A Parallel Software Pipeline for DMET Microarray Genotyping Data Analysis

• Published in: Biotech (Basel) Vol. 7; no. 2; p. 17
• Main Authors: Agapito, Giuseppe, Guzzi, Pietro Hiram, Cannataro, Mario
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 14.06.2018; MDPI
• Subjects: Computer programs; Data analysis; Data mining; Data processing; Datasets; Drug development; Gene polymorphism; Genome-wide association studies; Genomes; Genomics; Genotyping; Linux; Mass spectroscopy; Medical treatment; Metabolism; Next-generation sequencing; Operating systems; Pharmacogenomics; Phenotypes; Precision medicine; Single-nucleotide polymorphism; Software; Software utilities; Statistical analysis; User interface; overall survival curves; pharmacogenomics; single nucleotide polymorphisms; statistical analysis; multiple analysis pipeline; data mining
• ISSN: 2571-5135; 2571-5135; 2673-6284
• DOI: 10.3390/ht7020017

Personalized medicine is an aspect of the P4 medicine (predictive, preventive, personalized and participatory) based precisely on the customization of all medical characters of each subject. In personalized medicine, the development of medical treatments and drugs is tailored to the individual characteristics and needs of each subject, according to the study of diseases at different scales from genotype to phenotype scale. To make concrete the goal of personalized medicine, it is necessary to employ high-throughput methodologies such as Next Generation Sequencing (NGS), Genome-Wide Association Studies (GWAS), Mass Spectrometry or Microarrays, that are able to investigate a single disease from a broader perspective. A side effect of high-throughput methodologies is the massive amount of data produced for each single experiment, that poses several challenges (e.g., high execution time and required memory) to bioinformatic software. Thus a main requirement of modern bioinformatic softwares, is the use of good software engineering methods and efficient programming techniques, able to face those challenges, that include the use of parallel programming and efficient and compact data structures. This paper presents the design and the experimentation of a comprehensive software pipeline, named microPipe, for the preprocessing, annotation and analysis of microarray-based Single Nucleotide Polymorphism (SNP) genotyping data. A use case in pharmacogenomics is presented. The main advantages of using microPipe are: the reduction of errors that may happen when trying to make data compatible among different tools; the possibility to analyze in parallel huge datasets; the easy annotation and integration of data. microPipe is available under Creative Commons license, and is freely downloadable for academic and not-for-profit institutions.