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Internal Oncology Testing Program Offers Opportunity to Test SAP's New Sequence Analysis Software


NEW YORK (GenomeWeb) – A new cancer personalized treatment service that SAP is offering to employees living with the disease provides an opportunity for the company to put its newly minted SAP Genomic Analyzer solution — a sequence alignment and analysis software that runs on the SAP Hana infrastructure — to the test.

SAP said this week that its software will be used as part of a personalized treatment option service offered to SAP employees — being piloted in Europe and the US — who have been diagnosed with solid tumors. The program is being run in collaboration with MolecularHealth and GATC Biotech, which will provide sequencing services for employees in the US and Europe, respectively.

In addition, MolecularHealth will be responsible for analyzing all the data generated at both labs. In 2012, MolecularHealth tapped SAP's Hana platform to help it shorten the analysis time that its decision support software for oncology required. Now, under the auspices of this program, MolecularHealth will use the Genomic Analyzer solution, SAP said, along with its own software, which analyzes data from TreatmentMap, the company's targeted gene panel of over 500 relevant genetic variants. Together, these tools will be used to generate bespoke profiles for each patient and their tumor and provide an interpretation of relevant variants to help treating clinicians select the most appropriate treatments.

The benefits of personalizing treatments for employees with cancer was the main motivation for the SAP program, but, "obviously, a nice side effect is that it also uses Hana and the Genomic Analyzer," providing tangible proof that "our technology can improve people's lives," Werner Erberhart, SAP's chief health platform expert, told BioInform. The company is still mulling the duration of the pilot. It does plan to eventually expand the program to include employees that work in offices in other countries later on.

SAP unveiled the Genomic Analyzer this past March and kicked off an early-access program where a number of unnamed clients put the software through its paces. The company describes the Genomic Analyzer as an application for sequence alignment, annotation, and analysis that runs on SAP Hana, an analytics platform the company developed that implements its in-memory database technology. The platform provides a type of infrastructure where the data are stored and processed in the computer's main memory, which helps speed up the analysis process since it eliminates seek times when queries are run.

Based on internal benchmarks using whole-exome data, which pitted the Genomic Analyzer's alignment algorithm against an unnamed algorithm that shows up in other commercial software, SAP's solution was able to assemble the full exome in three minutes — which works out to about 300 times faster than the competition, SAP said.

SAP is now preparing to launch an early-adoption program that will last for a month or two, under which customers will be able to purchase, install, and run the Hana-based software for a special price that the firm has not disclosed, Erberhart said. The full launch date for broad availability of the solution, he said, will depend on the results of the early-adoption program. Pricing is still being discussed.

This is the second solution that SAP has launched for the genomic analysis market. In February, the company disclosed that it had developed a standalone solution, also based on Hana, called Medical Insights, which integrates and analyzes clinical and genomic data to help oncologists makes better treatment decisions for patients. It announced the product at the Healthcare Information and Management Systems Society conference and said that it was seeking early adopters for the solution ahead of a broad release planned for later this year. At the time of the launch, the company also announced a partnership with Canadian firm PHEMI Health Systems to build a solution that would make it possible to provide more personalized treatments for HIV patients.

Two years ago, SAP formed a partnership with Qiagen to develop tools for genome sequence alignment and mutation calling — but the SAP Genomic Analyzer is not the fruit of that collaboration. Werner did not comment directly on where that partnership stands at present. All he would say is that "Qiagen is focused on their recent investments in bioinformatics companies. We are a looking forward to deepening our partnership in this context as and where appropriate."

Other SAP activities in the life science space include a joint effort with the Technical University Munich's proteomics and bioanalytics department to launch ProteomicsDB, a free web-based repository of human proteins and peptides from mass spectrometry experiments that's also based on the SAP Hana platform.

Last month, SAP said that researchers at Stanford University School of Medicine were using its Hana platform to research the contributions of genetics, environmental exposures, behavior, and other factors to disease susceptibility. The solution had been used in a study, SAP said, that analyzed how the genetic risk of type 2 diabetes varies between populations. As part of the study, which was done in the laboratory of Atul Butte, an associate professor of pediatrics and genetics at Stanford, the researchers were able to query 125 variants associated with type 2 diabetes across 629 individuals in less time than traditional methods, according to SAP.

SAP has also joined the Global Alliance for Genomics and Health, an international non-profit alliance focused on sharing and analyzing genomic and clinical data.