QueryOR: a comprehensive web platform for genetic variant analysis and prioritization

Background: Whole genome and exome sequencing are contributing to the extraordinary progress in the study of human genetic variants. In this fast developing field, appropriate and easily accessible tools are required to facilitate data analysis. Results: Here we describe QueryOR, a web platform suitable for searching among known candidate genes as well as for finding novel gene-disease associations. QueryOR combines several innovative features that make it comprehensive, flexible and easy to use. Instead of being designed on specific datasets, it works on a general XML schema specifying formats and criteria of each data source. Thanks to this flexibility, new criteria can be easily added for future expansion. Currently, up to 70 user-selectable criteria are available, including a wide range of gene and variant features. Moreover, rather than progressively discarding variants taking one criterion at a time, the prioritization is achieved by a global positive selection process that considers all transcript isoforms, thus producing reliable results. QueryOR is easy to use and its intuitive interface allows to handle different kinds of inheritance as well as features related to sharing variants in different patients. QueryOR is suitable for investigating single patients, families or cohorts. Conclusions: QueryOR is a comprehensive and flexible web platform eligible for an easy user-driven variant prioritization. It is freely available for academic institutions at http://queryor.cribi.unipd.it/

Bioinformatics for personal genomics: development and application of bioinformatic procedures for the analysis of genomic data

In the last decade, the huge decreasing of sequencing cost due to the development of high-throughput technologies completely changed the way for approaching the genetic problems. In particular, whole exome and whole genome sequencing are contributing to the extraordinary progress in the study of human variants opening up new perspectives in personalized medicine. Being a relatively new and fast developing field, appropriate tools and specialized knowledge are required for an efficient data production and analysis. In line with the times, in 2014, the University of Padua funded the BioInfoGen Strategic Project with the goal of developing technology and expertise in bioinformatics and molecular biology applied to personal genomics. The aim of my PhD was to contribute to this challenge by implementing a series of innovative tools and by applying them for investigating and possibly solving the case studies included into the project. I firstly developed an automated pipeline for dealing with Illumina data, able to sequentially perform each step necessary for passing from raw reads to somatic or germline variant detection. The system performance has been tested by means of internal controls and by its application on a cohort of patients affected by gastric cancer, obtaining interesting results. Once variants are called, they have to be annotated in order to define their properties such as the position at transcript and protein level, the impact on protein sequence, the pathogenicity and more. As most of the publicly available annotators were affected by systematic errors causing a low consistency in the final annotation, I implemented VarPred, a new tool for variant annotation, which guarantees the best accuracy (>99%) compared to the state-of-the-art programs, showing also good processing times. To make easy the use of VarPred, I equipped it with an intuitive web interface, that allows not only a graphical result evaluation, but also a simple filtration strategy. Furthermore, for a valuable user-driven prioritization of human genetic variations, I developed QueryOR, a web platform suitable for searching among known candidate genes as well as for finding novel gene-disease associations. QueryOR combines several innovative features that make it comprehensive, flexible and easy to use. The prioritization is achieved by a global positive selection process that promotes the emergence of the most reliable variants, rather than filtering out those not satisfying the applied criteria. QueryOR has been used to analyze the two case studies framed within the BioInfoGen project. In particular, it allowed to detect causative variants in patients affected by lysosomal storage diseases, highlighting also the efficacy of the designed sequencing panel. On the other hand, QueryOR simplified the recognition of LRP2 gene as possible candidate to explain such subjects with a Dent disease-like phenotype, but with no mutation in the previously identified disease-associated genes, CLCN5 and OCRL. As final corollary, an extensive analysis over recurrent exome variants was performed, showing that their origin can be mainly explained by inaccuracies in the reference genome, including misassembled regions and uncorrected bases, rather than by platform specific errors

alns - A Searchable and filterable sequence alignment format

Nucleotides and amino acids are basic building units of RNA, DNA and protein. Although intensive studies on understanding how the change of these building blocks affect the phenotypes of these biopolymers are ever increasing, many popular alignment formats are generated by pairwise comparision tools such as the Basic Local Alignment Search Tool (BLAST). These alignments are user friendly to researchers but are not convenient for searching, filtering and storage, in particular when there are thousands of alignments generated from highly conserved sequences.. Here, we introduce a new alignment format, alns, to facilitate rapid and convenient association of genetic changes and similarity to other sources of information such as phenotypes, disease state, time, geography and taxonomy via simple spreadsheet functions. The format shall assist biologists from wide disciplines in knowledge discovery. ©2010 IEEE.Link_to_subscribed_fulltex

Alns: A new searchable and filterable sequence alignment format

Nucleotides and amino acids are basic building units of RNA, DNA and protein. Although intensive studies on understanding how changes in these building blocks affect the phenotypes of these biopolymers are ever increasing, many popular alignment formats are generated by pair-wise comparison tools such as the Basic Local Alignment Search Tool (BLAST). These alignments are user-friendly to researchers but are not convenient for searching, filtering and storage, in particular when there are thousands of alignments generated from highly conserved sequences. Here, we introduce a new alignment format, alns, to facilitate rapid and convenient association of genetic changes and similarity to other sources of information such as phenotypes, disease state, time, geography and taxonomy via simple spreadsheet functions. The format shall assist biologists from a wide range of disciplines in knowledge discovery. Copyright © 2013 Inderscience Enterprises Ltd.Link_to_subscribed_fulltex