> For the complete documentation index, see [llms.txt](https://help.tso500software.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.tso500software.illumina.com/dragen-tso-500-guides/dragen-tso-500-v2.5/analysis-output/dna-output/hrd-and-gis-outputs.md).
# HRD and GIS Outputs
The Illumina DRAGEN TruSight Oncology 500 Analysis Software allows for analysis of sequencing data generated from the TruSight Oncology 500 HRD assay. When HRD samples are analyzed new results and metrics are included in the CombinedVariantOutput and MetricsOutput files respectively. The following tables detail how these scores and QC metrics are derived.
| Metric | Description |
| ------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| Genomic Instability Score (GIS) | Proprietary Genomic Instability Score (GIS) indicating level of genomic instability in sample genome. Combination of Loss of Heterozygosity (LOH), Telomeric allelic imbalance and Large-scale State Transitions (LST) scores.
The GIS scores provided by TruSight Oncology 500 HRD show good correlation (R2= 0.98) with Myriad Genetics GIS however they are not identical (Refer to TruSight Oncology 500 HRD Product Data Sheet Doc# M-GL-00748 for more details). GIS from alternative HRD assays should be not be considered equivalent to Illumina/Myriad GIS.
|
{% hint style="warning" %}
The GIS algorithm within the TSO500 pipeline (which does not have a cell line mode due to the TSO500 pipeline being non-configurable) is only intended for FFPE samples. Cell line samples will not accurately report GIS results as the tumor fraction (>90%) is too high to reliably distinguish tumor vs germline variants.
{% endhint %}
### HRD Metrics Included in Metrics Output File
| Metric | Description | Section in Metrics Output |
| ----------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------ |
| PCT\_TARGET\_HRD\_50X | Percent of HRD probe SNP panel covered by at least 50X coverage | DNA Library QC Metrics for GIS |
| EXCESSIVE\_TF | EXCESSIVE TF indicates if there is excessive tumor content in sample. Troubleshooting: Samples with pure tumor fraction >90% are outside the design for GIS estimation (this includes pure tumor cell lines) | DNA Library QC Metrics for GIS |
| ALLELE\_DOSAGE\_RATIO | Proprietary Myriad Genetics estimate of b-allele dosage based on b-allele noise/signal ratio. B-Allele noise is correlated with coverage; lower coverage samples will have higher noise. B-allele signal is also correlated with tumor fraction; a higher tumor fraction produces a higher signal for b-allele sites. Samples with lower tumor fraction and higher amount of noise (or lower coverage) will have higher Allele Dosage Ratio. The upper limit of the score is 50, therefore any sample with 50 Allele Dosage Ratio can be assumed to have tumor fraction close to zero and typically has a GIS = 0. | DNA Expanded Metrics |
| MEDIAN\_TARGET\_HRD\_COVERAGE | Median target fragment coverage across all target positions in the genome. Coverage is the total number of non-duplicate pair alignments that overlap. | DNA Expanded Metrics |
---
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