Yang Cao

Chediak–Higashi syndrome (CHS) is a hereditary predisposition to hemophagocytic lymphohistiocytosis. We report an adolescent who presented with bicytopenia and progressed to an accelerated phase due to CHS. Neutrophils demonstrated impaired NETosis. Pseudoexon activation in the LYST gene was identified as the underlying molecular mechanism.

Germline variants in DEPDC5 are a cause of familial focal epilepsy with variable foci. Affected individuals may have focal cortical dysplasia if a second brain somatic variant occurs. As access to brain tissue is limited, the second somatic hit in the brain is usually presumed if a clear pathogenic germline variant is present. Here, we present a patient with structural focal epilepsy due to focal cortical dysplasia. He underwent epilepsy surgery at age 2 months. Clinical genetic testing revealed a germline variant of uncertain significance (VUS) DEPDC5 c.920T>G, p. (Leu307Arg). We hypothesized that if the proband's germline DEPDC5 variant was disease‐causal, a second somatic variant may be identifiable in affected cortical tissue. DNA was extracted from archived brain formalin‐fixed paraffin‐embedded tissue and subjected to deep gene panel analysis. This revealed an additional somatic pathogenic variant in DEPDC5 , which was confirmed using droplet digital PCR. Identification of the second somatic hit in brain tissue ( DEPDC5 c.982C>T, p.(Arg328*)) confirmed the two‐hit situation in this patient and supported disease causality of the germline variant. In conclusion, testing tissue for somatic variants may be clinically relevant at a patient‐specific level if a germline VUS affects a gene where a two‐hit mechanism is known.

Chromosome 11q13 microdeletion syndrome, or otodental syndrome, involves dental, auditory, and ocular anomalies linked to deletions in the 11q13.2q13.4 region. We report a 1‐year‐old girl with a 43 kb deletion of the FGF3 gene on chromosome 11q13.3, exhibiting otodental dysplasia, hearing difficulty, and developmental delay. Her family history includes permanent childhood hearing loss and otodental syndrome. Chromosomal microarray analysis (CMA) and sequencing confirmed a complete heterozygous deletion of FGF3. This case suggests that FGF3 haploinsufficiency is sufficient to cause the syndrome's key clinical features, emphasizing the need for further research and long‐term follow‐up.

Background: The joint College of American Pathologists/American College of Medical Genetics and Genomics Cytogenetics Committee works to ensure the competency and proficiency of clinical cytogenetic testing laboratories through proficiency testing (PT) programs for various clinical tests offered by such laboratories, including the evaluation of cytogenetic abnormalities in solid tumors. Methods: Review and analyze 25 years (1999–2023) of solid tumor chromosome analysis PT results, utilizing G-banded karyograms. A retrospective review of results from 1999 to 2023 was performed, identifying the challenges addressing solid tumors. The chromosomal abnormalities and overall performance were evaluated. Results: A total of 21 solid tumor challenges were administered during the period 1999–2018. No solid tumor challenges were administered during the period 2019–2023. Challenges consisted of metaphase images and accompanying clinical history for the evaluation of numerical and/or structural abnormalities. All 21 cases reached 80% grading consensus for abnormality recognition. However, five cases (24%) failed to reach consensus for nomenclature reporting by participating laboratories. These cases illustrate errors in reporting chromosomal abnormalities, including whole-arm translocations and those involving sex chromosomes. In addition, they highlight the challenges with differentiation of terminal and interstitial deletions, difficulties in identifying correct breakpoints, and omission of brackets in neoplastic cases. Conclusions: This comprehensive 25-year review demonstrates the exceptional proficiency of cytogenetic laboratories in accurately identifying chromosome abnormalities in solid tumors, while also highlighting the challenges of reporting specific types of chromosomal abnormalities.

Pathogenic variants in the receptor tyrosine kinase TIE2, encoded by TEK, are known to cause vascular malformations (VMs). In this study, we retrospectively reviewed the deidentified data generated through clinical NGS testing in our laboratory and found 88 VM cases with a total of 107 clinically significant TEK variants. Among those, 23 unique variants at the amino acid level were identified, including five novel (p.Cys1040Arg, p.Arg1099PhefsTer12, p.Glu1109Ter, p.Phe1111LeufsTer7, p.Phe1111ValfsTer7) and 18 previously published variants. Missense variants were identified more often in the tyrosine kinase domain, while all nonsense/frameshift variants were clustered in the C‐terminal tail (CTT). In addition, most variants occurred as solitary alterations, whereas certain variants always co‐occurred with a second TEK variant. Five patterns of TEK variants (P1–P5) were identified: (P1) Arg849 + another variant; (P2) Tyr897 + another variant; (P3) Leu914 single variants; (P4) Arg915/918 single variants; and (P5) CTT single /co‐occurring variants. This study provides the most comprehensive view of pathogenic TEK variants in VMs to date.