Case Study: The Barbara Ann Karmanos Cancer Center

The Barbara Ann Karmanos Cancer Center, located in midtown Detroit, is the only National Cancer Institute (NCI)-designated comprehensive cancer center in metro Detroit and one of just 51 centers of its kind in the United States. The comprehensive cancer center designation means patients can access treatments exclusive to Karmanos, as well as clinical trials, cancer prevention programs, and multidisciplinary teams of cancer specialists — a comprehensive approach you cannot find in many large hospitals or health systems. Because comprehensive cancer centers are at the forefront of cancer research, they can often handle patient cases that are more challenging and complex.

To receive the “comprehensive” NCI designation, an institution must demonstrate expertise in research, laboratory, clinical, and population-based research. Hospitals must also provide early-phase clinical trials and conduct community outreach and educational activities. KCI has four NCI recognized interdisciplinary programs, i.e. the Molecular Therapeutics Program, the Population Studies and Disparities Research Prevention Program, the Molecular Imaging, and Tumor Biology and Microenvironment Diagnostics Programs. The biostatistics core supports all four programs. Karmanos is conducting more than 800 cancer-specific scientific investigation programs and clinical trials each year?. This is where Advaita’s iPathwayGuide software comes to the picture.

Wei Chen graduated from the University of Michigan with a Ph.D. in Biostatistics. She works in the Biostatistics and Bioinformatics Core of the Karmanos Cancer Institute, which is also affiliated with Wayne State University. She also has an academic appointment in the Department of Oncology, School of Medicine. She has been in this Core since 2006.

She became familiar with Advaita through a past project that she was involved with and collaborated with the founder of Advaita. She says: “We both collaborated with the same investigator. That was many, many years ago when I first joined this institution. So, I came to know Dr. Draghici very well. I know he published books and I know he’s very good at doing computational work in this area. He is a recognized expert in the field. After a presentation that he gave to the Core members, we realized that iPathwayGuide is something that could be useful for our core because our core is quite heavy on the statistics expertise but needed help on the bioinformatics aspects. So, Advaita was a good fit and a strong need.”

Wei’s submits dozens of research proposals every year and she is involved in many other existing projects. Her Core supports the approximately 300 scientific members in the Karmanos Cancer Institute. These investigators include basic scientists, clinicians and epidemiologists who come with very diverse backgrounds and training. Wei and her colleagues in the core help them design their experiments, as well as analyze their data. The ultimate goal of most experiments is to understand the underlying biological phenomena. She says: “Investigators are always interested in knowing what the gene functions are, and what pathways are involved. Bioinformatics provides that component. That is the essence of the bioinformatics work in the Core. Most of us are trained as PhDs in statistics. But we need support in bioinformatics and that is what we use iPathwayGuide for.”

Wei says that the best part of iPathwayGuide is the quality of the output and the way it presents data to researchers. She adds: “I like the quality of the reports – the analytics are very sophisticated. And our investigators also like that the format, the form, and the presentation of the report in terms of a content. The product tells a story about the data and results.” Wei also mentions that as a statistician and not a life scientist, she cannot judge the outcomes and the conclusion of an experiment from a life science perspective. This is why she appreciates that the full results are easily shared with the life science investigators, who can perform additional queries specific to the hypotheses that underlined each given experiment.

She often gets positive feedback from the researchers about the iPathwayGuide analysis. She adds: “They, they were amazed by what they printed out and how comprehensive the results were – such a thick stack of informative reports. They were impressed by the output, the amount of information, and the interactive graphs. The presentation looks very pleasant and is very comprehensive. Keeping them happy and productive is important.”

iPathwayGuide is funded through the Core facility budget. Wei believes that this is an essential part of the budget and that it is mission critical to the researchers.

Wei says that Karmanos also has access to Ingenuity from a competitive company. She says that it is very expensive and does not offer the quality of output of iPathwayGuide and is not as fast in producing results as iPathwayGuide. “With only a couple of clicks, I generate a very nice package of results” she says. And then, with another click she sends it over. She also really prefers the meta-analysis of iPathwayGuide. She says that she now only uses iPathwayGuide for this multiple-experiments type of bioinformatics analysis.

Wei is pleased with the service and support from Advaita. She says that Advaita is quick to respond with questions and offers outstanding training and support. She is especially pleased with the fact that iPathwayGuide also has training and support built directly into the actual software. She says: “There are videos embedded in the product that show users precisely what do if they need help. This is really nice.”

Finally, when asked what she would tell other core facilities about Advaita, Wei says: “Advaita is more cost effective than competitive products and, for the output, it does saves a lot of time. You don’t have to come up with your own report, write-up and conclusions. It does a superior job of finishing the analysis for you. It’s just better.”