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 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. ExpansionHunter performs 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 (http://www.genome.org/cgi/doi/10.1101/gr.225672.117)

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Graph ExpansionHunter (https://doi.org/10.1101/572545)

These methods work only for whole human genome samples in PCR-free libraries. Repeats are only genotyped if the coverage at the locus is at least 10x.