Calculate HRD Score
Calculate HRD Score takes as input a region-level ploidy track (
) and outputs a report containing a homologous recombination deficiency (HRD) score along with related information.
The HRD score quantifies chromosomal events that can be more prevalent in certain tumors. The tool is designed for targeted research resequencing experiments with sufficient genomic coverage to reliably detect ploidy states. HRD calculation is therefore suitable for panels with targets distributed across all chromosomes. Panels that are limited to specific gene hotspots or exonic regions do not provide the necessary breadth for genome-wide structural assessment and are not recommended for HRD analysis.
The following chromosomal events contribute to the HRD score:
- Loss-of-heterozygosity (LOH)
- Large-scale state transition (LST)
- Telomeric allelic imbalance (TAI)
To run the tool, go to:
Tools | Biomedical Genomics Analysis (
) | Oncology Score Estimation (
) | Calculate HRD Score (
)
The following options can be configured (figure 8.9):
- Centromeres. An annotation track () containing the centromeric regions. Centromere positions are used to determine the chromosome arm for each ploidy region.
- Minimum LOH length (Mb). Regions shorter than this (in megabases) are excluded from LOH calculations.
- LOH weight. The weight of LOH in the HRD score.
- Minimum LST length (Mb). Regions shorter than this (in megabases) are excluded from LST calculations.
- Maximum LST region distance (Mb) Regions separated by a distance larger than this (in megabases) are excluded from LST calculations.
- LST weight. The weight of LST in the HRD score.
- TAI weight. The weight of TAI in the HRD score.
- Minimum score for HRD-positive status. An HRD score equal to or above this leads to an HRD-positive status of the sample.
Figure 8.9: Options for Calculate HRD Score.
Subsections