Chaitankar Vijender, Karakülah Gökhan, Ratnapriya Rinki, Giuste Felipe O, Brooks Matthew J, Swaroop Anand
Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA.
Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD, 20892-0610, USA.
Prog Retin Eye Res. 2016 Nov;55:1-31. doi: 10.1016/j.preteyeres.2016.06.001. Epub 2016 Jun 11.
The advent of high throughput next generation sequencing (NGS) has accelerated the pace of discovery of disease-associated genetic variants and genomewide profiling of expressed sequences and epigenetic marks, thereby permitting systems-based analyses of ocular development and disease. Rapid evolution of NGS and associated methodologies presents significant challenges in acquisition, management, and analysis of large data sets and for extracting biologically or clinically relevant information. Here we illustrate the basic design of commonly used NGS-based methods, specifically whole exome sequencing, transcriptome, and epigenome profiling, and provide recommendations for data analyses. We briefly discuss systems biology approaches for integrating multiple data sets to elucidate gene regulatory or disease networks. While we provide examples from the retina, the NGS guidelines reviewed here are applicable to other tissues/cell types as well.
高通量新一代测序（NGS）技术的出现加快了疾病相关基因变异的发现步伐以及表达序列和表观遗传标记的全基因组分析，从而使基于系统的眼部发育和疾病分析成为可能。NGS及其相关方法的快速发展在大数据集的采集、管理和分析以及提取生物学或临床相关信息方面带来了重大挑战。在此，我们阐述了常用的基于NGS的方法的基本设计，特别是全外显子组测序、转录组和表观基因组分析，并提供数据分析建议。我们简要讨论了整合多个数据集以阐明基因调控或疾病网络的系统生物学方法。虽然我们提供了来自视网膜的示例，但这里所综述的NGS指南也适用于其他组织/细胞类型。
