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.