Cancer is a group of related-but-different diseases with various underlying molecular networks that complicate treatment. Dr. Shraddha Pai’s research goal is to improve data-driven clinical decision-making by finding genomic and multi-omic signatures that match cancer patients to the most effective treatments with the fewest side effects. Her team uses population-scale data with multiple layers of information (e.g. transcriptomic, DNA methylation, proteomic, brain imaging, clinical), and develops algorithms and software that incorporate prior knowledge of genotype-phenotype impact and systems-level organization for predictive modeling.
As a postdoctoral fellow, Dr. Pai led the development of netDx, a general-purpose patient classifier algorithm that integrates heterogenous patient data into a single model to predict clinical outcome. It adapts a recommender system model similar to that used by Netflix (“find movies like this one”) to precision medicine (“find patients like non-responders”), and uses prior knowledge of cellular pathways to organize genomic data as well as machine learning. The lab is currently building on this work to create predictive modelling workflows for application to pre-clinical patient data.
Dr. Pai’s work and expertise in genomics and precision medicine apply to cancer as well as other diseases with genomic contribution. The lab collaborates broadly with clinical, genomic and computational scientists for method development and translational research.
Genomics and epigenomics of neurodevelopmental disorders
Dr. Pai’s lab also studies the role of developmental epigenetics in altering the risk of childhood- and adult-onset disease. This includes the study of neurodevelopmental disorders such as schizophrenia and cancers of neurodevelopmental origin, such as pediatric brain malignancies. Dr. Pai co-led the first epigenome-wide association study in neurons isolated from post-mortem brain samples in major psychosis. This study led to the identification of a novel biomarker that unifies two distinctive features of psychosis: dopaminergic increase and reduced synaptic structure. The study of genomics of pediatric brain malignancies is a new and fast-evolving research area in the lab, so Contact Dr. Pai for further details.
For more information please see the Pai Lab website.