Calculate HRD Score (beta)

The Calculate HRD Score (beta) tool is designed to calculate Homologous Recombination Deficiency (HRD) from targeted research resequencing experiments.

The tool takes a target-level ploidy track (from the Detect Regional Ploidy tool) and centromers as input.

To run the Calculate HRD Score (beta) tool, go to:

        Toolbox | Biomedical Genomics Analysis (Image biomedical_folder_closed_16_n_p) | Oncology Score Estimation (Image oncology_tools_folder_closed_16_h_p) | Calculate HRD Score (beta) (Image calculate_hrd_score_16_n_p)

Select the target-level ploidy track generated by the Detect Regional Ploidy tool and click Next.

You are now presented with choices regarding HRD calculation.

When finished with the settings, click Next to start the algorithm.

HRD calculation

The HRD score is a count of chromosomal rearrangements that can be increased in tumors with HRD. It is calculated as the weighted sum of three different chromosomal rearrangements: The number of Telomeric Allelic Imbalances (TAI), Large-scale Transitions (LST), and long regions of Loss of Heterozygosity (LOH). The calculations are based on identified regions of copy number variations (CNV) as well as variant frequencies in a sample, which are identified beforehand.

The LOH score is defined as the number of regions with a minor allele count of zero. If all regions on a chromosome are affected by LOH, the whole chromosome is excluded from the LOH score calculation.

The TAI score is defined as the number of regions that:

Calculation of the three scores is inspired by:

The LST score is the number of LST events. The LST score counts large rearrangements for each arm of a chromosome. The regions are merged and short regions removed iteratively. For each chromosome arm, as long as there are segments less than 3 MB, the segment at the first position, that is less than 3 MB is removed and adjacent segments across the whole chromosome arm with identical allele counts merged.

Calculate HRD score algorithm report

The report provides a table listing: