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Members of the Pediatric Cancer Genome Project have developed and validated a new algorithm to track down structural variation in cancer genomes based on soft-clipping data generated when sequence reads are partially aligned to a reference genome.

Researchers at St. Jude Children's Research Hospital found that even limited DNA sequencing can provide clues for more effective ALL treatments, and believe that more comprehensive sequencing could deliver additional clinically relevant results.

During a plenary session at the American Association for Cancer Research annual meeting this week, St. Jude's Children's Research Hospital Scientific Director James Downing discussed preliminary findings from the pediatric cancer genome project that his group is doing in conjunction with investigators at Washington University.

T-cell receptor sequencing is "a long way from being used clinically," said Robert Holt, head of sequencing at the BC Cancer Agency's Genome Sciences Center and senior author of a recent paper on the subject.

Insight is developing the tests using TaqMan probes on Life Technologies' ABI 7500 Fast Dx real-time PCR system to help physicians monitor cancer patients for mutations and upregulation in the ALK gene in order to make more effective treatment decisions.

In addition to developing a test to monitor ALK gene mutation status, Insight is working on a companion diagnostic directed at ALK.

Pairings: Sep 22, 2010


Allen Roses, Muin Khoury, Mary Relling, Martin Godbout

With a tide of data anticipated from St. Jude's ongoing genomic research, "the future's going to involve much more proteomics than we currently have capacity for."

Researchers at the AAAS annual meeting highlighted the use of ancestry markers and other genetic information rather than self-reported race for studying everything from disease association to population genetics.

Investigators from Washington University and St. Jude Children's Research Hospital are teaming on a three-year, $65 million pediatric cancer genome sequencing project.


The US National Institutes of Health's All of Us project awarded $4.6 million to the company Color to develop a genetic counseling resource for the program.

The Times of India reports on a pilot study that used genomic testing to determine whether patients had drug-resistant tuberculosis.

New guidelines say that more women may benefit from genetic testing for hereditary breast or ovarian cancer, according to the Los Angeles Times.

In Cell this week: small proteins identified among human microbiome, role for tumor microbes in pancreatic cancer survival, and more.