Optical Genome Mapping Reveals and Characterizes Recurrent Aberrations and New Fusion Genes in Adult ALL

Abstract

(1) Background: In acute lymphoblastic leukemia (ALL) the genetic characterization remains challenging. Due to the genetic heterogeneity of mutations in adult patients, only a small proportion of aberrations can be analyzed with standard routine diagnostics. Optical genome mapping (OGM) has recently opened up new possibilities for the characterization of structural variants on a genome-wide level, thus enabling simultaneous analysis for a broad spectrum of genetic aberrations. (2) Methods: 11 adult ALL patients were examined using OGM. (3) Results: Genetic results obtained by karyotyping and FISH were confirmed by OGM for all patients. Karyotype was redefined, and additional genetic information was obtained in 82% (9/11) of samples by OGM, previously not diagnosed by standard of care. Besides gross-structural chromosome rearrangements, e.g., ring chromosome 9 and putative isodicentric chromosome 8q, deletions in CDKN2A/2B were detected in 7/11 patients, defining an approx. 20 kb minimum region of overlap, including an alternative exon 1 of the CDKN2A gene. The results further confirm recurrent ALL aberrations (e.g., PAX5, ETV6, VPREB1, IKZF1). (4) Conclusions: Genome-wide OGM analysis enables a broad genetic characterization in adult ALL patients in one single workup compared to standard clinical testing, facilitating a detailed genetic diagnosis, risk-stratification, and target-directed treatment strategies.

Keywords: CDKN2A/B deletion; adult acute lymphoblastic leukemia (ALL); isodicentric chromosome; optical genome mapping (OGM); ring chromosome.

Figure 1

OGM detects different types of gross structural aberrations. (A) Additional Philadelphia-like chromosome in patient 2: visualized as interchromosomal translocation (9;22)(q34.12;q11.23) with BCR::ABL1 fusion in combination with neighboring copy number (CN) gains in close proximity to the translocation breakpoint region. CNV filter settings “no filter” were applied for visualization. (B) Presence of a ring chromosome of unknown origin previously detected by karyotyping could be confirmed and redefined by OGM to chromosome 9 material in patient 9. The ring chromosome presents as a translocation SV in combination with distal CN losses in circos plot and SV visualization. (C) Putative isodicentric chromosome idic(8q) presenting as CN gains on chromosome 8q and part of 8p in conjunction with an inverted duplication SV on 8p12 and a CN loss in close proximity (patient 4). CNV filter settings were set to “no filter” for visualization. Idic(8q) was not detected by karyotyping. Light blue and light red blocks depict gains and losses of chromosomal material in the respective regions. Blue blocks depict structural variants, green blocks depict masked regions including the centromeric region on chromosome depicted in yellow. Created with BioRender.com.

Figure 2

OGM detects rare or new gene fusions: Circos plots and respective SVs representing the gene fusions. Orientation of genes is indicated by arrows. (A) Three-way translocation involving the IGH locus on chromosome 14q, TRB locus on 7q, and MIR100HG micro-RNA on chromosome 11 (patient 5). (B) Circos plot and interchromosomal translocation SV reveal a t(7;15)(q22.1;q14) and the resulting CUX1::NUTM1 fusion breakpoint region (patient 7). (C) Circos plot and intrachromosomal fusion SV showing KMT2A fused to PRDM10 in patient 10. Created with BioRender.com.

Figure 3

Estimated minimal region of overlap for CDKN2A and CDKN2B deletions on chromosome 9p (minus strand) based on OGM data. Large 9p deletions (top) and detailed view of 9p21.3 CDKN2A and CDKN2B genomic region (middle, bottom) are depicted. Top: Large losses of genomic material are shown as red bars, small deletions as red dots at the top. Detailed view of CDKN2A and CDKN2B genomic region includes the CDKN2A alternative reading frame and respective transcripts (CDKN2A transcripts p16INK4a and p14ARF and CDKN2B transcript p15INK4b). Colors of the deleted regions correspond to the affected transcripts. OGM label positions at breakpoint regions are vertically extended to the bottom of the figure. A minimal region of overlap can be hypothesized that affects the alternative reading frame of CDKN2A (p14ARF transcript) based on OGM data. Created with BioRender.com.

Figure 4

ALL-gene deletions/partial deletions overlap in the studied patient group. Single patients are visualized by unique color clouds. Gene cloud overlap shows frequency of affected genes: bigger font size corresponds to higher deletion frequency in the analyzed patient samples; core genes CDKN2A/CDKN2B are most frequently (partially) deleted and are visualized with the biggest font. Deletions in genes only detected in single patients show smallest font size. * Indicates ALL-associated genes with unknown effect of gene deletions. Legend describes patient numbers. Created with BioRender.com.