Comput Methods Programs Biomed. 2023 Nov;241:107744. doi: 10.1016/j.cmpb.2023.107744. Epub 2023 Aug 10.

ABSTRACT

BACKGROUND AND OBJECTIVE: Primary ciliary dyskinesia (PCD) is a rare genetic disorder causing a defective ciliary structure, which predominantly leads to an impaired mucociliary clearance and associated airway disease. As there is currently no single diagnostic gold standard test, PCD is diagnosed by a combination of several methods comprising genetic testing and the examination of the ciliary structure and function. Among the approved diagnostic methods, only high-speed video microscopy (HSVM) allows to directly observe the ciliary motion and therefore, to directly assess ciliary function. In the present work, we present our recently developed freely available open-source software - termed "Cilialyzer", which has been specifically designed to support and facilitate the analysis of the mucociliary activity in respiratory epithelial cells captured by high-speed video microscopy.

METHODS: In its current state, the Cilialyzer software enables clinical PCD analysts to load, preprocess and replay recorded image sequences as well as videos with a feature-rich replaying module facilitating the commonly performed qualitative visual assessment of ciliary function (including the assessment of the ciliary beat pattern). The image processing methods made accessible through an intuitive user interface allow clinical specialists to comfortably compute the ciliary beating frequency (CBF), the activity map and the "frequency correlation length" - an observable getting newly introduced. Furthermore, the Cilialyzer contains a simple-to-use particle tracking interface to determine the mucociliary transport speed.

RESULTS: Cilialyzer is fully written in the Python programming language and freely available under the terms of the MIT license. The proper functioning of the computational analysis methods constituting the Cilialyzer software is demonstrated by using simulated and representative sample data from clinical practice. Additionally, the software was used to analyze high-speed videos showing samples obtained from healthy controls and genetically confirmed PCD cases (DNAI1 and DNAH11 mutations) to show its clinical applicability.

CONCLUSIONS: Cilialyzer serves as a useful clinical tool for PCD analysts and provides new quantitative information awaiting to be clinically evaluated using cohorts of PCD. As Cilialyzer is freely available under the terms of a permissive open-source license, it serves as a ground frame for further development of computational methods aiming at the quantification and automation of the analysis of mucociliary activity captured by HSVM.

PMID:37598471 | DOI:10.1016/j.cmpb.2023.107744

Lancet Neurol. 2023 Sep;22(9):812-825. doi: 10.1016/S1474-4422(23)00246-6.

ABSTRACT

BACKGROUND: Most neonatal and infantile-onset epilepsies have presumed genetic aetiologies, and early genetic diagnoses have the potential to inform clinical management and improve outcomes. We therefore aimed to determine the feasibility, diagnostic yield, and clinical utility of rapid genome sequencing in this population.

METHODS: We conducted an international, multicentre, cohort study (Gene-STEPS), which is a pilot study of the International Precision Child Health Partnership (IPCHiP). IPCHiP is a consortium of four paediatric centres with tertiary-level subspecialty services in Australia, Canada, the UK, and the USA. We recruited infants with new-onset epilepsy or complex febrile seizures from IPCHiP centres, who were younger than 12 months at seizure onset. We excluded infants with simple febrile seizures, acute provoked seizures, known acquired cause, or known genetic cause. Blood samples were collected from probands and available biological parents. Clinical data were collected from medical records, treating clinicians, and parents. Trio genome sequencing was done when both parents were available, and duo or singleton genome sequencing was done when one or neither parent was available. Site-specific protocols were used for DNA extraction and library preparation. Rapid genome sequencing and analysis was done at clinically accredited laboratories, and results were returned to families. We analysed summary statistics for cohort demographic and clinical characteristics and the timing, diagnostic yield, and clinical impact of rapid genome sequencing.

FINDINGS: Between Sept 1, 2021, and Aug 31, 2022, we enrolled 100 infants with new-onset epilepsy, of whom 41 (41%) were girls and 59 (59%) were boys. Median age of seizure onset was 128 days (IQR 46-192). For 43 (43% [binomial distribution 95% CI 33-53]) of 100 infants, we identified genetic diagnoses, with a median time from seizure onset to rapid genome sequencing result of 37 days (IQR 25-59). Genetic diagnosis was associated with neonatal seizure onset versus infantile seizure onset (14 [74%] of 19 vs 29 [36%] of 81; p=0·0027), referral setting (12 [71%] of 17 for intensive care, 19 [44%] of 43 non-intensive care inpatient, and 12 [28%] of 40 outpatient; p=0·0178), and epilepsy syndrome (13 [87%] of 15 for self-limited epilepsies, 18 [35%] of 51 for developmental and epileptic encephalopathies, 12 [35%] of 34 for other syndromes; p=0·001). Rapid genome sequencing revealed genetic heterogeneity, with 34 unique genes or genomic regions implicated. Genetic diagnoses had immediate clinical utility, informing treatment (24 [56%] of 43), additional evaluation (28 [65%]), prognosis (37 [86%]), and recurrence risk counselling (all cases).

INTERPRETATION: Our findings support the feasibility of implementation of rapid genome sequencing in the clinical care of infants with new-onset epilepsy. Longitudinal follow-up is needed to further assess the role of rapid genetic diagnosis in improving clinical, quality-of-life, and economic outcomes.

FUNDING: American Academy of Pediatrics, Boston Children's Hospital Children's Rare Disease Cohorts Initiative, Canadian Institutes of Health Research, Epilepsy Canada, Feiga Bresver Academic Foundation, Great Ormond Street Hospital Charity, Medical Research Council, Murdoch Children's Research Institute, National Institute of Child Health and Human Development, National Institute for Health and Care Research Great Ormond Street Hospital Biomedical Research Centre, One8 Foundation, Ontario Brain Institute, Robinson Family Initiative for Transformational Research, The Royal Children's Hospital Foundation, University of Toronto McLaughlin Centre.

PMID:37596007 | DOI:10.1016/S1474-4422(23)00246-6

BMC Neurol. 2023 Aug 17;23(1):305. doi: 10.1186/s12883-023-03354-9.

ABSTRACT

BACKGROUND: The leukodystrophy "Vanishing White Matter" (VWM) is an orphan disease with neurological decline and high mortality. Currently, VWM has no approved treatments, but advances in understanding pathophysiology have led to identification of promising therapies. Several investigational medicinal products are either in or about to enter clinical trial phase. Clinical trials in VWM pose serious challenges, as VWM has an episodic disease course; disease phenotype is highly heterogeneous and predictable only for early onset; and study power is limited by the small patient numbers. To address these challenges and accelerate therapy delivery, the VWM Consortium, a group of academic clinicians with expertise in VWM, decided to develop a core protocol to function as a template for trials, to improve trial design and facilitate sharing of control data, while permitting flexibility regarding other trial details. Overall aims of the core protocol are to collect safety, tolerability, and efficacy data for treatment assessment and marketing authorization.

METHODS: To develop the core protocol, the VWM Consortium designated a committee, including clinician members of the VWM Consortium, family and patient group advocates, and experts in statistics, clinical trial design and alliancing with industries. We drafted three age-specific protocols, to stratify into more homogeneous patient groups, of ages ≥ 18 years, ≥ 6 to < 18 years and < 6 years. We chose double-blind, randomized, placebo-controlled design for patients aged ≥ 6 years; and open-label non-randomized natural-history-controlled design for patients < 6 years. The protocol describes study populations, age-specific endpoints, inclusion and exclusion criteria, study schedules, sample size determinations, and statistical considerations.

DISCUSSION: The core protocol provides a shared uniformity across trials, enables a pool of shared controls, and reduces the total number of patients necessary per trial, limiting the number of patients on placebo. All VWM clinical trials are suggested to adhere to the core protocol. Other trial components such as choice of primary outcome, pharmacokinetics, pharmacodynamics, and biomarkers are flexible and unconstrained by the core protocol. Each sponsor is responsible for their trial execution, while the control data are handled by a shared research organization. This core protocol benefits the efficiency of parallel and consecutive trials in VWM, and we hope accelerates time to availability of treatments for VWM.

TRIAL REGISTRATION: NA. From a scientific and ethical perspective, it is strongly recommended that all interventional trials using this core protocol are registered in a clinical trial register.

PMID:37592248 | DOI:10.1186/s12883-023-03354-9

Hum Genomics. 2023 Aug 16;17(1):75. doi: 10.1186/s40246-023-00524-1.

ABSTRACT

BACKGROUND: Diagnostic efficacy is now well established for diagnostic genomic testing in rare disease. Assessment of overall utility is emerging as a key next step, however ambiguity in the conceptualisation and measurement of utility has impeded its assessment in a comprehensive manner. We propose a conceptual framework to approach determining the broader utility of diagnostic genomics encompassing patients, families, clinicians, health services and health systems to assist future evidence generation and funding decisions. BODY: Building upon previous work, our framework posits that utility of diagnostic genomics consists of three dimensions: the domain or type and extent of utility (what), the relationship and perspective of utility (who), and the time horizon of utility (when). Across the description, assessment, and summation of these three proposed dimensions of utility, one could potentially triangulate a singular point of utility axes of type, relationship, and time. Collectively, the multiple different points of individual utility might be inferred to relate to a concept of aggregate utility.

CONCLUSION: This ontological framework requires retrospective and prospective application to enable refinement and validation. Moving forward our framework, and others which have preceded it, promote a better characterisation and description of genomic utility to inform decision-making and optimise the benefits of genomic diagnostic testing.

PMID:37587497 | PMC:PMC10433656 | DOI:10.1186/s40246-023-00524-1

BMC Genomics. 2023 Aug 16;24(1):460. doi: 10.1186/s12864-023-09561-5.

ABSTRACT

BACKGROUND: Approximately 4-8% of the world suffers from a rare disease. Rare diseases are often difficult to diagnose, and many do not have approved therapies. Genetic sequencing has the potential to shorten the current diagnostic process, increase mechanistic understanding, and facilitate research on therapeutic approaches but is limited by the difficulty of novel variant pathogenicity interpretation and the communication of known causative variants. It is unknown how many published rare disease variants are currently accessible in the public domain.

RESULTS: This study investigated the translation of knowledge of variants reported in published manuscripts to publicly accessible variant databases. Variants, symptoms, biochemical assay results, and protein function from literature on the SLC6A8 gene associated with X-linked Creatine Transporter Deficiency (CTD) were curated and reported as a highly annotated dataset of variants with clinical context and functional details. Variants were harmonized, their availability in existing variant databases was analyzed and pathogenicity assignments were compared with impact algorithm predictions. 24% of the pathogenic variants found in PubMed articles were not captured in any database used in this analysis while only 65% of the published variants received an accurate pathogenicity prediction from at least one impact prediction algorithm.

CONCLUSIONS: Despite being published in the literature, pathogenicity data on patient variants may remain inaccessible for genetic diagnosis, therapeutic target identification, mechanistic understanding, or hypothesis generation. Clinical and functional details presented in the literature are important to make pathogenicity assessments. Impact predictions remain imperfect but are improving, especially for single nucleotide exonic variants, however such predictions are less accurate or unavailable for intronic and multi-nucleotide variants. Developing text mining workflows that use natural language processing for identifying diseases, genes and variants, along with impact prediction algorithms and integrating with details on clinical phenotypes and functional assessments might be a promising approach to scale literature mining of variants and assigning correct pathogenicity. The curated variants list created by this effort includes context details to improve any such efforts on variant curation for rare diseases.

PMID:37587458 | PMC:PMC10433598 | DOI:10.1186/s12864-023-09561-5

Chirurgie (Heidelb). 2023 Aug 14. doi: 10.1007/s00104-023-01937-3. Online ahead of print.

ABSTRACT

BACKGROUND: Pseudomyxoma peritonei syndrome (PMP) is an orphan disease. Surgery is the fundament of treatment.

METHOD: Short review summarizing the state of the art treatment.

RESULTS: Cytoreductive surgery (CRS) in combination with hyperthermic intraperitoneal chemotherapy (HIPEC) form the foundations of treatment for PMP. The peritoneal cancer index should be preoperatively determined based on imaging and/or laparoscopy, intraoperatively validated and both should be documented. An extraperitoneal surgical preparation technique leads to effective en bloc resection of the peritoneum and the affected abdominal area. The HIPEC technique should be performed with mitomycin C for 60-90 min. Complete CRS (CC = 0, CC = 1) and the histological subtype are relevant for the prognosis. Structured educational programs and mentoring can optimize the learning curve. The aftercare should be performed at the surgical center. After follow-up imaging at 3 months after CRS, in the first 2 years a control should be carried out every 6 months. Thereafter, the intervals can be extended to 1 year.

CONCLUSION: Standardized surgical treatment and HIPEC, optimized specific surgical training and structured follow-up at the center lead to an excellent long-term prognosis for patients with PMP.

PMID:37578542 | DOI:10.1007/s00104-023-01937-3

Expert Rev Respir Med. 2023 Aug 14. doi: 10.1080/17476348.2023.2247989. Online ahead of print.

ABSTRACT

INTRODUCTION: Pulmonary veno-occlusive disease (PVOD) is an orphan disease and uncommon etiology of pulmonary arterial hypertension (PAH) characterized by substantial small pulmonary vein and capillary involvement.

AREAS COVERED: PVOD, also known as 'PAH with features of venous/capillary involvement' in the current ESC/ERS classification.

EXPERT OPINION: In recent years, particular risk factors for PVOD have been recognized, including genetic susceptibilities and environmental factors (such as exposure to occupational organic solvents, chemotherapy, and potentially tobacco). The discovery of biallelic mutations in the EIF2AK4 gene as the cause of heritable PVOD has been a breakthrough in understanding the molecular basis of PVOD. Venous and capillary involvement (PVOD-like) has also been reported to be relatively common in connective tissue disease-associated PAH (especially systemic sclerosis), and in rare pulmonary diseases like sarcoidosis and pulmonary Langerhans cell granulomatosis. Although PVOD and pulmonary arterial hypertension (PAH) exhibit similarities, including severe precapillary PH, it is essential to differentiate between them since PVOD has a worse prognosis and requires specific management. Indeed, PVOD patients are characterized by poor response to PAH-approved drugs, which can lead to pulmonary edema and clinical deterioration. Due to the lack of effective treatments, early referral to a lung transplantation center is crucial.

PMID:37578057 | DOI:10.1080/17476348.2023.2247989

J Biomed Inform. 2023 Sep;145:104474. doi: 10.1016/j.jbi.2023.104474. Epub 2023 Aug 10.

ABSTRACT

Inferring knowledge from known relationships between drugs, proteins, genes, and diseases has great potential for clinical impact, such as predicting which existing drugs could be repurposed to treat rare diseases. Incorporating key biological context such as cell type or tissue of action into representations of extracted biomedical knowledge is essential for principled pharmacological discovery. Existing global, literature-derived knowledge graphs of interactions between drugs, proteins, genes, and diseases lack this essential information. In this study, we frame the task of associating biological context with protein-protein interactions extracted from text as a classification task using syntactic, semantic, and novel meta-discourse features. We introduce the Insider corpora, which are automatically generated PubMed-scale corpora for training classifiers for the context association task. These corpora are created by searching for precise syntactic cues of cell type and tissue relevancy to extracted regulatory relations. We report F1 scores of 0.955 and 0.862 for identifying relevant cell types and tissues, respectively, for our identified relations. By classifying with this framework, we demonstrate that the problem of context association can be addressed using intuitive, interpretable features. We demonstrate the potential of this approach to enrich text-derived knowledge bases with biological detail by incorporating cell type context into a protein-protein network for dengue fever.

PMID:37572825 | DOI:10.1016/j.jbi.2023.104474

Orphanet J Rare Dis. 2023 Aug 11;18(1):242. doi: 10.1186/s13023-023-02837-9.

ABSTRACT

BACKGROUND: A rare disease (RD) diagnosis and therapy can affect the family's quality of life and mental health. A lack of information and missing care options lead to helplessness and psychological stress within families. This work aims to identify patients' and parents' experiences in daily life and with the health care system as well as their needs and current pathways to psychosocial care to develop implementation strategies adapted to the families' needs.

METHODS: The present analysis is part of the national multicenter study "Children Affected by Rare Disease and Their Families-Network (CARE-FAM-NET)." We conducted semi-structured telephone interviews with children, adolescents, and young adults with RD (aged 12 to 21 years) and parents of children with RD (aged 0 to 17 years). We analyzed the transcribed and anonymized interviews using the method of focused interview analyses to identify previous experiences with medical and psychosocial care and possible needs for improvement and support.

RESULTS: Seventy-four parents of children with RD and 15 children, adolescents, and young adults with RD participated. Five main themes emerged. Daily life with an RD: RD affects the everyday and social life of the respondents, negatively impacting mental well-being. Experiences with the health care system: The long diagnostic path is stressful for families. Professionals' lack of information/education leads to inadequate care for those affected. Psychosocial support: Families do not know about psychosocial care services. In some cases, the families take advantage of psychosocial support services (such as support groups or advocacy groups), which are predominantly very helpful. Difficulties and barriers: Time, socio-legal and organizational problems burden families and lead to advantages in using psychosocial services. Improvements for patient-oriented support: Those affected wished for timely, preventive support (especially in administrative and socio-legal matters) and education regarding psychosocial care services.

CONCLUSION: RD represent a great challenge for all family members - patients, parents, and siblings. The patients' and parents' previous experiences in daily life, medical and psychosocial care show a need for target-group specific support, including training of health care professionals and low-threshold access care services and practical help for all family members.

PMID:37568186 | PMC:PMC10422846 | DOI:10.1186/s13023-023-02837-9

Orphanet J Rare Dis. 2023 Aug 11;18(1):241. doi: 10.1186/s13023-023-02850-y.

ABSTRACT

BACKGROUND: A rare muscle disease, GNE myopathy is caused by mutations in the GNE gene involved in sialic acid biosynthesis. Our recent phase II/III study has indicated that oral administration of aceneuramic acid to patients slows disease progression.

METHODS: We conducted a phase III, randomized, placebo-controlled, double-blind, parallel-group, multicenter study. Participants were assigned to receive an extended-release formulation of aceneuramic acid (SA-ER) or placebo. Changes in muscle strength and function over 48 weeks were compared between treatment groups using change in the upper extremity composite (UEC) score from baseline to Week 48 as the primary endpoint and the investigator-assessed efficacy rate as the key secondary endpoint. For safety, adverse events, vital signs, body weight, electrocardiogram, and clinical laboratory results were monitored.

RESULTS: A total of 14 patients were enrolled and given SA-ER (n = 10) or placebo (n = 4) tablets orally. Decrease in least square mean (LSM) change in UEC score at Week 48 with SA-ER (- 0.115 kg) was numerically smaller as compared with placebo (- 2.625 kg), with LSM difference (95% confidence interval) of 2.510 (- 1.720 to 6.740) kg. In addition, efficacy was higher with SA-ER as compared with placebo. No clinically significant adverse events or other safety concerns were observed.

CONCLUSIONS: The present study reproducibly showed a trend towards slowing of loss of muscle strength and function with orally administered SA-ER, indicating supplementation with sialic acid might be a promising replacement therapy for GNE myopathy.

TRIAL REGISTRATION NUMBER: ClinicalTrials.gov (NCT04671472).

PMID:37568154 | DOI:10.1186/s13023-023-02850-y

Orphanet J Rare Dis. 2023 Aug 10;18(1):240. doi: 10.1186/s13023-023-02847-7.

ABSTRACT

BACKGROUND: Genetic testing can facilitate the diagnosis and subsequent therapeutic management of rare diseases. However, there is a lack of data on the use of genetic testing for rare diseases. This study aims to describe the utilization rate and troubles encountered by clinicians in treating rare diseases with genetic testing.

METHODS: A cross-sectional electronic questionnaire survey was conducted between June and October 2022 among the medical staff from the hospitals covering all provinces, municipalities, and autonomous regions of China. The survey on genetic testing focused on whether genetic testing was used in the diagnosis and treatment of rare diseases, the specific methods of genetic testing, and the problems encountered when using genetic testing.

RESULTS: A total of 20,132 physicians who had treated rare diseases were included, of whom 35.5% were from the central region, 36.7% were from the eastern region, and 27.8% were from the western region. The total utilization rate of genetic testing for rare diseases was 76.0% (95%CI: 75.4-76.6). The use of genetic testing was highest in the Eastern region (79.2% [95% CI: 78.3-80.1]), followed by the Central (75.9% [95% CI: 74.9-76.9]) and Western regions (71.9% [95% CI: 70.7-73.1]). More than 90% (94.1% [95%CI: 93.4-94.8]) of pediatricians had used genetic testing to treat rare diseases, with surgeons having the lowest use of genetic testing (58.3% [95% CI: 56.6-60.0]). Physicians' departments and education levels affect the use of genetic testing. Most physicians have used a variety of genetic tests in the management of rare diseases, the most popular methods were "Whole-exome sequencing (Proband)" and "Whole-exome sequencing (families of three or more)". Doctors have encountered many problems with the use of genetic testing in the diagnosis and treatment of rare diseases, among which the high price was the main concern of medical workers.

CONCLUSION: Three-quarters of physicians used genetic testing in rare disease practice, and there were regional differences in the use of genetic testing. Recognition of the utilization of genetic testing can help identify patterns of resource utilization in different regions and provide a more comprehensive picture of the epidemiology of rare diseases in jurisdictions.

PMID:37563631 | PMC:PMC10416371 | DOI:10.1186/s13023-023-02847-7

Pediatr Ann. 2023 Aug;52(8):e282. doi: 10.3928/19382359-20230613-03. Epub 2023 Aug 1.

NO ABSTRACT

PMID:37561829 | DOI:10.3928/19382359-20230613-03

PLoS One. 2023 Aug 10;18(8):e0289921. doi: 10.1371/journal.pone.0289921. eCollection 2023.

ABSTRACT

BACKGROUND: Statistical analyses of clinical data are a cornerstone in understanding pathomechanisms of disorders. In rare disorders, cross-sectional datasets of sufficient size are usually not available. Taking AA amyloidosis as an example of a life-threatening rare disorder resulting from of uncontrolled chronic inflammation, we propose techniques from time series analysis to predict organ response to treatment. The advantage of time-series analysis is that it solely relies on temporal variation and therefore allows analyzing organ response to treatment even when the cross-sectional dimension is small.

METHODS: The joint temporal interdependence of inflammatory activity and organ response was modelled multivariately using vector autoregression (VAR) based on a unique 4.5 year spanning data set of routine laboratory, imaging data (e.g., 18F-Florbetaben-PET/CT) and functional investigations of a 68-year-old patient with multi-organ involvement of AA amyloidosis due to ongoing inflammatory activity of a malignant paraganglioma in stable disease for >20 years and excellent response to tocilizumab).

RESULTS: VAR analysis showed that alterations in inflammatory activity forecasted alkaline phosphatase (AP). AP levels, but not inflammatory activity at the previous measurement time point predicted proteinuria.

CONCLUSION: We demonstrate the feasibility and value of time series analysis for obtaining clinically reliable information when the rarity of a disease prevents conventional prognostic modelling approaches. We illustrate the comparative utility of blood, functional and imaging markers to monitor the development and regression of AA amyloidosis.

PMID:37561769 | PMC:PMC10414553 | DOI:10.1371/journal.pone.0289921

J Inherit Metab Dis. 2023 Sep;46(5):824-838. doi: 10.1002/jimd.12663.

ABSTRACT

Over the past decade high-throughput DNA sequencing approaches, namely whole exome and whole genome sequencing became a standard procedure in Mendelian disease diagnostics. Implementation of these technologies greatly facilitated diagnostics and shifted the analysis paradigm from variant identification to prioritisation and evaluation. The diagnostic rates vary widely depending on the cohort size, heterogeneity and disease and range from around 30% to 50% leaving the majority of patients undiagnosed. Advances in omics technologies and computational analysis provide an opportunity to increase these unfavourable rates by providing evidence for disease-causing variant validation and prioritisation. This review aims to provide an overview of the current application of several omics technologies including RNA-sequencing, proteomics, metabolomics and DNA-methylation profiling for diagnostics of rare genetic diseases in general and inborn errors of metabolism in particular.

PMID:37553850 | DOI:10.1002/jimd.12663

Orphanet J Rare Dis. 2023 Aug 9;18(1):236. doi: 10.1186/s13023-023-02839-7.

ABSTRACT

BACKGROUND: Rare diseases have become a major public health concern worldwide. However, detailed epidemiological data are lacking. With the development of the Internet, search queries have played an important role in disease surveillance. In this study, we explored a new method for the epidemiological research on rare diseases, using large-scale online search queries and reported case data. We distilled search logs related to rare diseases nationwide from 2016 to 2019. The case data were obtained from China's national database of rare diseases during the same period.

RESULTS: A total of 120 rare diseases were included in this study. From 2016 to 2019, the number of patients with rare diseases estimated using search data and those obtained from the case database showed an increasing trend. Rare diseases can be ranked by the number of search estimated patients and reported patients, and the rankings of each disease in both search and reported case data were generally stable. Furthermore, the disease rankings in the search data were relatively consistent with the reported case data in each year, with more than 50% of rare diseases having a ranking difference of -20 to 20 between the two systems. In addition, the relationship between the disease rankings in the two systems was generally stable over time. Based on the relationship between the disease rankings in the search and reported case data, rare diseases can be classified into two categories.

CONCLUSION: Online search queries may provide an important new resource for detecting rare diseases. Rare diseases can be classified into two categories to guide different epidemiological research strategies.

PMID:37559136 | PMC:PMC10411025 | DOI:10.1186/s13023-023-02839-7

G3 (Bethesda). 2023 Aug 9;13(8):jkad144. doi: 10.1093/g3journal/jkad144.

NO ABSTRACT

PMID:37556359 | PMC:PMC10411584 | DOI:10.1093/g3journal/jkad144

Genetics. 2023 Aug 9;224(4):iyad121. doi: 10.1093/genetics/iyad121.

NO ABSTRACT

PMID:37556311 | PMC:PMC10411596 | DOI:10.1093/genetics/iyad121

Hematology. 2023 Dec;28(1):2241226. doi: 10.1080/16078454.2023.2241226.

ABSTRACT

BACKGROUND: In China, conventional genetic testing methods can only detect common thalassemia variants. Accurate detection of rare thalassemia is crucial for clinical diagnosis, especially for children that need long-term blood transfusion. This study aims to explore the application value of third-generation sequencing (TGS) in the diagnosis of rare thalassemia in children with anemia.

METHODS: We enrolled 20 children with anemia, excluding from iron deficiency anemia (IDA). TGS was employed to identify both known and novel thalassemia genotypes, while sanger sequencing was used to confirm the novel mutation detected.

RESULTS: Among the 20 samples, we identified 5 cases of rare thalassemia. These included β-4.9 (hg38,Chr11:5226187-5231089) at HBB gene, α-91(HBA2:c.*91delT), αCD30(HBA2:c.91-93delGAG), Chinese Gγ+(Aγδβ)0(NG_000007.3: g .48795-127698 del 78904) and delta - 77(T > C)(HBD:c.-127T>C). Notably, the -SEA/α-91α genotype associated with severe non-deletional hemoglobin H disease (HbH disease) has not been previously reported. Patients with genotypes β654/β-4.9 and -SEA/α-91α necessitate long-term blood transfusions, and those with the -SEA/αCD30α, Chinese Gγ+(Aγδβ)0 and delta thalassemia demonstrate mild anemia.

CONCLUSIONS: TGS demonstrates promising potential as a diagnostic tool for suspected cases of rare thalassemia in children, especially those suspected to have transfusion-dependent thalassemia (TDT).

PMID:37548329 | DOI:10.1080/16078454.2023.2241226

Front Endocrinol (Lausanne). 2023 Jul 20;14:1211426. doi: 10.3389/fendo.2023.1211426. eCollection 2023.

ABSTRACT

X-linked hypophosphatemia (XLH) is a rare, progressive, genetic disease with multisystem impact that typically begins to manifest in early childhood. Two treatment options exist: oral phosphate in combination with active vitamin D ("conventional therapy") and a fully human monoclonal anti-FGF23 antibody, burosumab. The clinical benefit of conventional therapy in adults is limited, and poor tolerance and complications are common. Burosumab was first approved as a treatment for XLH in 2018 and its disease-modifying benefits in clinical trials in children suggest burosumab treatment could also alter the disease course in adults. Without long-term clinical data on multiple XLH-related sequelae available, the results of an elicitation exercise are reported, in which eight global experts in XLH posited how long-term treatment with burosumab is anticipated to impact the life course of clinical sequelae in adults with XLH. Based on their clinical experiences, the available evidence and their disease understanding, the experts agreed that some long-term benefits of using burosumab are likely in adults with XLH even if they have a misaligned skeleton from childhood. Burosumab treatment is anticipated to reduce the incidence of fractures and halt the progression of clinical sequelae associated with conventional therapy. While the trajectories for established dental abscesses are not expected to improve with burosumab treatment, dental abscess development may be prevented. Starting treatment with burosumab in childhood to increase the likelihood of an aligned skeleton and continuation into and throughout adulthood to maintain euphosphatemia may optimize patient outcomes, although future real-world investigation is required to support this hypothesis.

PMID:37547321 | PMC:PMC10400326 | DOI:10.3389/fendo.2023.1211426

J Allergy Clin Immunol Pract. 2023 Aug 4:S2213-2198(23)00815-2. doi: 10.1016/j.jaip.2023.07.042. Online ahead of print.

ABSTRACT

BACKGROUND: Debates on the allocation of medical resources during the COVID-19 pandemic revealed the need for a better understanding of immunologic risk. Studies highlighted variable clinical outcomes of SARS-CoV-2 infections in individuals with defects in both adaptive and innate immunity, suggesting additional contributions from other factors. Notably, none of these studies controlled for variables linked with social determinants of health.

OBJECTIVE: To determine the contributions of determinants of health to risk of hospitalization for SARS-CoV-2 infection among individuals with inborn errors of immunodeficiencies.

METHODS: This is a retrospective, single-center cohort study of 166 individuals with inborn errors of immunity, aged two months through 69 years, who developed SARS-CoV-2 infections from March 1, 2020 through March 31, 2022. Risks of hospitalization was assessed using a multivariable logistic regression analysis.

RESULTS: The risk of SARS-CoV-2-related hospitalization was associated with underrepresented racial and ethnic populations (odds ratio [OR] 4.50; confidence interval [CI], 1.57 - 13.4), a diagnosis of any genetically-defined immunodeficiency (OR 3.32; CI, 1.24 - 9.43), obesity (OR 4.24; CI, 1.38 - 13.3), and neurologic disease (OR 4.47; CI, 1.44 - 14.3. COVID-19 vaccination was associated with reduced hospitalization risk (OR 0.52; CI, 0.31 - 0.81). Defects in T cell and innate immune function, immune-mediated organ dysfunction, and social vulnerability were not associated with increased risk of hospitalization after controlling for covariates.

CONCLUSIONS: The associations between race, ethnicity, and obesity with increased risk of hospitalization for SARS-CoV-2 infection indicate the importance of variables linked with social determinants of health as immunologic risk factors for individuals with inborn errors of immunity.

PMID:37544429 | DOI:10.1016/j.jaip.2023.07.042