Advances, practice, and clinical perspectives in high‐throughput sequencing

Abstract

Remarkable advances in high-throughput sequencing technologies have fundamentally changed our understanding of the genetic and epigenetic molecular bases underlying human health and diseases. As these technologies continue to revolutionize molecular biology leading to fresh perspectives, it is imperative to thoroughly consider the enormous excitement surrounding the technologies by highlighting the characteristics of platforms and their global trends as well as potential benefits and limitations. To date, with a variety of platforms, the technologies provide an impressive range of applications, including sequencing of whole genomes and transcriptomes, identifying of genome modifications, and profiling of protein interactions. Because these applications produce a flood of data, simultaneous development of bioinformatics tools is required to efficiently deal with the big data and to comprehensively analyze them. This review covers the major achievements and performances of the high-throughput sequencing and further summarizes the characteristics of their applications along with introducing applicable bioinformatics tools. Moreover, a step-by-step procedure for a practical transcriptome analysis is described employing an analytical pipeline. Clinical perspectives with special consideration to human oral health and diseases are also covered. Oral Diseases (2016) 22, 353-364

ZBTB16 as a Downstream Target Gene of Osterix Regulates Osteoblastogenesis of Human Multipotent Mesenchymal Stromal Cells

“…We used the Tophat2 (v. 2.0.14)‐Cufflinks (v.2.2.1) pipeline [Trapnell et al, ] to gather the uniquely mapped reads to the human reference genome (hg19) and to quantify RefSeq gene expression as the unit of fragments per kilobase of exon per million mapped reads (FPKM). After combining nine samples using Cuffmerge, we performed Cuffdiff processing in the Cufflinks package to detect differentially expressed genes (DEGs) between the tissues via two‐group t ‐tests coupled to a Benjamini–Hochberg correction (q‐value) as previously described [Park et al, ]. We defined DEGs when the fold change of the FPKMs was >2.0 and the q‐value was <0.05.…”

Illumina-based sequencing analysis of pathogenic microorganisms in dental caries patients of different Chinese ethnic groups

“…High-throughput sequencing technology is a current research hotspot in microbial diversity, metagenomics, and metabolomics of microbiology to explore correlations between oral microbes and clinical diseases. 5 Schulze-Schweifing et al 6 compared traditional culture methods with highthroughput sequencing, and demonstrated that the latter has a faster sequencing speed and larger sequencing volume, and can determine the entire microbiological structure of oral samples, which accurately measures the proportion of dominant bacteria and identifies novel bacterial species. Previous studies indicated that highthroughput sequencing technology can be used to detect oral salivary microbes in patients with dental caries, and analyze the community structure and microbial diversity.…”

Molecular dynamics simulations for genetic interpretation in protein coding regions: where we are, where to go and when

“…According to the NCBI's dbSNP Short Genetic Variations database (build 151) [9], ∼1 billion uniquely mapped (non-redundant) human genetic variations have been reported, including single-and multiple-base variations, insertions and deletions (indels) and short tandem repeats. Advances in highthroughput sequencing techniques [10][11][12] have enabled wholeexome sequencing (WES) [13] and genome-wide association studies (GWAS) [14] on humans [15][16][17] and a number of model species [18][19][20][21], contributing to a better understanding of how single-nucleotide variations (SNVs), the most frequent variations present in DNA [22], are related to diseases. An accurate interpretation of SNVs constitutes a major challenge in genetics and health.…”