GIP: an open-source computational pipeline for mapping genomic instability from protists to cancer cells

Genome instability has been recognized as a key driver for microbial and cancer adaptation and thus plays a central role in many diseases. Genome instability encompasses different types of genomic alterations, yet most available genome analysis software are limited to just one type of mutation. To overcome this limitation and better understand the role of genetic changes in enhancing pathogenicity we established GIP, a novel, powerful bioinformatic pipeline for comparative genome analysis. Here, we show its application to whole genome sequencing datasets of Leishmania, Plasmodium, Candida and cancer. Applying GIP on available data sets validated our pipeline and demonstrated the power of our tool to drive biological discovery. Applied to Plasmodium vivax genomes, our pipeline uncovered the convergent amplification of erythrocyte binding proteins and identified a nullisomic strain. Re-analyzing genomes of drug adapted Candida albicans strains revealed correlated copy number variations of functionally related genes, strongly supporting a mechanism of epistatic adaptation through interacting gene-dosage changes. Our results illustrate how GIP can be used for the identification of aneuploidy, gene copy number variations, changes in nucleic acid sequences, and chromosomal rearrangements. Altogether, GIP can shed light on the genetic bases of cell adaptation and drive disease biomarker discovery.