Scientists at Albert Einstein College of Medicine of Yeshiva University have developed a desktop genome analyzer and browser that allows biologists to rapidly and easily analyze and process their high-throughput data. The open-source software, called GenPlay, is described in the May 19 online edition of Bioinformatics.
Currently, genomic data is analyzed mainly by information specialists rather than by the biologists who designed the experiments that produce the data. GenPlay was created with the goal of offering biologists a user-friendly, multi-purpose tool that can help them visualize, analyze and transform their raw data into biologically relevant tracks.
“The first human genome was sequenced 10 years ago by an international consortium at a cost of $7 billion,” notes GenPlay co-developer Eric Bouhassira, Ph.D., senior author of the Bioinformatics article, professor of medicine and of cell biology, and the Ingeborg and Ira Leon Rennert Professor of Stem Cell Biology and Regenerative Medicine at Einstein. “But today, a complete genome can be sequenced for less than $10,000 and the cost is predicted to drop to less than $1,000 in a few years. The dramatic dip in cost has led to the creation of an avalanche of new data that biologists are having trouble analyzing. GenPlay is intended to make it easier for biologists to make sense of their data.”
A dozen or so genome browsers are currently available. GenPlay offers a major advantage over the others, says Dr. Bouhassira, because it “emphasizes letting biologists take control of their own data by providing continuous visual feedback together with extremely rapid browsing at every decision point during an analysis.”
GenPlay handles three major types of data: data from gene expression studies, epigenetic data, and single nucleotide polymorphism (SNP) data. The free GenPlay software is available from http://www.genplay.net.
The Bioinformatics paper is titled “GenPlay, a Multi-Purpose Genome Analyzer and Browser.” The lead author of the paper is Julien Lajugie, M.S., associate in Einstein’s department of medicine, who co-developed GenPlay and wrote the GenPlay program. The project was funded by New York State Stem Cell Science (NYSTEM).
About Albert Einstein College of Medicine of Yeshiva University
Albert Einstein College of Medicine of Yeshiva University is one of the nation’s premier centers for research, medical education and clinical investigation. During the 2010-2011 academic year, Einstein is home to 724 M.D. students, 256 Ph.D. students, 122 students in the combined M.D./Ph.D. program, and 375 postdoctoral research fellows. The College of Medicine has 2,770 fulltime faculty members located on the main campus and at its clinical affiliates. In 2009, Einstein received more than $135 million in support from the NIH. This includes the funding of major research centers at Einstein in diabetes, cancer, liver disease, and AIDS. Other areas where the College of Medicine is concentrating its efforts include developmental brain research, neuroscience, cardiac disease, and initiatives to reduce and eliminate ethnic and racial health disparities. Through its extensive affiliation network involving five medical centers in the Bronx, Manhattan and Long Island – which includes Montefiore Medical Center, The University Hospital and Academic Medical Center for Einstein – the College of Medicine runs one of the largest post-graduate medical training programs in the United States, offering approximately 150 residency programs to more than 2,500 physicians in training. For more information, please visit www.einstein.yu.edu.
