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• The study of archival pediatric HGG samples provided valuable insights, including novel genetic features and subtypes, in this rare tumor type. • The use of gold standard karyotyping combined with array and sequencing in a lab without methylation array allowed for reclassification of all tumors. • The use of the 2021 WHO classification of CNS tumors refined each integrated tumor diagnosis. Though rare, pediatric high-grade gliomas (pHGG) are a leading cause of cancer-related mortality in children. We wanted to determine whether our currently available clinical laboratory methods could better define diagnosis for pHGG that had been archived at our institution for the past 20 years (1998 to 2017). We investigated 33 formalin-fixed paraffin-embedded pHGG using ThermoFisher Oncoscan SNP microarray with somatic mutation analysis, Sanger sequencing, and whole genome sequencing. These data were correlated with historical histopathological, chromosomal, clinical, and radiological data. Tumors were subsequently classified according to the 2021 WHO Classification of Paediatric CNS Tumours. All 33 tumors were found to have genetic aberrations that placed them within a 2021 WHO subtype and/or provided prognostic information; 6 tumors were upgraded from WHO CNS grade 3 to grade 4. New pHGG genetic features were found including two small cell glioblastomas with H3 G34 mutations not previously described; one tumor with STRN-NTRK2 fusion; and a congenital diffuse leptomeningeal glioneuronal tumor without a chromosomal 1p deletion but with KIAA1549-BRAF fusion. Overall, the combination of laboratory methods yielded key information for tumor classification. Thus, even small studies of these uncommon tumor types may yield new genetic features and possible new subtypes that warrant future investigations. [ABSTRACT FROM AUTHOR]

Juvenile myelomonocytic leukemia (JMML) is a rare aggressive childhood leukemia characterized by an excess proliferation of cells of granulocytic and monocytic lineages. The WHO classifies JMML with the myelodysplastic/myeloproliferative neoplasms. Myelodysplasia in JMML is usually minimal to mild. Auer rods have never been reported in JMML. We present a 2-year-old boy with splenomegaly, leukocytosis, thrombocytopenia, anemia, and excess myeloblasts with easily seen Auer rods, and marked dysgranulopoiesis and dyserythropoiesis. Conventional cytogenetic analysis showed a sole abnormality of t(3;5)(q25;q35). Microarray analysis showed a terminal 21 Mb region of copy-neutral loss of heterozygosity on 19q. Disease-related somatic NRAS mutation was detected. This case represents an unusual JMML with Auer rods and marked myelodysplasia. These unusual histopathologic features may be related to the t(3;5)(q25;q35). A t(3;5) with variable breakpoints has been reported in a small proportion of acute myeloid leukemias and myelodysplastic syndromes. To our knowledge, this is the first JMML case reported with this translocation. [ABSTRACT FROM AUTHOR]

Abstract: Dermatofibrosarcoma protuberans (DFSP) is a low-grade dermal and subcutaneous spindle cell neoplasm that most commonly occurs in the extremities and trunk of adults. It is rare in children and infants, and only few cases are reported as congenital. A 2-year-old girl presented with a rapidly enlarging left breast mass. The histology of the excised mass revealed a moderately cellular spindle cell tumor with large hypercellular fibrosarcoma-like areas, few myxoid areas, and other areas with multinucleated giant cells. By immunohistochemistry, the tumor cells were focally positive for CD34 and were negative in the fibrosarcomatous areas. The diagnosis of DFSP was confirmed by demonstrating an unbalanced translocation der(22)t(17;22)(q21.3;q13.1) by conventional cytogenetic and fluorescence in situ hybridization analyses. Positive immunoreactivity with PDGFR-β antibody indicated constitutional activation of PDGF receptor and provided an alternate indirect method of confirming the presence of dysregulated PDGF gene involved in this translocation. Although DFSP has been described in the adult female breast, this is the first such case in the breast of a 2-year-old girl. Dermatofibrosarcoma protuberans should be considered in the differential diagnosis of subcutaneous/dermal spindle cell tumors in children regardless of the site. CD 34 immunostaining should not be relied on, as it may be negative in fibrosarcomatous areas. Confirmation of the diagnosis in unusual sites requires identification of the characteristic t(17;22) chromosomal translocation. [Copyright &y& Elsevier]

Abstract: Chromosome anomalies have been shown to have prognostic significance in children with acute lymphoblastic leukemia (ALL). Chromosome 21 was evaluated for its ability to predict outcome when found in either a single copy (the Mono21 group) or when involved in a structural aberration (the Misc21 group). Both anomalies were associated with an increased risk of failure for patients with standard-risk ALL, rather than higher-risk ALL. Event-free survival was 50.0% at 5 years and 48.4% at 8 years for standard-risk patients with Mono21+Misc21, compared with 77.8 and 75.5%, respectively, for standard-risk patients without these anomalies of chromosome 21. There was no significant difference in outcome between the Mono21 and the Misc21 group (P = 0.10). Mono21 and Misc21 were determined to be independently prognostic whether or not the primary leukemic clone had fewer than 45 chromosomes. The frequency of an adverse outcome was comparable to other poor prognosis subgroups such as hypodiploidy (<45 chromosomes), t(9;22), or t(4;11), all of which have been targeted for aggressive therapy even if the case is otherwise standard risk. [Copyright &y& Elsevier]

• Quality assurance tool for improved patient results. • Design of a methods database, its use, and advantages of maintenance. • Methods provided in supplementary files. Chromosome analysis of solid tumors provides valuable information for diagnosis and patient management, yet successfully culturing solid tumors can be challenging. The Children's Mercy (CM) Cytogenetics laboratory has compiled a database of 1371 non-lymphoma solid tumors cultured since 2002. Analysis of the tumor culture data found a culture success rate of 91.6%. Abnormal karyotypes were identified in 47.0% of these tumors. A quality improvement project reviewed the database for methods, cell culture success, yield of clonally abnormal karyotypes, culture failure, tumor diagnostic category, and other. This review revealed processes that could be optimized with minor changes to methods in a subset of tumors. Three tumor/method pair examples are provided including adrenal cortical carcinomas (ACCs), choroid plexus tumors (CPTs), and neuroblastoma. The successful culture of tumors as defined by capture of clonally abnormal cells is dependent upon several factors including culture medium, monolayer versus suspension culture, length of time in culture, method of disaggregation and other. The database serves as a quality assurance tool that enables continuous improvement in culture success rate and abnormal yield. It is also an educational resource for laboratory technologists, residents and fellows. Using the database to track methods and results ensures consistency in routine tumor processing, facilitates oversight to optimize methods for quality, and improves results for patient care. [ABSTRACT FROM AUTHOR]

Copy number variations (CNVs) of the CNTN6 gene - a member of the contactin gene superfamily - have been previously proposed to have an association with neurodevelopmental and autism spectrum disorders. However, no functional evidence has been provided to date and phenotypically normal and mildly affected carriers complicate the interpretation of this aberration. In view of conflicting reports on the pathogenicity of CNVs involving CNTN6 and association with different phenotypes, we, independently, evaluated clinical features of nineteen patients with detected CNV of CNTN6 as part of their clinical microarray analysis at Children's Mercy and Nationwide Children's Hospitals for the period of 2008–2015. The clinical presentations of these patients were variable making it difficult to establish genotype-phenotype correlations. CNVs were inherited in six patients. For thirteen patients, inheritance pattern was not established due to unavailability of parental samples for testing. In three cases CNV was inherited from a healthy parent and in three cases from a parent with neurodevelopmental symptoms. Of the nineteen patients, four had a separate genetic abberation in addition to CNV of the CNTN6 that could independently explain their respective phenotypes. Separately, CNTN6 sequencing was performed on an autism spectrum disorder (ASD) research cohort of 94 children from 80 unrelated families. We found no difference in frequency of rare coding variants between the cohort of patients and controls. We conclude that CNVs involving CNTN6 alone seem to be most likely a neutral variant or a possible modifier rather than a disease-causing variant. Patients with CNVs encompassing CNTN6 could benefit from additional genetic testing since a clinical diagnosis due to a CNV of CNTN6 alone is still questionable. [ABSTRACT FROM AUTHOR]