Phelan-McDermid syndrome data network: Integrating patient reported outcomes with clinical notes and curated genetic reports.

The heterogeneity of patient phenotype data are an impediment to the research into the origins and progression of neuropsychiatric disorders. This difficulty is compounded in the case of rare disorders such as Phelan-McDermid Syndrome (PMS) by the paucity of patient clinical data. PMS is a rare syndromic genetic cause of autism and intellectual deficiency. In this paper, we describe the Phelan-McDermid Syndrome Data Network (PMS_DN), a platform that facilitates research into phenotype-genotype correlation and progression of PMS by: a) integrating knowledge of patient phenotypes extracted from Patient Reported Outcomes (PRO) data and clinical notes-two heterogeneous, underutilized sources of knowledge about patient phenotypes-with curated genetic information from the same patient cohort and b) making this integrated knowledge, along with a suite of statistical tools, available free of charge to authorized investigators on a Web portal https://pmsdn.hms.harvard.edu. PMS_DN is a Patient Centric Outcomes Research Initiative (PCORI) where patients and their families are involved in all aspects of the management of patient data in driving research into PMS. To foster collaborative research, PMS_DN also makes patient aggregates from this knowledge available to authorized investigators using distributed research networks such as the PCORnet PopMedNet. PMS_DN is hosted on a scalable cloud based environment and complies with all patient data privacy regulations. As of October 31, 2016, PMS_DN integrates high-quality knowledge extracted from the clinical notes of 112 patients and curated genetic reports of 176 patients with preprocessed PRO data from 415 patients.

Considerations in the evaluation and determination of minimal risk in pragmatic clinical trials.

Institutional review boards, which are charged with overseeing research, must classify the riskiness of proposed research according to a federal regulation known as the Common Rule (45 CFR 46, Subpart A) and by regulations governing the US Food and Drug Administration codified in 21 CFR 50. If an institutional review board determines that a clinical trial constitutes "minimal risk," there are important practical implications: the institutional review board may then allow a waiver or alteration of the informed consent process; the study may be carried out in certain vulnerable populations; or the study may be reviewed by institutional review boards using an expedited process. However, it is unclear how institutional review boards should assess the risk levels of pragmatic clinical trials. Such trials typically compare existing, widely used medical therapies or interventions in the setting of routine clinical practice. Some of the therapies may be considered risky of themselves but the study comparing them may or may not add to that pre-existing level of risk. In this article, we examine the common interpretations of research regulations regarding minimal-risk classifications and suggest that they are marked by a high degree of variability and confusion, which in turn may ultimately harm patients by delaying or hindering potentially beneficial research. We advocate for a clear differentiation between the risks associated with a given therapy and the incremental risk incurred during research evaluating those therapies as a basic principle for evaluating the risk of a pragmatic clinical trial. We then examine two pragmatic clinical trials and consider how various factors including clinical equipoise, practice variation, research methods such as cluster randomization, and patients' perspectives may contribute to current and evolving concepts of minimal-risk determinations, and how this understanding in turn affects the design and conduct of pragmatic clinical trials.

Caregiver perspectives on patient-focused drug development for Phelan-McDermid syndrome.

BACKGROUND: Phelan-McDermid syndrome (PMS) is a neurodevelopmental disorder caused by SHANK3 haploinsufficiency with clinical manifestations that can be devastating and profoundly affect quality of life. RESULTS: The Externally Led Patient-Focused Drug Development (EL-PFDD) meeting was an opportunity for families affected by PMS to share with the Food and Drug Administration (FDA) how symptoms impact their lives and how treatments could be most meaningful. The Voice of the Patient report serves as a summary of this meeting to influence upcoming drug development and clinical trials. The purpose of this report is to provide a clinical perspective on the results of the EL-PFDD meeting to amplify the voice of these caregivers to the scientific community. CONCLUSIONS: Caregivers prioritize an improved quality of life for their loved ones characterized by improved cognitive function, improved communication, increased independence, and reduced risk of regression. With these caregiver priorities in mind, this report provides the FDA and the scientific community with a clear understanding of which aspects of PMS should influence the development of future therapeutics.

A roadmap for SHANK3-related Epilepsy Research: recommendations from the 2023 strategic planning workshop.

On September 27, 2023, the CureSHANK nonprofit foundation sponsored a conference in Boston, Massachusetts, to identify gaps in knowledge surrounding SHANK3-related epilepsy with the goal of determining future research priorities and recommendations. In addition to patient families and members of the CureSHANK community, participants in the conference included a broad cross-section of preclinical and clinical researchers and clinicians with expertise in SHANK3-related epilepsy as well as representatives from the pharmaceutical industry. Here we summarize the outcomes from comprehensive premeeting deliberations and the final conference recommendations, including (1) gaps in knowledge related to clinical science, (2) gaps in knowledge related to preclinical science, and (3) research priorities moving forward.

A roadmap for SHANK3-related Epilepsy Research: recommendations from the 2023 strategic planning workshop Phelan-McDermid Syndrome, a rare genetic disorder linked to the SHANK3 gene, manifests in a spectrum of clinical phenotypes including intellectual disability, autism spectrum disorder, and epilepsy. Epilepsy has been particularly under-investigated in this syndrome, and most of the animal models studied to date do not display seizures. On September 27, 2023, the CureSHANK nonprofit foundation sponsored a conference in Boston, Massachusetts, to identity gaps in knowledge surrounding SHANK3-related epilepsy. Conference attendees included patient families, basic scientists, clinical researchers, clinicians and representatives from the pharmaceutical industry with interest in SHANK3-related epilepsy. This review summarizes the outcome of this conference, including a summary of current state of knowledge and resources available, gaps in our understanding, priorities for future research in this important manifestation of PMS.

Phenome-wide profiling identifies genotype-phenotype associations in Phelan-McDermid syndrome using family-sourced data from an international registry.

BACKGROUND: Phelan-McDermid syndrome (PMS) is a rare neurodevelopmental disorder caused by 22q13 deletions that include the SHANK3 gene or pathogenic sequence variants in SHANK3. It is characterized by global developmental delay, intellectual disability, speech impairment, autism spectrum disorder, and hypotonia; other variable features include epilepsy, brain and renal malformations, and mild dysmorphic features. Here, we conducted genotype-phenotype correlation analyses using the PMS International Registry, a family-driven registry that compiles clinical data in the form of family-reported outcomes and family-sourced genetic test results. METHODS: Data from the registry were harmonized and integrated into the i2b2/tranSMART clinical and genomics data warehouse. We gathered information from 401 individuals with 22q13 deletions including SHANK3 (n = 350, ranging in size from 10 kb to 9.1 Mb) or pathogenic or likely pathogenic SHANK3 sequence variants (n = 51), and used regression models with deletion size as a potential predictor of clinical outcomes for 328 phenotypes. RESULTS: Our results showed that increased deletion size was significantly associated with delay in gross and fine motor acquisitions, a spectrum of conditions related to poor muscle tone, renal malformations, mild dysmorphic features (e.g., large fleshy hands, sacral dimple, dysplastic toenails, supernumerary teeth), lymphedema, congenital heart defects, and more frequent neuroimaging abnormalities and infections. These findings indicate that genes upstream of SHANK3 also contribute to some of the manifestations of PMS in individuals with larger deletions. We also showed that self-help skills, verbal ability and a range of psychiatric diagnoses (e.g., autism, ADHD, anxiety disorder) were more common among individuals with smaller deletions and SHANK3 variants. LIMITATIONS: Some participants were tested with targeted 22q microarrays rather than genome-wide arrays, and karyotypes were unavailable in many cases, thus precluding the analysis of the effect of other copy number variants or chromosomal rearrangements on the phenotype. CONCLUSIONS: This is the largest reported case series of individuals with PMS. Overall, we demonstrate the feasibility of using data from a family-sourced registry to conduct genotype-phenotype analyses in rare genetic disorders. We replicate and strengthen previous findings, and reveal novel associations between larger 22q13 deletions and congenital heart defects, neuroimaging abnormalities and recurrent infections.

Bringing everyone to the table - findings from the 2018 Phelan-McDermid Syndrome Foundation International Conference.

BACKGROUND: Phelan-McDermid Syndrome (PMS) is a rare neurodevelopmental disorder characterized by global developmental delay, autism spectrum disorder, and numerous systemic complications including seizures, gastrointestinal dysfunction, and renal anomalies. The Phelan-McDermid Syndrome Foundation (PMSF) was created to improve the quality of life of people affected by PMS worldwide by supporting families, accelerating research, and raising awareness. To further this mission, the PMSF initiated the Phelan-McPosium in 2016 to bring families affected by PMS, clinicians, and researchers together to design patient-centered rigorous clinical and translational research. Here, we present findings from the 2018 Phelan-McPosium. RESULTS: The 2018 Phelan-McPosium was attended by 183 families and 35 researchers and clinicians. Overall, the Early Childhood parents raised the fewest number of concerns, families of Late-Childhood patients raised more concerns around epilepsy and behavioral problems, and Teen and Adult families were primarily concerned about implications of genetic testing, gastrointestinal dysfunction, and regression. All families were concerned with feasibility, safety and importance of clinical trials for PMS. CONCLUSIONS: The concerns raised by families across the sessions varied by age in a manner which may overlap with the emergence of various signs and symptoms through the natural history of PMS. The design of the Phelan-McPosium session has successfully generated thoughtful research questions that led to innovative investigations and clinical trials that are shaping the standard of care for PMS. This is an approach which could be employed by any rare disease group to align translational research efforts with a patient-centered focus.