Advances in Bioinformatics, Biostatistics and Omics Sciences

An Innovative Gene Prioritization Pipeline for DNA-Sequencing Analyses

Author(s): Luigi Donato, Simona Alibrandi, Rosalia D’Angelo, Concetta Scimone, Antonina Sidoti and Alessandra Costa

Pp: 53-73 (21)

DOI: 10.2174/9789811481802120010005

* (Excluding Mailing and Handling)


In recent decades, the development of next-generation sequencing (NGS) technologies has made it possible to understand molecular mechanisms at the basis of various genetic diseases. The huge amount of data obtained from these experiments must be carefully analyzed. One of the most sensitive steps consists of gene prioritization, already performed by several widely used computational tools such as Endeavour, ToppGene, and Candid, to obtain only the genes that are most probably associated with the disease of interest. Furthermore, among these genes, it is important to choose those that show the highest statistical significance, to obtain a more reliable result. This represents one of the major limitations for many researchers. In this work, we propose an innovative method that could help researchers reduce a large amount of data by applying filters before the prioritization process that is carried out by Toppgene, today considered the most powerful tool. We performed prioritization of candidate genes obtained by whole-exome sequencing (WES) on a patient affected by an orphan form of retinitis pigmentosa. We obtained new mutations and polymorphic variants in known associated/causative and yet unrelated genes. The upstream application of different filters allowed us to work with a smaller number of genes and therefore, to produce a lower statistical bias. Furthermore, Toppgene has proven to be a complete, reliable tool for carrying out the prioritization process.

Keywords: Bioinformatics, Biostatistics, Candid, Conditional Formatting, CLC Genomics Workbench, Disease Ontology, DNA, DNASTAR Lasergene Suite, Excel, Gene Prioritization, GO, Human Phenotype, Mouse Phenotype, Molecular Function, NGS, Pipeline, ToppGene, RP, WGS, WES.

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