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Genomics In The Journals: Mar 24, 2011

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – In Science Translational Medicine, researchers from the Memorial Sloan-Kettering Cancer Center and Johns Hopkins University report that breast cancer metastasis coincides with specific methylome patterns. The team used the Illumina Infinium HumanMethylation27 array to assess CpG methylation in 39 breast tumors from several sub-types that exhibited different metastatic behaviors and subsequently verified their methylation findings in another 132 individuals using mass spectrometry-based assays. Tumors that were less likely to metastasize tended to have excess methylation at certain genes, they found, showing a so-called "breast CpG island methylator phenotype" that seems to curb the expression of genes typically jacked up in metastatic tumors.

Doing a series of biopsies and genetic analyses over time may help squelch treatment-resistance in some long cancers, according to another study in Science Translational Medicine this week. American researchers tracked genotypic and histological changes in non-small cell lung cancer samples from 37 individuals before and after treatment. The participants all had tumors with mutations in the epidermal growth factor receptor gene EGFR that had become resistant to tyrosine kinase inhibiter therapy. Multiplex platform genotyping, fluorescence in situ hybridization, and other analyses of the tumors showed that tumor pathology, mutation and expression patterns, and even lung cancer type sometimes changed with time, suggesting ongoing profiling of tumors might be in order.

"Our findings suggest that, when feasible, oncogene-driven cancers should be interrogated with repeat biopsies throughout the course of the disease," co-lead author Lecia Sequist, an oncologist affiliated with the Massachusetts General Hospital Cancer Center and Harvard Medical School, said in a statement. "Doing so could both contribute to greater understanding of acquired resistance and give caregivers better information about whether resumption of targeted therapy or initiation of a standard therapy would be most appropriate for an individual patient."

A new study in the New England Journal of Medicine suggests a variant in the human leukocyte antigen gene HLA-A can help predict which individuals will have skin reactions and related side effects while taking the epilepsy drug carbamazepine in individuals of European descent. An international research team used Illumina arrays and HLA typing as part of their genome-wide association study involving 65 individuals who had mild or severe drug reactions while taking the drug and 3,987 who did not. Those with adverse reactions were more likely to carry the HLA-A*3101 allele, they reported, a pattern that held when they tested another 145 individuals with carbamazepine-induced hypersensitivity. The allele seems to up the risk of hypersensitivity from the five percent in the general population to 26 percent, they noted, whereas those lacking the allele have a slightly decreased risk of such side effects.

Previous studies have uncovered associations between adverse reactions to carbamazepine and the HLA-B*1502 allele in Han Chinese populations. That allele was successfully used to type and classify individuals taking the drug in Taiwan, according to a second new NEJM study this week.

Finally, as part of a special section on cancer this week, Science has a review article by Wellcome Trust Sanger Institute researcher Michael Stratton describing the progress being made using sequencing studies to tackle cancer. In the article, Stratton touches on everything from the role of sequencing technologies being employed to find driver mutations in cancer thus far to the future applications of sequencing for cancer diagnosis and treatment.

"[G]iven the rich seam of information that we know is buried in each cancer genome, the extraordinary pace of technological advance in sequencing, and the practical advantage of using a single test in diverse clinical contexts … it seems reasonable to look forward to a time in the not-so-distant future when we will consider a cancer genome sequence as a routine adjunct in clinical trials and a test we will perform on many newly diagnosed cancers," Stratton concluded.

Genomics In The Journals is a new weekly feature pointing readers to select, recently published articles involving genomics and related research.

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