仆从
纳米孔测序
变色
结构变异
计算生物学
基因组
基因组学
纳米孔
DNA测序
顺序装配
生物
大规模并行测序
遗传学
计算机科学
DNA
基因
基因组不稳定性
转录组
纳米技术
基因表达
材料科学
DNA损伤
作者
Mircea Cretu Stancu,Markus J. van Roosmalen,Ivo Renkens,Marleen M. Nieboer,Sjors Middelkamp,Joep de Ligt,Giulia Pregno,Daniela Giachino,Giorgia Mandrile,Jose Espejo Valle-Inclán,Jerome Korzelius,Ewart de Bruijn,Edwin Cuppen,Michael E. Talkowski,Tobias Marschall,Jeroen de Ridder,Wigard P. Kloosterman
标识
DOI:10.1038/s41467-017-01343-4
摘要
Despite improvements in genomics technology, the detection of structural variants (SVs) from short-read sequencing still poses challenges, particularly for complex variation. Here we analyse the genomes of two patients with congenital abnormalities using the MinION nanopore sequencer and a novel computational pipeline-NanoSV. We demonstrate that nanopore long reads are superior to short reads with regard to detection of de novo chromothripsis rearrangements. The long reads also enable efficient phasing of genetic variations, which we leveraged to determine the parental origin of all de novo chromothripsis breakpoints and to resolve the structure of these complex rearrangements. Additionally, genome-wide surveillance of inherited SVs reveals novel variants, missed in short-read data sets, a large proportion of which are retrotransposon insertions. We provide a first exploration of patient genome sequencing with a nanopore sequencer and demonstrate the value of long-read sequencing in mapping and phasing of SVs for both clinical and research applications.
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