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Genomics In The Journals: Oct 25, 2012

NEW YORK (GenomeWeb News) – A study in BMC Genetics suggests that the low level of genetic diversity found in the koala may have preceded the animal's population decline during the late 19th and early 20th centuries.

Researchers from Germany, Denmark, and the US sequenced a hyper-variable portion of the koala's mitochondrial genome sequence using DNA from more than a dozen museum samples. The samples, obtained from museums in Australia and beyond, represented koalas that had been collected in different parts of Australia from the late 1800s to the 1980s.

The team found surprisingly similar mitochondrial profiles in the historical koala samples and samples from modern day koalas. And all four of the mitochondrial haplotypes identified in the older museum samples persist in modern koala populations, the researchers said. That hints that relatively low genetic diversity has been present in koalas for at least 120 years — prior to dramatic population declines at the end of the 19th century, which have been attributed to factors such as hunting, habitat loss, and disease.

"The event which reduced the genetic diversity of koalas must have happened a long time ago, perhaps during the late Pleistocene when the larger species of koala, P. stirtoni, became extinct," Leibniz-Institute for Zoo and Wildlife Research's Alex Greenwood, the study's corresponding author, said in a statement.

Quantitative imaging and genomic analyses can offer complementary information about breast cancers, in some cases providing clues to patient survival, according to a new Science Translational Medicine study.

An international team headed by investigators in the UK came up with computational approaches for quantifying tumor cellularity — the proportion of cancerous cells, immune cells, and other stromal cells in a tumor sample — and combining this imaging-based information with genomics data. By doing imaging and histopathological assessments of 323 breast cancers in parallel with gene expression and copy number profiling of these tumors, for instance, the researchers demonstrated that they could improve tumor classification and patient prognoses — results that they verified in another 241 breast tumors. In particular, results of their analyses suggest that a combination of imaging and genomics data can help in classifying and predicting survival outcomes in estrogen-receptor negative breast cancer.

"Our approach has the potential to provide new clinical predictors and to better understand the tumor microenvironment by using already available histopathological information," senior author Florian Markowetz, a researcher affiliated with the University of Cambridge and the Cancer Research UK Cambridge Research Institute, and co-authors argued.

"Although the mechanistic basis underpinning the prognostic value of stromal patterns is not known," they added, "our findings highlight the importance of accounting for architectural differences in attempting to understand tumor-microenvironment interactions."

In the New England Journal of Medicine, a team from the US and Japan looked at the relationship between PIK3CA mutation status in colorectal cancer and survival patterns for patients taking aspirin. Using data for 964 rectal or colon cancer patients already enrolled in long-term studies, the researchers identified an aspirin-associated boost in survival for individuals with PIK3CA mutation-positive colorectal tumors — an effect that was not detected in colorectal cancer patients whose tumors lacked PIK3CA mutations. Of the 62 PIK3CA mutation-positive colorectal cancer patients who reported taking aspirin regularly, 60 had survived at least five years following their diagnosis, compared to 67 of 90 PIK3CA mutation-positive colorectal cancer patients who did not report taking the drug.

"Our data suggest that regular use of aspirin is suitable for testing as an adjuvant treatment in patients with mutated PIK3CA cancers and that PIK3CA mutations status may serve as a tumor biomarker that predicts the response to adjuvant aspirin treatment," authors of the study noted, though they cautioned that additional studies in larger colorectal cancer cohorts are needed to expand on the present findings.

A study by Chinese researchers in the American Journal of Human Genetics has implicated the same two genetic variants in elevated risk for lung, stomach, and esophageal cancers in the Han Chinese population.

The team started by doing a genome-wide association analysis of 5,368 Han Chinese individuals with lung cancer, non-cardia gastric cancer, or esophageal squamous cell carcinoma, looking for genetic variants that were overrepresented in these individuals compared to more than 4,000 unaffected controls from the same population. After testing the top five variants from the discovery phase of the study in another 9,001 cases and 11,436 controls, the investigators determined that two SNPs — one on chromosome 6 and another on chromosome 7 — were consistently tied to a rise in the risk of all three types of cancer considered.

"[O]ur study indicated variants at 6p21.1 and 7p15.3 as candidate susceptibility loci for multiple types of human cancer, though the biological mechanism remains to be elucidated," Nanjing Medical University researcher Hongbing Shen, the study's senior author, and co-authors concluded. "Further investigations are warranted to extend these findings to other types of human cancers and to other ethnic populations."

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

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