Optical Genome Mapping: Integrating Structural Variations for Precise Homologous Recombination Deficiency Score Calculation

Abstract

Homologous recombination deficiency (HRD) is characterized by the inability of a cell to repair the double-stranded breaks using the homologous recombination repair (HRR) pathway. The deficiency of the HRR pathway results in defective DNA repair, leading to genomic instability and tumorigenesis. The presence of HRD has been found to make tumors sensitive to ICL-inducing platinum-based therapies and poly(adenosine diphosphate [ADP]-ribose) polymerase (PARP) inhibitors (PARPi). However, there are no standardized methods to measure and report HRD phenotypes. Herein, we compare optical genome mapping (OGM), chromosomal microarray (CMA), and a 523-gene NGS panel for HRD score calculations. This retrospective study included the analysis of 196 samples, of which 10 were gliomas, 176 were hematological malignancy samples, and 10 were controls. The 10 gliomas were evaluated with both CMA and OGM, and 30 hematological malignancy samples were evaluated with both the NGS panel and OGM. To verify the scores in a larger cohort, 135 cases were evaluated with the NGS panel and 71 cases with OGM. The HRD scores were calculated using a combination of three HRD signatures that included loss of heterozygosity (LOH), telomeric allelic imbalance (TAI), and large-scale transitions (LST). In the ten glioma cases analyzed with OGM and CMA using the same DNA (to remove any tumor percentage bias), the HRD scores (mean ± SEM) were 13.2 (±4.2) with OGM compared to 3.7 (±1.4) with CMA. In the 30 hematological malignancy cases analyzed with OGM and the 523-gene NGS panel, the HRD scores were 7.6 (±2.2) with OGM compared to 2.6 (±0.8) with the 523-gene NGS panel. OGM detected 70.8% and 66.8% of additional variants that are considered HRD signatures in gliomas and hematological malignancies, respectively. The higher sensitivity of OGM to capture HRD signature variants might enable a more accurate and precise correlation with response to PARPi and platinum-based drugs. This study reveals HRD signatures that are cryptic to current standard of care (SOC) methods used for assessing the HRD phenotype and presents OGM as an attractive alternative with higher resolution and sensitivity to accurately assess the HRD phenotype.

Keywords: HRD scores; homologous recombination deficiency; optical genome mapping.

Figure 1

Validation of automated scoring with Access compared to expertly curated scores for HRD calculation using Optical Genome Mapping.

Figure 2

Comparison of HRD score calculated with CMA compared to OGM in 10 glioma samples.

Figure 3

Shows the visualization and comparison of HRD scores for a case of glioblastoma with optical genome mapping and chromosomal microarray. (A) Optical genome mapping: shows the circos plot with an overview of the structural variations, copy number variations, aneuploidy, translocations, and fusions in the sample. (B) Optical genome mapping: whole genome CNV view showing region with copy number gain (blue columns), and copy number loss (red columns). (C) Chromosomal microarray: HRD scars visualization in NxClinical using the decision tree with HRD scar and scoring filtration.

Figure 4

Shows the concordant call between optical genome mapping and chromosomal microarray. (A) Shows a >10 Mb <15 Mb copy number loss, resulting in TAI-1 (HRD score = 2). (B) Shows a <10 Mb copy number loss, which did not add to HRD score (HRD score = 0) (highlighted in red box).

Figure 5

Shows the zoomed-in view of Figure 4B (<10 Mb) copy number loss with optical genome mapping. (A) Shows the 5.3 Mb deletion. (B) Zoomed-in view of the 5.3 Mb deletion showing translocations t(16;19) at both breakpoints (highlighted in blue boxes). This segment resulted in a HRD score of 2 with OGM, and a HRD score of 0 with CMA.

Figure 6

Comparison of HRD score calculated with the 523-gene NGS panel compared to OGM in 30 hematological malignancy samples.

Figure 7

Additional structural variations detected with OGM that result from HRD. (A) Shows the comparison of OGM with CMA for a HRD scar, LOH-2 (>15 Mb deletion), that contributed a score of 3 with CMA and 4 with OGM as the deletion was part of a translocation t(9;11) (highlighted in red box). (B) Shows a large (>10 Mb) inversion with OGM that contributes a score of 2 towards HRD calculation.

Figure 8

Shows the comparison between optical genome mapping and the 523-gene NGS panel in a case of acute myeloid leukemia. (A) Circos plot with OGM, showing an interstitial deletion at 7q, and trisomies 13 and 21. (B) Shows the HRD scarring in NxClinical using 523-gene panel data. (C) Zoomed-in view of chromosome 13 showing two interstitial regions with gains (TAI-1 and LST-1) and limited coverage to assist the analyst to determine true/false positive calls. (D) Zoomed-in view of chromosome 21 showing a TAI-1. Both segmental calls at chromosomes 13 and 21 were determined to be false calls, as these were trisomies as observed with OGM and confirmed with karyotyping.