NGS catalog: A database of next generation sequencing studies in humans

Abstract

Next generation sequencing (NGS) technologies have been rapidly applied in biomedical and biological research since its advent only a few years ago, and they are expected to advance at an unprecedented pace in the following years. To provide the research community with a comprehensive NGS resource, we have developed the database Next Generation Sequencing Catalog (NGS Catalog, http://bioinfo.mc.vanderbilt.edu/NGS/index.html), a continually updated database that collects, curates and manages available human NGS data obtained from published literature. NGS Catalog deposits publication information of NGS studies and their mutation characteristics (SNVs, small insertions/deletions, copy number variations, and structural variants), as well as mutated genes and gene fusions detected by NGS. Other functions include user data upload, NGS general analysis pipelines, and NGS software. NGS Catalog is particularly useful for investigators who are new to NGS but would like to take advantage of these powerful technologies for their own research. Finally, based on the data deposited in NGS Catalog, we summarized features and findings from whole exome sequencing, whole genome sequencing, and transcriptome sequencing studies for human diseases or traits.

A Meta-analysis of Somatic Mutations from Next Generation Sequencing of 241 Melanomas: A Road Map for the Study of Genes with Potential Clinical Relevance

“…Similar to data collection procedures in our NGS Catalog database (8), we conducted a comprehensive literature search of melanoma NGS studies using the keywords “exome sequencing AND melanoma” and “whole genome sequencing AND melanoma” through PubMed (http://www.ncbi.nlm.nih.gov/pubmed). We performed a careful manual check of the search results.…”

“…We performed a careful manual check of the search results. Our query revealed at least ten melanoma NGS studies published from 2010 to 2012 (as of September, 2012, right before we started the analysis) (8). Studies were excluded if only part of the NGS mutation data was available.…”

Identification of phenylpropanoid biosynthetic genes and phenylpropanoid accumulation by transcriptome analysis of Lycium chinense

“…Compared with traditional gene cloning, NGS technology has high efficiency (whole-genome sequencing), fast run times (ranging from hours to days) and high accuracy [20, 22]. Among the different types of NGS technology, the Illumina Hiseq system has been widely used [23–25], owing to its high throughput, accuracy, and low costs.…”

Deep sequencing and in silico analyses identify MYB-regulated gene networks and signaling pathways in pancreatic cancer

“…With the advent of next generation sequencing (NGS), high resolution genomic and transcriptomic information can be retrieved through the whole genome sequencing (WGS) and RNA sequencing (RNA-seq)12. The transcriptome profiling is rapidly replacing the hybridization-based microarrays as it provides an unbiased, extensive and precise measurement of levels of transcripts and their isoforms13.…”