单位：[1]Institute for Genomic Medicine, Columbia University, New York, NY 10032,USA. [2]Nextomics Biosciences, Wuhan, Hubei 430000, China. [3]China-Japan Friendship Hospital, Beijing 100029, China. [4]Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA.
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.
基金：
National Institutes of HealthUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [HG006465]; NATIONAL HUMAN GENOME RESEARCH INSTITUTEUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Human Genome Research Institute (NHGRI) [R01HG006465] Funding Source: NIH RePORTER
第一作者单位：[1]Institute for Genomic Medicine, Columbia University, New York, NY 10032,USA.
通讯作者：
通讯机构：[1]Institute for Genomic Medicine, Columbia University, New York, NY 10032,USA. [4]Department of Biomedical Informatics, Columbia University, New York, NY 10032, USA.
推荐引用方式(GB/T 7714)：
Liu Qian,Zhang Peng,Wang Depeng,et al.Interrogating the "unsequenceable" genomic trinucleotide repeat disorders by long-read sequencing[J].GENOME MEDICINE.2017,9:doi:10.1186/s13073-017-0456-7.
APA：
Liu, Qian,Zhang, Peng,Wang, Depeng,Gu, Weihong&Wang, Kai.(2017).Interrogating the "unsequenceable" genomic trinucleotide repeat disorders by long-read sequencing.GENOME MEDICINE,9,
MLA：
Liu, Qian,et al."Interrogating the "unsequenceable" genomic trinucleotide repeat disorders by long-read sequencing".GENOME MEDICINE 9.(2017)
生物学