Ding, Qiliang

Background: Acute myeloid leukemia (AML) with CBFB::MYH11 fusion and myeloid/lymphoid neoplasms with eosinophilia and tyrosine kinase gene fusions (MLN-TK) are genetically defined and typically mutually exclusive entities. Case Presentation: We report a unique case of de novo AML harboring two clonal, transcriptionally active class-defining fusions: CBFB::MYH11 and GOLGA4::PDGFRB. A 61-year-old woman presented with leukocytosis with neutrophilia, eosinophilia, and monocytosis; circulating blasts; and a markedly hypercellular marrow. Cytogenetic analysis revealed inv(16)(p13.1q22) and t(3;5)(p21;q32) in all 20 metaphases, and RNA sequencing confirmed expression of both CBFB::MYH11 and GOLGA4::PDGFRB fusions. In addition, an oncogenic WT1 frameshift variant was identified. Hematopathologic findings were largely consistent with AML with CBFB::MYH11 fusion but exhibited features reminiscent of PDGFRB-rearranged MLN-TK. The patient achieved complete remission following the standard 7 + 3 induction chemotherapy regimen for AML with gemtuzumab ozogamicin. Conclusions: This case illustrates the diagnostic challenges posed by concomitant class-defining alterations in hematologic neoplasms and underscores the importance of integrated genomic assessment.

Abstract Background Pathogenic variants in the DMD gene are associated with Duchenne and Becker muscular dystrophy (DMD/BMD). Professional medical societies currently recommend DMD carrier screening for all patients who are pregnant or considering pregnancy. Such testing may identify intragenic duplications of DMD (i.e., involving one or more exons but fully contained with the gene) in patients without a personal or family history of DMD/BMD. These incidentally detected DMD intragenic duplications, however, pose significant challenges for variant interpretation. Pathogenicity of an intragenic duplication depends on its structural configuration. Tandem duplications may cause reading frame disruption and gene loss-of-function; conversely, non-tandem duplications may not disrupt gene function. Current carrier screening assays cannot determine the structural configuration of an intragenic duplication. The current guidelines (e.g., the ClinGen PVS1 decision tree) presume intragenic duplications are in tandem unless proven otherwise. If this presumption of tandem configuration is inaccurate, it may lead to overestimation of variant pathogenicity, potentially resulting in unnecessary invasive procedures (e.g., amniocentesis for prenatal diagnosis) and/or having other negative impacts with regards to prenatal decision-making. This study aims to evaluate the validity of this presumption for incidentally detected DMD intragenic duplications. Methods We performed high-coverage whole-genome long-read sequencing on the PromethION instrument (Oxford Nanopore Technologies) for 15 cases with previously identified DMD intragenic duplications. Among these cases, four had personal or family history of DMD/BMD, while 11 had no known history (i.e., incidentally detected). The structural configurations of the duplications were determined by an in-house bioinformatics tool and manual inspection of the alignment files. Results In all 4 cases with a known personal or family history of DMD/BMD, the DMD intragenic duplications were confirmed to be in tandem, aligning with expectations of their pathogenicity. Interestingly, among the 11 cases with incidentally detected DMD intragenic duplications, seven (64%) were found to involve interspersed duplications. In five of these seven interspersed duplication cases, the involved DMD exons were co-duplicated with distinct segments of the Xp arm located 0.5–30 Mb away, forming complex structural variants. In another case, the duplicated DMD exons have inserted into the Xq arm, about 90 Mb downstream of DMD. The final case involved the duplicated DMD exons inserted into a repetitive region most consistent with 9q12 (i.e., the 9qh region). Conclusions Our study reveals that while DMD intragenic duplications in patients with a personal or family history of DMD/BMD were consistently in tandem, a substantial 64% of incidentally detected DMD intragenic duplications were not in tandem. These findings have important implications for both clinicians and laboratorians. They challenge the presumption of tandem configuration for DMD intragenic duplications in individuals where the variants were identified incidentally, e.g., through carrier screening in those without a family history of DMD/BMD. In these cases, we recommend classifying the DMD intragenic duplications as variants of uncertain significance (VUS), unless there is evidence of tandem configuration.

ABSTRACT Objective Although fetal sex chromosome complement prediction by prenatal cell‐free DNA (cfDNA) screening is highly accurate, discordance between the cfDNA‐inferred chromosomal sex and phenotypic sex observed via ultrasonography or at birth, that is, “fetal sex discordance”, does rarely occur. Such discordance may be caused by differences in sex development (DSD) or technical or biological artifacts. This study aims to provide insights into the proportion of fetal sex discordance cases caused by DSD versus non‐DSD artifacts. Method We retrospectively reviewed 122,748 cases that underwent diagnostic testing at the Mayo Clinic Cytogenetics Laboratory between 2015 and 2023. Thirty‐three singleton‐gestation cases tested for fetal sex discordances were identified. Results Fetal sex discordance was attributed to non‐DSD artifacts in 24 (73%) of the 33 patients. In these cases, the phenotypic sex matched the chromosomal sex revealed by diagnostic cytogenetic testing. The remaining 9 patients included one with mosaic 46,X,psu idic(Y)(q11.21)/45,X, 5 with 46,XY DSD, and 3 with 46,XX DSD. Conclusion The majority of fetal sex discordance cases are caused by non‐DSD artifacts rather than DSD. Accurate clinical counseling of fetal sex discordance requires distinguishing between DSD and non‐DSD causes, emphasizing the need for diagnostic cytogenetic testing.

Abstract Objectives Protein-truncating variants in the TTN gene are a well-established cause of dilated cardiomyopathy (DCM). We report a novel case of DCM caused by a mobile element insertion (MEI) in TTN, through which we highlight the key features of MEIs in next-generation sequencing data. Because of the rarity of MEIs, the next-generation sequencing data features associated with these events may be mistaken as noise, potentially leading to missed diagnoses. Methods Next-generation sequencing gene panel testing for DCM was performed on a 17-year-old male patient presenting with severe left ventricular dilatation and systolic dysfunction. Manta was used for structural variant detection, followed by manual review of NGS data for potential structural variants. Results Manta detected a potential insertion in TTN. Manual review identified hallmark features consistent with a LINE-1 MEI. This finding was orthogonally confirmed by long-range polymerase chain reaction and gel electrophoresis, which indicated an insertion of approximately 4 to 5 kilobase pairs. The insertion disrupted the reading frame of TTN within an A-band exon, resulting in protein truncation that was classified as likely pathogenic. Conclusions This case expands the mutational spectrum of TTN protein-truncating variants. It also underscores the importance of recognizing rarer types of pathogenic variants (eg, MEIs) to produce accurate genetic diagnostics.

Cystic fibrosis is caused by biallelic pathogenic variants in the CFTR gene, which contains a polymorphic (TG)mTn sequence (the “poly-T/TG tract”) in intron 9. While T9 and T7 alleles are benign, T5 alleles with longer TG repeats, e.g., (TG)12T5 and (TG)13T5, are clinically significant. Thus, professional medical societies currently recommend reporting the TG repeat size when T5 is detected. Sanger sequencing is a cost-effective method of genotyping the (TG)mTn tract; however, its polymorphic length substantially complicates data analysis. We developed CFTR-TIPS, a freely available web-based software tool that infers the (TG)mTn genotype from Sanger sequencing data. This tool detects the (TG)mTn tract in the chromatograms, quantifies goodness of fit with expected patterns, and visualizes the results in a graphical user interface. It is broadly compatible with any Sanger chromatogram that contains the (TG)mTn tract ± 15 bp. We evaluated CFTR-TIPS using 835 clinical samples previously analyzed in a CLIA-certified, CAP-accredited laboratory. When operated fully automatically, CFTR-TIPS achieved 99.8% concordance with our clinically validated manual workflow, while generally taking less than 10 s per sample. There were two discordant samples: one due to a co-occurring heterozygous duplication that confounded the tool and the other due to incomplete (TG)mTn tract detection in the reverse chromatogram. No clinically significant misclassifications were observed. CFTR-TIPS is a free, accurate, and rapid tool for CFTR (TG)mTn tract genotyping using cost-effective Sanger sequencing. This tool is suitable both for automated use and as an aid to manual review to enhance accuracy and reduce analysis time.