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

BMC Research Notes
Daniela EvangelistaMario Rosario Guarracino

Abstract

The 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. OPENDoRM 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. OPENDoRM is a freely available web-oriented application for the planning of pooled...Continue Reading

References

Mar 25, 2000·American Journal of Human Genetics·C I AmosW Wang
Sep 14, 2000·American Journal of Human Genetics·J L Gastwirth
Jul 26, 2012·Journal of Biomedicine & Biotechnology·Lin LiuMaggie Law
Aug 3, 2012·Proceedings of the National Academy of Sciences of the United States of America·Michael W SchmittLawrence A Loeb
Jul 17, 2014·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Maria Brigida FerraroMario Rosario Guarracino

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Citations

Feb 12, 2021·Scientific Reports·Julius ŽilinskasMario R Guarracino

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Methods Mentioned

BETA
PCR

Software Mentioned

ZK
OPENDoRM
OPENDoRM interface
DiagWalks
J2EE
NoReplica
OptReplica
Transposition

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