STR visualisation¶

STR results are displayed in the Interpretation Portal and reviewing this plot is fundamental to the process of assessing the quality of the repeat size estimations computed by ExpansionHunter. Genomics England strongly advises GLHs to use the visualization plot to assess the quality of each call before validation of expansions with an alternative method. It is also advised to review normal alleles of the sizes larger than the read length (e.g. >49 repeats for trinucleotide repeat loci) and normal alleles very close to the threshold (e.g. +/- 2 repeat unit)

Analysing the reads that ExpansionHunter considers when assessing the repeat lengths is essential for determining the quality of the call but also for characterising interruptions (e.g. for Spinocerebellar Ataxias) or pathogenic-borderline cases, before orthogonal confirmation.

Below are visualisation plots and scenarios to illustrate how Expansion Hunter estimates STR genotypes.

Note

The software utilised to generate STR plots for DRAGEN v4.0.5 (NGIS Mira release) has been altered to REViewer. The output format from REViewer is .svg which can be downloaded and viewed in most web browsers.

A good quality STR call showing alleles within the normal range¶

An example of a visualisation plot that illustrates the reads used by ExpansionHunter when estimating expansions in HTT is shown in below. Both alleles have an STR repeat-length of 22 and accordingly, reads each containing the CAG motif 22 times are visible.

Good quality STR within normal range

A good quality STR showing one allele within the normal range and one expanded allele within read length¶

An example of a visualisation plot illustrating the reads used by ExpansionHunter when estimating expansions in HTT is shown below. Alleles of 18 and 40 repeat-lengths are shown in the plot. For the expanded allele, support is provided by:

"Flanking reads” that are anchored only on one side of the repeat. Some of these reads support more than 18 repeats but cannot be used to determine the exact number of repeats.
“Spanning reads” that are anchored on both sides of the repeat and support exactly 40 repeats for one of the alleles.
There are no “in repeat reads” that are not anchored at either end of the repeat

Good quality STR within normal range with one expanded allele within read length

A good quality STR showing one allele within the normal range and one expanded allele with "in repeat reads"¶

An example of a visualisation plot illustrating the reads used by ExpansionHunter when estimating expansions in HTT is shown below. Alleles of 17 and 67 repeat-lengths are shown in the plot. For the expanded allele, support is provided by:

"Flanking reads” that are anchored only on one side of the repeat. Some of these reads support more than 17 repeats but cannot be used to determine the exact number of repeats.
“In repeat reads” that are not anchored at either end of the repeat. These reads support at least 50 repeats.
There are no “spanning reads” that are anchored on both sides of the repeat.

Good quality STR within normal range with one expanded allele with "in repeat reads"

A good quality STR call with interruptions¶

An example plot with the reads used by ExpansionHunter when estimating expansions in ATXN1 is shown below. Interruptions (ATG rather than CTG) in the reads containing the ATXN1 repeat motif are visible (red As in figure). In certain disorders (i.e., ataxias) it is important to use the visualisation plots to check for such interruptions.

Good quality STR with interruptions