Journal
GENOME MEDICINE
Volume 9, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s13073-017-0456-7
Keywords
Trinucleotide repeats; Trinucleotide repeat disorders; Microsatellites; RepeatHMM; PacBio; Nanopore; Long-read sequencing
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Funding
- National Institutes of Health [HG006465]
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Microsatellite expansion, such as trinucleotide repeat expansion (TRE), is known to cause a number of genetic diseases. Sanger sequencing and next-generation short-read sequencing are unable to interrogate TRE reliably. We developed a novel algorithm called RepeatHMM to estimate repeat counts from long-read sequencing data. Evaluation on simulation data, real amplicon sequencing data on two repeat expansion disorders, and whole-genome sequencing data generated by PacBio and Oxford Nanopore technologies showed superior performance over competing approaches. We concluded that long-read sequencing coupled with RepeatHMM can estimate repeat counts on microsatellites and can interrogate the unsequenceable genomic trinucleotide repeat disorders.
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