Technological limitations have hindered the large-scale genetic investigation of tandem repeats in disease. We show that long-read sequencing with a single Oxford Nanopore Technologies PromethION flow cell per individual achieves 30× human genome coverage and enables accurate assessment of tandem repeats including the 10,000-bp Alzheimer's disease-associated ABCA7 VNTR. The Guppy "flip-flop" base caller and tandem-genotypes tandem repeat caller are efficient for large-scale tandem repeat assessment, but base calling and alignment challenges persist. We present NanoSatellite, which analyzes tandem repeats directly on electric current data and improves calling of GC-rich tandem repeats, expanded alleles, and motif interruptions.
CITATION STYLE
De Roeck, A., De Coster, W., Bossaerts, L., Cacace, R., De Pooter, T., Van Dongen, J., … Sleegers, K. (2019). NanoSatellite: Accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION. Genome Biology, 20(1). https://doi.org/10.1186/s13059-019-1856-3
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