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We characterized the world’s second case with ascertained extreme resilience to autosomal dominant Alzheimer’s disease (ADAD). Side-by-side comparisons of this male case and the previously reported female case with ADAD homozygote for the APOE3 Christchurch (APOECh) variant allowed us to discern common features. The male remained cognitively intact until 67 years of age despite carrying a PSEN1-E280A mutation. Like the APOECh carrier, he had extremely elevated amyloid plaque burden and limited entorhinal Tau tangle burden. He did not carry the APOECh variant but was heterozygous for a rare variant in RELN (H3447R, termed COLBOS after the Colombia–Boston biomarker research study), a ligand that like apolipoprotein E binds to the VLDLr and APOEr2 receptors. RELN-COLBOS is a gain-of-function variant showing stronger ability to activate its canonical protein target Dab1 and reduce human Tau phosphorylation in a knockin mouse. A genetic variant in a case protected from ADAD suggests a role for RELN signaling in resilience to dementia.

Progressive osseous heteroplasia (POH) is a rare, debilitating disorder characterized by heterotopic ossification in the skin and muscles, resulting in contractures of the joints and progressive loss of function. While 60-70% of the POH patients have paternally inherited, inactivating pathogenic variants in GNAS, the remaining 30-40% have no known etiology. FAM111B pathogenic variants, located on chromosome 11q12.1, cause POIKTMP (hereditary fibrosing poikiloderma with tendon contractures, myopathy, and pulmonary fibrosis), a very rare, autosomal-dominant disorder with high frequency of de novo missense pathogenic variants, which affects multiple tissues and organs, causing extensive fibrosis and muscle adiposis, though the exact mechanism is unknown. To our knowledge, there are no reports of FAM111B associated with POH. We describe the first case of POH phenotype associated with a novel de novo frameshift pathogenic variant in the FAM111B and present an analysis of the protein structure and function caused by this genomic disruption.A 15-year-old African-American male presented with generalized calcific nodules, progressive contractures, and muscle weakness leading to immobility, beginning at 6 years of age. Cutaneous examination showed generalized hard nodules varying from small to plaque-like ulcerated erupted skin lesions. Biochemical evaluation revealed 25(OH) vitamin D insufficiency (20 ng/mL), and normal levels of parathyroid hormone, FGF-23, alkaline phosphatase, calcium, and phosphorus. Skeletal survey radiographs and computed tomography (CT) of the chest, abdomen, and pelvis showed extensive soft tissue and muscle heterotopic ossifications involving shoulders, axillae, trunk, abdomen, pelvis, upper and lower extremities, in a clumped, conglomerate distribution within muscle, subcutaneous fat, and in some areas extending to the skin. There was no pulmonary fibrosis on the chest CT. The clinical and radiographic findings were most consistent with POH. A trio-clinical exome sequencing revealed a de novo heterozygous likely pathogenic variant in the FAM111B (OMIM # 615584) (c.1462delT [p.Cys488Valfs*21]). The resulted frameshift change in exon 4 replaced C-terminal region with 21 alternative amino acids. Multiple, previously reported disease-associated variants appear to localize within the trypsin-like cysteine/serine peptidase domain in which this variant occurs, supporting the functional significance of this region, though none have been previously reported to be associated with POH phenotype. Our 3D protein modeling showed obliteration of predicted protein folding and structure, and elimination of the zinc-binding domain, likely severely affecting protein function.This is the first case of POH phenotype associated with a novel de novo pathogenic frameshift variant in FAM111B. Whether the frameshift change in FAM111B predicts POH remains unclear. Further evaluations are necessary to fully elucidate this finding and the potential role and mechanism by which the FAM111B variants contributes to POH phenotype.

CIViC (Clinical Interpretation of Variants in Cancer; civicdb.org) is a crowd-sourced, public domain knowledgebase composed of literature-derived evidence characterizing the clinical utility of cancer variants. As clinical sequencing becomes more prevalent in cancer management, the need for cancer variant interpretation has grown beyond the capability of any single institution. CIViC contains peer-reviewed, published literature curated and expertly-moderated into structured data units (Evidence Items) that can be accessed globally and in real time, reducing barriers to clinical variant knowledge sharing. We have extended CIViC’s functionality to support emergent variant interpretation guidelines, increase interoperability with other variant resources, and promote widespread dissemination of structured curated data. To support the full breadth of variant interpretation from basic to translational, including integration of somatic and germline variant knowledge and inference of drug response, we have enabled curation of three new Evidence Types (Predisposing, Oncogenic and Functional). The growing CIViC knowledgebase has over 300 contributors and distributes clinically-relevant cancer variant data currently representing >3200 variants in >470 genes from >3100 publications.

To investigate the topography and etiologies of acute cerebellar infarcts (ACIs) that presented as isolated acute vestibular syndromes (AVSs).ACI was ascertained on magnetic resonance diffusion-weighted imaging combined with apparent diffusion coefficient sequence and was categorized into the simple (territory and small infarct) and the complicated (concomitant infarcts in territories of posterior circulation besides cerebellum). Infarct topography and etiologies were compared between ACI patients with isolated AVS and non-isolated AVS (general and/or local neurological symptoms and/or signs with or without AVS).We enrolled 129 ACI patients, and 53 patients (53/129, 41.1%) had isolated AVS. In isolated AVS, the infarct lesions could be territory infarcts, small infarcts involving cortical, subcortical, and areas directly related to vestibular structures, and the primary etiologies were of large artery atherosclerosis and small vessel disease. Compared with the patients with non-isolated AVS, those with isolated AVS had more prevalence of small vessel disease (OR 6.30, 2.16-18.39; p = 0.001) and more probability of small infarcts (OR 6.04, 95%CI 2.31-15.76; p 0.0001). In isolated AVS patients, the small infarct located more frequently in cerebellar hemispheres than the areas directly related to vestibular structures (27/35 vs 8/35), and the territory infarct located more frequently in the area supplied by posterior inferior cerebellar artery than the other areas (9/13 vs 4/13).Our study found that ACI could be presented as isolated AVS, which occurred more frequently in patients with small hemisphere infarct or infarct in the territory supplied by posterior inferior cerebellar artery.

Background The incidence and biology of IDH1/2 mutations in pediatric gliomas are unclear. Notably, current treatment approaches by pediatric and adult providers vary significantly. We describe the frequency and clinical outcomes of IDH1/2-mutant gliomas in pediatrics. Methods We performed a multi-institutional analysis of the frequency of pediatric IDH1/2-mutant gliomas, identified by next-generation sequencing (NGS). In parallel, we retrospectively reviewed pediatric IDH1/2-mutant gliomas, analyzing clinico-genomic features, treatment approaches, and outcomes. Results Incidence: Among 851 patients with pediatric glioma who underwent NGS, we identified 78 with IDH1/2 mutations. Among patients 0–9 and 10–21 years old, 2/378 (0.5%) and 76/473 (16.1%) had IDH1/2-mutant tumors, respectively. Frequency of IDH mutations was similar between low-grade glioma (52/570, 9.1%) and high-grade glioma (25/277, 9.0%). Four tumors were graded as intermediate histologically, with one IDH1 mutation. Outcome: Seventy-six patients with IDH1/2-mutant glioma had outcome data available. Eighty-four percent of patients with low-grade glioma (LGG) were managed observantly without additional therapy. For low-grade astrocytoma, 5-year progression-free survival (PFS) was 42.9% (95%CI:20.3–63.8) and, despite excellent short-term overall survival (OS), numerous disease-related deaths after year 10 were reported. Patients with high-grade astrocytoma had a 5-year PFS/OS of 36.8% (95%CI:8.8–66.4) and 84% (95%CI:50.1–95.6), respectively. Patients with oligodendroglioma had excellent OS. Conclusions A subset of pediatric gliomas is driven by IDH1/2 mutations, with a higher rate among adolescents. The majority of patients underwent upfront observant management without adjuvant therapy. Findings suggest that the natural history of pediatric IDH1/2-mutant glioma may be similar to that of adults, though additional studies are needed.

Exome reanalysis is useful for providing molecular diagnoses for previously uninformative samples. However, challenges exist in implementing a practical solution for clinicians and laboratories. This study complements the current literature by providing practical considerations for patient-level and cohort-level reanalyses. The Clinical and Laboratory Standards Institute assembled the Document Development Committee and an interpretation working group that developed the framework for reevaluation of exome-based data. We describe two distinct but complementary approaches toward exome reanalyses: clinician-initiated patient-level reanalysis, and laboratory-initiated cohort-level reanalysis. We highlight the advantages and constraints for both approaches, and provide a high-level conceptual guide for ordering clinicians and laboratories through the critical decision pathways. Because clinical exome sequencing continues to be the standard of care in genetics, exome reanalysis would be critical in increasing the overall diagnostic yield. A systematic guide will facilitate the efficient adoption of reevaluation of exome data for laboratories, health care professionals, genetic counselors, and clinicians.

Detection of somatic genetic drivers is important for risk stratification and treatment selection in pediatric leukemias; however, newly recognized genetic markers may not be detected by routine karyotyping and fluorescence in situ hybridization (FISH). To identify the combination of assays that provides the highest detection rate for clinically significant molecular abnormalities, we tested 160 B- lymphoblastic leukemia (B-ALL) by karyotyping, FISH, chromosomal microarray analysis (CMA) and the custom next-generation sequencing (NGS) panel, OncoKidsⓇ. In addition, we tested 40 myeloid malignancies with karyotyping, chromosomal microarray analysis (CMA), and OncoKidsⓇ; 36/40 myeloid malignancies were also tested with FISH. In B-ALL, individual testing methods had the following diagnostic yields for the key genetic drivers: karyotype 34%; basic FISH panel 45%; FISH panel with IGH and CRLF2 probes 65%; CMA 48%; OncoKidsⓇ 39%. CMA and OncoKidsⓇ testing allowed detection of key genetic drivers in 42% of the samples that remained unknown upon testing by conventional methods. In myeloid malignancies, OncoKidsⓇ had the highest yield for detection of both primary and secondary DNA mutations and RNA fusions. Our data highlights the complementarity between CMA and NGS and conventional cytogenetics/FISH in pediatric leukemia diagnostics. Due to rapid turn-around-time, FISH may be useful as an initial screening method in B-ALL. Our data also suggests NGS testing with a comprehensive panel, despite a longer turnaround time, is a good alternative to karyotyping and FISH in pediatric AML due to its superior detection rate.

The safety of intravenous tissue plasminogen activator (IV-tPA) in patients with stroke of unknown time of onset (SUTO) was unclear and mostly concerned. We sought to investigate the safety in terms of symptomatic intracranial hemorrhage (sICH) and death in SUTO patients treated with IV-tPA. We searched PubMed and EMBASE from inception to 2 December 2020 for eligible studies reporting IV-tPA in SUTO patients compared to conservative medical therapy, or to stroke of known onset time (SKOT) treated with IV-tPA within standard time window. We pooled relative risk (RR) with 95% confidence interval (95%CI) with random-effects model. Twenty-four studies were included, enrolling 77,398 patients. SUTO patients with IV-tPA had higher incidence of sICH than that in SUTO patients without IV-tPA (3.8% versus 0.96%; RR = 3.75, 95%CI: 2.69–5.22) but comparable to that in SKOT patients with IV-tPA (3.8% versus 4.1%; RR = 1.16, 95%CI: 0.94–1.44). There was no significant difference in death risk in SUTO patients with IV-tPA versus SUTO patients without IV-tPA (RR = 1.34, 95%CI: 0.60–3.01) and versus SKOT patients with IV-tPA (RR = 1.19, 95%CI: 0.95–1.50). Compared with SUTO patients without IV-tPA, SUTO patients with IV-tPA had higher likelihood of favorable functional outcome (adjusted RR = 1.28, 95%CI: 1.03–1.60) and functional independence (adjusted RR = 1.95, 95%CI: 1.24–3.06), comparable to that in SKOT patients with IV-tPA in favorable functional outcome (adjusted RR = 0.67, 95%CI: 0.38–1.20) and functional independence (adjusted RR = 0.84, 95%CI: 0.59–1.18). SUTO patients could be treated safely and effectively with IV-tPA under the guidance of imaging evaluation.

STAT1 gain-of-function (GOF) mutations are associated with a rare autosomal dominant immunodeficiency disorder with main clinical manifestations including chronic mucocutaneous candidiasis (CMC) and bronchiectasis. In addition, these patients show higher incidences of cerebral and extracerebral aneurysm, malignancies and various autoimmune conditions compared to the general population. Although previous publications have reported clinical findings in patients with STAT1 GOF mutation, they did not include histopathologic features. Herein, we describe the first case with detailed histologic findings in the lung of a 5-year-old patient with a de novo STAT1 GOF mutation, who presented with CMC and bronchiectasis. The biopsy showed severe bronchiolectasis with extensive airway dilatation and occasional disruptions. Peribronchiolar inflammation was not always present and evident mainly in areas of airway disruption; inflammation may have not been a main driver of the airway damage in this case. The airway dilatation often showed an interesting herniating pattern, possibly implying a connective tissue etiology. This case also demonstrates the diagnostic utility of whole exome sequencing as STAT1 GOF mutations are not detected by routine workup. The definitive diagnosis will lead to more specific treatments and increased surveillance for serious conditions, such as cerebral aneurysms and malignancies.

As guidelines, therapies, and literature on cancer variants expand, the lack of consensus variant interpretations impedes clinical applications. CIViC is a public domain, crowd-sourced, and adaptable knowledgebase of evidence for the Clinical Interpretation of Variants in Cancer, designed to reduce barriers to knowledge sharing and alleviate the variant interpretation bottleneck.

Central retina imaging is important for early Parkinson’s disease (PD) recognition. We aimed to investigate central retina changes using spectral domain-optical coherence tomography (SD-OCT) in PD patients. We systematically searched PubMed and EMBASE to identify studies comparing the whole or individual layer thickness of central retina between PD patients and health controls using SD-OCT from inception to April 25, 2020. Data were extracted at eye level. We pooled the mean difference with random effects model. Subgroup analysis and mete-regression were done to detect possible source of heterogeneity. We included 27 studies (28 sets of data) enrolling 1470 PD patients (2288 eyes) and 1552 health controls (2524 eyes) in our meta-analysis. Compared with control eyes, the whole thickness of central retina decreased significantly at fovea center by mean difference − 2.70 μm (95% CI [− 4.87, − 0.53], p = 0.01) and in all quadrants in PD eyes. The combination of ganglion cell layer and inner plexiform layer thinned by an average mean difference of − 3.17 μm (95% CI [− 5.07, − 1.26], p = 0.001). The nerve fiber layer thinned by an average mean difference − 0.66 μm (95% CI [− 1.09 to − 0.23], p = 0.003). There was no significant difference in the thickness of inner nuclear layer, outer plexiform layer and outer nuclear layer between eyes of PD and controls. The results of subgroup analysis and mete-regression were consistent. The whole thickness, the thickness of the combination of ganglion cell layer and inner plexiform layer, and nerve fiber layer of central retina decreased significantly in PD patients.

To investigate the association between the prevalence of silent brain infarction (SBI) and incompleteness of circle of Willis (CoW) in patients with internal carotid artery stenosis (ICA).We included patients with unilateral intra- or extracranial ICA stenosis ≥ 50% or occlusion without previous history of stroke or transient ischemic attack. SBIs were evaluated on magnetic resonance image. We compared SBI prevalence between patients with complete and incomplete CoW, and between ipsilateral and contralateral hemispheres to stenosed ICA.We included 257 patients with ICA stenosis, among them 120 patients had complete CoW and 137 patients had incomplete CoW. SBI prevalence was significantly higher in patients with incomplete CoW than those with complete CoW (73.0% vs 43.3%, OR 3.09, 95% CI 1.70-5.63). Further, in patients with incomplete CoW, SBIs prevalence was significantly higher in ipsilateral hemisphere than that in contralateral hemisphere (63.5% vs 46.7%, OR = 2.01, 95% CI 1.21-3.34). While, in patients with complete CoW, SBI prevalence was not significantly different between two hemispheres (31.7% vs 23.3%, OR = 1.51, 95% CI 0.83-2.73).In patients with ICA stenosis, SBI prevalence was associated with incompleteness of CoW.

Novel gene-disease discoveries, rapid advancements in technology, and improved bioinformatics tools all have the potential to yield additional molecular diagnoses through the reanalysis of exome sequencing data. Collaborations between clinical laboratories, ordering physicians, and researchers are also driving factors that can contribute to these new insights. Automation in ongoing natural history collection, evolving phenotype updates, advancements in processing next-generation sequencing data, and up-to-date variant-gene-disease databases are increasingly needed for systematic exome reanalysis. Here, we review some of the advantages and challenges for clinician-initiated and laboratory-initiated exome reanalysis, and we propose a model for the future that could potentially maximize the clinical utility of exome reanalysis by integrating information from electronic medical records and knowledge databases into routine clinical workflows.

PURPOSE: Beckwith–Wiedemann syndrome (BWS) is a human genomic imprinting disorder characterized by lateralized overgrowth, macroglossia, abdominal wall defects, congenital hyperinsulinism, and predisposition to embryonal tumors. One of the molecular etiologies underlying BWS is paternal uniparental isodisomy of chromosome 11p15.5 (pUPD11). About 8% of pUPD11 cases are due to genome-wide paternal uniparental isodisomy (GWpUPD). About 30 cases of live-born patients with GWpUPD have been described, most of whom were mosaic and female. We present male patients with BWS due to GWpUPD, elucidate the underlying mechanism, and make recommendations for management. METHODS: Three male patients with GWpUPD underwent clinical and molecular evaluation by single-nucleotide polymorphism (SNP) microarrays in different tissues. Previously published cases of GWpUPD were reviewed. RESULTS: SNP microarray demonstrated a GWpUPD cell population with sex chromosomes XX and biparental cell population with sex chromosomes XY, consistent with dispermic androgenetic chimerism. CONCLUSION: SNP microarray is necessary to distinguish GWpUPD cases and the underlying mechanisms. The percentage of GWpUPD cell population within a specific tissue type correlated with the amount of tissue dysplasia. Males with BWS due to GWpUPD are important to distinguish from other molecular etiologies because the mechanism indicates risk for germ cell tumors and autosomal recessive diseases in addition to other BWS features.

Diffuse leptomeningeal glioneuronal tumors (DLGNTs) are newly recognized as an entity in the 2016 revision of the WHO Classification of tumors of the central nervous system. They typically present as diffuse leptomeningeal infiltrates along the neuraxis with focal and superficial involvement of the parenchyma. Here, we report a DLGNT with unusual radiological and histological features. A 13-year-old girl presented with scoliosis and back pain. Magnetic resonance imaging demonstrated a syrinx from C2 to T11 and an intramedullary mass from T6 to T9-10. No leptomeningeal involvement was recognized. Histological examination of the gross total resection specimen revealed a low-grade neuroepithelial neoplasm predominantly infiltrating the spinal cord and only focally involving the leptomeninges. Chromosome microarray identified co-deletion of the short arm of chromosome 1 and the long arm of chromosome 19 as well as fusion of the KIAA1549 and BRAF genes. Next-generation sequencing demonstrated wild-type alleles at the mutational hotspots of IDH1 (R132) and IDH2 (R140 and R172). In contrast to most reported DLGNTs, the tumor described in this manuscript was characterized by a predominant parenchymal component and only minor leptomeningeal involvement both radiographically and histologically. Our case, therefore, expands the spectrum of radiological and histopathological features of this new entity. It also highlights the critical role of molecular genetic testing in establishing the diagnosis of DLGNT in unusual cases.

Childhood cancers present unique challenges for variant interpretation in a clinical context due to their rarity, low mutation burden, diversity of molecular alterations, and heterogeneity among patients. Consequently, genes and variants associated with childhood tumors are under-represented in public cancer databases and knowledgebases. A focused effort is needed for the structured curation of genetic variant-level data to document diagnostic, prognostic, and therapeutic biomarkers for childhood cancers. The Pediatric Cancer Curation Advancement Subcommittee (PCCAS), a collaboration between the Clinical Interpretations of Variants in Cancer knowledgebase (CIViC; civicdb.org), the ClinGen Somatic Pediatric Cancer Taskforce, Disease Ontology (DO; disease-ontology.org) and CIViCmine (bionlp.bcgsc.ca/civicmine/), is addressing this challenge through enhanced curation, tagging, and automation. PCCAS created a pediatric specific curation standard operating procedure (SOP) to harmonize pediatric evidence entered in CIViC. Our SOP provides general guidance and considerations to define and classify childhood cancers and to represent childhood cancer evidence on a spectrum of age-related incidence and presentation. For instance, pediatric evidence in CIViC is now tagged using Human Phenotype Ontology (HPO) age of onset terms, allowing pediatric evidence to be easily searched, tracked, and sorted. We also initiated the addition of new age of onset terms to enhance the granularity of these tags. WHO ICD-O nomenclature has been chosen for pediatric disease classification in CIViC. ICD-O provides updated terminology including specific genetic subtypes, which are important in pediatric cancers where their underlying molecular profiles often define the disease. To aid curator selection of disease, we verified pediatric relevant ICD-O terms inclusion in DO and restructured DO disease hierarchies to ensure proper mapping. CIViC highlights our pediatric cancer initiative in multiple areas including a homepage feature linking directly to a dedicated pediatric advanced search that returns all evidence tagged with pediatric or young adult age of onset. Most importantly, our childhood specific SOP and initiatives are included in all ClinGen Somatic Cancer and CIViC training sessions for consistent implementation. CIViCmine supports CIViC by using natural language processing to identify important cancer biomarkers in the literature. To better identify pediatric biomarkers, we are adapting and refining CIViCmine to use MeSH terms and other approaches to enhance accuracy in the identification of childhood evidence in both the literature and CIViC. In conclusion, implementation of these procedures, features, and automation are pushing to make childhood cancer variant evidence more accessible and interpretable. Citation Format: Jason Saliba, Jake Lever, Kilannin Krysiak, Arpad Danos, Alex Wagner, Heather E. Williams, Laveniya Satgunaseelan, David Meredith, Cameron J. Grisdale, Chimene Kesserwan, Jianling Ji, Shruti Rao, Catherine Cottrell, Alanna Church, Mark Evans, Yasmina Jaufeerally-Fakim, Lynn M. Schriml, Angshumoy Roy, Gordana Raca, Malachi Griffith, Obi L. Griffith. Enhancing pediatric cancer variant curation and representation through standardized classification and automation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1193.

Chromosomal rearrangements of the NTRK genes generate kinase fusions that are targetable oncogenic drivers in diverse adult and pediatric malignancies. Despite robust clinical response to targeted NTRK inhibition, the emergence of therapeutic resistance poses a formidable clinical challenge. Here we report the characterization of an ETV6-NTRK3 fusion–driven pediatric glioma that progressed through NTRK-targeted treatments with entrectinib and selitrectinib. Genetic analysis of multifocal recurrent/resistant lesions identified a previously uncharacterized NTRK3 p.G623A and a known p.G623E resistance mutation, in addition to other alterations of potential pathogenic impact. Functional studies using heterologous reconstitution model systems and patient-derived tumor cell lines establish that NTRK3G623A and NTRK3G623E mutated kinases exhibit reduced sensitivity to entrectinib and selitrectinib, as well as other NTRK inhibitors tested herein. In summary, this genetic analysis of multifocal recurrent/resistant glioma driven by ETV6-NTRK3 fusion captured a cross section of resistance-associated alterations that, based on in vitro analysis, likely contributed to resistance to targeted therapy and disease progression.

Isocitrate dehydrogenase (IDH) mutations are rare in pediatric and adolescent gliomas. We recently identified three adolescent/young adult (AYA) patients with IDH‐mutant low grade gliomas of the brainstem with several key clinicopathologic and molecular features in common. We discuss these three cases and review the current literature.

The safety of intravenous tissue plasminogen activator (IV-tPA) in patients with stroke of unknown time of onset (SUTO) was unclear and mostly concerned. We sought to investigate the safety in terms of symptomatic intracranial hemorrhage (sICH) and death in SUTO patients treated with IV-tPA. We searched PubMed and EMBASE from inception to 2 December 2020 for eligible studies reporting IV-tPA in SUTO patients compared to conservative medical therapy, or to stroke of known onset time (SKOT) treated with IV-tPA within standard time window. We pooled relative risk (RR) with 95% confidence interval (95%CI) with random-effects model. Twenty-four studies were included, enrolling 77,398 patients. SUTO patients with IV-tPA had higher incidence of sICH than that in SUTO patients without IV-tPA (3.8% versus 0.96%; RR = 3.75, 95%CI: 2.69-5.22) but comparable to that in SKOT patients with IV-tPA (3.8% versus 4.1%; RR = 1.16, 95%CI: 0.94-1.44). There was no significant difference in death risk in SUTO patients with IV-tPA versus SUTO patients without IV-tPA (RR = 1.34, 95%CI: 0.60-3.01) and versus SKOT patients with IV-tPA (RR = 1.19, 95%CI: 0.95-1.50). Compared with SUTO patients without IV-tPA, SUTO patients with IV-tPA had higher likelihood of favorable functional outcome (adjusted RR = 1.28, 95%CI: 1.03-1.60) and functional independence (adjusted RR = 1.95, 95%CI: 1.24-3.06), comparable to that in SKOT patients with IV-tPA in favorable functional outcome (adjusted RR = 0.67, 95%CI: 0.38-1.20) and functional independence (adjusted RR = 0.84, 95%CI: 0.59-1.18). SUTO patients could be treated safely and effectively with IV-tPA under the guidance of imaging evaluation.

Background Recent large-scale genomic studies have revealed a spectrum of genetic variants associated with specific subtypes of central nervous system (CNS) tumors. The aim of this study was to determine the clinical utility of comprehensive genomic profiling of pediatric, adolescent and young adult (AYA) CNS tumors in a prospective setting, including detection of DNA sequence variants, gene fusions, copy number alterations (CNAs), and loss of heterozygosity. Methods OncoKids, a comprehensive DNA- and RNA-based next-generation sequencing (NGS) panel, in conjunction with chromosomal microarray analysis (CMA) was employed to detect diagnostic, prognostic, and therapeutic markers. NGS was performed on 222 specimens from 212 patients. Clinical CMA data were analyzed in parallel for 66% (146/222) of cases. Results NGS demonstrated clinically significant alterations in 66% (147/222) of cases. Diagnostic markers were identified in 62% (138/222) of cases. Prognostic information and targetable genomic alterations were identified in 22% (49/222) and 18% (41/222) of cases, respectively. Diagnostic or prognostic CNAs were revealed by CMA in 69% (101/146) of cases. Importantly, clinically significant CNAs were detected in 57% (34/60) of cases with noncontributory NGS results. Germline cancer predisposition testing was indicated for 27% (57/212) of patients. Follow-up germline testing was performed for 20 patients which confirmed a germline pathogenic/likely pathogenic variant in 9 cases: TP53 (2), NF1 (2), SMARCB1 (1), NF2 (1), MSH6 (1), PMS2 (1), and a patient with 47,XXY Klinefelter syndrome. Conclusions Our results demonstrate the significant clinical utility of integrating genomic profiling into routine clinical testing for pediatric and AYA patients with CNS tumors.

Central retina imaging is important for early Parkinson's disease (PD) recognition. We aimed to investigate central retina changes using spectral domain-optical coherence tomography (SD-OCT) in PD patients.We systematically searched PubMed and EMBASE to identify studies comparing the whole or individual layer thickness of central retina between PD patients and health controls using SD-OCT from inception to April 25, 2020. Data were extracted at eye level. We pooled the mean difference with random effects model. Subgroup analysis and mete-regression were done to detect possible source of heterogeneity.We included 27 studies (28 sets of data) enrolling 1470 PD patients (2288 eyes) and 1552 health controls (2524 eyes) in our meta-analysis. Compared with control eyes, the whole thickness of central retina decreased significantly at fovea center by mean difference - 2.70 μm (95% CI [- 4.87, - 0.53], p = 0.01) and in all quadrants in PD eyes. The combination of ganglion cell layer and inner plexiform layer thinned by an average mean difference of - 3.17 μm (95% CI [- 5.07, - 1.26], p = 0.001). The nerve fiber layer thinned by an average mean difference - 0.66 μm (95% CI [- 1.09 to - 0.23], p = 0.003). There was no significant difference in the thickness of inner nuclear layer, outer plexiform layer and outer nuclear layer between eyes of PD and controls. The results of subgroup analysis and mete-regression were consistent.The whole thickness, the thickness of the combination of ganglion cell layer and inner plexiform layer, and nerve fiber layer of central retina decreased significantly in PD patients.

Background Disorders in the PIK3CA-related overgrowth spectrum because of somatic mosaicism are associated with segmental overgrowth of the body in conjunction with vascular, skeletal, and brain malformations such as hemimegalencephaly. A pathogenic variant may only be detectable in affected tissue and not in peripheral blood or saliva samples; therefore archival tissue may be the only relevant available specimen for testing. Although this is a common approach for cancer testing, it is not typically used for constitutional genetic disorders. Methods PIK3CA mosaicism was assessed with a custom pediatric oncology next-generation sequencing panel (OncoKids) designed to capture somatic mutations in pediatric malignancies. The panel covers a wide range of targets including PIK3CA and AKT1 hotspots. We used OncoKids on archival formalin-fixed, paraffin-embedded or frozen samples from seven patients with facial hemihypertrophy and lipomas, hemimegalencephaly, or hemihypertrophy with a lymphovascular malformation. The age of the archival tissue examined by next-generation sequencing ranged from two to 13 years (median 5 years). Every patient had clinical manifestations within the PIK3CA-related overgrowth spectrum and had a sample of an affected tissue available for testing from a prior surgical intervention. Results PIK3CA mosaicism was detected in all seven patients and the mutant allele fraction was lower in the lymphovascular malformation tissues (8% to 11%) than in brain (20% to 32%) and lipomatous (16% to 23%) tissues. Conclusions Our study highlights the clinical utility of using a robust, oncology-focused next-generation sequencing assay to identify PIK3CA mosaicism in noncancer cases. It is feasible to use archival samples that are more than a decade old to obtain a molecular diagnosis, which can then be used to improve health care management.

The OncoKids panel is an amplification-based next-generation sequencing assay designed to detect diagnostic, prognostic, and therapeutic markers across the spectrum of pediatric malignancies, including leukemias, sarcomas, brain tumors, and embryonal tumors. This panel uses low input amounts of DNA (20 ng) and RNA (20 ng) and is compatible with formalin-fixed, paraffin-embedded and frozen tissue, bone marrow, and peripheral blood. The DNA content of this panel covers the full coding regions of 44 cancer predisposition loci, tumor suppressor genes, and oncogenes; hotspots for mutations in 82 genes; and amplification events in 24 genes. The RNA content includes 1421 targeted gene fusions. We describe the validation of this panel by using a large cohort of 192 unique clinical samples that included a wide range of tumor types and alterations. Robust performance was observed for analytical sensitivity, reproducibility, and limit of detection studies. The results from this study support the use of OncoKids for routine clinical testing of a wide variety of pediatric malignancies.

Deletions of proximal chromosome 3p13p14 are infrequent chromosomal alterations. Variable sizes and breakpoints have been reported in patients with a wide range of phenotypes that are evolving as additional cases are reported. The routine use of high-density chromosomal microarrays (CMA) has allowed the identification of many more cases of this disorder and clinical phenotyping shows evidence for an emerging profile among patients with overlapping deletions of 3p13p14. Here, we review the currently reported cases, their phenotypes and where available, the genomic intervals delineated by CMA. Surprisingly, we found that a significant number of proximal chromosome 3p deletions involve structural rearrangements, especially insertions, that have been identified in balanced parental chromosome complements. This region is historically known as a common human chromosomal fragile site, although an underlying genomic mechanism related to its architecture has not been identified. We conclude that identification of an interstitial 3p deletion in a proband by CMA should prompt consideration of further structural chromosomal evaluation using more traditional cytogenetic techniques. While the variability in breakpoints does not suggest a unifying underlying mechanism for these alterations, identification of the haploinsufficient genes in each patient's deletion interval and their developmental roles can guide genotype-phenotype correlations and impact clinical management.

Chromosomal rearrangements of the NTRK genes generate kinase fusions that are targetable oncogenic drivers in diverse adult and pediatric malignancies. Despite robust clinical response to targeted NTRK inhibition, the emergence of therapeutic resistance poses a formidable clinical challenge. Here we report the characterization of an ETV6-NTRK3 fusion–driven pediatric glioma that progressed through NTRK-targeted treatments with entrectinib and selitrectinib. Genetic analysis of multifocal recurrent/resistant lesions identified a previously uncharacterized NTRK3 p.G623A and a known p.G623E resistance mutation, in addition to other alterations of potential pathogenic impact. Functional studies using heterologous reconstitution model systems and patient-derived tumor cell lines establish that NTRK3G623A and NTRK3G623E mutated kinases exhibit reduced sensitivity to entrectinib and selitrectinib, as well as other NTRK inhibitors tested herein. In summary, this genetic analysis of multifocal recurrent/resistant glioma driven by ETV6-NTRK3 fusion captured a cross section of resistance-associated alterations that, based on in vitro analysis, likely contributed to resistance to targeted therapy and disease progression.

Childhood cancers are driven by unique profiles of somatic genetic alterations, with a significant contribution from predisposing germline variants. Understanding the genomic landscape of pediatric cancers is complicated by their rarity, the heterogeneity of variation within a given disease, and the complex forms of structural variation they contain. Variants in childhood disease may differ from those in adult versions of the same cancer type, or may have different clinical significance. Currently, pediatric variants are underrepresented in cancer variant databases, and an urgent need exists for their publicly available expert curation. To address this, the Pediatric Cancer Taskforce (PCT) was formed within the Clinical Genome Resource (ClinGen) Somatic Cancer Clinical Domain Working Group (CDWG) (https://www.clinicalgenome.org/working-groups/somatic/). The PCT is a multi-institutional group of 39 members with broad experience in childhood cancer and variant curation, whose work consists of standardization and classification of genetic variants in pediatric cancers. The CIViC knowledgebase (www.civicdb.org) is a freely available resource for Clinical Interpretation of Variants in Cancer, which leverages public curation and expert moderation to address the problem of annotating the large volume of clinically actionable cancer variants. PCT curators work together with PCT expert members and the CIViC team on variant curation, and have submitted over 230 Evidence Items and over 10 Assertions to CIViC. To further address issues specific to pediatric curation, the PCT is working with CIViC to develop new pediatric-specific CIViC features and modifications of the data model that will aid in pediatric curation. A pediatric user interface, as well as representation of large scale structural and copy number variation are being developed for version two of CIViC, expected to be released in 1-2 years, which will enable curation of a new class of structural variants often encountered in pediatric cancer. A novel standard operating procedure for childhood cancer curation in CIViC is being developed by PCT experts, curators and the CIViC team. This SOP will cover topics including curation of structural variants, as well as pediatric-specific variant tiering guidelines which take into account the sparse nature of evidence in pediatric cases. A companion resource, CIViCmine (http://bionlp.bcgsc.ca/civicmine/), will be further developed to incorporate pediatric data. These and other joint efforts of the PCT and CIViC will significantly enhance pediatric variant representation for public use, to support the care of children with cancer. Citation Format: Arpad Danos, Wan-Hsin Lin, Jason Saliba, Angshumoy Roy, Alanna J. Church, Shruti Rao, Deborah Ritter, Kilannin Krysiak, Alex Wagner, Erica Barnell, Lana Sheta, Adam Coffman, Susanna Kiwala, Joshua F. McMichael, Laura Corson, Kevin Fisher, Heather E. Williams, Matthew Hiemenz, Katherine A. Janeway, Jianling Ji, Kesserwan A. Chimene, Laura Fuqua, Lisa Dyer, Huiling Xu, Jeffrey Jean, Laveniya Satgunaseelan, Liying Zhang, Ted W. Laetsch, Donald W. Parsons, Ryan Schmidt, Lynn M. Schriml, Kristen L. Sund, Shashikant Kulkarni, Subha Madhavan, Xinjie Xu, Rashmi Kanagal-Shamana, Marian Harris, Yasmine Akkari, Nurit Paz Yacov, Panieh Terraf, Malachi Griffith, Obi L. Griffith, Gordana Raca. Advancing knowledgebase representation of pediatric cancer variants through ClinGen/CIViC collaboration [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 210.

A 12 year-old male presented with a 2-month history of intermittent headaches, nausea, and vomiting. Magnetic resonance imaging (MRI) of the brain revealed a 2.2 x 3.5 x 2.6 cm lobulated, sellar/suprasellar mass, mildly T1/T2 hyperintense, with mild homogeneous enhancement and diffusion restriction. He underwent transsphenoidal and right craniotomies for gross total resection of the mass. Pathology demonstrated a hypercellular neoplasm with spindled to ovoid tumor cells arranged in fascicles and tight whirls, consistent with a spindle cell oncocytoma. OncoKids, a DNA- and RNA-based next generation sequencing panel, demonstrated an in-frame EML4 exon 2-ALK exon 19 fusion with a total of 179,872 supporting reads. The EML4-ALK fusion gene is predicted to encode a chimeric tyrosine kinase that facilitates multimerization and autophosphorylation of ALK, and activates its downstream targets, such as RAS/ERK, PI3K/AKT, and JAK/STAT pathways. This fusion is found in approximately 5% of patients with non-small cell lung cancer, a subset of inflammatory myofibroblastic tumors, as well as single cases of pulmonary atypical carcinoid, cholangiocarcinoma, and high-grade glioma. However, it has not been previously described in oncocytoma. Chromosomal microarray analysis demonstrated two interstitial non-contiguous deletions in 2p, and an interstitial deletion in 18q that does not include any known cancer-related genes. The deleted segment in 2p23.3p23.2 includes DNMT3A, which mediates DNA methylation and functions in modification of gene expression. DNMT3A mutations are frequent in hematological malignancies, however their role in oncocytoma is currently unknown. The proximal breakpoint of the deletion in 2p23.3p23.2 is in close proximity to but does not reside within ALK. Spindle cell oncocytoma is rarely reported in the pediatric population, with only one case described in the literature. This is the first case report of an oncocytoma with an EML4-ALK fusion. Additional studies are warranted to confirm its functional effect.

The 2016 World Health Organization (2016 WHO) classification of hematopoietic malignancies classifies neoplasms with a fusion between the FIP1L1 and PDGFRA genes in 4q12 into a group called “myeloid and lymphoid neoplasms with eosinophilia and abnormalities of PDGFRA, PDGFRB or FGFR1 or with PCM1-JAK2”. Neoplasms characterized by this fusion are pluripotent stem cell disorders that can show both myeloid and lymphoid differentiation. They typically occur in adult patients and most are characterized by eosinophilia. We describe identification of a FIP1L1-PDGFRA fusion in a 13-year-old boy who presented with T-lymphoblastic leukemia/lymphoma without eosinophilia. Detection of FIP1L1-PDGFRA driven neoplasms at diagnosis is usually critical for proper treatment, since almost all reported cases responded to tyrosine kinase inhibitors. However, our patient’s leukemia was refractory to standard chemotherapy, and did not show a meaningful response to tyrosine kinase inhibitor therapy. Testing for a FIP1L1-PDGFRA rearrangement is at present limited to patients with idiopathic hypereosinophilia, and we hypothesize that this abnormality may be under-diagnosed in children with acute leukemias.

We report a family in which two brothers had an undiagnosed genetic disorder comprised of dysmorphic features, microcephaly, severe intellectual disability (non-verbal), mild anemia, and cryptorchidism. Both developed osteosarcoma. Trio exome sequencing (using blood samples from the younger brother and both parents) was performed and a nonsense NM_000489.4: c.7156C>T (p.Arg2386*) mutation in the ATRX gene was identified in the proband (hemizygous) and in the mother’s peripheral blood DNA (heterozygous). The mother is healthy, does not exhibit any clinical manifestations of ATR-X syndrome and there was no family history of cancer. The same hemizygous pathogenic variant was confirmed in the affected older brother’s skin tissue by subsequent Sanger sequencing. Chromosomal microarray studies of both brothers’ osteosarcomas revealed complex copy number alterations consistent with the clinical diagnosis of osteosarcoma. Recently, somatic mutations in the ATRX gene have been observed as recurrent alterations in both osteosarcoma and brain tumors. However, it is unclear if there is any association between osteosarcoma and germline ATRX mutations, specifically in patients with constitutional ATR-X syndrome. This is the first report of osteosarcoma diagnosed in two males with ATR-X syndrome, suggesting a potential increased risk for cancer in patients with this disorder.

We identified a PSEN1 (presenilin 1) mutation carrier from the world's largest autosomal dominant Alzheimer's disease kindred, who did not develop mild cognitive impairment until her seventies, three decades after the expected age of clinical onset. The individual had two copies of the APOE3 Christchurch (R136S) mutation, unusually high brain amyloid levels and limited tau and neurodegenerative measurements. Our findings have implications for the role of APOE in the pathogenesis, treatment and prevention of Alzheimer's disease.

Advancing the clinical utility of whole-exome sequencing (WES) for patients with suspected genetic disorders is largely driven by bioinformatics approaches that streamline data processing and analysis. Herein, we describe our experience with implementing a semiautomated and phenotype-driven WES diagnostic workflow, incorporating both the DRAGEN pipeline and the Exomiser variant prioritization tool, at an academic children's hospital with an ethnically diverse pediatric patient population. We achieved a 41% molecular diagnostic rate for 66 duo-, quad-, or trio-WES cases, and 28% for 40 singleton-WES cases. Preliminary results were returned to ordering physicians within 1 wk for 12 of 38 (32%) probands with positive findings, which were instrumental in guiding the appropriate clinical management for a variety of patients, especially in critical care settings. The semiautomated and streamlined WES workflow also enabled us to identify novel variants in candidate disease genes in patients with developmental delay and autism and immune disorders and cancer, including ANK2, BPTF, BCL11A, FOXN1, PLAA, ATRX, DNAJC21, and RAD50. Together, we demonstrated the implementation of a streamlined WES workflow that was successfully applied for both clinical and research purposes.