Multiplex fusion gene testing in pediatric acute myeloid leukemia

Abstract

Background: Gene abnormalities, particularly chromosome rearrangements generating gene fusion, are associated with clinical characteristics and prognosis in pediatric acute myeloid leukemia (AML). Karyotyping is generally performed to enable risk stratification, but the results are not always consistent with those of reverse transcriptionpolymerase chain reaction (RT-PCR), and more accurate and rapid methods are required.Methods: A total of 487 samples from de novo AML patients enrolled in the Japanese Pediatric Leukemia/Lymphoma Study Group (JPLSG) AML-05 study (n = 448), and from acute promyelocytic leukemia (APL) patients enrolled in the JPLSG AML-P05 study (n = 39) were available for this investigation. Multiplex quantitative RT-PCR was performed to detect eight important fusion genes: MLL-ELL, MLL-AF6(MLLT4), FUS(TLS)-ERG, NUP98-HOXA9, and PML-RARA.Results: Fusion genes were detected in 207 (46.2%) of the 448 AML-05 patient samples. After exclusion of two samples with PML-RARA, no chromosomal abnormalities were identified on karyotyping in 19 of 205 patients (9.3%) positive for fusion genes on RT-PCR. Fusion genes were confirmed on fluorescence in situ hybridization (FISH) in 11 of these 19 patients. In contrast, fusion genes were detected in 37 of 39 patients (94.9%) from the AML-P05 study, and 33 of these results were consistent with the karyotyping. There were discrepancies in four patients (10.8%), three with normal karyotypes and one in whom karyotyping was not possible. All four of these patients were PML-RARA positive on FISH.Conclusions: Multiplex quantitative RT-PCR-based fusion gene screening may be effective for diagnosis of pediatric AML.

A genomic DNA‑based NGS method for the simultaneous detection of multiple fusion genes in pediatric leukemia

“…Each additional fusion gene detected was different (i.e., CBFA2T3/GLIS2, NIFA/CBFA2T1, ZEB2/RUNX1, MYO1F/KMT2A, NUP98/NSD1, HOXA11AS/PBX1 and EWSR/ELF5), demonstrating the more comprehensive capability of MTCS-270 in fusion gene detection. Notably, by combining both the MTCS-270 and MRTP-57 detection approaches, the frequently observed fusion genes in AML, such as the AML1/ETO, PML/RARA, CBFβ/MYH11 and MLL-related fusion genes, were detected in 5/46 (10.9%), 4/46 (8.7%), 2/46 (4.3%) and 9/46 (19.6%) samples, respectively, which was generally consistent with the findings reported in the literature (12,13). Furthermore, MTCS-270 was able to differentiate isoforms of affected fusion genes, which was beyond the detection capability of MRTP-57.…”

Genome-Wide Detection of Copy Number Variations and Evaluation of Candidate Copy Number Polymorphism Genes Associated With Complex Traits of Pigs

“…The role of CNV's is an increasingly discussed academic topic, and previous studies on CNV have been conducted in humans, cattle, sheep, and other species (37)(38)(39)(40). CNVs could destroy the normal expression of genes and ultimately cause phenotypic changes mainly through dosage effects, interruption, and position effects of gene deletion and duplication (41)(42)(43). As a type of essential variation in the genome, CNV polymorphisms play key roles in species evolution, environmental adaptation, disease resistance, and disease susceptibility (44)(45)(46).…”

A Simple RNA Target Capture NGS Strategy for Fusion Genes Assessment in the Diagnostics of Pediatric B‐cell Acute Lymphoblastic Leukemia

“…The characterization of their breakpoint coordinates enabled the design of diagnostic screening by both quantitative multiplex polymerase chain reaction (qPCR) and fluorescence in situ hybridization (FISH). 14 The recent introduction of NGS allowed a fast and accurate screening of the patient's genome at the nucleotide level, which lead to the discovery of a broad array of previously unknown fusion genes. 15 This reflects the increased capability of NGS to recognize subtle chromosomal rearrangements.…”