> For the complete documentation index, see [llms.txt](https://docs.omics.ai/products/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.omics.ai/products/workbench/variant-interpreter/reviewing-variants/tandem-repeats.md).

# Tandem repeats

Tandem repeats are short DNA motifs repeated back-to-back. When a repeat expands beyond a threshold it can cause disease (repeat-expansion disorders). Long reads can span large repeats in a single read, which makes accurate sizing possible where short reads fail.

## The candidate table

Each row is a genotyped repeat locus. You can search, sort, filter, and customize the columns in the table using the **Columns** dropdown.

The default columns in the candidate table include:

| Column                       | Description                                                                                                                |
| ---------------------------- | -------------------------------------------------------------------------------------------------------------------------- |
| **User Classification**      | The classification manually assigned to the repeat locus by a reviewer (e.g., Pathogenic, Likely Pathogenic, VUS, Benign). |
| **Automated Classification** | The automated classification generated by the system's pipeline based on repeat expansion thresholds.                      |
| **Tandem Repeat ID**         | The unique identifier of the tandem repeat locus.                                                                          |
| **MC**                       | Motif copy counts (the number of times the motif is repeated) for each allele.                                             |
| **Motifs**                   | The repeated DNA sequence motifs defining the tandem repeat.                                                               |
| **LPS Motifs**               | The specific motifs associated with the longest pure segments of the repeat.                                               |
| **LPS**                      | Longest pure segment length (the length of the longest uninterrupted repeat motif segment) for each allele.                |
| **LPS Median**               | The median length of the longest pure segment in reference cohorts.                                                        |
| **LPS P99**                  | The 99th percentile length of the longest pure segment in reference cohorts, used to identify abnormal expansions.         |
| **LPS Ratio to median**      | The ratio of the sample's LPS to the reference median, helping highlight potential outliers.                               |
| **LPS Outlier**              | A flag indicating if the repeat segment length is a statistical outlier compared to controls (e.g., `LPS_OUTLIER`).        |
| **ALLR**                     | Allele length range (a confidence interval indicating the range of the repeat length for each allele).                     |
| **SD**                       | Spanning reads (the number of PacBio HiFi reads spanning and supporting the repeat allele).                                |
| **AP**                       | Allele purity (a score representing how pure/uninterrupted the repeat sequence is).                                        |
| **Average Methylation**      | The average CpG methylation level across the repeat locus.                                                                 |
| **Genotype**                 | The zygosity and allele calls for the tandem repeat.                                                                       |

## Views

The calls can be shown as a **table** or a **locus view**. For a trio, the locus view shows the proband alongside paternal and maternal data when all three are provided; otherwise it shows the proband alone.

## Filters

The filter drawer offers:

* **User Classification**: Pathogenic, Likely Pathogenic, VUS, Likely Benign, Benign.
* **Chromosome**: chr1 to chr22, chrX, chrY.
* **Position**: a genomic-coordinate range.
* **LPS Outlier**: Outlier or Non-outlier. This tab opens pre-filtered to Outlier (longest pure segment greater than P99 × 1.2 and greater than 72 bp).

## How to review

1. Focus on loci flagged as near or above a known pathogenic threshold.
2. Compare the two allele sizes; note expansions and confirm read support.
3. Record findings for the [report](/products/workbench/variant-interpreter/generating-a-report.md).


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