英国诺丁汉大学Matthew Loose小组利用工具包“Readfish”，实现了对千兆碱基大小基因组进行靶向纳米孔测序。2020年11月30日出版的《自然—生物技术》发表了这一研究成果。

先前，人们使用动态时间扭曲将信号映射到参考基因组来实现对基因进行富集和删除，但是该方法需要大量的计算资源，并且无法缩放到千兆字节大小的序列。

研究人员通过使用图形处理单元（GPU）调用来克服纳米孔测序的局限。研究人员实现了人类基因组特定染色体的富集和混合人群中低丰度生物性状的富集，而无需对样品成分具有先验知识。最后，研究人员从10000个人类基因中富集了25,600个外显子和717个与癌症相关的基因，从而在<15 h测序中鉴定了NB4细胞系中存在PML-RARA的融合。

该方法可用于有效筛选任何目标基因组，而无需使用任何计算机和合适GPU进行专门的样品制备。该工具包Readfish可从https://www.github.com/looselab/readfish获得。

据介绍，纳米孔测序仪通过反转单个纳米孔上的电压以消除特定序列，从而选择性富集样品中的某些DNA分子来实现富集和删除以解决生物学问题。

附：英文原文

Title: Readfish enables targeted nanopore sequencing of gigabase-sized genomes

Author: Alexander Payne, Nadine Holmes, Thomas Clarke, Rory Munro, Bisrat J. Debebe, Matthew Loose

Issue&Volume: 2020-11-30

Abstract: Nanopore sequencers can be used to selectively sequence certain DNA molecules in a pool by reversing the voltage across individual nanopores to reject specific sequences, enabling enrichment and depletion to address biological questions. Previously, we achieved this using dynamic time warping to map the signal to a reference genome, but the method required substantial computational resources and did not scale to gigabase-sized references. Here we overcome this limitation by using graphical processing unit (GPU) base-calling. We show enrichment of specific chromosomes from the human genome and of low-abundance organisms in mixed populations without a priori knowledge of sample composition. Finally, we enrich targeted panels comprising 25,600 exons from 10,000 human genes and 717 genes implicated in cancer, identifying PML–RARA fusions in the NB4 cell line in <15h sequencing. These methods can be used to efficiently screen any target panel of genes without specialized sample preparation using any computer and a suitable GPU. Our toolkit, readfish, is available at https://www.github.com/looselab/readfish.

DOI: 10.1038/s41587-020-00746-x

Source: https://www.nature.com/articles/s41587-020-00746-x