Interrogating the "unsequenceable" genomic trinucleotide repeat disorders by long-read sequencing

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 l...

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Veröffentlicht in:Genome medicine 2017-07, Vol.9 (1), p.65-65, Article 65
Hauptverfasser: Liu, Qian, Zhang, Peng, Wang, Depeng, Gu, Weihong, Wang, Kai
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Sprache:eng
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Zusammenfassung: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.
ISSN:1756-994X
1756-994X
DOI:10.1186/s13073-017-0456-7