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Sweden's Halo Genomics and Uppsala University collaborate on study to identify mutations that cause colon cancer

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UPPSALA, Sweden—Aimed at providing state-of-the-art diagnostic tools for individualized cancer treatment, Halo Genomics AB has launched a joint study with the Department of Immunology, Genetics and Pathology at Uppsala University to identify mutations that cause colon cancer.
To accomplish this feat, researchers are using HaloPlex PCR, a new analytical method that provides scientists the ability to analyze a large number of samples in record time, according to a Nov. 7 news release. Thus far, results show that HaloPlex PCR technology is useful for so-called companion diagnostics, as required to select the optimal cancer treatment for each individual patient.
Halo Genomics has developed an assay to selectively amplify 563 genes in 11 pathways in a total of 228 tumor samples, according to the company. Uppsala University has made the selection of genes and will also sequence and analyze the data.
Researchers selected 560 genes in 192 tumor samples, and Halo Genomics produced a so-called HaloPlex PCR-analysis of the genes. 
"With this analytical method, it took a week for one person to prepare the 192 samples for sequencing, without any need for special equipment," says Mats Nilsson, project director at the Department of Immunology, Genetics and Pathology at Rudbeck Laboratory, a translation research center that houses routine clinic, clinical and preclinical research in immunology, cancer and genetics.
The samples are now being sequenced at SciLifeLab in Uppsala, one of the largest universities in Scandinavia with 35,000 students, Nilsson says. The researchers expect to be able to identify exactly what molecules are affected in tumor cells from individual patients. 
"This information will be of significance when it comes to selecting the right kind of targeted treatment for patients in the future," Nilsson tells ddn. "The method is promising for use in diagnostics because of its low cost and high efficiency. The goal of our project is to improve therapy of cancer by improved companion diagnostics—that is, guiding therapy by knowledge about the exact molecular cause of disease. The reason why we are going this way is that most of the drugs in the drug development pipelines at the pharma companies are molecularly targeted drugs. They usually aim to block some signaling pathway that is overexpressed in cancer by targeting a specific receptor or kinase.
"If genes in that particular pathway are mutated, then the drug won't work," Nilsson continues. "These drugs are usually very expensive and do have some adverse effects, so it very important to select the right drug for each patient, based on the mutational profile of that particular patient's tumor."
The idea to focus on colon cancer came from renowned oncologist Dr. Bengt Glimelius, a leading expert in colon cancer therapy. He has collected colon cancer material with a very good track record of patient data for a very long time, Nilsson says.
Glimelius was responsible for specifying the surgical procedures for operating on colon cancer patients, thus reducing the number of patient complaints and post-surgical problems to nearly nil. He also was one of the first oncologists to champion a "psycho-social" approach—or a caring, psychological and empathetic approach—to treating cancer patients and their families.
Glimelius also believes in preventative medicine. An early diagnosis of colon cancer benefits the patient by providing the right therapy as early as possible and to avoid unproductive treatments that delay a proper treatment and can cause adverse effects, Nilsson says.
Colon cancer is the third most common cancer worldwide with 5,700 new cancers yearly in Sweden, he says. About 40 percent of these patients die within five years.
Excluding skin cancers, colorectal cancer is the third most common cancer diagnosed in both men and women in the United States. The American Cancer Society's most recent estimates on the number of colorectal cancer cases in the United States for 2011 are 101,700 new cases of colon cancer, 39,510 new cases of rectal cancer and an estimated 49,380 deaths.

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