner Res. 2024 Aug 20:zjae137. doi: 10.1093/jbmr/zjae137. Online ahead of print.

ABSTRACT

Familial hypocalciuric hypercalcemia (FHH) is typically a benign condition characterized by elevated serum calcium, low urinary calcium excretion, and non-suppressed circulating levels of parathyroid hormone (PTH), usually requiring no intervention. FHH is inherited in an autosomal-dominant manner. Three subtypes are described, representing variants in genes with critical roles in extracellular calcium-sensing. FHH1, due to heterozygous inactivating variants in the calcium-sensing receptor gene (CASR) accounts for the majority of cases. FHH2, due to variants in GNA11, encoding the α-subunit of the downstream signaling protein, G11, is the rarest form of FHH. FHH3, resulting from variants in AP2S1, may present with a more pronounced phenotype than FHH1 or FHH2. We describe herein a newborn girl presenting with in utero femoral fractures, hypercalcemia, hypophosphatemia, and elevated circulating PTH. She was diagnosed with mild hyperparathyroidism and provided supplemental phosphate upon hospital discharge. However, serum calcium and PTH remained elevated at 5 months of age. The combination of low-calcium formula and cinacalcet improved the biochemical profile. No pathogenic variants in the coding region of CASR were identified; subsequent whole exome sequencing revealed a G->T transition at c.44 (p.R15L) in AP2S1. Family studies identified this variant in the father and an affected brother. The mother was unexpectedly found to be hypocalcemic and was diagnosed with idiopathic hypoparathyroidism. This case demonstrates successful treatment of FHH3 using a low-calcium formula to limit dietary calcium availability and cinacalcet to modify PTH levels.

PMID:39163488 | DOI:10.1093/jbmr/zjae137

Nature. 2024 Aug;632(8026):711. doi: 10.1038/d41586-024-02611-2.

NO ABSTRACT

PMID:39152343 | DOI:10.1038/d41586-024-02611-2

medRxiv [Preprint]. 2024 Aug 9:2024.08.08.24307445. doi: 10.1101/2024.08.08.24307445.

ABSTRACT

IMPORTANCE: Epilepsy is the most common neurological disorder of childhood. Identifying genetic diagnoses underlying epilepsy is critical to developing effective therapies and improving outcomes. Most children with non-acquired (unexplained) epilepsy remain genetically unsolved, and the utility of genome sequencing after nondiagnostic exome sequencing is unknown.

OBJECTIVE: To determine the diagnostic (primary) and clinical (secondary) utility of genome sequencing after nondiagnostic exome sequencing in individuals with unexplained pediatric epilepsy.

DESIGN: This cohort study performed genome sequencing and comprehensive analyses for 125 participants and available biological parents enrolled from August 2018 to May 2023, with data analysis through April 2024 and clinical return of diagnostic and likely diagnostic genetic findings. Clinical utility was evaluated.

SETTING: Pediatric referral center.

PARTICIPANTS: Participants with unexplained pediatric epilepsy and previous nondiagnostic exome sequencing; biological parents when available.

EXPOSURES: Short-read genome sequencing and analysis.

MAIN OUTCOMES AND MEASURES: Primary outcome measures were the diagnostic yield of genome sequencing, defined as the percentage of participants receiving a diagnostic or likely diagnostic genetic finding, and the unique diagnostic yield of genome sequencing, defined as the percentage of participants receiving a diagnostic or likely diagnostic genetic finding that required genome sequencing. The secondary outcome measure was clinical utility of genome sequencing, defined as impact on evaluation, treatment, or prognosis for the participant or their family.

RESULTS: 125 participants (58 [46%] female) were enrolled with median age at seizure onset 3 [IQR 1.25, 8] years, including 44 (35%) with developmental and epileptic encephalopathies. The diagnostic yield of genome sequencing was 7.2% (9/125), with diagnostic genetic findings in five cases and likely diagnostic genetic findings in four cases. Among the solved cases, 7/9 (78%) required genome sequencing for variant detection (small copy number variant, three noncoding variants, and three difficult to sequence small coding variants), for a unique diagnostic yield of genome sequencing of 5.6% (7/125). Clinical utility was documented for 4/9 solved cases (44%).

CONCLUSIONS AND RELEVANCE: These findings suggest that genome sequencing can have diagnostic and clinical utility after nondiagnostic exome sequencing and should be considered for patients with unexplained pediatric epilepsy.

PMID:39148850 | PMC:PMC11326351 | DOI:10.1101/2024.08.08.24307445

Lancet Neurol. 2024 Sep;23(9):857-858. doi: 10.1016/S1474-4422(24)00333-8.

NO ABSTRACT

PMID:39152020 | DOI:10.1016/S1474-4422(24)00333-8

Lancet Glob Health. 2024 Sep;12(9):e1398. doi: 10.1016/S2214-109X(24)00311-5.

NO ABSTRACT

PMID:39151974 | DOI:10.1016/S2214-109X(24)00311-5

JCI Insight. 2024 Aug 15:e175257. doi: 10.1172/jci.insight.175257. Online ahead of print.

ABSTRACT

Pediatric diffuse midline gliomas (DMG) with H3-K27M-altered are aggressive brain tumors that arise during childhood. Despite advances in genomic knowledge and the significant number of clinical trials testing new targeted therapies, patient outcomes are still insufficient. Immune checkpoint blockades with small molecules, such as aptamers, are opening new therapeutic options that represent hope for this orphan disease. Here, we demonstrated that a TIM-3 aptamer as monotherapy increased the immune infiltration and elicited a strong specific immune response with a tendency to improve the overall survival of treated DMG-bearing mice. Importantly, combining TIM-3 Apt with radiotherapy increased the overall median survival and led to long-term survivor mice in two pediatric DMG orthotopic murine models. Interestingly, TIM-3 aptamer administration increased the number of myeloid populations and the pro-inflammatory ratios of CD8: Tregs in the tumor microenvironment as compared to non-treated groups after radiotherapy. Importantly, the depletion of T-cells led to a major loss of the therapeutic effect achieved by the combination. This work uncovers TIM-3 targeting as an immunotherapy approach to improve the radiotherapy outcome in DMGs and offers a strong foundation for propelling a phase I clinical trial using radiotherapy and TIM-3 blockade combination as a treatment for these tumors.

PMID:39146023 | DOI:10.1172/jci.insight.175257

Orphanet J Rare Dis. 2024 Aug 14;19(1):297. doi: 10.1186/s13023-024-03319-2.

ABSTRACT

BACKGROUND: People with a rare disease commonly experience long delays from the onset of symptoms to diagnosis. Rare diseases are challenging to diagnose because they are clinically heterogeneous, and many present with non-specific symptoms common to many diseases. We aimed to explore the experiences of people with myositis, primary immunodeficiency (PID), and sarcoidosis from symptom onset to diagnosis to identify factors that might impact receipt of a timely diagnosis.

METHODS: This was a qualitative study using semi-structured interviews. Our approach was informed by Interpretive Phenomenological Analysis (IPA). We applied the lens of uncertainty management theory to tease out how patients experience, assess, manage and cope with puzzling and complex health-related issues while seeking a diagnosis in the cases of rare diseases.

RESULTS: We conducted interviews with 26 people with a rare disease. Ten participants had been diagnosed with a form of myositis, 8 with a primary immunodeficiency, and 8 with sarcoidosis. Time to diagnosis ranged from 6 months to 12 years (myositis), immediate to over 20 years (PID), and 6 months to 15 years (sarcoidosis). We identified four themes that described the experiences of participants with a rare disease as they sought a diagnosis for their condition: (1) normalising and/or misattributing symptoms; (2) particularising by clinicians; (3) asserting patients' self-knowledge; and (4) working together through the diagnosable moment.

CONCLUSIONS: Managing medical uncertainty in the time before diagnosis of a rare disease can be complicated by patients discounting their own symptoms and/or clinicians discounting the scale and impact of those symptoms. Persistence on the part of both clinician and patient is necessary to reach a diagnosis of a rare disease. Strategies such as recognising pattern failure and accommodating self-labelling are key to diagnosis.

PMID:39143641 | DOI:10.1186/s13023-024-03319-2

Orphanet J Rare Dis. 2024 Aug 14;19(1):298. doi: 10.1186/s13023-024-03312-9.

ABSTRACT

BACKGROUND: Given the geographical sparsity of Rare Diseases (RDs), assembling a cohort is often a challenging task. Common data models (CDM) can harmonize disparate sources of data that can be the basis of decision support systems and artificial intelligence-based studies, leading to new insights in the field. This work is sought to support the design of large-scale multi-center studies for rare diseases.

METHODS: In an interdisciplinary group, we derived a list of elements of RDs in three medical domains (endocrinology, gastroenterology, and pneumonology) according to specialist knowledge and clinical guidelines in an iterative process. We then defined a RDs data structure that matched all our data elements and built Extract, Transform, Load (ETL) processes to transfer the structure to a joint CDM. To ensure interoperability of our developed CDM and its subsequent usage for further RDs domains, we ultimately mapped it to Observational Medical Outcomes Partnership (OMOP) CDM. We then included a fourth domain, hematology, as a proof-of-concept and mapped an acute myeloid leukemia (AML) dataset to the developed CDM.

RESULTS: We have developed an OMOP-based rare diseases common data model (RD-CDM) using data elements from the three domains (endocrinology, gastroenterology, and pneumonology) and tested the CDM using data from the hematology domain. The total study cohort included 61,697 patients. After aligning our modules with those of Medical Informatics Initiative (MII) Core Dataset (CDS) modules, we leveraged its ETL process. This facilitated the seamless transfer of demographic information, diagnoses, procedures, laboratory results, and medication modules from our RD-CDM to the OMOP. For the phenotypes and genotypes, we developed a second ETL process. We finally derived lessons learned for customizing our RD-CDM for different RDs.

DISCUSSION: This work can serve as a blueprint for other domains as its modularized structure could be extended towards novel data types. An interdisciplinary group of stakeholders that are actively supporting the project's progress is necessary to reach a comprehensive CDM.

CONCLUSION: The customized data structure related to our RD-CDM can be used to perform multi-center studies to test data-driven hypotheses on a larger scale and take advantage of the analytical tools offered by the OHDSI community.

PMID:39143600 | DOI:10.1186/s13023-024-03312-9

Orphanet J Rare Dis. 2024 Aug 13;19(1):295. doi: 10.1186/s13023-024-03300-z.

ABSTRACT

BACKGROUND: Rare disorders comprise of ~ 7500 different conditions affecting multiple systems. Diagnosis of rare diseases is complex due to dearth of specialized medical professionals, testing labs and limited therapeutic options. There is scarcity of data on the prevalence of rare diseases in different populations. India being home to a large population comprising of 4600 population groups, of which several thousand are endogamous, is likely to have a high burden of rare diseases. The present study provides a retrospective overview of a cohort of patients with rare genetic diseases identified at a tertiary genetic test centre in India.

RESULTS: Overall, 3294 patients with 305 rare diseases were identified in the present study cohort. These were categorized into 14 disease groups based on the major organ/ organ system affected. Highest number of rare diseases (D = 149/305, 48.9%) were identified in the neuromuscular and neurodevelopmental (NMND) group followed by inborn errors of metabolism (IEM) (D = 47/305; 15.4%). Majority patients in the present cohort (N = 1992, 61%) were diagnosed under IEM group, of which Gaucher disease constituted maximum cases (N = 224, 11.2%). Under the NMND group, Duchenne muscular dystrophy (N = 291/885, 32.9%), trinucleotide repeat expansion disorders (N = 242/885; 27.3%) and spinal muscular atrophy (N = 141/885, 15.9%) were the most common. Majority cases of β-thalassemia (N = 120/149, 80.5%) and cystic fibrosis (N = 74/75, 98.7%) under the haematological and pulmonary groups were observed, respectively. Founder variants were identified for Tay-Sachs disease and mucopolysaccharidosis IVA diseases. Recurrent variants for Gaucher disease (GBA:c.1448T > C), β-thalassemia (HBB:c.92.+5G > C), non-syndromic hearing loss (GJB2:c.71G > A), albinism (TYR:c.832 C > T), congenital adrenal hyperplasia (CYP21A2:c.29-13 C > G) and progressive pseudo rheumatoid dysplasia (CCN6:c.298T > A) were observed in the present study.

CONCLUSION: The present retrospective study of rare disease patients diagnosed at a tertiary genetic test centre provides first insight into the distribution of rare genetic diseases across the country. This information will likely aid in drafting future health policies, including newborn screening programs, development of target specific panel for affordable diagnosis of rare diseases and eventually build a platform for devising novel treatment strategies for rare diseases.

PMID:39138584 | DOI:10.1186/s13023-024-03300-z

J Biomed Sci. 2024 Aug 13;31(1):79. doi: 10.1186/s12929-024-01070-1.

ABSTRACT

Gene therapy has made considerable strides in recent years. More than 4000 protein-coding genes have been implicated in more than 6000 genetic diseases; next-generation sequencing has dramatically revolutionized the diagnosis of genetic diseases. Most genetic diseases are considered very rare or ultrarare, defined here as having fewer than 1:100,000 cases, but only one of the 12 approved gene therapies (excluding RNA therapies) targets an ultrarare disease. This article explores three gene supplementation therapy approaches suitable for various rare genetic diseases: lentiviral vector-modified autologous CD34+ hematopoietic stem cell transplantation, systemic delivery of adeno-associated virus (AAV) vectors to the liver, and local AAV delivery to the cerebrospinal fluid and brain. Together with RNA therapies, we propose a potential business model for these gene therapies.

PMID:39138523 | DOI:10.1186/s12929-024-01070-1

Cell Mol Life Sci. 2024 Aug 13;81(1):347. doi: 10.1007/s00018-024-05389-8.

ABSTRACT

CDKL5 Deficiency Disorder (CDD) is a debilitating epileptic encephalopathy disorder affecting young children with no effective treatments. CDD is caused by pathogenic variants in Cyclin-Dependent Kinase-Like 5 (CDKL5), a protein kinase that regulates key phosphorylation events in neurons. For therapeutic intervention, it is essential to understand molecular pathways and phosphorylation targets of CDKL5. Using an unbiased phosphoproteomic approach we identified novel targets of CDKL5, including GTF2I, PPP1R35, GATAD2A and ZNF219 in human iPSC-derived neuronal cells. The phosphoserine residue in the target proteins lies in the CDKL5 consensus motif. We validated direct phosphorylation of GTF2I and PPP1R35 by CDKL5 using complementary approaches. GTF2I controls axon guidance, cell cycle and neurodevelopment by regulating expression of neuronal genes. PPP1R35 is critical for centriole elongation and cilia morphology, processes that are impaired in CDD. PPP1R35 interacts with CEP131, a known CDKL5 phospho-target. GATAD2A and ZNF219 belong to the Nucleosome Remodelling Deacetylase (NuRD) complex, which regulates neuronal activity-dependent genes and synaptic connectivity. In-depth knowledge of molecular pathways regulated by CDKL5 will allow a better understanding of druggable disease pathways to fast-track therapeutic development.

PMID:39136782 | DOI:10.1007/s00018-024-05389-8

Trans Am Clin Climatol Assoc. 2024;134:113-122.

ABSTRACT

Adrenocortical carcinoma (ACC) is an orphan cancer with 35% five-year survival that has been unchanged for last five decades. Patients often present with severe hypercortisolism or with mass effects. The only Food and Drug Administration (FDA)-approved drug for ACC is mitotane, an insecticide derivative, which provides only limited additional months of survival, but with toxicities. Little progress in the field has occurred due to a lack of preclinical models. We recently developed new human ACC in vitro and in vivo research models. We produced the first two new ACC cell lines for the field, CU-ACC1 and CU-ACC2, which we have distributed for global collaborations. In addition, we developed 10 ACC patient-derived xenograft (PDX) and two humanized ACC-PDX models to test new therapeutics and examine the mechanism of mitotane action in combination with immunotherapy. These new preclinical models allow us to identify novel targets and test new therapeutics for our patients with adrenal cancer.

PMID:39135585 | PMC:PMC11316896

Nature. 2024 Aug;632(8026):747-748. doi: 10.1038/d41586-024-02434-1.

NO ABSTRACT

PMID:39134763 | DOI:10.1038/d41586-024-02434-1