Comprehensive elaboration of database resources utilized in next-generation sequencing-based tumor somatic mutation detection

Biochim Biophys Acta Rev Cancer. 2019 Aug;1872(1):122-137. doi: 10.1016/j.bbcan.2019.06.004. Epub 2019 Jun 29.

Abstract

The rapid evolution of next-generation sequencing (NGS)-based tumor genomic profile detection and the emergence of molecularly targeted therapies have enabled precision oncology. In NGS-based analysis, various types of databases have been developed to perform different functions. However, many problems still exist when using these public databases. Therefore, it is important to better understand the characteristics and limitations of each database and have them complement each other to provide useful clinical evidence for NGS testing. In this review, we elaborate on the important role of databases and their concrete applications in NGS-based somatic mutation detection. We introduce the typically used databases for sequence alignment, variant filtration, and variant interpretation, and compare the differences between the databases with similar functions. Subsequently, we determine the limitations of each database and provide the corresponding solutions. Furthermore, we present an overview diagram to clearly illustrate the database used in the entire NGS-based somatic mutation detection pipeline.

Keywords: Database; Next-generation sequencing; Precision oncology; Somatic mutation; Tumor.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • DNA Mutational Analysis*
  • Databases, Genetic*
  • Genome, Human / genetics
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Mutation
  • Neoplasms / genetics*
  • Precision Medicine
  • Sequence Analysis, DNA / methods