Orphan or Rare Diseases

Basophils play a protective role in the recovery of skin barrier function from mechanical injury in mice

Mon, 2024-01-29 06:00

J Invest Dermatol. 2024 Jan 27:S0022-202X(24)00079-4. doi: 10.1016/j.jid.2023.12.024. Online ahead of print.

ABSTRACT

Physical trauma disrupts skin barrier function. How the skin barrier recovers is not fully understood. We evaluated in mice the mechanism of skin barrier recovery following mechanical injury inflicted by tape stripping. Tape stripping disrupted skin barrier function as evidenced by increased trans epidermal water loss. We show that tape stripping induces IL-1, IL-23 and TCRγδ+ dependent upregulation of cutaneous Il17a and Il22 expression. We demonstrate that IL-17A and IL-22 induce epidermal hyperplasia, promote neutrophil recruitment, and delay skin barrier function recovery. Neutrophil depletion improved the recovery of skin barrier function and decreased epidermal hyperplasia. scRNAseq and flow cytometry analysis of skin cells revealed basophil infiltration into tape stripped skin. Basophil depletion upregulated Il17a expression, increased neutrophil infiltration, and delayed skin barrier recovery. Comparative analysis of genes differentially expressed in tape stripped skin of basophil depleted mice and Il17a-/- mice, indicated that basophils counteract the effects of IL-17A on the expression of epidermal and lipid metabolism genes important for skin barrier integrity. Our results demonstrate that basophils play a protective role by downregulating Il17a expression following mechanical skin injury, thereby counteracting the adverse effect of IL-17A on skin barrier function recovery and suggest novel interventions to accelerate this recovery.

PMID:38286187 | DOI:10.1016/j.jid.2023.12.024

Categories: Literature Watch

Incontinentia pigmenti Stage 1 is not simply vesiculo-bullous but vesiculo-pustular

Mon, 2024-01-29 06:00

Pediatr Dermatol. 2024 Jan-Feb;41(1):182-183. doi: 10.1111/pde.15465.

ABSTRACT

Incontinentia pigmenti (IP) is a rare X-linked dominant, male-lethal disorder characterized by pathognomic skin lesions. As described in the literature the typical cutaneous changes follow the pattern of Blaschko's lines and develop in four stages that usually start at birth. Stage 1 is called vesicular, bullous or inflammatory. The vesicles are rapidly filled with eosinophils and thus turn into pustules. Thus, the term "pustular" is relevant to the first phase of IP, and the stage can be considered as "vesiculopustular/inflammatory" to be more precise than "vesicular" or "bullous."

PMID:38284782 | DOI:10.1111/pde.15465

Categories: Literature Watch

Knowledge, awareness, and perception on genetic testing for primary immunodeficiency disease among parents in Malaysia: a qualitative study

Mon, 2024-01-29 06:00

Front Immunol. 2024 Jan 12;14:1308305. doi: 10.3389/fimmu.2023.1308305. eCollection 2023.

ABSTRACT

BACKGROUND: Primary Immunodeficiency Disease (PID), also known as Inborn Errors of Immunity (IEI), comprises a group of rare genetic disorders that impair the body's immune responses. These conditions result from monogenic germline mutations that affect the function of genes governing the innate and adaptive immune system. Therefore, individuals with PID are more susceptible to infectious diseases, allergies, and autoimmune and autoinflammatory conditions. The prevalence of PID has been on the rise, with the number of classified diseases reaching 404, and 430 genetic defects reported to cause these conditions. However, in Malaysia, genetic testing for PID is currently limited and needs to be outsourced to overseas laboratories, posing financial challenges for families. Moreover, limited research has focused on the knowledge and awareness of genetic testing among parents of children with PID in Malaysia. This study aims to address this gap and provide valuable insights into the knowledge, awareness, and perception of genetic testing among this specific population.

METHOD: This qualitative cross-sectional study utilised online open-ended, semi-structured focus group interviews to explore the perceptions and experiences of parents of children with Primary Immunodeficiency (PID). Participants were recruited through convenience sampling from the Malaysian Patient Organisation for Primary Immunodeficiencies (MyPOPI), a non-governmental organisation dedicated to providing support and raising awareness about PID. The study spanned from May 2023 to July 2023 and included participants from diverse regions of Malaysia who had undergone different diagnostic journeys in various hospitals.

RESULT: The focus group discussions yielded 11 sub-themes that highlighted the experiences, understanding and challenges of the participants regarding genetic testing based on the semi-structured questions. These sub-themes were then grouped into four main themes that are awareness and understanding of genetic testing, the journey towards diagnosis and treatment, emotional impact and psychological factors, and the importance of medical experts in diagnosing and managing PID, as well as public perception and awareness.

CONCLUSION: In conclusion, this study highlights the diverse knowledge, awareness, and perception surrounding genetic testing for PID. Factors such as access to services, family history, and personal circumstances shape individuals' understanding of genetic testing. The importance of healthcare professionals, along with the need for improved accessibility and targeted communication strategies, is underscored to enhance understanding and reduce stigma surrounding genetic testing for rare diseases like PID.

PMID:38283358 | PMC:PMC10811462 | DOI:10.3389/fimmu.2023.1308305

Categories: Literature Watch

A web-based psychological support program for caregivers of children with rare chronic diseases: a randomized controlled trial

Sat, 2024-01-27 06:00

Orphanet J Rare Dis. 2024 Jan 27;19(1):27. doi: 10.1186/s13023-024-03029-9.

ABSTRACT

BACKGROUND: Approximately 50% of rare diseases have symptom onset during childhood. A high level of nursing care and an often uncertain prognosis put caregivers of the affected children at high risk for psychological distress. At the same time, their caregivers have limited access to appropriate psychological care. The aim of this study was to evaluate a web-based psychological support program for caregivers of children with chronic rare diseases (WEP-CARE).

METHODS: German-speaking parents (recruited between May 2016 and March 2018) caring for children aged 0-25 years with a rare disease showing clinically relevant anxiety symptoms, were assigned to either the WEP-CARE (n = 38) or treatment as usual (n = 36) condition within a randomized controlled trial. The primary outcome measure was parental anxiety, assessed with the Generalized Anxiety Disorder Questionnaire (GAD-7). Secondary outcomes were fear of disease progression, depression, coping, quality of life and user satisfaction. The group differences were tested through repeated-measures analyses of variance. The WEP-CARE group was additionally followed up three months after the treatment.

RESULTS: A significant time-group interaction was found for anxiety (F (1,35) = 6.13, p = .016), fear of disease progression (F (1,331) = 18.23, p < .001), depression (F (1,74) = 10.79, p = .002) and coping (F (1,233) = 7.02, p = .010), suggesting superiority of the WEP-CARE group. Sustainability of the treatment gains regarding anxiety, fear of disease progression and coping was confirmed at the 6-month follow-up assessment (p < .01). A significant interaction effect could not be found for quality of life (F(1,2) = 0.016; p = .899). Both participating parents and therapists were satisfied with WEP-CARE.

CONCLUSIONS: Our results underline the efficacy and feasibility of WEP-CARE for parents of children with various rare diseases.

PMID:38281056 | PMC:PMC10821309 | DOI:10.1186/s13023-024-03029-9

Categories: Literature Watch

Coding undiagnosed rare disease patients in health information systems: recommendations from the RD-CODE project

Sat, 2024-01-27 06:00

Orphanet J Rare Dis. 2024 Jan 27;19(1):28. doi: 10.1186/s13023-024-03030-2.

ABSTRACT

BACKGROUND: In European Union countries, any disease affecting less than 5 people in 10,000 is considered rare. As expertise is scarce and rare diseases (RD) are complex, RD patients can remain undiagnosed for many years. The period of searching for a diagnosis, called diagnostic delay, sometimes leads to a diagnostic dead end when the patient's disease is impossible to diagnose after undergoing all available investigations. In recent years, extensive efforts have been made to support the implementation of ORPHA nomenclature in health information systems (HIS) so as to allow RD coding. Until recently, the nomenclature only encompassed codes for specific RD. Persons suffering from a suspected RD who could not be diagnosed even after full investigation, could not be coded with ORPHAcodes. The recognition of the RD status is necessary for patients, even if they do not have a precise diagnosis. It can facilitate reimbursement of care, be socially and psychologically empowering, and grant them access to scientific advances.

RESULTS: The RD-CODE project aimed at making those patients identifiable in HIS in order to produce crucial epidemiological data. Undiagnosed patients were defined as patients for whom no clinically-known disorder could be confirmed by an expert center after all reasonable efforts to obtain a diagnosis according to the state-of-the-art and diagnostic capabilities available. Three recommendations for the coding of undiagnosed RD patients were produced by a multi-stakeholder panel of experts: 1/ Capture the diagnostic ascertainment for all rare disease cases; 2/ Use the newly created ORPHAcode (ORPHA:616874 "Rare disorder without a determined diagnosis after full investigation"), available in the Orphanet nomenclature: as the code is new, guidelines are essential to ensure its correct and homogeneous use for undiagnosed patients' identification in Europe and beyond; 3/ Use additional descriptors in registries.

CONCLUSIONS: The recommendations can now be implemented in HIS (electronic health records and/or registries) and could be a game-changer for patients, clinicians and researchers in the field, enabling assessment of the RD population, including undiagnosed patients, adaptation of policy measures including financing for care and research programs, and to improved access of undiagnosed patients to research programs.

PMID:38280999 | PMC:PMC10822150 | DOI:10.1186/s13023-024-03030-2

Categories: Literature Watch

A new drug for rare diseases: pozelimab for CHAPLE disease

Fri, 2024-01-26 06:00

Lancet. 2024 Feb 17;403(10427):592-593. doi: 10.1016/S0140-6736(23)02652-1. Epub 2024 Jan 23.

NO ABSTRACT

PMID:38278169 | DOI:10.1016/S0140-6736(23)02652-1

Categories: Literature Watch

Lipodystrophy in methylmalonic acidemia associated with elevated FGF21 and abnormal methylmalonylation

Thu, 2024-01-25 06:00

JCI Insight. 2024 Feb 22;9(4):e174097. doi: 10.1172/jci.insight.174097.

ABSTRACT

A distinct adipose tissue distribution pattern was observed in patients with methylmalonyl-CoA mutase deficiency, an inborn error of branched-chain amino acid (BCAA) metabolism, characterized by centripetal obesity with proximal upper and lower extremity fat deposition and paucity of visceral fat, that resembles familial multiple lipomatosis syndrome. To explore brown and white fat physiology in methylmalonic acidemia (MMA), body composition, adipokines, and inflammatory markers were assessed in 46 patients with MMA and 99 matched controls. Fibroblast growth factor 21 levels were associated with acyl-CoA accretion, aberrant methylmalonylation in adipose tissue, and an attenuated inflammatory cytokine profile. In parallel, brown and white fat were examined in a liver-specific transgenic MMA mouse model (Mmut-/- TgINS-Alb-Mmut). The MMA mice exhibited abnormal nonshivering thermogenesis with whitened brown fat and had an ineffective transcriptional response to cold stress. Treatment of the MMA mice with bezafibrates led to clinical improvement with beiging of subcutaneous fat depots, which resembled the distribution seen in the patients. These studies defined what we believe to be a novel lipodystrophy phenotype in patients with defects in the terminal steps of BCAA oxidation and demonstrated that beiging of subcutaneous adipose tissue in MMA could readily be induced with small molecules.

PMID:38271099 | DOI:10.1172/jci.insight.174097

Categories: Literature Watch

Are the European reference networks for rare diseases ready to embrace machine learning? A mixed-methods study

Thu, 2024-01-25 06:00

Orphanet J Rare Dis. 2024 Jan 25;19(1):25. doi: 10.1186/s13023-024-03047-7.

ABSTRACT

BACKGROUND: The delay in diagnosis for rare disease (RD) patients is often longer than for patients with common diseases. Machine learning (ML) technologies have the potential to speed up and increase the precision of diagnosis in this population group. We aim to explore the expectations and experiences of the members of the European Reference Networks (ERNs) for RDs with those technologies and their potential for application.

METHODS: We used a mixed-methods approach with an online survey followed by a focus group discussion. Our study targeted primarily medical professionals but also other individuals affiliated with any of the 24 ERNs.

RESULTS: The online survey yielded 423 responses from ERN members. Participants reported a limited degree of knowledge of and experience with ML technologies. They considered improved diagnostic accuracy the most important potential benefit, closely followed by the synthesis of clinical information, and indicated the lack of training in these new technologies, which hinders adoption and implementation in routine care. Most respondents supported the option that ML should be an optional but recommended part of the diagnostic process for RDs. Most ERN members saw the use of ML limited to specialised units only in the next 5 years, where those technologies should be funded by public sources. Focus group discussions concluded that the potential of ML technologies is substantial and confirmed that the technologies will have an important impact on healthcare and RDs in particular. As ML technologies are not the core competency of health care professionals, participants deemed a close collaboration with developers necessary to ensure that results are valid and reliable. However, based on our results, we call for more research to understand other stakeholders' opinions and expectations, including the views of patient organisations.

CONCLUSIONS: We found enthusiasm to implement and apply ML technologies, especially diagnostic tools in the field of RDs, despite the perceived lack of experience. Early dialogue and collaboration between health care professionals, developers, industry, policymakers, and patient associations seem to be crucial to building trust, improving performance, and ultimately increasing the willingness to accept diagnostics based on ML technologies.

PMID:38273306 | PMC:PMC10809751 | DOI:10.1186/s13023-024-03047-7

Categories: Literature Watch

Rescue of secretion of rare-disease-associated misfolded mutant glycoproteins in UGGT1 knock-out mammalian cells

Thu, 2024-01-25 06:00

Traffic. 2024 Jan;25(1):e12927. doi: 10.1111/tra.12927.

ABSTRACT

Endoplasmic reticulum (ER) retention of misfolded glycoproteins is mediated by the ER-localized eukaryotic glycoprotein secretion checkpoint, UDP-glucose glycoprotein glucosyl-transferase (UGGT). The enzyme recognizes a misfolded glycoprotein and flags it for ER retention by re-glucosylating one of its N-linked glycans. In the background of a congenital mutation in a secreted glycoprotein gene, UGGT-mediated ER retention can cause rare disease, even if the mutant glycoprotein retains activity ("responsive mutant"). Using confocal laser scanning microscopy, we investigated here the subcellular localization of the human Trop-2-Q118E, E227K and L186P mutants, which cause gelatinous drop-like corneal dystrophy (GDLD). Compared with the wild-type Trop-2, which is correctly localized at the plasma membrane, these Trop-2 mutants are retained in the ER. We studied fluorescent chimeras of the Trop-2 Q118E, E227K and L186P mutants in mammalian cells harboring CRISPR/Cas9-mediated inhibition of the UGGT1 and/or UGGT2 genes. The membrane localization of the Trop-2 Q118E, E227K and L186P mutants was successfully rescued in UGGT1-/- cells. UGGT1 also efficiently reglucosylated Trop-2-Q118E-EYFP in cellula. The study supports the hypothesis that UGGT1 modulation would constitute a novel therapeutic strategy for the treatment of pathological conditions associated to misfolded membrane glycoproteins (whenever the mutation impairs but does not abrogate function), and it encourages the testing of modulators of ER glycoprotein folding quality control as broad-spectrum rescue-of-secretion drugs in rare diseases caused by responsive secreted glycoprotein mutants.

PMID:38272446 | PMC:PMC10832616 | DOI:10.1111/tra.12927

Categories: Literature Watch

Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges

Thu, 2024-01-25 06:00

Brief Bioinform. 2024 Jan 22;25(2):bbad508. doi: 10.1093/bib/bbad508.

ABSTRACT

Next-generation sequencing (NGS) has revolutionized the field of rare disease diagnostics. Whole exome and whole genome sequencing are now routinely used for diagnostic purposes; however, the overall diagnosis rate remains lower than expected. In this work, we review current approaches used for calling and interpretation of germline genetic variants in the human genome, and discuss the most important challenges that persist in the bioinformatic analysis of NGS data in medical genetics. We describe and attempt to quantitatively assess the remaining problems, such as the quality of the reference genome sequence, reproducible coverage biases, or variant calling accuracy in complex regions of the genome. We also discuss the prospects of switching to the complete human genome assembly or the human pan-genome and important caveats associated with such a switch. We touch on arguably the hardest problem of NGS data analysis for medical genomics, namely, the annotation of genetic variants and their subsequent interpretation. We highlight the most challenging aspects of annotation and prioritization of both coding and non-coding variants. Finally, we demonstrate the persistent prevalence of pathogenic variants in the coding genome, and outline research directions that may enhance the efficiency of NGS-based disease diagnostics.

PMID:38271481 | PMC:PMC10810331 | DOI:10.1093/bib/bbad508

Categories: Literature Watch

Clinical and genetic manifestations of left ventricular non-compaction in children

Thu, 2024-01-25 06:00

G Ital Cardiol (Rome). 2024 Feb;25(2):98-105. doi: 10.1714/4187.41758.

ABSTRACT

Left ventricular non-compaction (LVNC) is a myocardial disease characterized by a two-layered structure typically seen at the apical and lateral left portions of the ventricular myocardium, distal to the papillary muscles. While considered a rare disease, its prevalence in children is increasing due to the increased awareness of this condition and improved resolution of imaging techniques. The etiology is heterogeneous, ranging from inherited conditions to acquired diseases. Although many patients are asymptomatic, some patients may experience adverse events, including heart failure, arrhythmias, or thromboembolic events. Several echocardiographic or cardiac magnetic resonance imaging diagnostic criteria have been proposed for diagnosing LVNC. However, their application in children is significantly limited. This review aims to describe the clinical and genetic characteristics of children with LVNC and discuss the role of the proposed diagnostic criteria.

PMID:38270365 | DOI:10.1714/4187.41758

Categories: Literature Watch

Cross-border rare disease advocacy: Preethi Krishnaraj interviews Harsha Rajasimha

Thu, 2024-01-25 06:00

Dis Model Mech. 2024 Jun 1;17(6):dmm050672. doi: 10.1242/dmm.050672. Epub 2024 Jan 25.

NO ABSTRACT

PMID:38270284 | PMC:PMC10846506 | DOI:10.1242/dmm.050672

Categories: Literature Watch

Rare Diseases in Citizen Science - Preliminary Experiences in Developing a Personal Health App

Thu, 2024-01-25 06:00

Stud Health Technol Inform. 2024 Jan 25;310:1151-1155. doi: 10.3233/SHTI231145.

ABSTRACT

SelEe is a German citizen science project aiming to develop a smartphone app for a patient-managed record. The goal is to study rare diseases with the support of interested citizens and people affected by rare diseases. We established a core research team, including professional researchers (leading the project) and citizens. Citizens have the opportunity to discuss the progress, make suggestions regarding the app's design and data entry and contribute to the dissemination of the project. To gather feedback and experiences from the core research team, we performed an online questionnaire regarding the topics "influence and communication", "improvements and learning effect", and "satisfaction". Finally, 9 citizens of the core research team participated. The results show that the citizens are very satisfied with the design of the app, their participation opportunities and the communication in the project.

PMID:38269995 | DOI:10.3233/SHTI231145

Categories: Literature Watch

User Centered Rare Disease Clinical Trial Knowledge Graph (RCTKG)

Thu, 2024-01-25 06:00

Stud Health Technol Inform. 2024 Jan 25;310:94-98. doi: 10.3233/SHTI230934.

ABSTRACT

Drug development in rare diseases is challenging due to the limited availability of subjects with the diseases and recruiting from a small patient population. The high cost and low success rate of clinical trials motivate deliberate analysis of existing clinical trials to understand status of clinical development of orphan drugs and discover new insight for new trial. In this project, we aim to develop a user centered Rare disease based Clinical Trial Knowledge Graph (RCTKG) to integrate publicly available clinical trial data with rare diseases from the Genetic and Rare Disease (GARD) program in a semantic and standardized form for public use. To better serve and represent the interests of rare disease users, user stories were defined for three types of users, patients, healthcare providers and informaticians, to guide the RCTKG design in supporting the GARD program at NCATS/NIH and the broad clinical/research community in rare diseases.

PMID:38269772 | DOI:10.3233/SHTI230934

Categories: Literature Watch

Caecal malakoplakia: a rare mimic of malignancy

Tue, 2024-01-23 06:00

BMJ Case Rep. 2024 Jan 23;17(1):e257130. doi: 10.1136/bcr-2023-257130.

ABSTRACT

Malakoplakia is a rare granulomatous disease. Its aetiology is unclear but possible theories include infection with microorganisms (especially Escherichia coli), immunosuppression and impaired lysosomal function. It has been commonly documented to affect the genitourinary tract but can affect any organ, with the gastrointestinal system being the next most affected. We present a woman in her 70s, with a 2-week history of right-sided abdominal pain, 13 years following her renal transplant. She was admitted for treatment of an E. coli bacteraemia. CT scan had shown a caecal pole mass, highly suspicious for malignancy. It was surgically resected, and histology revealed findings of malakoplakia within the colon. Surgical intervention was combined with a prolonged course of antibiotics for successful treatment. We highlight the ability of malakoplakia to mimic malignancy and should be considered in the differentials in the context of an immunosuppressed patient with radiological findings of a colonic mass.

PMID:38262716 | PMC:PMC10826489 | DOI:10.1136/bcr-2023-257130

Categories: Literature Watch

Advanced Cellular Models for Rare Disease Study: Exploring Neural, Muscle and Skeletal Organoids

Tue, 2024-01-23 06:00

Int J Mol Sci. 2024 Jan 13;25(2):1014. doi: 10.3390/ijms25021014.

ABSTRACT

Organoids are self-organized, three-dimensional structures derived from stem cells that can mimic the structure and physiology of human organs. Patient-specific induced pluripotent stem cells (iPSCs) and 3D organoid model systems allow cells to be analyzed in a controlled environment to simulate the characteristics of a given disease by modeling the underlying pathophysiology. The recent development of 3D cell models has offered the scientific community an exceptionally valuable tool in the study of rare diseases, overcoming the limited availability of biological samples and the limitations of animal models. This review provides an overview of iPSC models and genetic engineering techniques used to develop organoids. In particular, some of the models applied to the study of rare neuronal, muscular and skeletal diseases are described. Furthermore, the limitations and potential of developing new therapeutic approaches are discussed.

PMID:38256087 | PMC:PMC10815694 | DOI:10.3390/ijms25021014

Categories: Literature Watch

Targeted long-read sequencing identified a causal structural variant in X-linked nephrogenic diabetes insipidus

Tue, 2024-01-23 06:00

BMC Med Genomics. 2024 Jan 22;17(1):29. doi: 10.1186/s12920-024-01801-1.

ABSTRACT

BACKGROUND: X-linked nephrogenic diabetes insipidus (NDI) is a rare genetic renal disease caused by pathogenic variants in the AVPR2 gene. Single nucleotide variants and small insertions/deletions in AVPR2 are reliably detected by routine clinical sequencing. Nevertheless, structural variants involving AVPR2 are challenging to identify accurately by conventional genetic testing. Here, we report a novel deletion of AVPR2 in a Czech family identified for the first time by targeted long-read sequencing (T-LRS).

METHODS: A male proband with X-linked NDI underwent clinical sequencing of the AVPR2 gene that failed and thus indicated possible whole-gene deletion. Therefore, PCR mapping and subsequent targeted long-read sequencing (T-LRS) using a Pacific Biosciences sequencer were applied to search for the suspected deletion. To validate the deletion breakpoints and prove variant segregation in the family with X-linked NDI, Sanger sequencing of the deletion junction was performed. Quantitative real-time PCR was further carried out to confirm the carrier status of heterozygous females.

RESULTS: By T-LRS, a novel 7.5 kb deletion of AVPR2 causing X-linked NDI in the proband was precisely identified. Sanger sequencing of the deletion junction confirmed the variant breakpoints and detected the deletion in the probands´ mother, maternal aunt, and maternal cousin with X-linked NDI. The carrier status in heterozygous females was further validated by quantitative real-time PCR.

CONCLUSIONS: Identifying the 7.5 kb deletion gave a precise molecular diagnosis for the proband, enabled genetic counselling and genetic testing for the family, and further expanded the spectrum of structural variants causing X-linked NDI. Our results also show that T-LRS has significant potential for accurately identifying putative structural variants.

PMID:38254165 | PMC:PMC10804598 | DOI:10.1186/s12920-024-01801-1

Categories: Literature Watch

Developing a community-led rare disease ELSI research agenda

Tue, 2024-01-23 06:00

Orphanet J Rare Dis. 2024 Jan 22;19(1):23. doi: 10.1186/s13023-023-02986-x.

ABSTRACT

BACKGROUND: Research priorities are best defined through engagement with communities who will be impacted by the research and have lived experience of the topics to be studied. We aimed to establish a pediatric rare disease community stakeholder group and empower them in (1) eliciting perspectives from affected families in the wider region and (2) synthesizing collective ideas into a research agenda focused on shared ethical, legal, and social implications (ELSI) across rare disease.

METHODS: This two-year project utilized a community-centered approach to engage rare disease community members as equal partners in developing a research agenda for ELSI in rare disease. We established "Rare Voices" (RV), a 22-member stakeholder group of patients, parents, clinicians and researchers. Following capacity-building trainings, RV designed and conducted listening sessions with teen patients and parents of children with rare diseases to explore challenges, positive experiences, and ethical concerns. Listening session findings were synthesized and contextualized into research topics, which RV members further refined and prioritized. We used established measures to assess RV member engagement and satisfaction.

RESULTS: From 14 listening sessions with parents (n = 52) and teen patients (n = 13), RV identified eight core research topics as most important for future rare disease research: coordinating care, communication, accessing resources and care, impact on family unit, community and support in society, mental health and identity, ethical aspects of care, and uncertainty. RV members were highly engaged throughout the two-year project and reported high levels of satisfaction with the experience and research agenda.

CONCLUSIONS: Through capacity-building and authentic engagement, this project resulted in a community-led rare disease research agenda to guide future rare disease ELSI research that aligns with patients' and families' priorities. An environment of equal partnership and respect created a space for mutual learning where community members were empowered to shape the research agenda based on their collective experiences. The agenda recognizes the shared psychosocial and healthcare experiences of rare disease and offers practical areas of research to address patient and family needs.

PMID:38254122 | PMC:PMC10801933 | DOI:10.1186/s13023-023-02986-x

Categories: Literature Watch

Pangenome graphs improve the analysis of structural variants in rare genetic diseases

Mon, 2024-01-22 06:00

Nat Commun. 2024 Jan 22;15(1):657. doi: 10.1038/s41467-024-44980-2.

ABSTRACT

Rare DNA alterations that cause heritable diseases are only partially resolvable by clinical next-generation sequencing due to the difficulty of detecting structural variation (SV) in all genomic contexts. Long-read, high fidelity genome sequencing (HiFi-GS) detects SVs with increased sensitivity and enables assembling personal and graph genomes. We leverage standard reference genomes, public assemblies (n = 94) and a large collection of HiFi-GS data from a rare disease program (Genomic Answers for Kids, GA4K, n = 574 assemblies) to build a graph genome representing a unified SV callset in GA4K, identify common variation and prioritize SVs that are more likely to cause genetic disease (MAF < 0.01). Using graphs, we obtain a higher level of reproducibility than the standard reference approach. We observe over 200,000 SV alleles unique to GA4K, including nearly 1000 rare variants that impact coding sequence. With improved specificity for rare SVs, we isolate 30 candidate SVs in phenotypically prioritized genes, including known disease SVs. We isolate a novel diagnostic SV in KMT2E, demonstrating use of personal assemblies coupled with pangenome graphs for rare disease genomics. The community may interrogate our pangenome with additional assemblies to discover new SVs within the allele frequency spectrum relevant to genetic diseases.

PMID:38253606 | PMC:PMC10803329 | DOI:10.1038/s41467-024-44980-2

Categories: Literature Watch

About a case of Fraser syndrome. Autopsy of a 37 weeks gestation fetus with multiple malformations

Sun, 2024-01-21 06:00

Rev Esp Patol. 2024 Jan-Mar;57(1):64-66. doi: 10.1016/j.patol.2023.07.002. Epub 2023 Oct 14.

ABSTRACT

Fraser syndrome or cryptophthalmos-syndactyly syndrome is a rare genetic disease, the diagnosis of which is based on a series of major and minor clinical criteria and that can be supported by genetic tests. This article presents the case of a fetal autopsy at 37 weeks of gestation with suspicion of CHAOS syndrome (congenital obstructive syndrome of the upper airways).

PMID:38246713 | DOI:10.1016/j.patol.2023.07.002

Categories: Literature Watch

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