Swiss Med Wkly. 2024 Jun 3;154:3401. doi: 10.57187/s.3401.

ABSTRACT

AIMS OF THE STUDY: This pilot study aims to enhance understanding by examining parents' specific views on the requirements, content and objectives of case management and advanced care coordination for children with rare diseases during childhood. The findings of this study are expected to offer valuable insights and recommendations for existing and future initiatives in clinical practice and research, with the goal of improving the comprehensive, child-centred and family-orientated approach to case management.

METHODS: This pilot study is part of an ongoing prospective study (SPACE), involving parents and families from various networks in Switzerland. Participants were parents recruited from the Children with Rare Diseases (KMSK) network consisting of families with children with rare diseases. The survey questionnaire covered demographic information; expectations and perceived need for case management; assessment of their quality of life and their child's suffering; and evaluation of interprofessional and interdisciplinary communication. Qualitative data from free-response answers were analysed using Mayring's content analysis and descriptive statistics were used to analyse quantitative data from Likert-scale questions.

RESULTS: The study included 108 respondent families from among the 775 in the KMSK, a 14% response rate. The age of their children ranged from 0.4 to 24 years (mean: 8) and their level of suffering in the past six months varied, with 31.5% indicating intense or very intense suffering. In terms of case management, 15.8% of families reported access while 32.4% expressed a need but did not have access to it. The study identified three categories of parental expectations regarding case management, emphasising the importance of interprofessional collaboration, effective communication and comprehensive support.

CONCLUSIONS: The findings shed light on the high need for case management support with a current undersupply in Switzerland and an association with reduced parental quality of life, highlighting the necessity for diverse support and assistance to effectively manage the challenges faced by families with children with rare diseases.

PMID:38875522 | DOI:10.57187/s.3401

JCO Clin Cancer Inform. 2024 Jun;8:e2400008. doi: 10.1200/CCI.24.00008.

ABSTRACT

PURPOSE: Rare cancers constitute over 20% of human neoplasms, often affecting patients with unmet medical needs. The development of effective classification and prognostication systems is crucial to improve the decision-making process and drive innovative treatment strategies. We have created and implemented MOSAIC, an artificial intelligence (AI)-based framework designed for multimodal analysis, classification, and personalized prognostic assessment in rare cancers. Clinical validation was performed on myelodysplastic syndrome (MDS), a rare hematologic cancer with clinical and genomic heterogeneities.

METHODS: We analyzed 4,427 patients with MDS divided into training and validation cohorts. Deep learning methods were applied to integrate and impute clinical/genomic features. Clustering was performed by combining Uniform Manifold Approximation and Projection for Dimension Reduction + Hierarchical Density-Based Spatial Clustering of Applications with Noise (UMAP + HDBSCAN) methods, compared with the conventional Hierarchical Dirichlet Process (HDP). Linear and AI-based nonlinear approaches were compared for survival prediction. Explainable AI (Shapley Additive Explanations approach [SHAP]) and federated learning were used to improve the interpretation and the performance of the clinical models, integrating them into distributed infrastructure.

RESULTS: UMAP + HDBSCAN clustering obtained a more granular patient stratification, achieving a higher average silhouette coefficient (0.16) with respect to HDP (0.01) and higher balanced accuracy in cluster classification by Random Forest (92.7% ± 1.3% and 85.8% ± 0.8%). AI methods for survival prediction outperform conventional statistical techniques and the reference prognostic tool for MDS. Nonlinear Gradient Boosting Survival stands in the internal (Concordance-Index [C-Index], 0.77; SD, 0.01) and external validation (C-Index, 0.74; SD, 0.02). SHAP analysis revealed that similar features drove patients' subgroups and outcomes in both training and validation cohorts. Federated implementation improved the accuracy of developed models.

CONCLUSION: MOSAIC provides an explainable and robust framework to optimize classification and prognostic assessment of rare cancers. AI-based approaches demonstrated superior accuracy in capturing genomic similarities and providing individual prognostic information compared with conventional statistical methods. Its federated implementation ensures broad clinical application, guaranteeing high performance and data protection.

PMID:38875514 | DOI:10.1200/CCI.24.00008

Orphanet J Rare Dis. 2024 Jun 13;19(1):234. doi: 10.1186/s13023-024-03242-6.

ABSTRACT

BACKGROUND: The low prevalence of rare diseases poses a significant challenge in advancing their understanding. This study aims to delineate the clinical and genetic characteristics of patients with rare eye diseases (RED) enrolled in the Spanish Rare Diseases Patient Registry.

METHODS: A total of 864 patients from the registry database were included. Diseases were categorized into inherited retinal dystrophies (n=688); anterior segment diseases (n=48); congenital malformations (n=27); and syndromic diseases with ocular involvement including muscular (n=46), neurological (n=34), or metabolic (n=13); inflammatory diseases (n=4); and tumors (n=4). Data on visual acuity (VA) and/or visual field (VF), symptoms and signs, concurrent diseases in syndromic cases, age of onset and at diagnosis, affected genes, disability rating, inability to work and dependency grade recognition were collected.

RESULTS: A mean diagnostic delay of 7 years from symptom onset was observed. Commonly reported symptoms included photophobia, night blindness, and progressive vision loss (≥57% of patients). Cataract was the most prevalent secondary disease (46%), with pseudophakia being the most common ocular surgery (26%). Hearing loss and cardiovascular diseases were the most prevalent concurrent systemic diseases (≥13%). Certificates of disability, incapacity for work, and dependency were held by 87%, 42%, and 19% of patients, respectively. Among the 719 patients with available VA data, 193 (27%) were blind, and 188 (26%) had moderate to severe visual impairment. Over half of the patients (54%) exhibited VF defects, and 216 (25%) had concentric contraction ≤5° or abolished VF. Most had genetic diseases with autosomal recessive (55%), autosomal dominant (30%), X-linked (9%), and mitochondrial (6%) patterns. One patient had mutations in both recessive USH2A and dominant RHO genes simultaneously. Of the 656 patients (75.7%) who underwent genetic testing, only 461 (70.3%) received a positive result (pathogenic or likely pathogenic mutations explaining the phenotype). We found 62 new gene variants related to RED not previously reported in databases of genetic variants related to specific phenotypes.

CONCLUSIONS: This study delineates the clinical and genotypic profiles of RED in Spain. Genetic diseases, particularly retinal disorders, predominate, but a significant proportion of affected patients remain genetically undiagnosed, hindering potential gene therapy endeavors. Despite notable improvements in reducing diagnosis delays, it is still remarkable. RED frequently lead to disability and blindness among young populations.

PMID:38872169 | DOI:10.1186/s13023-024-03242-6

Curr Treat Options Oncol. 2024 Jun 12. doi: 10.1007/s11864-024-01219-y. Online ahead of print.

ABSTRACT

Anaplastic thyroid cancer presents formidable challenges, particularly in cases of recurrence or metastasis. Timely BRAF V600E testing is imperative at diagnosis, initially through immunohistochemistry, followed by comprehensive genomic profiling encompassing genes such as NTRK, RET, ALK, and assessment of tumor mutation burden (TMB). FDA-approved treatment options include dabrafenib and trametinib for patients with BRAF mutations, while those exhibiting high TMB may benefit from pembrolizumab. Further therapeutic decisions hinge upon mutational profile, urgency of response required, airway integrity, and access to targeted therapies There is growing use of immunotherapy for ATC based on published reports of activity, but currently there is no FDA approved agent for ATC. The off-label utilization of "precision medicine" combinations imposes a considerable financial strain, underscoring the necessity for further clinical trials to elucidate promising therapeutic avenues for this orphan disease. There is a pressing need for the development and support of clinical trials investigating genomically driven and immune-based therapies for anaplastic thyroid cancer.

PMID:38862695 | DOI:10.1007/s11864-024-01219-y

Health Informatics J. 2024 Apr-Jun;30(2):14604582241259322. doi: 10.1177/14604582241259322.

ABSTRACT

Patients with rare diseases commonly suffer from severe symptoms as well as chronic and sometimes life-threatening effects. Not only the rarity of the diseases but also the poor documentation of rare diseases often leads to an immense delay in diagnosis. One of the main problems here is the inadequate coding with common classifications such as the International Statistical Classification of Diseases and Related Health Problems. Instead, the ORPHAcode enables precise naming of the diseases. So far, just few approaches report in detail how the technical implementation of the ORPHAcode is done in clinical practice and for research. We present a concept and implementation of storing and mapping of ORPHAcodes. The Transition Database for Rare Diseases contains all the information of the Orphanet catalog and serves as the basis for documentation in the clinical information system as well as for monitoring Key Performance Indicators for rare diseases at the hospital. The five-step process (especially using open source tools and the DataVault 2.0 logic) for set-up the Transition Database allows the approach to be adapted to local conditions as well as to be extended for additional terminologies and ontologies.

PMID:38855877 | DOI:10.1177/14604582241259322

Genet Med. 2024 Jun 6:101177. doi: 10.1016/j.gim.2024.101177. Online ahead of print.

ABSTRACT

PURPOSE: Critically ill infants from marginalized populations disproportionately receive care in neonatal intensive care units (NICUs) that lack access to state-of-the-art genomic care, leading to inequitable outcomes. We sought provider perspectives to inform our implementation study (VIGOR) providing rapid genomic sequencing within these settings.

METHODS: We conducted semi-structured focus groups with neonatal and genetics providers at five NICUs at safety-net hospitals, informed by the Promoting Action on Research Implementation in Health Services framework, which incorporates evidence, context, and facilitation domains. We iteratively developed codes and themes until thematic saturation was reached.

RESULTS: Regarding evidence, providers felt that genetic testing benefits infants and families. Regarding context, the major barriers identified to genomic care were genetic testing cost, lack of genetics expertise for disclosure and follow-up, and navigating the complexity of selecting and ordering genetic tests. Providers had negative feelings about the current status quo and inequity in genomic care across NICUs. Regarding facilitation, providers felt that a virtual support model like VIGOR would address major barriers and foster family-centered care and collaboration.

CONCLUSION: NICU providers at safety-net hospitals believe that access to state-of-the-art genomic care is critical for optimizing infant outcomes, yet substantial barriers exist that the VIGOR study may address.

PMID:38855852 | DOI:10.1016/j.gim.2024.101177

Recenti Prog Med. 2024 Jun;115(6):267-270. doi: 10.1701/4274.42525.

ABSTRACT

Pdta Net, established and managed by Research and Health Foundation (ReS), is a database aimed at gathering and analysing the Regional Care Pathways (CPs) approved in Italy. A comprehensive search was conducted within institutional websites to retrieve all CPs approved by Italian Regions and Autonomous Provinces until December 2023, by utilizing specific keywords. Compared to the previous year, 51 new approvals were recorded. By now, Pdta Net collects 856 CPs, of which 476 are for high-impact chronic diseases and 380 for rare diseases.

PMID:38853728 | DOI:10.1701/4274.42525

Clin Chim Acta. 2024 Jun 7:119765. doi: 10.1016/j.cca.2024.119765. Online ahead of print.

ABSTRACT

BACKGROUND AND AIMS: Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations to the CF transmembrane conductance regulator (CFTR). Symptoms and severity of the disease can be quite variable suggesting modifier genes play an important role.

MATERIALS AND METHODS: Exome sequencing was performed on six individuals carrying homozygous deltaF508 for CFTR genotype but present with rapidly progressing CF (RPCF). Data was analyzed using an unbiased genome-wide genetic burden test against 3076 controls. Single cell RNA sequencing data from LungMAP was utilized to evaluate unique and co-expression of candidate genes, and structural modeling to evaluate the deleterious effects of identified candidate variants.

RESULTS: We have identified solute carrier family 26 member 9 (SLC26A9) as a modifier gene to be associated with RPCF Two rare missense SLC26A9 variants were discovered in three of six individuals deemed to have RPCF: c.229G > A; p.G77S (present in two patients), and c.1885C > T; p.P629S. Co-expression of SLC26A9 and CFTR mRNA is limited across different lung cell types, with the highest level of co-expression seen in human (6.3 %) and mouse (9.0 %) alveolar type 2 (AT2) cells. Structural modeling suggests deleterious effects of these mutations as they are in critical protein domains which might affect the anion transport capability of SLC26A9.

CONCLUSION: The enrichment of rare and potentially deleterious SLC26A9 mutations in patients with RPCF suggests SLC26A9 may act as an alternative anion transporter in CF and is a modifier gene associated with this lung phenotype.

PMID:38852790 | DOI:10.1016/j.cca.2024.119765

Gait Posture. 2024 Jul;112:174-180. doi: 10.1016/j.gaitpost.2024.05.033. Epub 2024 Jun 1.

ABSTRACT

BACKGROUND: Rare bone diseases (RBD) cause physical and sensory disability that affects quality of life. Mobility challenges are common for people with RBDs, and travelling to gait analysis labs can be very complex. Smartphone sensors could provide remote monitoring.

RESEARCH QUESTION: This study aimed to search for and identify variables that can be used to discriminate between people with RBD and healthy people by using built-in smartphone sensors in a real-world setting.

METHODS: In total, 18 participants (healthy: n=9; RBD: n=9), controlled by age and sex, were included in this cross-sectional study. A freely available App (Phyphox) was used to gather data from built-in smartphone sensors (accelerometer & gyroscope) at 60 Hz during a 15-min walk on a level surface without turns or stops. Temporal gait parameters like cadence, mean stride time and, coefficient variance (CoVSt) and nonlinear analyses, as the largest Lyapunov exponent (LLE) & sample entropy (SE) in the three accelerometer axes were used to distinguish between the groups and describe gait patterns.

RESULTS: The LLE (p=0.04) and the SE of the z-axis (p=0.01), which are correlated with balance control during walking and regularity of the gait, are sufficiently sensitive to distinguish between RBD and controls.

SIGNIFICANCE: The use of smartphone sensors to monitor gait in people with RBD allows for the identification of subtle changes in gait patterns, which can be used to inform assessment and management strategies in larger cohorts.

PMID:38850844 | DOI:10.1016/j.gaitpost.2024.05.033

Brain. 2024 Jun 8:awae183. doi: 10.1093/brain/awae183. Online ahead of print.

ABSTRACT

Intracellular trafficking involves an intricate machinery of motor complexes including the dynein complex to shuttle cargo for autophagolysosomal degradation. Deficiency in dynein axonemal chains as well as cytoplasmic light and intermediate chains have been linked with ciliary dyskinesia and skeletal dysplasia. The cytoplasmic dynein 1 heavy chain protein (DYNC1H1) serves as a core complex for retrograde trafficking in neuronal axons. Dominant pathogenic variants in DYNC1H1 have been previously implicated in peripheral neuromuscular disorders (NMD) and neurodevelopmental disorders (NDD). As heavy-chain dynein is ubiquitously expressed, the apparent selectivity of heavy-chain dyneinopathy for motor neuronal phenotypes remains currently unaccounted for. Here, we aimed to evaluate the full DYNC1H1-related clinical, molecular and imaging spectrum, including multisystem features and novel phenotypes presenting throughout life. We identified 47 cases from 43 families with pathogenic heterozygous variants in DYNC1H1 (aged 0-59 years) and collected phenotypic data via a comprehensive standardized survey and clinical follow-up appointments. Most patients presented with divergent and previously unrecognized neurological and multisystem features, leading to significant delays in genetic testing and establishing the correct diagnosis. Neurological phenotypes include novel autonomic features, previously rarely described behavioral disorders, movement disorders, and periventricular lesions. Sensory neuropathy was identified in nine patients (median age of onset 10.6 years), of which five were only diagnosed after the second decade of life, and three had a progressive age-dependent sensory neuropathy. Novel multisystem features included primary immunodeficiency, bilateral sensorineural hearing loss, organ anomalies, and skeletal manifestations, resembling the phenotypic spectrum of other dyneinopathies. We also identified an age-dependent biphasic disease course with developmental regression in the first decade and, following a period of stability, neurodegenerative progression after the second decade of life. Of note, we observed several cases in whom neurodegeneration appeared to be prompted by intercurrent systemic infections with double-stranded DNA viruses (Herpesviridae) or single-stranded RNA viruses (Ross-River fever, SARS-CoV-2). Moreover, the disease course appeared to be exacerbated by viral infections regardless of age and/or severity of NDD manifestations, indicating a role of dynein in anti-viral immunity and neuronal health. In summary, our findings expand the clinical, imaging, and molecular spectrum of pathogenic DYNC1H1 variants beyond motor neuropathy disorders and suggest a life-long continuum and age-related progression due to deficient intracellular trafficking. This study will facilitate early diagnosis and improve counselling and health surveillance of affected patients.

PMID:38848546 | DOI:10.1093/brain/awae183

Am J Hum Genet. 2024 Jul 11;111(7):1271-1281. doi: 10.1016/j.ajhg.2024.05.006. Epub 2024 Jun 5.

ABSTRACT

There is mounting evidence of the value of clinical genome sequencing (cGS) in individuals with suspected rare genetic disease (RGD), but cGS performance and impact on clinical care in a diverse population drawn from both high-income countries (HICs) and low- and middle-income countries (LMICs) has not been investigated. The iHope program, a philanthropic cGS initiative, established a network of 24 clinical sites in eight countries through which it provided cGS to individuals with signs or symptoms of an RGD and constrained access to molecular testing. A total of 1,004 individuals (median age, 6.5 years; 53.5% male) with diverse ancestral backgrounds (51.8% non-majority European) were assessed from June 2016 to September 2021. The diagnostic yield of cGS was 41.4% (416/1,004), with individuals from LMIC sites 1.7 times more likely to receive a positive test result compared to HIC sites (LMIC 56.5% [195/345] vs. HIC 33.5% [221/659], OR 2.6, 95% CI 1.9-3.4, p < 0.0001). A change in diagnostic evaluation occurred in 76.9% (514/668) of individuals. Change of management, inclusive of specialty referrals, imaging and testing, therapeutic interventions, and palliative care, was reported in 41.4% (285/694) of individuals, which increased to 69.2% (480/694) when genetic counseling and avoidance of additional testing were also included. Individuals from LMIC sites were as likely as their HIC counterparts to experience a change in diagnostic evaluation (OR 6.1, 95% CI 1.1-∞, p = 0.05) and change of management (OR 0.9, 95% CI 0.5-1.3, p = 0.49). Increased access to genomic testing may support diagnostic equity and the reduction of global health care disparities.

PMID:38843839 | DOI:10.1016/j.ajhg.2024.05.006

Nervenarzt. 2024 Jun;95(6):564-572. doi: 10.1007/s00115-024-01674-w. Epub 2024 Jun 6.

ABSTRACT

Reversible cerebral vasoconstriction syndrome (RCVS) is a complex and etiologically diverse neurovascular disorder that typically presents with severe thunderclap headaches (TCH) as the primary symptom, accompanied by reversible vasoconstriction of the cerebral arteries. The clinical course may include focal neurological deficits or epileptic seizures. There are two types: idiopathic RCVS and secondary RCVS, the latter triggered by various substances, medical interventions, or diseases. In clinical practice, various medical specialists may initially encounter this condition, underscoring the importance of accurate recognition and diagnosis of RCVS. The clinical course often appears monophasic and self-limiting, with recurrences reported in only 1.7% of cases annually. Complications such as cerebral hemorrhages and cerebral ischemia can lead to death in 5-10% of cases. This article utilizes a case study to explore RCVS, its complications, and the diagnostic procedures involved.

PMID:38842549 | DOI:10.1007/s00115-024-01674-w

Endocr Connect. 2024 Jun 1:EC-24-0091. doi: 10.1530/EC-24-0091. Online ahead of print.

ABSTRACT

Prader Willi syndrome (PWS) is a rare orphan disease and complex genetic neurodevelopmental disorder, with a birth incidence of approximately 1 in 10,000-30,000. Management of people with PWS requires a multi-disciplinary approach, ideally through a multi-disciplinary team (MDT) clinic with community support. Hypotonia, poor feeding and faltering growth are characteristic features in the neonatal period, followed by hyperphagia and risk of rapid weight gain later in childhood. Children and adolescents (CA) with PWS usually display developmental delay and mild learning disability, and can develop endocrinopathies, scoliosis, respiratory difficulties (both central and obstructive sleep apnoea), challenging behaviours, skin picking, and mental health issues especially into adulthood. This consensus statement is intended to be a reference document for clinicians managing children and adolescents (up to 18 years of age) with PWS. It considers the bio-psycho-social domains of diagnosis, clinical assessment, and management in the paediatric setting as well as during and after transition to adult services. The guidance has been developed from information gathered from peer-reviewed scientific reports and from the expertise of a range of experienced clinicians in the United Kingdom and Ireland involved in the care of patients with PWS.

PMID:38838713 | DOI:10.1530/EC-24-0091

N Engl J Med. 2024 Jun 6;390(21):1985-1997. doi: 10.1056/NEJMoa2314761.

ABSTRACT

BACKGROUND: Genetic variants that cause rare disorders may remain elusive even after expansive testing, such as exome sequencing. The diagnostic yield of genome sequencing, particularly after a negative evaluation, remains poorly defined.

METHODS: We sequenced and analyzed the genomes of families with diverse phenotypes who were suspected to have a rare monogenic disease and for whom genetic testing had not revealed a diagnosis, as well as the genomes of a replication cohort at an independent clinical center.

RESULTS: We sequenced the genomes of 822 families (744 in the initial cohort and 78 in the replication cohort) and made a molecular diagnosis in 218 of 744 families (29.3%). Of the 218 families, 61 (28.0%) - 8.2% of families in the initial cohort - had variants that required genome sequencing for identification, including coding variants, intronic variants, small structural variants, copy-neutral inversions, complex rearrangements, and tandem repeat expansions. Most families in which a molecular diagnosis was made after previous nondiagnostic exome sequencing (63.5%) had variants that could be detected by reanalysis of the exome-sequence data (53.4%) or by additional analytic methods, such as copy-number variant calling, to exome-sequence data (10.8%). We obtained similar results in the replication cohort: in 33% of the families in which a molecular diagnosis was made, or 8% of the cohort, genome sequencing was required, which showed the applicability of these findings to both research and clinical environments.

CONCLUSIONS: The diagnostic yield of genome sequencing in a large, diverse research cohort and in a small clinical cohort of persons who had previously undergone genetic testing was approximately 8% and included several types of pathogenic variation that had not previously been detected by means of exome sequencing or other techniques. (Funded by the National Human Genome Research Institute and others.).

PMID:38838312 | DOI:10.1056/NEJMoa2314761

BMC Med Res Methodol. 2024 Jun 4;24(1):128. doi: 10.1186/s12874-024-02239-w.

ABSTRACT

BACKGROUND: Clinical prediction models can help identify high-risk patients and facilitate timely interventions. However, developing such models for rare diseases presents challenges due to the scarcity of affected patients for developing and calibrating models. Methods that pool information from multiple sources can help with these challenges.

METHODS: We compared three approaches for developing clinical prediction models for population screening based on an example of discriminating a rare form of diabetes (Maturity-Onset Diabetes of the Young - MODY) in insulin-treated patients from the more common Type 1 diabetes (T1D). Two datasets were used: a case-control dataset (278 T1D, 177 MODY) and a population-representative dataset (1418 patients, 96 MODY tested with biomarker testing, 7 MODY positive). To build a population-level prediction model, we compared three methods for recalibrating models developed in case-control data. These were prevalence adjustment ("offset"), shrinkage recalibration in the population-level dataset ("recalibration"), and a refitting of the model to the population-level dataset ("re-estimation"). We then developed a Bayesian hierarchical mixture model combining shrinkage recalibration with additional informative biomarker information only available in the population-representative dataset. We developed a method for dealing with missing biomarker and outcome information using prior information from the literature and other data sources to ensure the clinical validity of predictions for certain biomarker combinations.

RESULTS: The offset, re-estimation, and recalibration methods showed good calibration in the population-representative dataset. The offset and recalibration methods displayed the lowest predictive uncertainty due to borrowing information from the fitted case-control model. We demonstrate the potential of a mixture model for incorporating informative biomarkers, which significantly enhanced the model's predictive accuracy, reduced uncertainty, and showed higher stability in all ranges of predictive outcome probabilities.

CONCLUSION: We have compared several approaches that could be used to develop prediction models for rare diseases. Our findings highlight the recalibration mixture model as the optimal strategy if a population-level dataset is available. This approach offers the flexibility to incorporate additional predictors and informed prior probabilities, contributing to enhanced prediction accuracy for rare diseases. It also allows predictions without these additional tests, providing additional information on whether a patient should undergo further biomarker testing before genetic testing.

PMID:38834992 | DOI:10.1186/s12874-024-02239-w

Brain. 2024 Jun 4:awae175. doi: 10.1093/brain/awae175. Online ahead of print.

ABSTRACT

Congenital hydrocephalus (CH), characterized by cerebral ventriculomegaly, is one of the most common reasons for pediatric brain surgery. Recent studies have implicated lin-41 (lineage variant 41)/TRIM71 (tripartite motif 71) as a candidate CH risk gene, however, TRIM71 variants have not been systematically examined in a large patient cohort or conclusively linked with an OMIM syndrome. Through cross-sectional analysis of the largest assembled cohort of patients with cerebral ventriculomegaly, including neurosurgically-treated CH (totaling 2,697 parent-proband trios and 8,091 total exomes), we identified 13 protein-altering de novo variants (DNVs) in TRIM71 in unrelated children exhibiting variable ventriculomegaly, CH, developmental delay, dysmorphic features, and other structural brain defects including corpus callosum dysgenesis and white matter hypoplasia. Eight unrelated patients were found to harbor arginine variants, including two recurrent missense DNVs, at homologous positions in RPXGV motifs of different NHL domains. Seven additional patients with rare, damaging, unphased or transmitted variants of uncertain significance were also identified. NHL-domain variants of TRIM71 exhibited impaired binding to the canonical TRIM71 target CDKN1A; other variants failed to direct the subcellular localization of TRIM71 to processing bodies. Single-cell transcriptomic analysis of human embryos revealed expression of TRIM71 in early first-trimester neural stem cells of the brain. These data show TRIM71 is essential for human brain morphogenesis and that TRIM71 mutations cause a novel neurodevelopmental syndrome featuring ventriculomegaly and CH.

PMID:38833623 | DOI:10.1093/brain/awae175

Eur J Med Genet. 2023 Dec;66(12):104871. doi: 10.1016/j.ejmg.2023.104871. Epub 2023 Oct 29.

ABSTRACT

Rare diseases encompass a diverse group of genetic disorders that affect a small proportion of the population. Identifying the underlying genetic causes of these conditions presents significant challenges due to their genetic heterogeneity and complexity. Conventional short-read sequencing (SRS) techniques have been widely used in diagnosing and investigating of rare diseases, with limitations due to the nature of short-read lengths. In recent years, long read sequencing (LRS) technologies have emerged as a valuable tool in overcoming these limitations. This minireview provides a concise overview of the applications of LRS in rare disease research and diagnosis, including the identification of disease-causing tandem repeat expansions, structural variations, and comprehensive analysis of pathogenic variants with LRS.

PMID:38832911 | DOI:10.1016/j.ejmg.2023.104871

Eur J Med Genet. 2023 Dec;66(12):104868. doi: 10.1016/j.ejmg.2023.104868. Epub 2023 Oct 30.

ABSTRACT

BACKGROUND: knowledge on the natural history of rare diseases is necessary to improve outcomes. Disease registries may play a key role in covering these unmet needs in the rare bone and mineral community.

OBJECTIVE: to map existing bone and mineral conditions registries in Europe and their characteristics.

METHODS: online survey about the use of registries/databases and their characteristics. This survey was disseminated among members of the European Reference Network on Rare Bone Diseases (ERN BOND) and non-ERN experts in the field of bone and mineral conditions as well as patient organisations.

RESULTS: sixty-three responses from health care providers (HCPs) and 10 responses from patient groups (PGs) were collected. The response rate for ERN BOND members was 55%. Of 63 HCPs, 37 declared using a registry. Osteogenesis imperfecta (OI) was the most registered condition. We mapped 3 international registries, all were disease-specific.

CONCLUSIONS: There is a need for developing a common high-quality platform for registering rare bone and mineral conditions.

PMID:38832910 | DOI:10.1016/j.ejmg.2023.104868

bioRxiv [Preprint]. 2024 May 22:2024.05.22.595175. doi: 10.1101/2024.05.22.595175.

ABSTRACT

Recurrent copy number variation represents one of the most well-established genetic drivers in neurodevelopmental disorders, including autism spectrum disorder (ASD). Duplication of 15q11.2-13.1 (dup15q) is a well-described neurodevelopmental syndrome that increases the risk of ASD by over 40-fold. However, the effects of this duplication on gene expression and chromatin accessibility in specific cell types in the human brain remain unknown. To identify the cell-type-specific transcriptional and epigenetic effects of dup15q in the human frontal cortex we conducted single-nucleus RNA-sequencing and multi-omic sequencing on dup15q cases (n=6) as well as non-dup15q ASD (n=7) and neurotypical controls (n=7). Cell-type-specific differential expression analysis identified significantly regulated genes, critical biological pathways, and differentially accessible genomic regions. Although there was overall increased gene expression across the duplicated genomic region, cellular identity represented an important factor mediating gene expression changes. Neuronal subtypes, showed greater upregulation of gene expression across a critical region within the duplication as compared to other cell types. Genes within the duplicated region that had high baseline expression in control individuals showed only modest changes in dup15q, regardless of cell type. Of note, dup15q and ASD had largely distinct signatures of chromatin accessibility, but shared the majority of transcriptional regulatory motifs, suggesting convergent biological pathways. However, the transcriptional binding factor motifs implicated in each condition implicated distinct biological mechanisms; neuronal JUN/FOS networks in ASD vs. an inflammatory transcriptional network in dup15q microglia. This work provides a cell-type-specific analysis of how dup15q changes gene expression and chromatin accessibility in the human brain and finds evidence of marked cell-type-specific effects of this genetic driver. These findings have implications for guiding therapeutic development in dup15q syndrome, as well as understanding the functional effects CNVs more broadly in neurodevelopmental disorders.

PMID:38826276 | PMC:PMC11142199 | DOI:10.1101/2024.05.22.595175

Zhongguo Ying Yong Sheng Li Xue Za Zhi. 2023 Dec 23;39:e20230008. doi: 10.62958/j.cjap.2023.008.

ABSTRACT

In the United States, cancer is one of the major causes of death. In 2010 alone, over 1.5 million fresh instances were recorded and over 0.5 billion died. After the completion of human genome sequence, significant progress in characterizing human epigenomes, proteomes and metabolomes has been made; a stronger knowledge of pharmacogenomics has been established and the capacity for individual personalization of health care has grown considerably. Personalized medicine has recently been primarily used to systematically select or optimize the prevention and therapeutic care of the patient through genetic or other data about the particular patient. Molecular profiling in healthy samples and cancer patients can allow for more personalized medications than is currently available. Patient protein, genetic and metabolic information may be used for adapting medical attention to the needs of that individual. The development of complementary diagnostics is a key attribute of this medicinal model. Molecular tests measuring the level of proteins, genes or specific mutations are used to provide a specific treatment for a particular individual by stratify the status of a disease, selecting the right drugs and tailoring dosages to the particular needs of the patient. These methods are also available for assessing risk factors for a patient for a number of conditions and for tailoring individual preventive therapies. Recent advances of personalized cancer medicine, challenges and futures perspectives are discussed.

PMID:38830754 | DOI:10.62958/j.cjap.2023.008