Orphan or Rare Diseases

Parental Attitudes Toward Standard Newborn Screening and Newborn Genomic Sequencing: Findings From the BabySeq Study

Mon, 2022-05-16 06:00

Front Genet. 2022 Apr 27;13:867371. doi: 10.3389/fgene.2022.867371. eCollection 2022.

ABSTRACT

Introduction: With increasing utility and decreasing cost of genomic sequencing, augmentation of standard newborn screening (NBS) programs with newborn genomic sequencing (nGS) has been proposed. Before nGS can be integrated into newborn screening, parents' perspectives must be better understood. Objective: Using data from surveys administered to parents of healthy newborns who were enrolled in the BabySeq Project, a randomized clinical trial of nGS alongside NBS, this paper reports parents' attitudes regarding population-based NBS and nGS assessed 3 months after results disclosure. Methods: Parental attitudes regarding whether all newborns should receive, and whether informed consent should be required for, NBS and nGS, as well as whether nGS should be mandated were assessed using 5-point scales from strongly disagree (=1) to strongly agree (=5). Parents' interest in receiving types of results from nGS was assessed on a 5-point scale from not at all interested (=1) to very interested (=5). Survey responses were analyzed using Fisher's exact tests, paired t-tests, and repeated measures ANOVA. Results: At 3 months post-disclosure, 248 parents of 174 healthy newborns submitted a survey. Support for every newborn receiving standard NBS (mean 4.67) was higher than that for every newborn receiving nGS (mean 3.60; p < 0.001). Support for required informed consent for NBS (mean 3.44) was lower than that for nGS (mean 4.27, p < 0.001). Parents' attitudes toward NBS and nGS were not significantly associated with self-reported political orientation. If hypothetically receiving nGS outside of the BabySeq Project, most parents reported being very interested in receiving information on their baby's risk of developing a disease in childhood that can be prevented, treated, or cured (86.8%) and their risk of developing a disease during adulthood that can be prevented, treated, or cured (84.6%). Discussion: Parents' opinions are crucial to inform design and delivery of public health programs, as the success of the program hinges on parents' trust and participation. To accommodate parents' preferences without affecting the current high participation rates in NBS, an optional add-on consent to nGS in addition to NBS may be a feasible approach. Trial Registration ClinicalTrials.gov Identifier: NCT02422511.

PMID:35571041 | PMC:PMC9091188 | DOI:10.3389/fgene.2022.867371

Categories: Literature Watch

Robotic Surgery for Bladder Cancer

Sun, 2022-05-15 06:00

JAMA. 2022 Jun 7;327(21):2085-2087. doi: 10.1001/jama.2022.6417.

NO ABSTRACT

PMID:35569078 | DOI:10.1001/jama.2022.6417

Categories: Literature Watch

Systematic Collaborative Reanalysis of Genomic Data Improves Diagnostic Yield in Neurologic Rare Diseases

Sun, 2022-05-15 06:00

J Mol Diagn. 2022 May;24(5):529-542. doi: 10.1016/j.jmoldx.2022.02.003.

ABSTRACT

Many patients experiencing a rare disease remain undiagnosed even after genomic testing. Reanalysis of existing genomic data has shown to increase diagnostic yield, although there are few systematic and comprehensive reanalysis efforts that enable collaborative interpretation and future reinterpretation. The Undiagnosed Rare Disease Program of Catalonia project collated previously inconclusive good quality genomic data (panels, exomes, and genomes) and standardized phenotypic profiles from 323 families (543 individuals) with a neurologic rare disease. The data were reanalyzed systematically to identify relatedness, runs of homozygosity, consanguinity, single-nucleotide variants, insertions and deletions, and copy number variants. Data were shared and collaboratively interpreted within the consortium through a customized Genome-Phenome Analysis Platform, which also enables future data reinterpretation. Reanalysis of existing genomic data provided a diagnosis for 20.7% of the patients, including 1.8% diagnosed after the generation of additional genomic data to identify a second pathogenic heterozygous variant. Diagnostic rate was significantly higher for family-based exome/genome reanalysis compared with singleton panels. Most new diagnoses were attributable to recent gene-disease associations (50.8%), additional or improved bioinformatic analysis (19.7%), and standardized phenotyping data integrated within the Undiagnosed Rare Disease Program of Catalonia Genome-Phenome Analysis Platform functionalities (18%).

PMID:35569879 | DOI:10.1016/j.jmoldx.2022.02.003

Categories: Literature Watch

Mental health care for rare disease in the UK - recommendations from a quantitative survey and multi-stakeholder workshop

Sun, 2022-05-15 06:00

BMC Health Serv Res. 2022 May 14;22(1):648. doi: 10.1186/s12913-022-08060-9.

ABSTRACT

BACKGROUND: Rare disease patients and carers report significant impacts on mental health but studies on UK populations have focussed on relatively few, specific conditions. Collectively rare conditions represent a substantial health burden, with an estimated 3.5 million affected individuals in the UK.

METHOD: We explored the impact on mental health of living with a rare condition, and experiences of health service support, through an online survey. The survey assessed the impact of specific experiences commonly reported by those affected by a rare condition through multiple choice questions and Likert scale items, and open text question boxes. Through a multi-stakeholder workshop that involved facilitated discussion of our findings with patients/carers, clinicians and a government advisor, we developed recommendations for policy and practice toward a more person-centred and integrated approach.

RESULTS: Eligible responses came from 1231 patients and 564 carers. Due to their rare condition, the majority of respondents (> 90%) had felt worried/anxious; stressed; and /or low/depressed. Thirty-six percent of patients and 19% of carers had had suicidal thoughts. Challenges that are particular to rare conditions and which negatively affect mental health included limited knowledge of the condition amongst healthcare professionals (88%), and not being believed or taken seriously by them. Only 23% of respondents felt healthcare professionals considered mental and physical health as equally important. Almost half reported never having been asked about mental health by healthcare professionals. Our findings indicate that access to, and appropriateness of, professional psychological support needs to be improved. Peer group support is important but signposting is inadequate. Our recommendations are for healthcare professionals to be supported to effectively and sensitively recognise and address patients' and carers' mental health needs; and for service level coordination of care to integrate professional psychological support with rare disease services.

CONCLUSION: Living with a rare disease substantially impacts mental health. Many of the drivers of poor mental health reflect issues specific to managing rare conditions. To meet UK government commitments, there should be a focus on empowering healthcare professionals who treat rare disease patients and on integration of mental health support with rare disease services.

PMID:35568910 | PMC:PMC9107210 | DOI:10.1186/s12913-022-08060-9

Categories: Literature Watch

Anxiety-like behavior and anxiolytic treatment in the Rett syndrome natural history study

Sun, 2022-05-15 06:00

J Neurodev Disord. 2022 May 14;14(1):31. doi: 10.1186/s11689-022-09432-2.

ABSTRACT

BACKGROUND: Rett syndrome (RTT) is a neurodevelopmental disorder most often related to a pathogenic variant in the X-linked MECP2 gene. Internalizing behaviors appear to be common, but standard methods of diagnosing anxiety are not readily applied in this population which typically has cognitive impairment and limited expressive language. This study aims to describe the frequency of anxiety-like behavior and anxiolytic treatments along with associated clinical features in individuals with RTT.

METHODS: Parental reports and medication logs provided data from 1380 females with RTT participating in two iterations of the multicenter U.S. RTT Natural History Study (RNHS) from 2006 to 2019.

RESULTS: Most participants with RTT (77.5%) had at least occasional anxious or nervous behavior. Anxiety was reported to be the most troublesome concern for 2.6%, and within the top 3 concerns for 10.0%, of participants in the second iteration. Parents directly reported treatment for anxious or nervous behavior in 16.6% of participants in the second iteration with most reporting good control of the behavior (71.6%). In the medication logs of both RNHS iterations, the indication of anxiety was listed for a similar number of participants (15% and 14.5%, respectively). Increased use of anxiolytics and selective serotonin reuptake inhibitors (SSRIs) was related to more frequent anxiety-like behaviors (P < 0.001), older age (P < 0.001), and mild MECP2 variants (P = 0.002).

CONCLUSION: Anxiety-like behavior is frequent at all ages and is a significant parental concern in RTT. Older individuals and those with mild MECP2 variants are more likely to be treated with medications. Better diagnosis and treatment of anxiety in RTT should be a goal of both future studies and clinical care.

TRIAL REGISTRATION: NCT00299312 and NCT02738281.

PMID:35568815 | PMC:PMC9107202 | DOI:10.1186/s11689-022-09432-2

Categories: Literature Watch

Biomarkers in Rare Diseases 2.0

Sat, 2022-05-14 06:00

Int J Mol Sci. 2022 Apr 21;23(9):4582. doi: 10.3390/ijms23094582.

ABSTRACT

It is estimated that there are over 7000 rare diseases, collectively affecting more than 350 million individuals worldwide [...].

PMID:35562973 | PMC:PMC9104062 | DOI:10.3390/ijms23094582

Categories: Literature Watch

Immune-Based Therapy in Triple-Negative Breast Cancer: From Molecular Biology to Clinical Practice

Sat, 2022-05-14 06:00

Cancers (Basel). 2022 Apr 23;14(9):2102. doi: 10.3390/cancers14092102.

ABSTRACT

Triple-negative breast cancer (TNBC) has been considered for many years an orphan disease in terms of therapeutic options, with conventional chemotherapy (CT) still representing the mainstay of treatment in the majority of patients. Although breast cancer (BC) has been historically considered a "cold tumor", exciting progress in the genomic field leading to the characterization of the molecular portrait and the immune profile of TNBC has opened the door to novel therapeutic strategies, including Immune Checkpoint Inhibitors (ICIs), Poly ADP-Ribose Polymerase (PARP) inhibitors and Antibody Drug Conjugates (ADCs). In particular, compared to standard CT, the immune-based approach has been demonstrated to improve progression-free survival (PFS) and overall survival (OS) in metastatic PD-L1-positive TNBC and the pathological complete response rate in the early setting, regardless of PD-L1 expression. To date, PD-L1 has been widely used as a predictor of the response to ICIs; however, many patients do not benefit from the addition of immunotherapy. Therefore, PD-L1 is not a reliable predictive biomarker of the response, and its accuracy remains controversial due to the lack of a consensus about the assay, the antibody, and the scoring system to adopt, as well as the spatial and temporal heterogeneity of the PD-L1 status. In the precision medicine era, there is an urgent need to identify more sensitive biomarkers in the BC immune oncology field other than just PD-L1 expression. Through the characterization of the tumor microenvironment (TME), the analysis of peripheral blood and the evaluation of immune gene signatures, novel potential biomarkers have been explored, such as the Tumor Mutational Burden (TMB), Microsatellite Instability/Mismatch Repair Deficiency (MSI/dMMR) status, genomic and epigenomic alterations and tumor-infiltrating lymphocytes (TILs). This review aims to summarize the recent knowledge on BC immunograms and on the biomarkers proposed to support ICI-based therapy in TNBC, as well as to provide an overview of the potential strategies to enhance the immune response in order to overcome the mechanisms of resistance.

PMID:35565233 | DOI:10.3390/cancers14092102

Categories: Literature Watch

Facial dysmorphologies in genetic disorders: exploring the ancestry component in a Colombian population

Fri, 2022-05-13 06:00

FASEB J. 2022 May;36 Suppl 1. doi: 10.1096/fasebj.2022.36.S1.R5134.

ABSTRACT

Currently there are more than 10,000 rare diseases that affect about 7% of the world's population. Up to 40% of rare genetic disorders present craniofacial dysmorphologies, which can vary from subtle facial anomalies to severe malformations. Visual assessment of facial dysmorphology is commonly used for clinical diagnosis, patient management and treatment monitoring. However, qualitative descriptions are usually vague and quantitative approaches using craniofacial phenotypes for the diagnosis of rare diseases are based on North American and European populations, disregarding the influence of population ancestry on facial variation, as in Latin-America. In this study, we assessed facial dysmorphologies associated to three different genetic disorders (Down (DS), Morquio (MS) and Noonan syndrome (NS)) in a Latin-American population from Cali (Colombia). We recorded the coordinates of 18 facial landmarks in 2D images from 34 pediatric patients (19 DS, 8 MS, 6 NS) and 75 controls and quantified facial differences between patients and control groups using Euclidean Distance Matrix Analysis (EDMA). Comparisons between control and syndromic phenotypes indicated that individuals diagnosed with DS and MS presented the largest percentage of dysmorphologies, with respectively 56.2% and 54.9% of significantly different facial traits. In NS, the percentage decreased to 12.4%. Each syndrome presented a characteristic facial pattern. In DS, all facial structures were affected, with a 6% increase of relative distance between the eyes and a 7-10% reduction in facial height. The eyes and nose were most affected in MS, but not the mouth, with higher hypertelorism and facial reduction than in DS (9% and 8-17%). In NS, facial differences were more subtle and affected mainly the eyes and mouth, reducing the relative distance between them from 1 to 4% in patients as compared to controls. Our study provides a precise quantitative comparison of facial dysmorphologies in three genetic disorders that in the future can be compared with other world-wide populations to test whether facial traits associated to disease are altered by different evolutionary and adaptive histories of human populations.

PMID:35560709 | DOI:10.1096/fasebj.2022.36.S1.R5134

Categories: Literature Watch

Unlocking sociocultural and community factors for the global adoption of genomic medicine

Fri, 2022-05-13 06:00

Orphanet J Rare Dis. 2022 May 12;17(1):191. doi: 10.1186/s13023-022-02328-3.

ABSTRACT

Advances in genomic sequencing and genetic testing are increasingly transforming the diagnosis and treatment of diseases-specifically, rare diseases. However, the application and benefit of such technologies remain inequitable globally. There is a clear and urgent need to provide genomic sequencing to people across the global population, including people living in under-resourced areas and/or underrepresented populations. Financial considerations are the most obvious barriers to the adoption of genomic medicine, yet there are many other factors that are not so obvious, such as geography, language, communication, and culture. Herein, we use the lens of rare diseases and focus on firstly, selected socio-cultural factors, and in particular stigma; and secondly, empowering community factors such as education, advocacy and connectivity amongst people living with rare diseases globally. These are critical areas of need and opportunity if genomic medicine is to achieve equitable and global adoption in the patient best-interest across low- middle- and high-income country health systems. Furthermore, we touch on specific child health aspects and how they can point towards opportunities to build on specific infrastructures.

PMID:35549752 | PMC:PMC9097338 | DOI:10.1186/s13023-022-02328-3

Categories: Literature Watch

Healthcare access, satisfaction, and health-related quality of life among children and adults with rare diseases

Fri, 2022-05-13 06:00

Orphanet J Rare Dis. 2022 May 12;17(1):196. doi: 10.1186/s13023-022-02343-4.

ABSTRACT

BACKGROUND: Research in a variety of countries indicates that healthcare access and health-related quality of life are challenged among people with a variety of rare diseases (RDs). However, there has been little systematic research on the experiences of children and adults with RDs in the American healthcare system that identifies commonalities across RDs. This research aimed to: (1) Describe demographics, disease characteristics, diagnostic experiences, access to healthcare, knowledge about RDs, support from healthcare professionals, and patient satisfaction among people with RDs and their caregivers; (2) examine predictors of patient satisfaction among adults with RDs; (3) compare health-related quality of life and stigma to US population norms; 4) examine predictors of anxiety and depression among adults and children with RDs.

RESULTS: This large-scale survey included (n = 1128) adults with RD or parents or caregivers of children with RDs representing 344 different RDs. About one third of participants waited four or more years for a diagnosis and misdiagnosis was common. A subset of participants reported experiencing insurance-related delays or denials for tests, treatments, specialists, or services. Approximately half of participants felt their medical and social support was sufficient, yet less than a third had sufficient dental and psychological support. Patients were generally neither satisfied or dissatisfied with their healthcare providers. Major predictors of satisfaction were lower stigma, lower anxiety, shorter diagnostic odyssey, greater physical function, and less pain interference. Adults and children with RDs had significantly poorer health-related quality of life and stigma in all domains compared to US norms. Predictors of both anxiety and depression were greater stigma/poor peer relationships, fatigue, sleep disturbance, limited ability to participate in social roles, and unstable disease course.

CONCLUSIONS: People in the U.S. with RDs have poor health-related quality of life and high stigma. These factors are related to patient satisfaction and healthcare access, including diagnostic delays and misdiagnosis. Advocacy work is needed in order to improve healthcare access and ultimately health-related quality of life for children and adults with RDs.

PMID:35549731 | PMC:PMC9096775 | DOI:10.1186/s13023-022-02343-4

Categories: Literature Watch

Parental segregation study reveals rare benign and likely benign variants in a Brazilian cohort of rare diseases

Fri, 2022-05-13 06:00

Sci Rep. 2022 May 11;12(1):7764. doi: 10.1038/s41598-022-11932-z.

ABSTRACT

Genomic studies may generate massive amounts of data, bringing interpretation challenges. Efforts for the differentiation of benign and pathogenic variants gain importance. In this article, we used segregation analysis and other molecular data to reclassify to benign or likely benign several rare clinically curated variants of autosomal dominant inheritance from a cohort of 500 Brazilian patients with rare diseases. This study included only symptomatic patients who had undergone molecular investigation with exome sequencing for suspected diseases of genetic etiology. Variants clinically suspected as the causative etiology and harbored by genes associated with highly-penetrant conditions of autosomal dominant inheritance underwent Sanger confirmation in the proband and inheritance pattern determination because a "de novo" event was expected. Among all 327 variants studied, 321 variants were inherited from asymptomatic parents. Considering segregation analysis, we have reclassified 51 rare variants as benign and 211 as likely benign. In our study, the inheritance of a highly penetrant variant expected to be de novo for pathogenicity assumption was considered as a non-segregation and, therefore, a key step for benign or likely benign classification. Studies like ours may help to identify rare benign variants and improve the correct interpretation of genetic findings.

PMID:35546177 | PMC:PMC9095660 | DOI:10.1038/s41598-022-11932-z

Categories: Literature Watch

Patients With Infantile Nephropathic Cystinosis in Germany and Austria: A Retrospective Cohort Study

Fri, 2022-05-13 06:00

Front Med (Lausanne). 2022 Apr 25;9:864554. doi: 10.3389/fmed.2022.864554. eCollection 2022.

ABSTRACT

BACKGROUND: Infantile nephropathic cystinosis (INC) is a rare lysosomal storage disorder resulting in progressive chronic kidney disease (CKD) and a variety of extrarenal manifestations. This orphan disease remains a challenge for patients, their families and health care providers. There is currently no comprehensive study on patients' clinical course in Germany and Austria.

METHODS: A retrospective cohort study including 74 patients at eleven centers of care was conducted. Data on time of diagnosis, CKD stage, leukocyte cystine levels (LCL), extrarenal manifestations, and treatment was collected from medical charts and subsequently analyzed using explorative statistics. Age at initiation of kidney replacement therapy (KRT) was evaluated by Kaplan-Meier analyses for different groups of patients.

RESULTS: Patients were diagnosed at a median age of 15 months (IQR: 10-29, range: 0-110), more recent year of birth was not associated with earlier diagnosis. Oral cystine-depleting therapy (i.e., cysteamine) was prescribed at a median dose of 1.26 g/m2 per day (IQR: 1.03-1.48, range: 0.22-1.99). 69.2% of all 198 LCL measurements of 67 patients were within the desired target range (≤ 1 nmol cystine/mg protein). Median time-averaged LCLs per patient (n = 65) amounted to 0.57 nmol cystine/mg protein (IQR: 0.33-0.98, range: 0.07-3.13) when considering only values at least 1 year after initiation of therapy. The overall median height of 242 measurements of 68 patients was at the 7th percentile (IQR: 1-25, range: 1-99). 40.5% of the values were ≤ the 3rd percentile. Patient sex and year of birth were not associated with age at initiation of KRT, but patients diagnosed before the age of 18 months required KRT significantly later than those patients diagnosed at the age of ≥ 18 months (p = 0.033): median renal survival was 21 years (95% CI: 16, -) vs. 13 years (95% CI, 10, -), respectively.

CONCLUSION: Early diagnosis and initiation of cystine depleting therapy is important for renal survival in children with INC. Cysteamine doses and LCL showed that treatment in this cohort met international standards although there is great interindividual variety. Patient growth and other aspects of the disease should be managed more effectively in the future.

PMID:35547226 | PMC:PMC9082678 | DOI:10.3389/fmed.2022.864554

Categories: Literature Watch

A year in pharmacology: new drugs approved by the US Food and Drug Administration in 2021

Wed, 2022-05-11 06:00

Naunyn Schmiedebergs Arch Pharmacol. 2022 May 11. doi: 10.1007/s00210-022-02250-2. Online ahead of print.

ABSTRACT

The second year of the COVID-19 pandemic had no adverse effect on the number of new drug approvals by the US Food and Drug Administration (FDA). Quite the contrary, with a total of 50 new drugs, 2021 belongs to the most successful FDA years. We assign these new drugs to one of three levels of innovation: (1) first drug against a condition ("first-in-indication"), (2) first drug using a novel molecular mechanism ("first-in-class"), and (3) "next-in-class", i.e., a drug using an already exploited molecular mechanism. We identify 21 first-in-class, 28 next-in-class, and only one first-in-indication drugs. By treatment area, the largest group is once again cancer drugs, many of which target specific genetic alterations. Every second drug approved in 2021 targets an orphan disease, half of them being cancers. Small molecules continue to dominate new drug approvals, followed by antibodies and non-antibody biopharmaceuticals. In 2021, the FDA continued to approve drugs without strong evidence of clinical effects, best exemplified by the aducanumab controversy.

PMID:35543739 | DOI:10.1007/s00210-022-02250-2

Categories: Literature Watch

Seven years since the launch of the Matchmaker Exchange: The evolution of genomic matchmaking

Tue, 2022-05-10 06:00

Hum Mutat. 2022 Jun;43(6):659-667. doi: 10.1002/humu.24373. Epub 2022 May 10.

ABSTRACT

The Matchmaker Exchange (MME) was launched in 2015 to provide a robust mechanism to discover novel disease-gene relationships. It operates as a federated network connecting databases holding relevant data using a common application programming interface, where two or more users are looking for a match for the same gene (two-sided matchmaking). Seven years from its launch, it is clear that the MME is making outstanding contributions to understanding the morbid anatomy of the genome. The number of unique genes present across the MME has steadily increased over time; there are currently >13,520 unique genes (~68% of all protein-coding genes) connected across the MME's eight genomic matchmaking nodes, GeneMatcher, DECIPHER, PhenomeCentral, MyGene2, seqr, Initiative on Rare and Undiagnosed Disease, PatientMatcher, and the RD-Connect Genome-Phenome Analysis Platform. The collective data set accessible across the MME currently includes more than 120,000 cases from over 12,000 contributors in 98 countries. The discovery of potential new disease-gene relationships is happening daily and international collaborative teams are moving these advances forward to publication, now numbering well over 500. Expansion of data sharing into routine clinical practice by clinicians, genetic counselors, and clinical laboratories has ensured access to discovery for even more individuals with undiagnosed rare genetic diseases. Tens of thousands of patients and their family members have been directly or indirectly impacted by the discoveries facilitated by two-sided genomic matchmaking. MME supports further connections to the literature (PubCaseFinder) and to human and model organism resources (Monarch Initiative) and scientists (ModelMatcher). Efforts are now underway to explore additional approaches to matchmaking at the gene or variant level where there is only one querier (one-sided matchmaking). Genomic matchmaking has proven its utility over the past 7 years and will continue to facilitate discoveries in the years to come.

PMID:35537081 | DOI:10.1002/humu.24373

Categories: Literature Watch

Rescue of behavioral and electrophysiological phenotypes in a Pitt-Hopkins syndrome mouse model by genetic restoration of <em>Tcf4</em> expression

Tue, 2022-05-10 06:00

Elife. 2022 May 10;11:e72290. doi: 10.7554/eLife.72290. Online ahead of print.

ABSTRACT

Pitt-Hopkins syndrome (PTHS) is a neurodevelopmental disorder caused by monoallelic mutation or deletion in the transcription factor 4 (TCF4) gene. Individuals with PTHS typically present in the first year of life with developmental delay and exhibit intellectual disability, lack of speech, and motor incoordination. There are no effective treatments available for PTHS, but the root cause of the disorder, TCF4 haploinsufficiency, suggests that it could be treated by normalizing TCF4 gene expression. Here we performed proof-of-concept viral gene therapy experiments using a conditional Tcf4 mouse model of PTHS and found that postnatally reinstating Tcf4 expression in neurons improved anxiety-like behavior, activity levels, innate behaviors, and memory. Postnatal reinstatement also partially corrected EEG abnormalities, which we characterized here for the first time, and the expression of key TCF4-regulated genes. Our results support a genetic normalization approach as a treatment strategy for PTHS, and possibly other TCF4-linked disorders.

PMID:35535852 | DOI:10.7554/eLife.72290

Categories: Literature Watch

Massively parallel identification of functionally consequential noncoding genetic variants in undiagnosed rare disease patients

Mon, 2022-05-09 06:00

Sci Rep. 2022 May 9;12(1):7576. doi: 10.1038/s41598-022-11589-8.

ABSTRACT

Clinical whole genome sequencing has enabled the discovery of potentially pathogenic noncoding variants in the genomes of rare disease patients with a prior history of negative genetic testing. However, interpreting the functional consequences of noncoding variants and distinguishing those that contribute to disease etiology remains a challenge. Here we address this challenge by experimentally profiling the functional consequences of rare noncoding variants detected in a cohort of undiagnosed rare disease patients at scale using a massively parallel reporter assay. We demonstrate that this approach successfully identifies rare noncoding variants that alter the regulatory capacity of genomic sequences. In addition, we describe an integrative analysis that utilizes genomic features alongside patient clinical data to further prioritize candidate variants with an increased likelihood of pathogenicity. This work represents an important step towards establishing a framework for the functional interpretation of clinically detected noncoding variants.

PMID:35534523 | DOI:10.1038/s41598-022-11589-8

Categories: Literature Watch

Application of Bayesian methods to accelerate rare disease drug development: scopes and hurdles

Sat, 2022-05-07 06:00

Orphanet J Rare Dis. 2022 May 7;17(1):186. doi: 10.1186/s13023-022-02342-5.

ABSTRACT

BACKGROUND: Design and analysis of clinical trials for rare and ultra-rare disease pose unique challenges to the practitioners. Meeting conventional power requirements is infeasible for diseases where sample sizes are inherently very small. Moreover, rare disease populations are generally heterogeneous and widely dispersed, which complicates study enrollment and design. Leveraging all available information in rare and ultra-rare disease trials can improve both drug development and informed decision-making processes.

MAIN TEXT: Bayesian statistics provides a formal framework for combining all relevant information at all stages of the clinical trial, including trial design, execution, and analysis. This manuscript provides an overview of different Bayesian methods applicable to clinical trials in rare disease. We present real or hypothetical case studies that address the key needs of rare disease drug development highlighting several specific Bayesian examples of clinical trials. Advantages and hurdles of these approaches are discussed in detail. In addition, we emphasize the practical and regulatory aspects in the context of real-life applications.

CONCLUSION: The use of innovative trial designs such as master protocols and complex adaptive designs in conjunction with a Bayesian approach may help to reduce sample size, select the correct treatment and population, and accurately and reliably assess the treatment effect in the rare disease setting.

PMID:35526036 | PMC:PMC9077995 | DOI:10.1186/s13023-022-02342-5

Categories: Literature Watch

Recommendations from the IRDiRC Working Group on methodologies to assess the impact of diagnoses and therapies on rare disease patients

Sat, 2022-05-07 06:00

Orphanet J Rare Dis. 2022 May 7;17(1):181. doi: 10.1186/s13023-022-02337-2.

ABSTRACT

Rare disease patients face many challenges including diagnostic delay, misdiagnosis and lack of therapies. However, early access to diagnosis and therapies can modify the management and the progression of diseases, which in return positively impacts patients, families and health care systems. The International Rare Diseases Research Consortium set up the multi-stakeholder Working Group on developing methodologies to assess the impact of diagnoses and therapies on rare disease patients. Using the patients' journey on the diagnostic paradigm, the Working Group characterized a set of metrics, tools and needs required for appropriate data collection and establishment of a framework of methodologies to analyze the socio-economic burden of rare diseases on patients, families and health care systems. These recommendations are intended to facilitate the development of methodologies and to better assess the societal impact of rare diseases.

PMID:35526001 | PMC:PMC9078009 | DOI:10.1186/s13023-022-02337-2

Categories: Literature Watch

Big picture initiatives in bleeding disorders

Fri, 2022-05-06 06:00

Haemophilia. 2022 May;28 Suppl 4:53-60. doi: 10.1111/hae.14532.

ABSTRACT

INTRODUCTION: The inherited bleeding disorders (IBD) community has witnessed significant therapeutic advances recently, yet important gaps persist, particularly for those with rare disorders and historically underserved populations.

AIMS: -To create a national research blueprint agenda, led by the National Hemophilia Foundation (NHF), enhancing patient-centric principles, accelerate research progress and address important gaps in care. -To review critical gaps that remain to be addressed in women with IBDs, who face specific bleeding challenges.

METHODS: The NHF research blueprint research agenda was defined by input from across the community, including caregivers and patients who are considered subject matter experts of their IBD, research leaders, allied health professionals and specialists, and representatives of the biopharmaceutical industry. In addition, two medical experts in the field of IBDs performed a comprehensive review to address the knowledge gaps in women with IBDs.

RESULTS: Two foundational principles of the NHF blueprint are: (1) it must deliver on key issues that significantly impact the lives of those affected by IBDs, and (2) the priorities defined are relevant and actionable aimed to achieve health equity among all those affected by IBDs. A multidisciplinary approach is necessary for an optimal management of puberty, transition to adulthood and pregnancy. Even if strict guidelines are followed, recent studies show that women with IBDs are still facing a high burden.

CONCLUSION: NHF blueprint will be issued in 2022. A specific research agenda is needed in women with IBDs to further improve their management and quality of life.

PMID:35521733 | DOI:10.1111/hae.14532

Categories: Literature Watch

Diagnosis of rare bleeding disorders

Fri, 2022-05-06 06:00

Haemophilia. 2022 May;28 Suppl 4:119-124. doi: 10.1111/hae.14561.

ABSTRACT

Rare bleeding disorders result in significant morbidity but are globally underdiagnosed. Advances in genomic testing and specialist laboratory assays have greatly increased the diagnostic armamentarium. This has resulted in the discovery of new genetic causes for rare diseases and a better understanding of the underlying molecular pathology.

PMID:35521730 | DOI:10.1111/hae.14561

Categories: Literature Watch

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