Clinical Utility of Optical Genome Mapping for Improved Cytogenomic Analysis of Gliomas

Abstract

A glioma is a solid brain tumor which originates in the brain or brain stem area. The diagnosis of gliomas based on standard-of-care (SOC) techniques includes karyotyping, fluorescence in situ hybridization (FISH), and chromosomal microarray (CMA), for detecting the pathogenic variants and chromosomal abnormalities. But these techniques do not reveal the complete picture of genetic complexity, thus requiring an alternative technology for better characterization of these tumors. The present study aimed to evaluate the clinical performance and feasibility of using optical genome mapping (OGM) for chromosomal characterization of gliomas. Herein, we evaluated 10 cases of gliomas that were previously characterized by CMA. OGM analysis showed concordance with the results of CMA in identifying the characterized Structural Variants (SVs) in these cases. More notably, it also revealed additional clinically relevant aberrations, demonstrating a higher resolution and sensitivity. These clinically relevant SVs included cryptic translocation, and SVs which are beyond the detection capabilities of CMA. Our analysis highlights the unique capability of OGM to detect all classes of SVs within a single assay, thereby unveiling clinically significant data with a shorter turnaround time. Adopting this diagnostic tool as a standard of care for solid tumors like gliomas shows potential for improving therapeutic management, potentially leading to more personalized and timely interventions for patients.

Keywords: chromosomal microarray; glioma; optical genome mapping; solid tumor; structural variants.

Figure 1

Whole genome view showing the concordance of the copy number variations detected +2, 6q-, +7, -10, -14, 19q-, and -22 by OGM (A) and CMA (B).

Figure 2

(A) The chromothripsis event detected on chromosome 8 in microarray, (B) the enlarged view of the same event indicating the various breakpoints by microarray where blue is gain and red is loss of CN.

Figure 3

The OGM circus plot (A) showing the chromothripsis event observed on chromosome 8 with an enlarged view of chromosome 8 and (B) showing the SV events related to the chromothripsis call. On the bottom (C) is the OGM whole genome view as a secondary visualization confirming the chromothripsis event in this case, blue color indicates CMV gain segment and red color indicates CNV loss in chromosomes.

Figure 4

The copy number loss and the nested deletion involving the CDKN2A and CDKN2B genes identified by CMA analysis in one of the glioma cases. Light red is the CNV event and dark red is the nested deleted present in the CNV loss event which contain the CDKN2A and CDKN2B genes.

Figure 5

OGM reveals additional details for a glioma case presented in Figure 4. (A) unbalanced translocation event between chromosome 9 and 7 which resulted in the CN loss on chromosome 9, and the nested deletion present on chromosome 9, (B) shows the enlarge view of nested deletion having the CN state of approximately 0.5 surrounded by CN state of 1.3 which contain CDKN2A and CDKN2B genes. Green map shows the reference map and blue map shows the nested deletion detected in this case.

Figure 5

OGM reveals additional details for a glioma case presented in Figure 4. (A) unbalanced translocation event between chromosome 9 and 7 which resulted in the CN loss on chromosome 9, and the nested deletion present on chromosome 9, (B) shows the enlarge view of nested deletion having the CN state of approximately 0.5 surrounded by CN state of 1.3 which contain CDKN2A and CDKN2B genes. Green map shows the reference map and blue map shows the nested deletion detected in this case.

Figure 6

Graphic depiction of (A) the original chromosome involved in the translocation event between chromosome 7 and chromosome 9, (B) the resulting derivative chromosomes, including the lost section of chromosome 9 that encompasses CDKN2A and CDKN2B for the glioma case examined by CMA in Figure 4 and OGM in Figure 5.

Figure 7

An unbalanced, complex translocation was detected in glioma case. (A) Circos plot showing the loss of p-arm on chromosome 3 and a copy number gain on chromosome 5 in SV track. (B) Enlarged view of the SV track showing three breakpoints on chromosome 3 involved in the translocation with chromosome 5, labeled with red rectangular boxes. One breakpoint at position 89.23 M on chromosome 3 results in the disruption of the EPHA3 gene. In CN track, red is loss of copy number state and blue is copy number gain.

Figure 8

Graphic depiction of (A) the original chromosomes involved, (B) the movement of genetic material between chromosome 3 and chromosome 5 in the translocation identified by OGM. This translocation results in a loss of genetic material on 3p, a disruption of EPHA3 on chromosome 3, a duplication on chromosome 5q (110.54–113.90 M), and a gain of chromosome 5q from 5q22.3/114.5 to the q-terminus.

Figure 9

A three-way translocation between chromosomes 3, 11, and 17, as revealed by OGM in glioma case. (A) Circos plot of the translocation event, (B) enlarged SV view of a breakpoint between chromosome 3 and chromosome 17 involving gene GSK3B, and (C) enlarged SV view of a breakpoint between chromosome 11 and the inverted chromosome 17.

Figure 10

(A) Graphic depiction of the original chromosomes involved in the 3-way translocations and the original location of the genes that are affected by the translocation. (B) The derivative chromosomes identified by OGM and formed as a result of the 3-way translocation.

Figure 11

(A) OGM showing the balanced translocation event in which gene fusion was observed between ETNK1 and ADAMTSL1 gene. (B,C) No change in either of gene was observed in the CMA analysis.