City of Hope’s DNA sequencing core facility has both a new leader and more powerful equipment than ever before.

Harry Gao, Ph.D., formerly associate director of the facility, has succeeded Jerry Forrest, Ph.D., as director. Forrest retired from City of Hope on Feb. 2 after 34 years of dedicated service.

From left, Jinhui Wang, Basilio Gonzalez and Harry Gao ready samples and load them into the new Solexa genome analyzer. (Photo by Darrin S. Joy)

Gao, who joined City of Hope as an assistant research scientist in 2004, oversees one of the many core facilities on campus — a laboratory where City of Hope researchers can have DNA samples analyzed for studies of genetic mechanisms behind cancer, diabetes and other diseases.

The facility has more than a new director, though. It also has a new- generation sequencing machine that will dramatically speed genetic analysis. It is called an Illumina Genome Analyzer, though scientists often call it a Solexa, after the original company that manufactured it. According to Gao, the genome analyzer will significantly upgrade their ability to analyze DNA.

DNA — short for deoxyribonucleic acid — carries all hereditary information in a genetic code consisting of only four molecular “letters,” called bases.

DNA sequencers or analyzers tell researchers the order of bases that make up the code in a segment of DNA. The machines the sequencing lab has used for many years — capillary-based ABI 3730 sequencers — can read as many as 800 bases of DNA sequence in 48 samples at a time. The new genome analyzer, however, can read as many as 20 billion bases in one run, according to Gao. That represents the entire human genome about seven times over.

“We can also do much more varied and in-depth analysis than our current technology,” said Gao. The Solexa can sequence and analyze samples of RNA, or ribonucleic acid, a genetic material that is chemically related to DNA.

The Solexa also can determine where, within an entire genome, a given protein can bind to DNA or RNA, giving researchers clues about what genes a protein might control.

The machine can analyze methylation patterns of DNA, as well. Methylation is a chemical change to DNA that cells use to control which genes are active and which are silent. Many new and investigational cancer drugs work by controlling methylation patterns on DNA.

Due to the power and versatility of Solexa technology, the name of the core facility has changed to the DNA Sequencing/Solexa Core Facility.

“This machine does so much more than what we’ve been able to offer up until now,” he said. “It will really take us to the next level of genome analysis.”

The Solexa currently is available for sequencing, and the advanced procedures it offers will be available soon. Because this instrument generates massive amounts of data, major efforts also are under way by the bioinformatics core and information technology services to facilitate data storage and analysis.

In addition to the changes to the sequencing core facility, the DNA Cloning Lab, another shared resource established by Forrest, is transitioning to the Research Storeroom. The DNA Cloning Lab provided enzymes, chemicals, bacteria and other common molecular biology resources to researchers on campus.

“Much of what the Cloning Lab did can more efficiently be handled by the Research Storeroom,” said Gao. “It just makes more sense to centralize those resources now.”