Stephen J. Salipante, MD, PhD

Clinical and Research Background

Dr. Salipante’s group focuses on the development and application of massively parallel (or “next-generation”) DNA sequencing technologies to areas relevant to human health. Our diverse research projects involve both basic science investigation and clinical test development. The purpose of our efforts is to develop and explore new applications of high-throughput sequencing technologies, to translate these technologies to novel clinical diagnostics and basic science discoveries, and to develop bioinformatics tools and data analysis pipelines for these purposes. We aim to learn about the basic biology of human diseases and to apply this new knowledge directly to disease diagnosis, prevention, and treatment.

Our current work is focused on three major areas of translational investigation:

Large‑Scale Sequencing of Clinical Bacterial Isolates

We have developed methods enabling the whole genome sequencing and analysis of large numbers (hundreds to thousands) of clinical bacterial isolates. These data can be applied to explore many aspects of bacterial infectious diseases, including molecular epidemiology, characterization of the diverse complement of genes that they harbor, and the identification of genes responsible for clinically important properties such as virulence and antibiotic resistance.

Detection of Low-Prevalence Cancer Mutations

With some modifications, sequencing technologies can now be employed to robustly detect actionable mutations present at very low frequencies (1 in 10,000 to 1 in 100,000 cells). These approaches hold translational opportunities in the sensitive detection of small numbers of cancer cells which persist after therapy (minimal residual disease) and for the early detection of cancers, potentially allowing earlier therapeutic intervention. Reliable detection of very low prevalence mutations also allows basic properties of malignancy to be explored, such the genomic evolution of tumors over time.

Development of Novel Next-Generation Sequencing Technologies and Diagnostic Tools

One of our activities is to develop novel applications and methods which utilize next-generation DNA sequencing and leverage its unique properties in various ways. These technologies are applied in translational research activities, and/or are adapted and validated for clinical use in the care of patients.