PURPOSE:Undiagnosed rare genetic diseases (RGD) can go unrecognized by health care providers, delaying appropriate genetic testing. This proof-of-concept study aimed to address this barrier through the development of a rule-based search algorithm called "ThinkRare." METHODS:The algorithm used structured electronic medical record data and clinical criteria to identify patients who may have a complex undiagnosed RGD, are eligible for clinical exome sequencing, and are not yet referred to genetics (true positives). Iterative testing on gold standard and test data sets (input) informed algorithm design and optimization. Medical record reviews were conducted to verify whether the algorithm identified patients (output) were true positives or false positives, and these outcomes informed algorithm modifications. Physicians of identified patients were notified with the option to refer to genetics. RESULTS:The search algorithm was applied retrospectively to 262,296 patients (test data set), excluding 99.9% of patients and identifying 30 patients eligible for exome sequencing. The algorithm's estimated recall (sensitivity) was 60% and precision (positive predictive value) was 15%. This process resulted in the diagnosis of 50% of patients (4/8) referred and evaluated in genetics. CONCLUSION:The search algorithm effectively identified patients retrospectively with an RGD and prospective deployment will ultimately help physicians "think rare."

Purpose: ARID1A/ARID1B haploinsufficiency leads to Coffin-Siris syndrome, duplications of ARID1A lead to a distinct clinical syndrome, whilst ARID1B duplications have not yet been linked to a phenotype. Methods: We collected patients with duplications encompassing ARID1A and ARID1B duplications. Results: 16 ARID1A and 13 ARID1B duplication cases were included with duplication sizes ranging from 0.1 to 1.2 Mb (1-44 genes) for ARID1A and 0.9 to 10.3 Mb (2-101 genes) for ARID1B. Both groups shared features, with ARID1A patients having more severe intellectual disability, growth delay, and congenital anomalies. DNA methylation analysis showed that ARID1A patients had a specific methylation pattern in blood, which differed from controls and from patients with ARID1A or ARID1B loss-of-function variants. ARID1B patients appeared to have a distinct methylation pattern, similar to ARID1A duplication patients, but further research is needed to validate these results. Five cases with duplications including ARID1A or ARID1B initially annotated as duplications of uncertain significance were evaluated using PhenoScore and DNA methylation reanalysis, resulting in the reclassification of 2 ARID1A and 2 ARID1B duplications as pathogenic. Conclusion: Our fi ndings reveal that ARID1B duplications manifest a clinical phenotype, and ARID1A duplications have a distinct episignature that overlaps with that of ARID1B duplications, providing further evidence for a distinct and emerging BAFopathy caused by whole-gene duplication rather than haploinsufficiency. (c) 2024 The Authors. Published by Elsevier Inc. on behalf of American College of Medical Genetics and Genomics. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

This paper reports the findings of an international survey of health data ecosystems (HDEs) in 12 countries plus the H3 Africa project using live, structured interviews with senior project team members under the auspices of Canada's All for One Precision Health Initiative. We note the high level of interest in HDEs around the world, as well as in Canada, despite the financial, jurisdictional, and other barriers that continue to hold back widespread data sharing. We present results detailing operational profiles for each of the 13 participants, including whether their healthcare systems are centralized (national) or decentralized (regional), project start date, funding, information technology (IT) infrastructure, and the extent to which participants have implemented a data-sharing mandate. We find no evidence to confirm common assumptions about features conferring an advantage on HDE development, such as early launch date or top-down government mandate. We also find no evidence of a reference model to explain what makes any HDE effective, valuable, or successful and conclude, on the basis of our interviews, that the diversity that makes each of these projects unique may undermine collective actions like data sharing. While participants provided useful cautions about pitfalls they encountered, more research on these issues is required, and we anticipate that advanced assessment tools like the maturity level model (MLM) developed by the European Union (EU) may help countries understand what stage of the HDE development process they have reached and what strategies will be most effective for them in later stages.

PURPOSE:Exome sequencing (ES) and genome sequencing (GS) can improve rare disease diagnosis but are not routinely available in many jurisdictions. To inform implementation, we report on a randomized implementation effectiveness trial comparing ES and GS. METHODS:Eligible trios were randomized to receive ES or GS in the same clinically accredited laboratory. Patient-level data on diagnostic utility and turnaround times were collected. Outcomes were compared statistically between clinically important subgroups. RESULTS:Of 1048 patients, 68.5% had syndromic intellectual disability/developmental delay (ID/DD) and 20.5% had multisystem disorders without ID/DD. Most had prior genetic test(s) that were nondiagnostic (95.5%), and of these, 91.6% included chromosome microarray. Diagnostic yields were 33.8% and 33.6%, for ES (n = 526) and GS (n = 522), respectively. Within sequencing groups, diagnostic results were more frequent among those with ID/DD than those without (P < .005). For routine (ie, nonexpedited) patients (n = 1020), 87.0% were reported in <12 weeks, and the mean turnaround time was 55.5 days (SD: 24.0). Turnaround time for ES and GS did not differ; however, result type (P < .001) and age of onset (P < .005) significantly affected turnaround time. CONCLUSION:Findings provide robust evidence of diagnostic utility and timeliness of ES and GS and will inform policy related to the organization, delivery, and reimbursement of clinical-grade genome diagnostics for rare diseases.

Trichilemmal cysts are benign organoid nevi derived from the outer root sheath of the hair follicle that were first described as a distinct entity in 2007 (Tantcheva-Poor et al. 2007). The keratin-filled, epithelial-lined cysts arise most frequently on the scalp but may also develop on the face, neck, and extremities (Al Aboud et al. 2024). These lesions are the most common type of skin cyst and occur in less than 10% of the US population (Al Aboud et al. 2024). Transformation of trichilemmal cysts into trichilemmal tumors or carcinomas has been observed on occasion (Kearns-Turcotte et al. 2022; Alici et al. 2015; Garg et al. 2009). Multiple trichilemmal cysts appearing in a Blaschko-linear arrangement constitute nevus trichilemmocysticus, an epidermal nevus syndrome that may co-occur with bone lesions (Happle 2010). Currently, there are no definitive treatments for this syndrome; management is centered around symptom control and prevention of complications. Surgical excision of cysts may be considered for symptomatic or aesthetically concerning lesions, and long-term follow-up is needed to monitor for new systemic or cutaneous manifestations. Trichilemmal cysts occur as sporadic lesions or follow an autosomal dominant pattern of inheritance with incomplete penetrance (Seidenari et al. 2013). Efforts to identify the predisposing gene were undertaken by Eiberg et al. (2005) by means of a genome-wide linkage analysis on a large Danish family with 11 affected relatives across three generations; the authors identified a ~10.3 Mb candidate locus on chromosome 3p24-p21.2, termed TRICY1 (MIM# 609649), suspected to harbor the causative gene. Subsequent exome and Sanger sequencing studies performed in 2019/2020 by (Hörer et al. 2019; Kolodney et al. 2020) on individuals with hereditary trichilemmal cysts revealed a mono-allelic, two-hit mechanism involving the phospholipase C delta 1 (PLCD1) gene underpinning hereditary trichilemmal cyst formation—the mechanism involved the inheritance of a predisposing PLCD1 "risk allele" most frequently c.1379G>A, p.(Ser460Leu), with subsequent acquisition of a somatic hotspot variant in cis (most frequently c.2234C>T, p.(Ser745Leu)) leading to cyst formation. The c.1379G>A, p.(Ser460Leu) "risk allele" variant is relatively common in the general population, with a Grpmax filtering AF of 0.03799 in gnomAD v4.1.0, and is classified as benign in ClinVar (Variation ID: 3058968). PLCD1 lies within the TRICY1 locus, and the encoded protein is a tumor suppressor that functions in intracellular signal transduction via hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2) into diacylglycerol (DAG; which activates protein kinase C) and inositol triphosphate (IP3; an important regulator of Ca2+ release) (Tall et al. 1997). Germline variants in PLCD1 have been reported in association with leukonychia totalis (MIM# 151600), which is characterized by complete whitening of the nail plate, with phenotypic variability and incomplete penetrance. A literature review performed by Zhang et al. (2023) to investigate genotype–phenotype correlations for hereditary leukonychia revealed that PLCD1 variants predicted to truncate the protein may underlie an autosomal recessive form of the disorder, whereas missense PLCD1 variants were more frequently associated with an autosomal dominant presentation. Trichilemmal cysts and leukonychia totalis co-occur in the rare, autosomal dominant Familial LeukOnychia, Trichilemmomas, Ciliary dystrophy, Hereditary (FLOTCH) syndrome (no assigned MIM number), suggesting a common genetic etiology (Rodríguez-Lojo et al. 2011). We report the genetic testing results for a previously reported female proband with nevus trichilemmocysticus (Larralde et al. 2011), which revealed a mosaic PLCD1 variant detectable in blood-derived DNA—the girl presented at birth with extensive linear dermatosis on the head, neck, trunk, limbs, palms, and soles of the feet, which consisted of yellow-colored plaques covered by verrucous papules and filiform hyperkeratosis (Figure 1A). At 4 years of age, she underwent treatment for ichthyosis hystrix, involving a 12-month course of isotretinoin, with no significant improvement. Cystic transformation of the lesions on the limbs was noted at around 6 years of age. Histopathological examination of several lesions was performed—a biopsy from a plaque on the right arm revealed a keratotic plug within a dilated hair follicle with parakeratotic columns resembling coronoid lamella; the surrounding epidermis showed hyperkeratosis, acanthosis, and papillomatosis. A biopsy of a cystic lesion demonstrated a cystic wall lined by stratified squamous epithelium, with compact keratinization, and a diagnosis of nevus trichilemmocysticus was established (Larralde et al. 2011). The patient remained under clinical follow-up—she experienced flare-ups with spontaneous lesion secretion, predominantly during the summer months (Figure 1B). By the age of 20 years, she began to experience joint pain, particularly in the shoulders, knees, and hands, along with morning stiffness (Figure 1C (I)). The rheumatologic profile laboratory tests were within normal parameters. Radiographic studies revealed no specific osteoarticular abnormalities. The cutaneous lesions distributed along the Blaschko lines of the left arm extended to the palm of the hand and reached the nail of the left middle finger, causing dystrophy, melanonychia, leukonychia, and onycholysis (Figure 1C (II)). Given the late-onset systemic features in the setting of a dermatological condition, and considering the syndromic context, genetic testing was pursued. We performed short read whole genome sequencing at an average depth of coverage of 120× on DNA derived from peripheral blood and a trichilemmal cyst (from the left upper arm; no cell culturing or micro-dissection was performed). A hotspot NM_006225.4:c.2234C>T, p.(Ser745Leu) PLCD1 variant was detected at 6% (7/116 reads) variant allele fraction (VAF) in blood-derived DNA, and at 11.76% VAF (14/199 reads) in the cyst-derived DNA. A droplet digital PCR (ddPCR) experiment was performed to validate these findings: the variant was detected at 5.3% and 6.6% VAF in the blood- and cyst-derived DNA, respectively (Figure 2A), for an average VAF of 5.7% and 9.2%, respectively, across technologies. The variant is rare (0 alleles in gnomAD v4.1.0) and is predicted to be probably damaging by in silico prediction tools (CADD 24.3, PolyPhen2 0.997, SIFT 0.01). The so-called germline "risk allele" was not detected in our proband, and no other strongly compelling variants were identified in her genome. A heterozygous germline NM_006225.4:c.1902+19G>A intronic PLCD1 variant was detected; however, this variant was not predicted to impact splicing by in silico prediction tools (SpliceAI score 0.04), has not been reported in ClinVar, and is frequent in population databases (5076 alleles in gnomAD v4.1.0; 10 homozygotes; AF 0.003145). A deep intronic NM_006225.4:c.199+975C>A PLCD1 variant was identified at similar VAFs to the p.(Ser745Leu) variant: 8% (11/141 reads) and 12% (13/112 reads) in blood- and cyst-derived DNA, respectively (vs. 6% and 12% for the hotspot variant); however, the deep intronic variant is not predicted to cause aberrant splicing (SpliceAI score 0.00), and has not been reported previously in ClinVar or in population databases; the biological and clinical significance of the latter two variants is therefore uncertain. The p.(Ser745Leu) PLCD1 hotspot variant has previously been identified as a somatic variant in approximately 44 trichilemmal cysts from 36 individuals (Table 1) (Kolodney et al. 2020; Hörer et al. 2019; Aoki et al. 2024). 33 out of 36 tested individuals harbored a predisposing PLCD1 "risk allele" (most frequently p.(Ser460Leu), or the haplotype containing p.(Ser460Leu) and p.(Pro301Pro)), in addition to the somatic hotspot variant in each tested cyst. Kolodney et al. (2020) identified 9 individuals with sporadic trichilemmal cysts who did not harbor a "risk allele"; cysts from 3 out of 6 (50%) of these individuals harbored an isolated p.(Ser745Leu) PLCD1 somatic variant. This is in contrast to the 41 trichilemmal cysts that arose in patients bearing a "risk allele" which all bore the p.(Ser745Leu) somatic hotspot variant. The "risk allele" and hotspot variant were confirmed to be in cis in all 11 cysts that were tested, fulfilling the mono-allelic two-hit mechanism of PLCD1-related trichilemmal cyst formation (Kolodney et al. 2020; Hörer et al. 2019; Aoki et al. 2024) (Table 1). Hörer et al. (2019) were unable to detect the "cyst-specific" variants [p.(Ser745Leu), p.(Ser710Phe), or p.(Ser711Phe)] in blood-, or buccal mucosa-derived DNA, nor in hair root-derived cDNA from their cohort, supporting a somatic provenance. However, it must be noted that sensitive/deep sequencing technologies to permit detection of the variants at low levels were not employed (Hörer et al. 2019). Our report is the fourth demonstration of a hotspot p.(Ser745Leu) PLCD1 variant occurring in the absence of a predisposing germline "risk allele" in a trichilemmal cyst and appears to be the first demonstration of the p.(Ser745Leu) variant occurring as a predisposing mosaic variant detectable at a low level in peripheral blood in a patient presenting with nevus trichilemmocysticus. Germline PLCD1 "risk alleles" Somatic PLCD1 variants 21/21 (100%) cysts from n = 10 patients with p.S460L/p.E455Kd 13 cysts from n = 13 patients with p.S460Ld The identified p.(Ser745Leu) hotspot variant is located at a highly conserved serine residue in the C2 domain of PLCδ1 (Figure 2B). The domain is important for the enzymatic activation of PLCδ1 through Ca2+-dependent binding to membrane-bound phosphatidylserine. Functional studies were conducted by Hörer et al. to investigate the impact of the identified variants on protein function in vitro. They determined that PLCδ1-dependent TRPC4 channel activation was slightly reduced in cells overexpressing the PLCδ1 "risk allele" haplotype [p.(Pro301Pro) + p.(Ser460Leu)] relative to wildtype; in contrast, cells overexpressing the "cyst-specific" variants [p.(Pro301Pro) + p.(Ser460Leu) + p.(Ser745Leu)], or the somatic hotspot mutation combined with an "artificial" dominant-negative lipase-deficient variant [p.(Ser745Leu) + p.(His311Ala)], resulted in no channel activation relative to wildtype (Hörer et al. 2019). Furthermore, an experiment measuring reaction products of PIP2 hydrolysis generated by the enzymatic action of PLCδ1 revealed that cells overexpressing the latter two variant combinations showed significantly reduced DAG concentrations compared to cells overexpressing the wildtype protein; DAG concentrations in cells overexpressing the "risk allele" protein variant (which lacked the p.(Ser745Leu) hotspot variant in cis) were not significantly reduced compared to wildtype (Hörer et al. 2019). Of note is that the authors did not investigate the impact of the p.(Ser745Leu) variant on PLCδ1 function in isolation, and therefore, it remains to be determined whether the single hit deleteriously impacts PLCδ1's function. With that said, in light of the earlier-mentioned finding in which 3 cysts were found to harbor the somatic hotspot p.(Ser745Leu) PLCD1 variant in the absence of a predisposing germline "risk allele" (Kolodney et al. 2020), together with the detection of the p.(Ser745Leu) variant as mosaic in our proband's peripheral blood, supports the hypothesis that the hotspot variant may be capable, albeit rarely, of inducing trichilemmal cyst formation in the absence of the "risk allele," and furthermore, when acquired as a mosaic alteration, depending on allelic fraction and tissue distribution, could potentially result in a more extensive phenotype with systemic manifestations in keeping with nevus trichilemmocysticus. Additional investigations into the functional impact of the hotspot variant are required, along with studies investigating the interplay between somatic and predisposing variants at this locus. In summary, this case demonstrates that mosaic PLCD1 hotspot variants occurring in the absence of the recognized germline "risk allele" may be a rare but important genetic cause of nevus trichilemmocysticus. When a PLCD1 "risk allele" is not detected in affected individuals, testing of DNA derived from uncultured affected tissue should be pursued, along with the use of higher sensitivity sequencing technologies that would permit detection of mosaicism of a hotspot variant in constitutional DNA samples. Clinically, a multidisciplinary approach involving dermatologists, geneticists, and other specialists is key to managing nevus trichilemmocysticus given its potential for delayed systemic manifestations. L.K. and M.N. drafted the manuscript with input from all authors. M.N. and M.L. collected samples and clinical data. W.M. performed sample acquisition and processing. L.K. and M.C. processed and analyzed the genomic data. Care4Rare Canada Consortium oversaw project administration. A.J.E., K.D.K. and K.M.B. critically revised the manuscript, and all authors gave final approval. We thank the family for their participation in the study. This study was performed under the Care4Rare Canada Consortium funded by Genome Canada and the Ontario Genomics Institute (OGI-147), the Canadian Institutes of Health Research, the Ontario Research Fund, Genome Alberta, Genome British Columbia, Genome Quebec, and the Children's Hospital of Eastern Ontario Foundation. L.K. was a recipient of a Banting Postdoctoral Fellowship. K.M.B. was supported by a CIHR Foundation Grant (FDN-154279) and is a Tier 1 Canada Research Chair in Rare Disease Precision Health. The authors declare no conflicts of interest. Care4Rare Canada deposits multi-omic data in Genomics4RD (genomics4rd.ca), a national platform that facilitates data sharing. As per obtained participant consent, selected phenotypic and DNA sequencing datasets from this participant can be made available through a controlled access request to Genomics4RD ([email protected]).

The major spliceosome contains five small nuclear RNAs (snRNAs; U1, U2, U4, U5 and U6) essential for splicing. Variants in RNU4-2, encoding U4, cause a neurodevelopmental disorder called ReNU syndrome. We investigated de novo variants in 50 snRNA-encoding genes in a French cohort of 23,649 individuals with rare disorders and gathered additional cases through international collaborations. Altogether, we identified 145 previously unreported probands with (likely) pathogenic variants in RNU4-2 and 21 individuals with de novo and/or recurrent variants in RNU5B-1 and RNU5A-1, encoding U5. Pathogenic variants typically arose de novo on the maternal allele and cluster in regions critical for splicing. RNU4-2 variants mainly localize to two structures, the stem III and T-loop/quasi-pseudoknot, which position the U6 ACAGAGA box for 5' splice site recognition and associate with different phenotypic severity. RNU4-2 variants result in specific defects in alternative 5' splice site usage and methylation patterns (episignatures) that correlate with variant location and clinical severity. This study establishes RNU5B-1 as a neurodevelopmental disorder gene, suggests RNU5A-1 as a strong candidate and highlights the role of de novo variants in snRNAs.

ABSTRACT Background and Objectives Spinocerebellar ataxias (SCA) represent a clinically and genetically heterogeneous group of progressive neurodegenerative diseases with prominent cerebellar atrophy. Recently, a novel pathogenic repeat expansion in intron 1 of FGF14 was identified, causing adult‐onset SCA (SCA27B). We aimed to determine the proportion of our unsolved adult‐onset ataxia cohort harboring this expansion using several technologies, and to characterize the phenotypic presentation within our population. Methods Individuals presenting with adult‐onset ataxia (> 30 years old) and negative previous genetic testing were selected from the Care4Rare patient repository. Affected individuals were from all ethnicities, and 90% had a family history suggestive of dominant ataxia, representing 19 of the 23 families included. We used multiple tools (PCR, long‐read genome sequencing and optical genome mapping (OGM)) to identify the pathogenic GAA repeat in FGF14. Results Of the 23 families included in this study, 65.2% harbored a pathogenic GAA expansion in FGF14. Individuals of French‐Canadian descent (FC) represented most of our cohort and had a 64.7% diagnostic yield. Affected individuals presented with gaze‐evoked nystagmus, gait ataxia, cerebellar dysarthria, and early episodic features. The GAA expansion in FGF14 was visible by OGM in all individuals tested. Interpretation Our diagnostic yield demonstrates this expansion may be the most common cause of adult‐onset SCA in dominant families of FC ancestry. Our FC participants have a phenotype distinct from previously published FC patients, with gaze‐evoked nystagmus being the most common eye anomaly. From a diagnostic standpoint, the pathogenic GAA repeat can be identified by OGM, but additional tests are required to complement the interpretation.

Autosomal dominant spinocerebellar ataxia 27B (SCA27B), caused by an intronic (GAA•TTC) repeat expansion in FGF14, is a common cause of late-onset cerebellar ataxia, but its genotypic and phenotypic spectrum remains to be fully established. We analysed the FGF14 (GAA•TTC) repeat expansion in a cohort of 134 patients with ataxia and 822 controls from Quebec. We conducted segregation study in large families to further characterize intergenerational repeat instability. We found a significant enrichment of (GAA•TTC)≥200 alleles in the ataxia cohort compared to controls (53.0

OBJECTIVE:Biallelic pathogenic MBOAT7 variants are associated with neurodevelopmental disorders, intellectual disability (ID), epilepsy, and neuropsychiatric disorders such as attention-deficit/hyperactivity disorder and autism spectrum disorders. We aimed to characterize the epilepsy phenotype in a cohort of patients affected by this syndrome. METHODS:We describe epilepsy features, electroencephalography, magnetic resonance imaging (MRI) findings, antiseizure treatment response, and neurodevelopment of 15 patients with biallelic MBOAT7 variants. RESULTS:All 15 patients had ID or developmental delay (DD). Twelve suffered from epilepsy, with mean age at seizure onset of 36 months (range = 2 months-6.5 years) and 10 of 12 showing signs of DD before seizure onset. Patients with epilepsy presented with focal motor seizures with impaired awareness (n = 3), focal tonic-clonic seizures and epileptic spasms (n = 1), focal to bilateral tonic-clonic seizures (n = 1), unknown onset bilateral tonic-clonic seizures (n = 2), myoclonic seizures (n = 4), myoclonic-atonic seizures (n = 1), atonic seizures (n = 1), tonic seizures (n = 1), and myoclonic absences (n = 2). Seizure freedom was achieved in 66.7% (8/12), with variable antiseizure treatment regimes. We reviewed electroencephalograms of the patients with epilepsy. Background activity was normal in 64%, whereas 36% had either a generalized or a focal slowing. Interictal epileptiform discharges (IEDs) were reported in 83%. Generalized spikes/polyspikes were found in 53%, multifocal IEDs in 23%, and parasagittal focal IEDs in 26%. The most frequent abnormal brain MRI findings, reported in 58% of patients, included high-intensity signal in T2 and fluid-attenuated inversion recovery (FLAIR) sequences in dentate nuclei and globus pallidus. Biallelic missense variants seemed to be associated with better cognitive and motor outcomes compared to truncating variants and in-frame deletions. SIGNIFICANCE:Biallelic MBOAT7 variants are associated with global developmental impairment in all affected patients and epilepsy in the majority. The seizure semiology is heterogenous. One third of our cohort had persistent seizures despite treatment. The most frequent MRI findings were hyperintensities in T2/FLAIR sequences in dentate nuclei and globus pallidus.

Microcephaly affects 1 in 2,500 babies per year. Primary microcephaly results from aberrant neurogenesis leading to a small brain at birth. This is due to altered patterns of proliferation and/or early differentiation of neurons. Premature differentiation of neurons is associated with defects in the centrosome and/or primary cilia. In this study, we report on the first patients identified with NUBP2 -deficiency and utilize a conditional mouse model to ascertain the molecular mechanisms associated with NUBP2 -deficient primary microcephaly. We identified homozygous NUBP2 variants in these patients who displayed profound primary microcephaly in addition to intrauterine growth restriction, cervical kyphosis, severe contractures of joints, and facial dysmorphia. We then generated a mouse model using Emx1-Cre to ablate Nubp2 from the forebrain. The mice presented with severe microcephaly starting at E18.5. Neurospheres generated from the forebrain of Emx1-Cre; Nubp2 flox/flox conditional deletion mice were used to support the pathogenicity of the patient variants. We show that loss of Nubp2 increases both canonical and non-canonical cell death, but that loss of p53 fails to rescue microcephaly in the mouse model. Examination of neurogenesis in Emx1-Cre; Nubp2 flox/flox mice revealed distinct alterations in proliferation and cellular migration accompanied by supernumerary centrosomes and cilia. We therefore propose that NUBP2 is a novel primary microcephaly-related gene and that the role of Nubp2 in centrosome and cilia regulation is crucial for proper neurogenesis.

Background:Genomic matchmaking-the process of identifying individuals with overlapping phenotypes and rare variants in the same gene-is an important tool facilitating gene discoveries for unsolved rare genetic disease (RGD) patients. Current approaches are two-sided, meaning both patients being matched must have the same candidate gene flagged. This limits the number of RGD patients eligible for matchmaking. One-sided matchmaking, in which a gene of interest is queried in the genome-wide sequencing data of RGD patients, would make matchmaking possible for previously undiscoverable individuals. However, platforms and workflows for this approach have not been well established. Result:We released a beta version of the One-Sided Matching Portal (OSMP), a platform capable of performing one-sided matchmaking queries across thousands of participants stored in genomic databases. The OSMP returns variant-level and participant-level information on each variant occurrence (VO) identified in a queried gene. A workflow for one-sided matchmaking was developed so that researchers could prioritize the many VOs returned from a given query. This workflow was tested through pilot studies where two sets of genes were queried in over 2500 individuals: 130 genes that were newly associated with disease in OMIM and 178 novel candidate genes that were not associated with a disease-gene association in OMIM. These pilots returned a large number of initial VOs (12,872 and 20,308, respectively); however, the workflow filtered out over 99.8% of these VOs prior to review by a participant's clinician. Filters on participant-level information, including variant zygosity, participant phenotype, and whether a variant was also present in unaffected participants, were effective at reducing the number of false positive matches. Conclusion:As demonstrated through the two pilot studies, one-sided matchmaking queries can be efficiently performed using the OSMP. The availability of variant-level and participant-level data is key to ensuring this approach is practical for researchers.

BACKGROUND: Sharing health data within and across jurisdictions is important for research and improving healthcare quality; however, researchers, governments and funders must balance the benefits of data sharing with data privacy. Though frameworks exist to guide data sharing it can be difficult to translate these into practice. Therefore, our aim was to create a practical example of data sharing for researchers in pediatric rheumatology. METHODS: We utilized expert consultation with leaders in child health, genomics, rheumatology, bioethics, privacy and records, bioinformatics, and legal counsel to better understand barriers and enablers for sharing of health data. We used these barriers to frame the learnings of UCAN CAN-DU (Understanding Childhood Arthritis Network Canada-Netherlands Personalized Medicine Network in Childhood Arthritis and Rheumatic Diseases) which is a collaboration that collects and shares phenotypic, genomic, health economic and patient reported data across centers in Canada and the Netherlands in order to provide a real-life, practical example of data sharing across borders in pediatric rheumatology. RESULTS: Barriers to data sharing include lack of standardized consent, ethics review processes for multi-site projects, developing data governance frameworks aligned with institutional and regulatory requirements, differing data standards and a lack of interoperability, and managing data access. UCAN CAN-DU provides lessons for navigating these barriers through standardized consent forms, centralized ethics review and reciprocity agreements; building a network to support data interoperability and harmonization of procedures; documentation to support data sharing, including legal agreements, utilization of a secure healthcare data storage compute facility, and a data access advisory committee with clear policies for secondary data use. CONCLUSION: We have shared how UCAN CAN-DU navigated barriers to data sharing, providing an example of data sharing for researchers in pediatric rheumatology. This work highlights the importance of research networks in establishing interoperability including minimal data sets, standard operating procedures, and institutional legal/contracts partnerships that ultimately support data sharing. The barriers and enablers presented are broadly applicable across countries and provide direction on areas for future research and initiatives to foster data sharing.

Long-read sequencing (LRS) is a promising technology positioned to study the significant proportion of rare diseases (RDs) that remain undiagnosed as it addresses many of the limitations of short-read sequencing, detecting and clarifying additional disease-associated variants that may be missed by the current standard diagnostic workflow for RDs. Some key areas where additional diagnostic yields may be realized include: (1) detection and resolution of structural variants (SVs); (2) detection and characterization of tandem repeat expansions; (3) coverage of regions of high sequence similarity; (4) variant phasing; (5) the use of de novo genome assemblies for reference-based or graph genome variant detection; and (6) epigenetic and transcriptomic evaluations. Examples from over 50 studies support that the main areas of added diagnostic yield currently lie in SV detection and characterization, repeat expansion assessment, and phasing (with or without DNA methylation information). Several emerging studies applying LRS in cohorts of undiagnosed RDs also demonstrate that LRS can boost diagnostic yields following negative standard-of-care clinical testing and provide an added yield of 7%-17% following negative short-read genome sequencing. With this evidence of improved diagnostic yield, we discuss the incorporation of LRS into the diagnostic care pathway for undiagnosed RDs, including current challenges and considerations, with the ultimate goal of ending the diagnostic odyssey for countless individuals with RDs.

Purpose: To develop and assess the face and construct validity of the Clinician-reported Genetic Testing Utility Index (C-GUIDE) for genetic testing in prenatal care. Methods: After a literature review and consultation with clinical experts, a preliminary draft of C-GUIDE Prenatal was developed. Its face and content validity were then assessed by 19 prenatal genetics' providers using interviews and surveys. Feedback informed further revisions. To test construct validity, 4 geneticist raters completed C-GUIDE on a retrospective sample of cases that received prenatal genetic testing and completed a concurrent global assessment of utility of these cases using an anchor item. A generalized estimating equations model was used to adjust for rater correlation and measure the association between C-GUIDE scores, global item scores, and potential clinical variables. Results: To develop C-GUIDE Prenatal, 7 items were removed, 10 items were modified, and 4 items were added. For 101 cases rated for validation, on average, a 1-point increase in the global item score was associated with an increase of 1.1 in the C-GUIDE score (P = .04). Compared with uninformative results, informative positive and informative negative results were associated with a mean increase of 10.7 (SE = 1.05) (P < .001) and 5.6 (SE = 1.85) (P < .001), respectively. As indications for testing, known/familial variants were associated with a mean increase in the C-GUIDE score of 4.7 (SE = 2.21) (P < .001) compared with ultrasound findings. C-GUIDE scores increased by a mean of 3.0 (SE = 0.23) among cases for whom pregnancies were ongoing compared with those for whom they were not (P < .01). Conclusion: The significant positive associations between C-GUIDE total and the global item score and between C-GUIDE total, result type, indication for testing, and pregnancy status in the expected directions provide evidence of construct validity. (c) 2024 American College of Medical Genetics and Genomics. Published by Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.

Introduction Rare diseases (RD) are collectively common and often genetic. Families value and can benefit from precise molecular diagnoses. Prolonged diagnostic odysseys exacerbate the burden of RD on patients, families and the healthcare system. Genome sequencing (GS) is a near-comprehensive test for genetic RD, but existing care models—where consultation with a medical geneticist is a prerequisite for testing—predate GS and may limit access or delay diagnosis. Evidence is needed to guide the optimal positioning of GS in care pathways. While initiating GS prior to geneticist consultation has been trialled in acute care settings, there are no data to inform the utility of this approach in outpatient care, where most patients with RD seek genetics services. We aim to evaluate the diagnostic yield, time to diagnosis, clinical and personal utility and incremental cost-effectiveness of GS initiated at the time of referral triage (pre-geneticist evaluation) compared with standard of care. Methods and analysis 200 paediatric patients referred to one of two large genetics centres in Ontario, Canada, for suspected genetic RD will be randomised into a 1:1 ratio to the intervention (GS first) or standard of care (geneticist first) arm. An unblinded, permuted block randomisation design will be used, stratified within each recruitment site by phenotype and prior genetic testing. The primary outcome measure is time to genetic diagnosis or to cessation of active follow-up. Survival analysis will be used to analyse time-to-event data. Additional measures will include patient-reported and family-reported measures of satisfaction, understanding and perceived test utility, clinician-reported measures of perceived test utility and management impact, and healthcare system utilisation and costs. Ethics and dissemination This study was approved by Clinical Trials Ontario. Results will be disseminated, at minimum, via peer-reviewed journals, professional conferences and internal reports to funding bodies. Efforts will be made to share aggregated study results with participants and their families. Trial registration number NCT06935019.