GIP

GIP maps and analyzes genomic instability from whole-genome sequencing data to characterize aneuploidy, gene copy number variations (CNVs), nucleotide sequence changes, and chromosomal rearrangements across organisms ranging from protists to cancer cells.

Key Features:

• Comprehensive detection: Detects aneuploidy, gene copy number variations (CNVs), nucleotide sequence changes, and chromosomal rearrangements to provide a broad characterization of genome instability.
• Comparative genomics: Facilitates comparative analysis across species and strains using whole-genome sequencing datasets, with applied examples in Leishmania, Plasmodium, Candida, and various cancer types.
• Biological discovery: Enables discovery of genomic events such as convergent amplification in erythrocyte binding proteins and identification of a nullisomic Plasmodium vivax strain, and reveals correlated CNVs among functionally related genes in drug-adapted Candida albicans supporting epistatic adaptation through gene-dosage interactions.
• Disease biomarker discovery: Identifies recurrent genomic instabilities that can be used to nominate biomarkers and candidate therapeutic targets linked to cell adaptation and pathogenicity.

Scientific Applications:

• Cross-species genome comparison: Comparative analysis of whole-genome sequencing data to study evolutionary adaptations and strain variation across protists, fungi, and cancer genomes.
• Pathogenesis and adaptation studies: Investigation of genomic changes underlying pathogenicity and adaptation, exemplified by findings in Plasmodium vivax and Candida albicans.
• Biomarker and target identification: Use of detected genomic instabilities to support identification of disease biomarkers and potential therapeutic targets in infectious disease and cancer contexts.

Methodology:

Processes whole-genome sequencing data to detect and compare genomic alterations (aneuploidy, CNVs, nucleotide sequence changes, chromosomal rearrangements) across datasets and produces visualizations of these changes.