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Genomics in the Journals: Apr 18, 2013

NEW YORK (GenomeWeb News) – In Nature Genetics, members of the St. Jude Children's Research Hospital-Washington University Pediatric Cancer Genome Project described findings from a genomic and transcriptomic study of low-grade glioma and low-grade glioneuronal tumors.

The researchers did whole-genome sequencing on 39 matched tumor-normal samples from children with LGG or LGGNT for the childhood brain cancer study. Coupled with transcriptome information for nearly four-dozen tumors and other types of data on around 100 more tumors, the genome sequences led them to suspicious alterations in both new and known cancer genes.

Even so, the group's analyses suggested that some 62 percent of the glioma tumors harbor only one gene mutation with predicted protein-altering potential.

Moreover, in more than half of the diffuse LGG cases, the investigators found either recurrent duplications involving part of the FGFR1 gene or rearrangements affecting a gene called MYB. The mutually exclusive FGFR1 and MYB mutations are drawing interest as potential treatment targets, they noted, particularly since initial mouse experiments indicate that the alterations converge on signaling pathways susceptible to specific drug inhibitors.

"We were surprised to find that many of these tumors could be traced to a single genetic alteration," co-author Richard Wilson, director of the Genome Institute at Washington University, said in a statement.

"This is a major pathway through which low-grade gliomas develop," he continued, "and it provides new clues to explore as we search for better treatments."

Circumcision causes a shift in penis microbial community structure that might curb the risk of HIV infection, according to a new mBio study. Researchers from the US and Uganda used 16S ribosomal gene sequencing to assess the sorts of microbial community members present in pre- and post-circumcision penis swab samples from 79 recently circumcised adult men in Uganda. Those samples were also compared with penis swab samples from 77 uncircumcised control individuals from the same population.

In the year following circumcision, the team saw an overall decline in both the number and diversity of microbes present in the penis microbiome. Compared to microbial communities in samples taken prior to circumcision or from the uncircumcised control individuals, the circumcision-associated microbiome showed decreased representation by at least a dozen anaerobic organisms, the group reported, along with a more modest boost in the numbers of aerobic bacteria.

Such findings hint that the penis microbiome might play a part in the circumcision-related dip in HIV infection risk that's been described in some past studies. For instance, authors of the new study noted that certain anaerobic microbes in the uncircumcised penis microbiome may contribute to inflammation and/or other processes that increase HIV infection risk — possibilities that they plan to explore in future studies.

"From a public health perspective the findings are really interesting because some of these [anaerobic] organisms that are decreasing could cause inflammation," senior author Lance Price, a researcher affiliated with the Translational Genomics Research Institute and George Washington University, said in a statement.

"The work that we're doing — by potentially revealing the underlying biological mechanisms — could reveal alternatives to circumcision that would have the same biological impact," he added. "In other words, if we find that it's a group of anaerobes that are increasing the risk for HIV, we can find alternative ways to bring down those anaerobes."

A University of California, San Francisco-led team looked at genetic factors associated with the risk of lymphedema — a chronic condition characterized by lymphatic fluid build up and painful swelling— in women treated for breast cancer. As they reported in PLOS One, the researchers assessed 157 SNPs in 17 candidate genes using blood samples from 155 breast cancer patients who developed lymphedema and 387 who did not.

Along with non-genetic factors with apparent ties to lymphedema risk, such as weight, disease stage, and lymph node removal patterns, the group found lymphedema-associated variants in four genes. These genes appear to participate in pathways impacting blood vessel formation and lymphatic vessel formation, authors of the study explained, pointing to a potential role for such process in lymphedema development during or after breast cancer treatment.

"These findings suggest that complex interactions may exist between a variety of patient characteristics and genetic markers that place some women at higher risk for the development of lymphedema," UCSF's Christine Miaskowski, first author on the study, said in a statement.

"Our hope is that once our findings are confirmed in a future study, we will be able to identify women at higher risk for lymphedema prior to breast cancer surgery, and initiate measures to prevent the development of this devastating condition," she added.

Finally, a pair of Science Translational Medicine studies focus on the feasibility of — and findings from — a crowd-sourcing study aimed to bring together genome-level data to find markers and models that better predict survival patterns in individuals with breast cancer.

For the first of these papers, Columbia University's Dimitris Anastassiou and colleagues described the prognostic model that they developed as winners of the study, dubbed the Sage Bionetworks/DREAM Breast Cancer Prognosis Challenge. In an accompanying study, meanwhile, a Sage Bionetworks-led group considered the nature and performance of the set of prognostic models submitted for the challenge, as well as the disease perspectives provided by these models.

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