A web-oriented software for the optimization of pooled experiments in NGS for detection of rare mutations.

Algirdas Lančinskas,Antonio Zuccaro,Julius Žilinskas,Mario R. Guarracino,Daniela Evangelista

doi:10.1186/s13104-016-1889-6

Abstract

BackgroundThe cost per patient of next generation sequencing for detection of rare mutations may be significantly reduced using pooled experiments. Recently, some techniques have been proposed for the planning of pooled experiments and for the optimal allocation of patients into pools. However, the lack of a user friendly resource for planning the design of pooled experiments forces the scientists to do frequent, complex and long computations.ResultsOPENDoRM is a powerful collection of novel mathematical algorithms usable via an intuitive graphical user interface. It enables researchers to speed up the planning of their routine experiments, as well as, to support scientists without specific bioinformatics expertises. Users can automatically carry out analysis in terms of costs associated with the optimal allocation of patients in pools. They are also able to choose between three distinct pooling mathematical methods, each of which also suggests the optimal configuration for the submitted experiment. Importantly, in order to keep track of the performed experiments, users can save and export the results of their experiments in standard tabular and charts contents.ConclusionOPENDoRM is a freely available web-oriented application for the planning of pooled NGS experiments, available at: http://www-labgtp.na.icar.cnr.it/OPENDoRM. Its easy and intuitive graphical user interface enables researchers to plan theirs experiments using novel algorithms, and to interactively visualize the results.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-016-1889-6) contains supplementary material, which is available to authorized users.

Highlights

The cost per patient of generation sequencing for detection of rare mutations may be significantly reduced using pooled experiments
We propose OPENDoRM, a new web tool for planning Next generation sequencing (NGS) experiments with a simple graphical user interface (GUI)
It provides flexibility to the users for automatically carrying out analysis in terms of costs associated with the optimal allocation of patients in pools, suggesting the optimal configurations of their experiments

Summary

Introduction

The cost per patient of generation sequencing for detection of rare mutations may be significantly reduced using pooled experiments. Some techniques have been proposed for the planning of pooled experiments and for the optimal allocation of patients into pools. We propose OPENDoRM (optimization of pooled experiments in NGS for detection of rare mutations), a new web tool for planning NGS experiments with a simple graphical user interface (GUI). It is able to: (i) describe the pooling of high-throughput generated data using four different algorithms; (ii) identify the optimal number of patients in each pool with respect to minimization of the cost of the experiment; (iii) generate easyto-read reports and charts for better understanding the planning of the experiments

Methods

Results

Conclusion