揭开新兴的批量 RNA-Seq 应用的神秘面纱：生物信息学方法的应用和实用性。

Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology.

机构信息

University of Wollongong, Wollongong, Australia.

Illawarra Health and Medical Research Institute, Wollongong, Australia.

出版信息

Brief Bioinform. 2021 Nov 5;22(6). doi: 10.1093/bib/bbab259.

DOI:10.1093/bib/bbab259

PMID:34329375

Abstract

Significant innovations in next-generation sequencing techniques and bioinformatics tools have impacted our appreciation and understanding of RNA. Practical RNA sequencing (RNA-Seq) applications have evolved in conjunction with sequence technology and bioinformatic tools advances. In most projects, bulk RNA-Seq data is used to measure gene expression patterns, isoform expression, alternative splicing and single-nucleotide polymorphisms. However, RNA-Seq holds far more hidden biological information including details of copy number alteration, microbial contamination, transposable elements, cell type (deconvolution) and the presence of neoantigens. Recent novel and advanced bioinformatic algorithms developed the capacity to retrieve this information from bulk RNA-Seq data, thus broadening its scope. The focus of this review is to comprehend the emerging bulk RNA-Seq-based analyses, emphasizing less familiar and underused applications. In doing so, we highlight the power of bulk RNA-Seq in providing biological insights.

摘要

下一代测序技术和生物信息学工具的重大创新，影响了我们对 RNA 的认识和理解。随着序列技术和生物信息学工具的进步，实用的 RNA 测序 (RNA-Seq) 应用也在不断发展。在大多数项目中，批量 RNA-Seq 数据用于测量基因表达模式、异构体表达、选择性剪接和单核苷酸多态性。然而，RNA-Seq 还包含更多隐藏的生物学信息，包括拷贝数改变、微生物污染、转座元件、细胞类型（去卷积）和新抗原的详细信息。最近开发的新型和先进的生物信息学算法提高了从批量 RNA-Seq 数据中检索这些信息的能力，从而拓宽了其应用范围。本综述的重点是理解新兴的基于批量 RNA-Seq 的分析方法，强调不太熟悉和未充分利用的应用。这样做，我们强调了批量 RNA-Seq 在提供生物学见解方面的强大功能。