The power and challenges of single cell gene expression technology

For many common diseases, a significant percentage of patients simply do not respond effectively or have adverse side-effects to any given treatment. To more successfully focus our disease intervention targets, comparatively diverse species with high-resolution starting points are required. An understanding of cell type–specific variation in gene expression is key to deciphering the roles of genes in disease. Accordingly, newly developed single-cell methods have started to fill our gaps in knowledge of disease by allowing us to peer deeply into the molecular microenvironments of tissues and organs. Multiple lipid emulsion techniques for isolating and evaluating single cells have been developed;…

The promise of precision medicine: A focus on genomics and bioinformatics

Chromosomal rearrangements leading to the generation of gene fusions are more common in pediatric malignancies compared to adults and possess diagnostic and prognostic value. Identification of novel gene fusions provides a means for patient stratification and the foundation for the development of targeted therapeutics. The innovations discussed will include: the development of custom Next Generation Sequencing (NGS) gene panels for pediatric leukemias, and a newborn screening assay that detects germline events in high-risk populations.

Use of Powerful Tools for Meaningful Conclusions from Sparse Data

At any given time, over 10 million women are pregnant or lactating in the United States, about 80% of these pregnancies result in a normal pregnancy and life birth. The remaining are associated with a wide range of pregnancy related diseases, an even lower percent of patients present with complications not related to the pregnancy itself. The size of the data is at first glance exciting for the informatics researcher however, the low incidence of positive cases of each type of disease results in sparse data difficult to analyze resulting in less than ideal models for data mining and knowledge…

Big Data Colloquium Distinguished Speaker – Dr. Jianjiong Gao

Thanks to the advancements of technology such as next-generation sequencing, an overwhelming amount of cancer genomics data has been generated by large-scale cancer genomics projects such as The Cancer Genome Atlas (TCGA). This has imposed an increasing challenge in the translation of the wealth of the resulting “big data” into biological discoveries and clinical applications. In this talk, I will present two major platforms we developed at Memorial Sloan Kettering Cancer Center to address this challenge: cBioPortal and OncoKB. The cBioPortal for Cancer Genomics (http://cbioportal.org/) collects, integrates, and visualizes multi-dimensional, high-level cancer genomics and clinical data. It was specifically…