New CHOP Investigator Combines Bioinformatics and Cancer Genomics

Feb 16 2016

New CHOP Investigator Combines Bioinformatics and Cancer Genomics

bioinformatics“I’m excited being here at the right time,” said Kai Tan, PhD. “Hopefully we can really push translational medicine in cancer, faster, with our new algorithms.”

It is the “right time” because Dr. Tan, a cancer genomics and bioinformatics researcher, joined The Children’s Hospital of Philadelphia in January. Within weeks of his arrival, Vice President Joe Biden launched the cancer “moonshot” initiative during a visit with cancer researchers from the University of Pennsylvania and CHOP at Penn’s Abramson Cancer Center.

The rapid expansion of precision medicine in cancer — in which researchers aim to develop clinical treatments precisely targeted to a tumor’s genetic profile — has created an urgent need for scientists like Dr. Tan, who has pioneered the development of novel computational strategies and systems biology to identify molecular events that drive cancers.

The bioinformatics component of Dr. Tan’s lab, about 60 percent of his team’s focus, is of vital importance to cancer research in this era of big data and translational medicine. Scientists using next-generation sequencing technologies to generate data about patients’ genomes and gene expression patterns, both in their healthy cells and in cancer cells, are finding themselves with vast amounts of information at their fingertips. That information is becoming available faster and cheaper than ever before — but it is not so cheap or easy to make sense of that data and find meaningful signals in the noise, such as identifying the specific genes or pathways that are most promising to target with new therapies.

“If we cannot generate new hypotheses, if we cannot identify new targets, it’s a waste of data,” Dr. Tan said.

bioinformaticsHis bioinformatics lab, which includes a team that came with him from the University of Iowa, develops algorithms to help do exactly that, focusing on analyzing next-generation sequencing data and gene network data. In addition, he is beginning to develop algorithms to interpret data now available from analyses of single cells, a method intended to find minute differences in the mutations present in different cells within tumors, but which is more error-prone because it cannot smooth out its errors across a large sample size.

In his bench work as a basic scientist, Dr. Tan studies the development pathways of hematopoetic stem cells (blood stem cells). These stem cells develop in similar ways in healthy development and in blood cancers such as leukemia. Dr. Tan is comparing genomic and epigenomic mechanisms that regulate gene expression in both cell types to gain insight into cancer’s differences — and its weaknesses.

In his new role as a faculty member in the Division of Oncology and in the Department for Biomedical and Health Informatics at CHOP, and an associate professor of Pediatrics at the Perelman School of Medicine at Penn, Dr. Tan will collaborate with CHOP clinicians and engage with the robust cancer and genomic research communities at both CHOP and Penn Medicine. He also is a principal investigator of several active National Institutes of Health grants.

“CHOP’s cancer center is one of the best, so I’m excited to apply our basic science skills to really do something that can eventually lead to new therapeutics,” Dr. Tan said. “That’s what really excites me.”