PhD-SNPg: updating a webserver and lightweight tool for scoring nucleotide variants

Author:

Capriotti Emidio1ORCID,Fariselli Piero2ORCID

Affiliation:

1. BioFolD Unit, Department Pharmacy and Biotechnology (FaBiT), University of Bologna , Via F. Selmi 3, Bologna 40126, Italy

2. Department of Medical Sciences, University of Torino , Via Santena 19, 10126 , Torino , Italy

Abstract

Abstract One of the primary challenges in human genetics is determining the functional impact of single nucleotide variants (SNVs) and insertion and deletions (InDels), whether coding or noncoding. In the past, methods have been created to detect disease-related single amino acid changes, but only some can assess the influence of noncoding variations. CADD is the most commonly used and advanced algorithm for predicting the diverse effects of genome variations. It employs a combination of sequence conservation and functional features derived from the ENCODE project data. To use CADD, a large set of pre-calculated information must be downloaded during the installation process. To streamline the variant annotation process, we developed PhD-SNPg, a machine-learning tool that is easy to install and lightweight, relying solely on sequence-based features. Here we present an updated version, trained on a larger dataset, that can also predict the impact of the InDel variations. Despite its simplicity, PhD-SNPg performs similarly to CADD, making it ideal for rapid genome interpretation and as a benchmark for tool development.

Funder

Italian Ministry for Education, University and Research

Publisher

Oxford University Press (OUP)

Subject

Genetics

Reference27 articles.

1. Genomic analysis in the age of Human genome sequencing;Lappalainen;Cell,2019

2. Bioinformatics for personal genome interpretation;Capriotti;Brief. Bioinform.,2012

3. A map of human genome variation from population-scale sequencing;Durbin;Nature,2010

4. A global reference for human genetic variation;1000 Genomes Project Consortium;Nature,2015

5. Pan-cancer analysis of whole genomes;ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium;Nature,2020

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