Last updated: September 01, 2006
Berkeley Drosophila Genome Project and Celera Shake Hands Over Plans to Sequence Fruit Fly Genome
BETHESDA, Md. - The publicly funded Berkeley Drosophila Genome Project and Celera Genomics, a business unit of The Perkin-Elmer Corporation (NYSE: PKN), have become formal partners in an effort to decode, or sequence, the genetic instructions of the fruit fly.
Officially called a "Memorandum of Understanding (MOU)," the agreement was signed last week by fly researcher Dr. Gerald Rubin at the University of California, Berkeley (UCB), and Dr. J. Craig Venter, president of Celera Genomics. Rubin leads a UCB-based, federally funded consortium to sequence the fruit fly's 150 million base-pair genome.
"We are delighted. This collaboration will be good for science and ultimately for medicine," said Venter.
According to the MOU, combining the skills of the two groups will allow them to finish the job this year. "It is also a test of whether a public-private collaboration can expedite and lower the cost of the generation and use of genomic information that will ultimately benefit agriculture, and prevention, diagnosis and treatment of important human illnesses," the document says. Both parties intend to encourage participation in this collaboration by other members of the international community doing research on the fruit fly.
Speaking Monday at the fourth annual James D. Watson lecture in Washington, D.C., Dr. Francis Collins, director of the National Human Genome Research Institute (NHGRI), which funds the Berkeley Drosophila Genome Project said, "This agreement marks the beginning of a productive collaboration between the public and private genome sequencing programs that should give the research community the fruit fly sequence more rapidly than previously predicted. It will also provide an important pilot for the development of a similar partnership effort to obtain the human sequence."
Because the fruit fly is so well studied, "the animal has provided an extraordinarily deep and broad understanding of the function of genes in disease," said Rubin. And, he added, "because the fruit fly is more similar to humans than any other animal sequenced so far, its genetic information can be directly related to humans in many cases."
Researchers at Berkeley have already produced about 20 percent of the fly's DNA sequence in high-quality form. Under the new arrangement, the Berkeley group will increase their activities in parceling up the fly genome for sequencing by copying and mapping overlapping DNA pieces that span the fly's genome. Meanwhile, researchers at Celera will try out a sequencing strategy, known as whole-genome shotgun sequencing. The whole-genome shotgun method will produce sequence from many small, random DNA fragments, using high-throughput machines. By combining that sequence with map information and additional sequence provided by the Berkeley group, the team aims to assemble the data into long stretches of correctly ordered, continuous genomic sequence. Both groups will work to fill in any remaining gaps and ensure the sequence meets quality standards. Celera will deposit the data it produces in batches in the public domain database, GenBank.
The complete set of shotgun data is expected to be in GenBank by the end of 1999. If the experiment works as hoped, the collaboration could save the government DNA sequencing project $10 million, and shave two years off the timetable for obtaining the fruit fly genome sequence.
"The fruit fly genome sequence will be an enormously useful tool for studying a variety of critical questions in biology, with important applications to human health," said Dr. Harold Varmus, who, as director of the National Institutes of Health (NIH), heads the nation's largest public funding agency for biomedical research. "This effort to get that information into the hands of the research community more quickly and at less public expense should be applauded." NHGRI, a component of the NIH, funds the U.S. Human Genome Project along with the Department of Energy. The public Human Genome Project is international in scope, with important contributions coming from several countries, especially the United Kingdom.
The fruit fly has been an important animal in genetics studies for most of this century. Its genome is organized among four chromosomes and is estimated to contain some 12,000 genes. Genetic experiments in the fly have revealed many important features, including the signals that establish body regions - what, for example, makes the head form at one end of the body and the tail at the other? Genes that control organization of the fly's body also have counterparts in humans and can help explain developmental problems that result in birth defects.
A copy of the MOU is available upon request.
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