> 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. ## Clinically relevant loci Most repeat loci in the genome are not associated with disease. The **Clinically Relevant** dropdown in the toolbar narrows the list to the loci that matter: | Option | Shows | | ------------ | ----------------------------------------------------------------------------------------------------------------------------------------------- | | **Clinical** | Loci with an established pathogenic range (from the STRchive catalogue), plus a small number of candidate loci that don't have a threshold yet. | | **Outlier** | Loci flagged as an LPS outlier: the longest pure segment is greater than P99 × 1.2 and greater than 72 bp. | | **Other** | Loci outside the Clinical set. | Checked options add together. For example, **Clinical** plus **Outlier** shows every clinical locus and every outlier. A badge on the button shows how many options are checked. Click **Clear**, or check both **Clinical** and **Other**, to show every locus. The tab opens with **Clinical** and **Outlier** checked. The same setting appears in the filter drawer as the **Clinically Relevant** facet. The two stay in sync. {% hint style="info" %} Tandem-repeat priority findings on the [Summary tab](/products/workbench/variant-interpreter/getting-started/the-summary-tab.md) count **LPS outliers only**, not the clinical loci. The Summary count and this tab's default view can therefore differ. {% endhint %} ## 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. Per-allele measures are split into separate **Allele 1** and **Allele 2** columns, so you can sort on either allele. 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). | | **Tandem Repeat ID** | The unique identifier of the tandem repeat locus. | | **MC (Allele 1)**, **MC (Allele 2)** | 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. For loci with several motifs, the highest value is shown. | | **LPS P99** | The 99th percentile length of the longest pure segment in reference cohorts, used to identify abnormal expansions. For loci with several motifs, the highest value is shown. | | **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 1)**, **ALLR (Allele 2)** | Allele length range (a confidence interval indicating the range of the repeat length for each allele). | | **SD (Allele 1)**, **SD (Allele 2)** | Spanning reads (the number of PacBio HiFi reads spanning and supporting the repeat allele). | | **AP (Allele 1)**, **AP (Allele 2)** | Allele purity (a score representing how pure/uninterrupted the repeat sequence is). | | **Average Methylation (Allele 1)**, **Average Methylation (Allele 2)** | The average CpG methylation level across the repeat locus, per allele. | | **Genotype** | The zygosity and allele calls for the tandem repeat. | You can sort by **Tandem Repeat ID**, the per-allele count, spanning-read, purity, and methylation columns, **LPS Median**, **LPS P99**, and **LPS Ratio to median**. ## 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. In the **Locus** view, a **Status** dropdown filters loci by where the proband's more severe allele falls against the pathogenic range: **pathogenic**, **intermediate**, **normal**, or **no threshold**. Each option shows its count for the loci currently loaded. ## 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. * **Clinically Relevant**: Clinical, Outlier, Other. This facet mirrors the toolbar dropdown and opens with Clinical and Outlier checked. Set the operator to **IS NOT** to exclude an option instead. ## The variant detail Opening a locus shows two headline cards: * **Motif Counts**: the **Highest motif count**, the largest repeat count across all motifs and both alleles. * **Avg Methylation**: the **Highest allele methylation**. The **Evidence in this sample** card shows allele purity for the call. ## How to review 1. Start from the default view of clinical loci and outliers. 2. Focus on loci flagged as near or above a known pathogenic threshold. The **Locus** view's **Status** filter brings these forward. 3. Compare the two allele sizes; note expansions and confirm read support. 4. [Classify](/products/workbench/variant-interpreter/classifying-variants.md) the locus so it can be included in the [report](/products/workbench/variant-interpreter/generating-a-report.md). --- # Agent Instructions This documentation is published with GitBook. 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