Repeat Expansion Detection with Expansion Hunter

Short tandem repeats (STRs) are regions of the genome consisting of repetitions of short DNA segments called repeat units. STRs can expand to lengths beyond the normal range and thereby cause mutations called repeat expansions. Repeat expansions are responsible for many diseases including Fragile X syndrome, amyotrophic lateral sclerosis, and Huntington's disease.

DRAGEN includes a repeat-expansion detection method called ExpansionHunter. This method works by performing an accurate sequence-graph based realignment of reads that originate inside and around each target repeat. It then genotypes the length of the repeat in each allele based on these graph alignments. More information and analysis is available in the following ExpansionHunter papers:

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ExpansionHunter (original version)

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Graph ExpansionHunter (new version integrated in DRAGEN)

It is important to note that these methods work only for whole human genome samples generated with PCR-free methods. Repeats are only genotyped if the coverage at the locus is at least 10x.