July 7, 2019  |  

Interrogating the “unsequenceable” genomic trinucleotide repeat disorders by long-read sequencing.

Authors: Liu, Qian and Zhang, Peng and Wang, Depeng and Gu, Weihong and Wang, Kai

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.

Journal: Genome medicine
DOI: 10.1186/s13073-017-0456-7
Year: 2017

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