Optical Genome Mapping for Comprehensive Assessment of Chromosomal Aberrations and Discovery of New Fusion Genes in Pediatric B-Acute Lymphoblastic Leukemia

Abstract

Purpose: To assess the potential added value of Optical Genomic Mapping (OGM) for identifying chromosomal aberrations. Methods: We utilized Optical Genomic Mapping (OGM) to determine chromosomal aberrations in 46 children with B-cell Acute lymphoblastic leukemia ALL (B-ALL) and compared the results of OGM with conventional technologies. Partial detection results were verified by WGS and PCR. Results: OGM showed a good concordance with conventional cytogenetic techniques in identifying the reproducible and pathologically significant genomic SVs. Two new fusion genes (LMNB1::PPP2R2B and TMEM272::KDM4B) were identified by OGM and verified by WGS and RT-PCR for the first time. OGM has a greater ability to detect complex chromosomal aberrations, refine complicated karyotypes, and identify more SVs. Several novel fusion genes and single-gene alterations, associated with definite or potential pathologic significance that had not been detected by traditional methods, were also identified. Conclusion: OGM addresses some of the limitations associated with conventional cytogenomic testing. This all-in-one process allows the detection of most major genomic risk markers in one test, which may have important meanings for the development of leukemia pathogenesis and targeted drugs.

Optical Genome Mapping Identifies Novel Recurrent Structural Alterations in Childhood ETV6::RUNX1+ and High Hyperdiploid Acute Lymphoblastic Leukemia

“…These included 2 cryptic deletions within the highly repetitive region of the IKZF1 gene 33 that were missed by SNP‐array likely due to poor probe coverage and low allele frequency. Other studies showed that OGM may become a particularly useful tool to identify patients belonging to the prognostically relevant IKZF1 plus group in a simple, fast, and cost‐effective way 12 , 17 . Of note, IKZF1 plus detection is usually assessed either by SNP‐array or multiplex ligation‐depended probe amplification, 25 which are comparable in respect to detection limit and sensitivity of ≈20%.…”

“…The cohesin complex is involved in chromosome segregation in dividing cells, but is also implicated in more wide‐ranging functions, such as DNA damage repair and regulation of gene expression, as indicated by the loss‐of‐function developmental syndrome, Cornelia de Lange 44 . Previous studies based on the short‐read sequencing, conventional technologies, and OGM reported somatic alterations of STAG2 in BCP‐ALL 3 , 17 , 38 and showed that germline SNVs/indels in cohesin complex members, such as NIPBL or RAD21, could be involved in BCP‐ALL predisposition 45 , 46 . Consistently, studies in conditional knockout mice demonstrated that Stag2 deletion in hematopoietic stem/progenitor cells increased their self‐renewal capacity and impaired B‐cell differentiation by decreasing chromatin accessibility and transcription of important B‐cell transcription factors, such as PAX5 47 .…”

“…The applicability of this approach has recently been shown for various hematological malignancies, and some researchers even advocate for further replacing the existing routine diagnostics methods of those neoplasms with optical genome mapping (OGM). 11–17…”

“…The applicability of this approach has recently been shown for various hematological malignancies, and some researchers even advocate for further replacing the existing routine diagnostics methods of those neoplasms with optical genome mapping (OGM). [11][12][13][14][15][16][17] Here, we present a study focusing on 60 HD and ETV6::RUNX1+ BCP-ALL cases analyzed by whole exome sequencing (WES) and OGM to decipher the landscape of genomic alterations in both entities, with a special focus on their SVs. We report several novel recurrently altered genes, which are not described in previous studies that applied SNP-arrays or WGS.…”

“…The recently introduced genome‐wide optical mapping technology analyzes long linear DNA molecules (>150 kb) and covers more repetitive and complicated regions, which allows for the detection of SVs, including inversions, insertions, deletions and translocations, with a size cut‐off of 500 bp in length for de novo assembled genomes. The applicability of this approach has recently been shown for various hematological malignancies, and some researchers even advocate for further replacing the existing routine diagnostics methods of those neoplasms with optical genome mapping (OGM) 11–17 …”