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.

高通量下一代测序（NGS）的出现加快了疾病相关遗传变异的发现速度以及表达序列和表观遗传标记的全基因组分布分析，从而允许对眼部发育和疾病进行基于系统的分析。NGS和相关方法的快速发展对大数据集的获取，管理和分析以及提取生物学或临床相关信息提出了重大挑战。在这里，我们说明了常用的基于NGS的方法的基本设计，特别是整个外显子组测序，转录组和表观基因组分析，并为数据分析提供了建议。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。