Predicting the pathogenicity of missense variants based on protein instability to support diagnosis of patients with novel variants of ARSL

Rare diseases are estimated to affect 3.5%-5.9% of the population worldwide and are difficult to diagnose. Genome analysis is useful for diagnosis. However, since some variants, especially missense variants, are also difficult to interpret, tools to accurately predict the effect of missense variants are very important and needed. Here we developed a method, "VarMeter", to predict whether a missense variant is damaging based on Gibbs free energy and solvent-accessible surface area calculated from the AlphaFold 3D protein model. We applied this method to the whole-exome sequencing data of 900 individuals with rare or undiagnosed disease in our in-house database, and identified four who were hemizygous for missense variants of arylsulfatase L (ARSL; known as the genetic cause of chondrodysplasia punctata 1, CPDX1). Two individuals had a novel Ser89 to Asn (Ser89Asn) or Arg469 to Trp (Arg469Trp) substitution, respectively predicted as "damaging" or "benign"; the other two had an Arg111 to His (Arg111His) or Gly117 to Arg (Gly117Arg) substitution, respectively predicted as "damaging" or "possibly damaging" and previously reported in patients showing clinical manifestations of CDPX1. Expression and analysis of the missense variant proteins showed that the predicted pathogenic variants (Ser89Asn, Arg111His, and Gly117Arg) had complete loss of sulfatase activity and reduced protease resistance due to destabilization of protein structure, while the predicted benign variant (Arg469Trp) had activity and protease resistance comparable to those of wild-type ARSL. The individual with the novel pathogenic Ser89Asn variant exhibited characteristics of CDPX1, while the individual with the benign Arg469Trp variant exhibited no such characteristics. These findings demonstrate that VarMeter may be used to predict the deleteriousness of variants found in genome sequencing data and thereby support disease diagnosis.

Planning anesthesia of a child with a rare disease: useful tools

Up to 8,000 rare diseases are currently described in the scientific literature. The presence of a rare disease constitutes an additional challenge for the practitioner given its implications on the management of anesthesia. Moreover, it is not possible for an anesthesiologist to know them all especially as the sources of information are scattered. This narrative review aims at proposing pre-anesthetic evaluation clear tools to summarize the individual aspects of a known or suspected rare disease in a patient and to define an adapted anesthetic strategy. It also describes a decision-making process, called « the rare disease reflex », to guide the practitioner to quickly initiate diagnostic investigations in the presence of unusual perioperative clinical signs suggestive of an undiagnosed rare disease.

Identification of barriers at the primary care provider level to improve inflammatory breast cancer diagnosis and management

The purpose of this study, based in the United States, was to evaluate knowledge gaps and barriers related to diagnosis and care of inflammatory breast cancer (IBC), a rare but lethal breast cancer subtype, amongst Primary Care Providers (PCP) as they are often the first point of contact when patients notice initial symptoms. PCP participants in the Duke University Health System, federally qualified health center, corporate employee health and community practices, nearby academic medical center, Duke physician assistant and advanced practice nurse leadership program alumni were first selected in a convenience sample and for semi-structured interviews (n = 11). Based on these data, an online survey tool was developed and disseminated (n = 78) to assess salient measures of IBC diagnosis, health disparity factors, referral and care coordination practices, COVID-19 impact, and continuing medical education (CME). PCP reported access to care and knowledge gaps in symptom recognition (mean = 3.3, range 1-7) as major barriers. Only 31 % reported ever suspecting IBC in a patient. PCP (n = 49) responded being challenged with referral delays in diagnostic imaging. Additionally, since the COVID-19 pandemic started, 63 % reported breast cancer referral delays, and 33 % reported diagnosing less breast cancer. PCP stated interest in CME in their practice for improved diagnosis and patient care, which included online (53 %), lunch time or other in-service training (33 %), patient and provider-facing websites (32 %). Challenges communicating rare cancer information, gaps in confidence in diagnosing IBC, and timely follow-up with patients and specialists underscores the need for developing PCP educational modules to improve guideline-concordant care.

Identification of novel homozygous nonsense SLC10A7 variant causing short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis and surgical management of spine

BACKGROUND

Short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis is a rare, autosomal recessive, skeletal disorder first described in 2018. This syndrome starts with pre- and postnatal developmental delay, and gradually presents with variable facial dysmorphisms, a short stature, amelogenesis imperfecta, and progressive skeletal dysplasia affecting the limbs, joints, hands, feet, and spine.

CASE PRESENTATION

We identified a homozygous novel nonsense mutation in exon 1 of SLC10A7 (NM_001300842.2: c.100G > T / p.Gly34*) segregating with the typical disease phenotype in a Han Chinese family. We reviewed the 12-year surgical treatment history with seven interventions on spine.

CONCLUSION

To date, only 12 cases of the SLC10A7 mutation have been reported, mainly from consanguineous families. Our patient showed a relatively severe and broad clinical phenotype compared with previously reported cases. In this patient, annual check-ups and timely surgeries led to a good outcome.

Qualified placebo for trials of herbal medicine treatment in rare diseases? A cross-sectional analysis

BACKGROUND

While substantial placebos have been used in herbal medicine (HM) clinical trials for rare diseases, the use and quality of reporting of HM-placebo remain unclear. We aim to describe the use of HM-placebo in clinical trials for rare diseases and determine the quality of reporting in these trials.

METHODS

This is a cross-sectional study. We searched PubMed, Embase, Web of Science, SinoMed, China National Knowledge Infrastructure, WanFang database, China Science and Technology Journal Database, National Institute of Informatics Support Academic Information Services, ClinicalTrials.gov and Chinese Clinical Trials Registry from their inception date to 14 February 2023 to identify registered and published trials that use placebos as a comparator in rare diseases. We collected data on placebo use reporting and the efficacy and safety of placebo. Descriptive statistics, the Chi-square test, and Binary multivariable logistic regression analysis were used to determine the placebo characteristics of the HM trial and its effect on reporting.

RESULTS

Among the 55 studies, we included that with a median administration time of placebo of 84 days (IQR 42-180) and a median placebo sample size of 30 (IQR 24-54). About half of the trials (27, 49.1%) did not provide their ethical approvals, and one trial had details of informed consent. None of the studies were fully reported and more than half of the items reported less than 50%. A total of 10 trials (18.2%) of placebo has active ingredients even though none of them performed pharmacological inert tests. Of the 29 studies with available data on adverse events, 5 (17.2%) trials did not show a better safety profile in the placebo group. Under the context that a relatively high-quality report is defined as a report with more than 9 items, there was a statistically significant difference between the two groups in the rate of relatively high-quality reports of the administration time (p = 0.047, OR 0.10, 95% CI 0.01 to 0.90), but the results are not representative.

CONCLUSION

The overall situation of HM-placebo in the field of rare diseases was poor. In particular, the placebo is tied to the quality of trials, and poor placebo hinders the generation of high-quality evidence for herbal clinical trials in the field of rare diseases. We summarize the current methods of assessment involved in the use of placebos and propose various considerations for placebos in different contexts. Our study can greatly promote rare disease researchers to review the quality of their placebo and clinical trials. It is imperative to guarantee that meticulously conducted research generates clinical evidence of the highest caliber. We also expect that in the future, more rigorous relevant standards about the reporting and design of HM-placebo will be developed. High-quality clinical trials are the prerequisite for the wide clinical application of herbal medicines for rare diseases.

Efficacy and safety of compassionate use for rare diseases: a scoping review from 1991 to 2022

BACKGROUND

Compassionate use is a system that provides patients with expedited access to drugs which has not yet been approved, but currently in clinical trials. The investigational drugs have been authorized for compassionate use in cases involving patients suffered from life-threatening diseases and with no alternative treatments. For instance, patients afflicted with highly heterogeneous rare diseases are eligible for treatment assistance through the compassionate use program. This study aims to investigate the characteristics of compassionate use in the context of rare diseases, evaluate the efficacy and safety of compassionate use for rare diseases, and analyze the marketing approval of investigational drugs.

METHODS

The case reports/case series of compassionate use were collected by conducting searches on Embase, PubMed, Web of Science, CNKI and SinoMed, spanning from January 1991 to December 2022. Subsequently, two independent reviewers evaluated these reports. Case reports/case series that met the inclusion criteria and exclusion criteria were enrolled. Information extracted from these reports and series included patients' basic information, the investigational drug's name, its indication, adverse events, treatment outcomes, and other relevant data.

RESULTS

A total of forty-six studies were included, encompassing 2079 patients with an average age of 38.1 years. Thirty-nine different drugs were involved in 46 studies. Furthermore, neoplasms emerged as the most common therapeutic area for compassionate use in rare disease management (23/46, 50.0%). Regarding the treatment efficacy, four studies reported successful disease resolution, while 35 studies observed symptom improvement among patients. Conversely, four studies documented no significant effects on patients' diseases. Moreover, one study reported worsened results following compassionate use, while the efficacy was not described in 2 studies. Adverse events were reported in 31 studies (67.4%) because of the compassionate use, while no adverse events occurred in 13 studies (28.3%). In other 2 studies, there was no description about whether treatment-emergent adverse events (TEAEs) were happened. 136 patients (6.5%) had Grade 5 adverse events (death), of which 19 deaths (0.9%) were considered to be related to compassionate use. Furthermore, the investigational drugs in 33 studies (33/46, 71.7%) received new drug approval at the end of January 31, 2023.The time lag from the start of the compassionate use to the formal approval of the investigational drug was 790.5 (IQR 359-2199.3) days. We found that in 11 studies, encompassing 9 different drugs, some compassionate use indications had not received regulatory authorities at the end of January 31, 2023.

CONCLUSION

The current status of compassionate use for rare diseases was clarified systematically in this study. Compassionate use of investigational drug is a significant treatment option for rare disease. In general, compassionate use appears to demonstrate favorable efficacy in the context of rare diseases, with a significant proportion of compassionate use drugs subsequently receiving marketing approval. However, the safety of drugs for compassionate use cannot be fully evaluated due to the safety data were not covered in some enrolled studies. Therefore, the establishment of an adverse event reporting system specific to compassionate use is warranted.

Inflammatory breast cancer (IBC) advocacy-Past, present and future!

Patient advocates, referring to those individuals that have been diagnosed with the disease for which they advocate, are essential stake holders in healthcare. For those facing the stages of being diagnosed with Inflammatory Breast Cancer (IBC), the "call to advocate" is an immediate response to being diagnosed with a rare and aggressive disease that progresses rapidly, often in a matter of weeks or months. There is a great stigma and bias in the medical community that has inhibited the education and study of IBC. A lack of understanding of the disease, how it presents and how to treat it leaves many IBC patients facing misdiagnosis. Communication is a cornerstone of healthcare; this goes beyond the patient-provider dynamic. Education of IBC must be a grassroots initiative. There should be no barrier to care in the diagnosis, treatment, study and survivorship of inflammatory Breast Cancer. It is not just an oncologist's lesson to learn, but that of all providers in healthcare. In this chapter you will hear how 4 women who were diagnosed with IBC faced the difficult tasks of navigating through the healthcare system on their own and came out on the other side using their experience to help others. In conclusion, in defining the evolving roles of Patient Advocacy in IBC over the past 25 years, we examine what has been done, along with its challenges, and what work still remains from the perspectives of different patient advocates.

Study methodology and insights from the palovarotene clinical development program in fibrodysplasia ossificans progressiva

BACKGROUND

The design of clinical trials in rare diseases is often complicated by a lack of real-world translational knowledge. Fibrodysplasia ossificans progressiva (FOP) is an ultra-rare genetic disorder characterized by skeletal malformations and progressive heterotopic ossification (HO). Palovarotene is a selective retinoic acid receptor gamma agonist. Here, we describe the methodology of three studies in the palovarotene clinical development program in FOP and discuss insights that could inform future research, including endpoint suitability and the impact of trial design.

METHODS

PVO-1A-001 (NCT02322255) was a prospective, protocol-specified, longitudinal FOP natural history study (NHS). PVO-1A-201 (NCT02190747) was a randomized, double-blind, placebo-controlled phase II trial; PVO-1A-202 (NCT02279095) was its open-label extension. Trial designs, including treatment regimens and imaging assessments, were refined between PVO-1A-201 and PVO-‍1A-202, and within PVO-1A-202, based on emerging data as the studies progressed. Palovarotene doses were administered using a flare-up treatment regimen (higher dose for 2/4 weeks, followed by lower dose for 4/≥8 weeks; from flare-up onset), with or without accompanying chronic (daily) treatment. Flare-up and disease progression outcomes were assessed, including incidence and volume of new HO during flare-ups and/or annually, as well as other clinical, patient-reported, and exploratory outcomes. Safety was monitored throughout all studies.

RESULTS

Overall, 114 and 58 individuals with FOP were enrolled in the NHS and phase II trials, respectively. Results of the NHS and PVO-1A-201 were published in 2022; complete results of PVO-1A-202 will be publicly available in due course. Together the studies yielded important information on endpoint suitability, including that low-dose whole-body computed tomography was the optimum imaging modality for assessing HO progression annually and that long study durations are needed to detect substantial changes in functional and patient-reported outcomes.

CONCLUSIONS

A flexible clinical development program is necessary for underexplored rare diseases to overcome the many challenges faced. Here, the NHS provided a longitudinal evaluation of FOP progression and interventional trials were based on emerging data. The studies described informed the design and endpoints implemented in the phase III MOVE trial (NCT03312634) and provide a foundation for future clinical trial development.

TRIAL REGISTRATION

NCT02322255 (registered 23/12/2014); NCT02190747 (registered 15/07/2014); NCT02279095 (registered 30/10/2014).

A single-center observational study on long-term neurodevelopmental outcomes in children with tuberous sclerosis complex

BACKGROUND

Tuberous sclerosis complex (TSC) is a rare multisystem disorder caused by mutations in the TSC1 or TSC2 gene. More than 90% of patients with TSC develop neurological and/or neuropsychiatric manifestations. The aim of the present study was to determine the developmental and cognitive long-term outcomes of pediatric TSC patients.

METHODS

This cross-sectional, monocenter study included pediatric TSC patients who received multidisciplinary long-term care with a last visit between 2005 and 2019. Neurological manifestations and cognitive development (BSID, K-ABC) were analyzed in relation to age and type of mutation.

RESULTS

Thirty-five patients aged 13.5 ± 7.8 years were included in the study. Diagnosis was confirmed genetically in 65.7% of patients (TSC1, 26.1%; TSC2, 65.2%; NMI, 8.7%). Mean age at diagnosis was 1.3 ± 3.5 years; 74.3% of the patients had been diagnosed within the first year of life due to seizures (62.9%) or/and cardiac rhabdomyomas (28.6%). The most common TSC manifestations included structural brain lesions (cortical tubers, 91.4%; subependymal nodules, 82.9%), epilepsy (85.7%), and cardiac rhabdomyomas (62.9%). Mean age at seizure onset was 1.5 ± 2.3 years, with onset in 80.0% of patients within the first two years of life. Infantile spasms, which were the first seizure type in 23.3% of the patients, developed earlier (0.6 ± 0.4 years) than focal seizures (1.8 ± 2.5 years). Refractory epilepsy was present in 21 (70.0%) patients, mild or severe intellectual impairment in 66.6%, and autism spectrum disorders in 11.4%. Severe cognitive impairment (33.3%) was significantly associated with epilepsy type and age at seizure onset (p < 0.05).

CONCLUSIONS

The results emphasized the phenotypic variability of pediatric-onset TSC and the high rate of neurological and neuropsychiatric morbidity. Early-onset refractory epilepsy was associated with impaired cognitive development. Children of all ages with TSC require multidisciplinary long-term care and individual early-intervention programs.

Expanding access to high-cost medicines under the Universal Health Coverage scheme in Thailand: review of current practices and recommendations

BACKGROUND

There has been an increasing demand to reimburse high-cost medicines, through public health insurance schemes in Thailand.

METHODS

A mixed method approach was employed. First, a rapid review of select high-income countries was conducted, followed by expert consultations and an in-depth review of three countries: Australia, England and Republic of Korea to understand reimbursement mechanisms of high-cost medicines. In Thailand, current pathways for reimbursing high-cost medicines reviewed, the potential opportunity cost estimated, and stakeholder consultations were conducted to identify context specific considerations.

RESULTS

High-income countries reviewed have implemented a variety of pathways and mechanisms for reimbursing high-cost medicines under specific eligibility criteria, listing processes, varying cost-effectiveness thresholds and special funding arrangements. In Thailand, high-cost medicines that do not offer good value-for-money are excluded from the reimbursement process. A framework for reimbursing high-cost medicines that are not cost-effective at the current willingness-to-pay threshold was proposed for Thailand. Under this framework, specific criteria are proposed to determine their eligibility for reimbursement such life-saving nature, treatment of conditions with no alternative treatment options, and affordability.

CONCLUSION

High-cost medicines may become eligible for reimbursement through alternative mechanisms based on specific criteria which depend on each context. The application of HTA methods and processes is important in guiding these decisions to support sustainable access to affordable healthcare in pursuit of Universal Health Coverage (UHC).

Comment reconnaître et distinguer les anomalies de structure dentaire ?

Introduction

The precise diagnosis of dental structural anomalies is an essential step preceding our restorative and orthodontic therapies. Indeed, first of all, it is necessary to identify the type of structural anomaly and to determine if it is an isolated or a syndromic form: the dental anomaly could be included in a more complex clinical picture combining other clinical signs. Moreover, the establishment of the diagnosis will allow the practitioner to adapt his clinical protocol according to the observed dental structure anomaly. The choice of the bonding material, the type of preparation (no prep, prep less, complete eviction), and the application of a deproteinization protocol with sodium hypochlorite depend to the structural defect.

Material and Method

The diagnosis of dental structural anomalies is based on several key points described in this article in order to facilitate the practitioner's diagnostic approach.

Conclusion

The diagnosis of amelogenesis or dentinogenesis imperfecta should justify the search for other signs to determine whether the anomaly of tooth structure is isolated or syndromic.

Neurovascular unit disruption and blood-brain barrier leakage in MCT8 deficiency

BACKGROUND

The monocarboxylate transporter 8 (MCT8) plays a vital role in maintaining brain thyroid hormone homeostasis. This transmembrane transporter is expressed at the brain barriers, as the blood-brain barrier (BBB), and in neural cells, being the sole known thyroid hormone-specific transporter to date. Inactivating mutations in the MCT8 gene (SLC16A2) cause the Allan-Herndon-Dudley Syndrome (AHDS) or MCT8 deficiency, a rare X-linked disease characterized by delayed neurodevelopment and severe psychomotor disorders. The underlying pathophysiological mechanisms of AHDS remain unclear, and no effective treatments are available for the neurological symptoms of the disease.

METHODS

Neurovascular unit ultrastructure was studied by means of transmission electron microscopy. BBB permeability and integrity were evaluated by immunohistochemistry, non-permeable dye infiltration assays and histological staining techniques. Brain blood-vessel density was evaluated by immunofluorescence and magnetic resonance angiography. Finally, angiogenic-related factors expression was evaluated by qRT-PCR. The studies were carried out both in an MCT8 deficient subject and Mct8/Dio2KO mice, an AHDS murine model, and their respective controls.

RESULTS

Ultrastructural analysis of the BBB of Mct8/Dio2KO mice revealed significant alterations in neurovascular unit integrity and increased transcytotic flux. We also found functional alterations in the BBB permeability, as shown by an increased presence of peripheral IgG, Sodium Fluorescein and Evans Blue, along with increased brain microhemorrhages. We also observed alterations in the angiogenic process, with reduced blood vessel density in adult mice brain and altered expression of angiogenesis-related factors during brain development. Similarly, AHDS human brain samples showed increased BBB permeability to IgG and decreased blood vessel density.

CONCLUSIONS

These findings identify for the first time neurovascular alterations in the MCT8-deficient brain, including a disruption of the integrity of the BBB and alterations in the neurovascular unit ultrastructure as a new pathophysiological mechanism for AHDS. These results open a new field for potential therapeutic targets for the neurological symptoms of these patients and unveils magnetic resonance angiography as a new non-invasive in vivo technique for evaluating the progression of the disease.

Analysis on the Marketing Trend and Approval Lag of Imported Orphan Drugs from 2010 to 2021 in China

BACKGROUND

In order to meet the unmet needs of rare disease patients in China, importing orphan drugs is an important way. The objectives of this study were to investigate the marketing trend of orphan drugs approved by the US Food and Drug Administration (FDA) and imported by China, to examine the orphan drug lag between China and the United States.

METHODS

This study analyzes the orphan drugs approved by FDA and imported by China from January 2010 to December 2021. The approval lag for orphan drugs between China and the US was calculated and analyzed by approval time. Factors potentially affecting the approval lag, such as target disease, ATC classification, formulation, corporation name, drug type, and whether the indications belong to the first batch of rare diseases catalogue were investigated.

RESULTS

The number of FDA-approved orphan drugs imported by China is increasing year by year, and the approval lag of these drugs is gradually decreasing, especially in the classification of Non-L, Injections, Non-United States, and biological product. Compared with 2010-2015, the approval lag of total drugs in the study was significantly improved in 2016-2021 (1977 days) compared with 2010-2015 (3928 days).

CONCLUSION

China's groundbreaking regulatory reforms of drugs since 2015 had made significant progress in reducing orphan drug lags, but there is still considerable room for progress. We should more actively promote the approval of rare disease drugs in China, establish a better approval mechanism, and enable Chinese patients with rare diseases to receive drug treatment in a timely manner.

[Recommendations for the healthcare of patients with FOP]

BACKGROUND

Fibrodysplasia ossificans progressiva (FOP) is a very rare, severe genetic disorder triggered by a gain-of-function mutation in the ACVR1 gene that codes for the type I bone morphogenetic protein (BMP) receptor ACVR1 (activin A receptor-type 1), also known as ALK2 (activin receptor-like kinase-2). It leads to the onset and progression of heterotopic ossification (HO) in soft and connective tissue. HO is often preceded by episodes of soft tissue swelling or flare-ups. Flare-ups, characteristic of FOP, may be induced by trauma, infection, vaccination, or other medications, as well as surgical procedures or may occur spontaneously. As patients age, they develop severe mobility limitations due to progressive HO formation, including immobility, causing a shortened life expectancy. FOP's first characteristic clinical sign is the congenital malformation of one or both big toes with valgus axis deviation, which is present in almost all patients. To confirm the diagnosis, molecular genetic analysis of the ACVR1 gene is possible.

AIM OF THE RECOMMENDATIONS

This white paper aims to provide an overview of the necessary prerequisites and conditions for the care of patients with FOP and positively contribute to patients with FOP by improving the overall availability of knowledge. To achieve this, relevant aspects of the care of the very rare disease FOP are presented, from the initial diagnosis to the care in regular care based on the authors' knowledge (German FOP network) and the international FOP Treatment Guidelines. The recommendations presented here are addressed to all actors and decision-makers in the health care system and are also intended to inform patients and the public.

Exome and genome sequencing for rare genetic disease diagnosis: A scoping review and critical appraisal of clinical guidance documents produced by genetics professional organizations

PURPOSE

Exome and genome sequencing have rapidly transitioned from research methods to widely used clinical tests for diagnosing rare genetic diseases. We sought to synthesize the topics covered and appraise the development processes of clinical guidance documents generated by genetics professional organizations.

METHODS

We conducted a scoping review of guidance documents published since 2010, systematically identified in peer-reviewed and gray literature, using established methods and reporting guidelines. We coded verbatim recommendations by topic using content analysis and critically appraised documents using the Appraisal of Guidelines Research and Evaluation (AGREE) II tool.

RESULTS

We identified 30 guidance documents produced by 8 organizations (2012-2022), yielding 611 recommendations covering 21 topics. The most common topic related to findings beyond the primary testing indication. Mean AGREE II scores were low across all 6 quality domains; scores for items related to rigor of development were among the lowest. More recently published documents generally received higher scores.

CONCLUSION

Guidance documents included a broad range of recommendations but were of low quality, particularly in their rigor of development. Developers should consider using tools such as AGREE II and basing recommendations on living knowledge syntheses to improve guidance development in this evolving space.

Risks and benefits of anesthesia for combined pediatric procedures in the NIH undiagnosed diseases program

PURPOSE

The NIH Undiagnosed Diseases Program (UDP) aims to provide diagnoses to patients who have previously received exhaustive evaluations yet remain undiagnosed. Patients undergo procedural anesthesia for deep phenotyping for analysis with genomic testing.

METHODS

A retrospective chart review was performed to determine the safety and benefit of procedural anesthesia in pediatric patients in the UDP. Adverse perioperative events were classified as anesthesia-related complications or peri-procedural complications. The contribution of procedures performed under anesthesia to arriving at a diagnosis was also determined.

RESULTS

From 2008 to 2020, 249 pediatric patients in the UDP underwent anesthesia for diagnostic procedures. The majority had a severe systemic disease (American Society for Anesthesiology status III, 79%) and/or a neurologic condition (91%). Perioperative events occurred in 45 patients; six of these were attributed to anesthesia. All patients recovered fully without sequelae. Nearly half of the 249 patients (49%) received a diagnosis, and almost all these diagnoses (88%) took advantage of information gleaned from procedures performed under anesthesia.

CONCLUSIONS

The benefits of anesthesia involving multiple diagnostic procedures in a well-coordinated, multidisciplinary, research setting, such as in the pediatric UDP, outweigh the risks.

Strategy for Generating Blinded Evidence for Single-Arm Trials with External Controls Using Expert Review of Home Video

INTRODUCTION

Neurodegenerative diseases cause developmental delays and loss of milestones in infants and children. However, scalable outcome measures that quantify features meaningful to parents/caregivers (P/CGs) and have regulatory precedence are lacking for assessing the effectiveness of treatments in clinical trials of neurodegenerative disorders. To address this gap, we developed an innovative, blinded strategy for single-arm trials with external controls using expert panel review of home video.

METHOD

We identified meaningful, observable, and objective developmental milestones from iterative interviews with P/CGs and clinical experts. Subsequently, we standardized video recording procedures and instructions to ensure consistency in how P/CGs solicited each activity. In practice, videos would be graded by an expert panel blinded to treatment. To ensure blinding and quality control, video recordings from interim time points would be randomly interspersed. We conducted a pilot study and a pretest of grading to test feasibility and improve the final strategy.

RESULTS

The five P/CGs participating in the pilot study found the instructions clear, selected activities important and reflective of their children's abilities, and recordings at-home preferrable to in-clinic assessments. The three grading experts found the videos easy to grade and the milestones clinically meaningful.

CONCLUSION

Our standardized strategy enables expert panel grading of developmental milestone achievements using at-home recordings, blinded to treatment and post-baseline time points. This rigorous and objective scoring system has broad applicability in various disease contexts, with or without external controls. Moreover, our strategy facilitates flexible, continued data collection and the videos can be archived for future analyses.

Simultaneous thyroglossal duct cyst with parathyroid cyst: A case report

BACKGROUND

Thyroglossal duct cysts (TDC) are common congenital deformities. Most of them are cysts formed by the thyroglossal ducts that do not disappear and degenerate in the early embryonic stage. TDC exists alone and is rarely complicated by other congenital embryonic malformations. Only a few reports of TDC with branchial cleft cysts, thyroid cancer, thyroid hematoma, and epidermoid cysts have been reported. Therefore, we report a patient with TDC and parathyroid cyst (PC), a rare disease that has never been reported.

CASE SUMMARY

A 47-year-old woman presented to clinic in April 2021 with a neck tumor which she had noticed 5 d earlier. We perfected the relevant examinations, such as ultrasound and computed tomography, and resected the tumor. After surgical treatment, the pathology revealed a cervical thyroglossal duct cyst and a left lobe parathyroid cyst. The patient was followed up for 1 year without significant recurrence.

CONCLUSION

We report a patient with a simultaneous TDC and a PC to explore the correlation between the two congenital anomalies.

Beyond structural bioinformatics for genomics with dynamics characterization of an expanded KRAS mutational landscape

Current capabilities in genomic sequencing outpace functional interpretations. Our previous work showed that 3D protein structure calculations enhance mechanistic understanding of genetic variation in sequenced tumors and patients with rare diseases. The KRAS GTPase is among the critical genetic factors driving cancer and germline conditions. Because KRAS-altered tumors frequently harbor one of three classic hotspot mutations, nearly all studies have focused on these mutations, leaving significant functional ambiguity across the broader KRAS genomic landscape observed in cancer and non-cancer diseases. Herein, we extend structural bioinformatics with molecular simulations to study an expanded landscape of 86 KRAS mutations. We identify multiple coordinated changes strongly associated with experimentally established KRAS biophysical and biochemical properties. The patterns we observe span hotspot and non-hotspot alterations, which can all dysregulate Switch regions, producing mutation-restricted conformations with different effector binding propensities. We experimentally measured mutation thermostability and identified shared and distinct patterns with simulations. Our results indicate mutation-specific conformations, which show potential for future research into how these alterations reverberate into different molecular and cellular functions. The data we present is not predictable using current genomic tools, demonstrating the added functional information derived from molecular simulations for interpreting human genetic variation.

Phenotypic presentation of Mendelian disease across the diagnostic trajectory in electronic health records

PURPOSE

To investigate the phenotypic presentation of Mendelian disease across the diagnostic trajectory in the electronic health record (EHR).

METHODS

We applied a conceptual model to delineate the diagnostic trajectory of Mendelian disease to the EHRs of patients affected by 1 of 9 Mendelian diseases. We assessed data availability and phenotype ascertainment across the diagnostic trajectory using phenotype risk scores and validated our findings via chart review of patients with hereditary connective tissue disorders.

RESULTS

We identified 896 individuals with genetically confirmed diagnoses, 216 (24%) of whom had fully ascertained diagnostic trajectories. Phenotype risk scores increased following clinical suspicion and diagnosis (P < 1 × 10-4, Wilcoxon rank sum test). We found that of all International Classification of Disease-based phenotypes in the EHR, 66% were recorded after clinical suspicion, and manual chart review yielded consistent results.

CONCLUSION

Using a novel conceptual model to study the diagnostic trajectory of genetic disease in the EHR, we demonstrated that phenotype ascertainment is, in large part, driven by the clinical examinations and studies prompted by clinical suspicion of a genetic disease, a process we term diagnostic convergence. Algorithms designed to detect undiagnosed genetic disease should consider censoring EHR data at the first date of clinical suspicion to avoid data leakage.

RDDL: A systematic ensemble pipeline tool that streamlines balancing training schemes to reduce the effects of data imbalance in rare-disease-related deep-learning applications

Identifying lowly prevalent diseases, or rare diseases, in their early stages is key to disease treatment in the medical field. Deep learning techniques now provide promising tools for this purpose. Nevertheless, the low prevalence of rare diseases entangles the proper application of deep networks for disease identification due to the severe class-imbalance issue. In the past decades, some balancing methods have been studied to handle the data-imbalance issue. The bad news is that it is verified that none of these methods guarantees superior performance to others. This performance variation causes the need to formulate a systematic pipeline with a comprehensive software tool for enhancing deep-learning applications in rare disease identification. We reviewed the existing balancing schemes and summarized a systematic deep ensemble pipeline with a constructed tool called RDDL for handling the data imbalance issue. Through two real case studies, we showed that rare disease identification could be boosted with this systematic RDDL pipeline tool by lessening the data imbalance problem during model training. The RDDL pipeline tool is available at https://github.com/cobisLab/RDDL/.

Effects of asfotase alfa in adults with pediatric-onset hypophosphatasia over 24 months of treatment

BACKGROUND

Hypophosphatasia (HPP) is a rare, heritable metabolic disorder caused by deficient activity of tissue-nonspecific alkaline phosphatase (TNSALP). Asfotase alfa (AA) is a human recombinant TNSALP that promotes bone mineralization and is approved to treat eligible patients with HPP.

METHODS

This prospective single-center observational study evaluated AA in adults with pediatric-onset HPP over 2 years of treatment (ClinicalTrials.govNCT03418389). Primary outcomes evaluated physical function; secondary outcomes assessed quality of life (QoL) and pain.

RESULTS

The study included 17 females and 5 males (mean age: 48.7 years). Median distance walked in the 6-Minute Walk Test increased significantly from baseline to 12 months (P = 0.034) and results were sustained. Median Timed Up and Go test time significantly decreased from baseline at 12 (P = 0.003) and 24 months (P = 0.005), as did the median chair rise time test at 12 (P = 0.003) and 24 months (P < 0.002). The change from baseline in usual gait speed was significant at 12 (P = 0.003) and 24 months (P = 0.015). Mean dominant and nondominant hand grip strength improved at 24 months (P = 0.029 and P = 0.019, respectively). Median Short Form 36 Physical Component Summary scores significantly improved from baseline at 12 (P = 0.012) and 24 (P = 0.005) months, and median Lower Extremity Functional Scale scores improved from baseline at 12 (P = 0.001) and 24 (P = 0.002) months. No significant change was noted in pain level at these timepoints. While injection site reactions occurred in 86.4 % of the participants, there were no severe side effects or safety findings.

CONCLUSIONS

Adults with pediatric-onset HPP treated with AA experienced marked improvement in functional and QoL outcomes that were observed as early as within 3 months of initial treatment and were sustained over 24 months.

Zebras Among Us: Advocating for the 30 Million Americans Living with Rare Disease

Nearly 30 million (about 1 in 10) Americans have a rare disease. On average, rare disease patients wait 6 years for an accurate and definitive diagnosis and see as many as 12 specialists along their diagnostic journey. In this brief article, we highlight some of what is being done across patient care, medical education, policy, and innovation in order to improve the diagnostic and treatment journeys of rare disease patients. We hope that members of the medical education community will appreciate this call to action and engage in the rare disease space.

Panels, Exomes, Genomes, and More-Finding the Best Path Through the Diagnostic Odyssey

Selecting the ideal test to evaluate an individual with a suspected genetic disorder can be challenging. While several clinical testing options are available, no single test yet captures all potentially causative genetic variants. Thus, clinicians may order testing in a stepwise fashion, and what to order after non-diagnostic testing can be challenging to determine. Here, we provide an overview of commonly used clinical genetic tests, guidance on when they are best used, and what they may miss. We conclude with a discussion of how new technologies might be used to identify challenging variants and simplify clinical testing in the future.

Policy-making and implementation for newborn bloodspot screening in Europe: a comparison between EURORDIS principles and UK practice

Newborn bloodspot screening (NBS) policy is a contentious area in Europe. Variation in the screening panels on offer, in the approach to evidence assessment and in the use of health economic modelling are some of the issues which are debated on the topic. In this paper we focus on a set of patient-driven principles for newborn screening published by EURORDIS and use these as a reference point for exploration and comparison with NBS policy development and screening practice in the UK. In doing so, we share UK practice; we note the UK is generally well aligned with many of the recommended principles, but we also discuss areas of controversy and challenges. Some of these, like 'actionability', will undoubtedly continue to be debated and may never reach consensus. For others, such as patient and public voice participation in newborn screening systems, there are opportunities to continue improving existing processes and developing new mechanisms for stakeholder participation. Screening bodies in other European countries should also compare their policy-making and implementation practices with the EURORDIS principles to stimulate further discussion on the challenges and opportunities of newborn screening and provide a cross-European baseline.