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Genomics in the Journals: 2013.06.27

NEW YORK (GenomeWeb News) – In Nature Genetics, members of the International Headache Genetics Consortium reported on a dozen apparent risk loci for migraine headaches, including five not described in the past.

The team tracked down the migraine-associated sites through a meta-analysis of data from dozens of past genome-wide association studies involving nearly 23,300 migraine sufferers and more than 95,400 unaffected individuals from the same populations.

Using genotyping information for these cases and controls, the study's authors narrowed in on 12 loci with significant ties to migraine susceptibility and another 134 loci containing variants with more tenuous migraine associations. Five of the significant risk sites were new, they noted, including some loci with links to migraine sub-groups such as migraines with aura symptoms.

"The molecular mechanisms of migraine are poorly understood," co-author Kári Stefánsson, a University of Iceland researcher and CEO of Decode Genetics, said in a statement. "The sequence variants uncovered through this meta-analysis could become a foothold for further studies to better understanding the pathophysiology of migraine."


A Massachusetts General Hospital-, Dana-Farber Cancer Institute-, and Harvard Medical School-led team has found evidence that ongoing aspirin use may slightly curb the risk of developing colorectal cancer. But that benefit appears to be absent for individuals whose tumors contain mutations in the BRAF gene.

As they reported in the Journal of the American Medical Association, investigators looked at data for 127,865 individuals whose aspirin use and cancer diagnoses had been documented over several years using questionnaires and other information sources. During the follow-up period, 1,226 individuals developed cancer originating in the colon or rectum.

Among those who reported regular aspirin use, the risk of developing BRAF mutation-negative colorectal cancer dipped by around 27 percent, on average, according to the team's analysis. That protective effect was more pronounced in individuals taking more aspirin each week. On the other hand, the group did not detect a significant aspirin-associated decrease in the risk of colorectal cancer characterized by BRAF mutation.

"These findings suggest that BRAF-mutant colon tumor cells may be less sensitive to the effect of aspirin," the study's authors concluded. "Given the modest absolute risk, further investigations are necessary to determine clinical implications of our findings."


An American Journal of Human Genetics study by researchers in the US, Thailand, the UK, Singapore, and Vietnam described a chromosome 2 deletion found in some children with language delay and so-called white matter hyperintensities — brain lesions associated with brain aging, declining cognition, and/or vascular problems affecting the brain.

Drawing from array-based genome-wide array-comparative genomic hybridization data on nearly 15,500 children tested at Baylor College of Medicine's medical genetics lab, the team noticed that a small group of children with language delay and white matter hyperintensities carried the same 4,000-base deletion on chromosome 2, which lops off part of a gene called TM4SF20.

From that data and follow-up analyses, the investigators found the characteristic deletion in 15 unrelated families with late-talking children who had white matter hyperintensities. Most of the families had either come from Southeast Asia, they noted, or had ancestry that could be traced back to Vietnam, Burma, Thailand, Indonesia, the Philippines, or Micronesia.

The chromosome 2 alteration appears to be found at higher-than-usual frequency in Vietnam's Kinh populations, according to their data, where roughly 2 percent of individuals carry the deletion.

"It is important to follow these children longitudinally to see how these late-talkers develop as they grow," corresponding author Seema Lalani, a clinical geneticist and researcher in molecular and human genetics at Baylor College of Medicine, said in a statement.

"We have also seen this deletion in children whose parents clearly were late-talkers themselves, but overcame the earlier problems to become doctors and professionals," she added. "The variability within the deletion carriers is fascinating and brings into question genetic and environmental modifiers that contribute to the extent of disease in these children."


If current climate predictions come to pass, members of soil microbial communities that dominate in arid desert environments may be pushed out by species better able to tolerate warmer temperatures, according to a study in Science.

Researchers affiliated with centers in the US and Spain used 16S RNA gene sequencing to look at the structure of soil microbe communities at 20 sampling locales in the US Southwest, including spots in the Colorado Plateau, the Great Basin, and the Sonoran, Mojave, and Chihuahuan deserts.

In the cooler, northern sites, the team found that the cyanobacterial species Microcoleus vaginatus (already known for its prevalence in biocrust samples) tended to dominate soil microbiomes. On the other hand, a distantly related species called M. steenstrupii often overshadowed M. vaginatus in microbe communities from soil samples collected at warmer, more southerly sites.

Based on these findings, the researchers speculated that temperature might play a key role in these soil community structure differences — a notion supported by their subsequent M. steenstrupii and M. vaginatus growth experiments in the lab. If so, they argued that anticipated temperature increases over the coming decades may lead to M. vaginatus's replacement by M. steenstrupii.

"By using our data with current climate models, we can predict that in 50 years, the cyanobacterium that fares better in warmer temperatures will push the cold-loving one off our map," Arizona State University's Ferran Garcia-Pichel, the corresponding author on the study, said in a statement.

"M. steenstrupii could completely dominate the crusts everywhere in our study area by then," he added. "Unfortunately, we simply don't know much about this microbe or what will happen to the ecosystem in the absence of M. vaginatus."


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

The Scan

Shape of Them All

According to BBC News, researchers have developed a protein structure database that includes much of the human proteome.

For Flu and More

The Wall Street Journal reports that several vaccine developers are working on mRNA-based vaccines for influenza.

To Boost Women

China's Ministry of Science and Technology aims to boost the number of female researchers through a new policy, reports the South China Morning Post.

Science Papers Describe Approach to Predict Chemotherapeutic Response, Role of Transcriptional Noise

In Science this week: neural network to predict chemotherapeutic response in cancer patients, and more.