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Genomics In The Journals: Oct 11, 2012

NEW YORK (GenomeWeb News) – In the journal Cancer, National Cancer Institute researchers have described the strategy they used to find a genetic variant that seems to dial back lung cancer risk.

The team used an Illumina oligonucleotide pooling array to genotype 378 individuals with lung cancer and 450 unaffected controls at 1,429 SNPs falling in inflammation and/or immune related genes. These included genes from oxidative response pathways, for instance, as well as genes involved in cell adhesion, cytokine, and other related processes.

The search led to 81 variants with apparent ties to lung cancer, including one SNP that was significantly associated with the disease in thousands more cases and controls tested for prior lung cancer genome-wide association studies. The variant, which landed in the inflammation and innate immune-related gene NFKB1, appeared to be associated with somewhat reduced lung cancer risk in both groups.

"Our study provides further evidence that inflammation may be associated with lung cancer risk," NCI cancer epidemiology and genetics researcher Meredith Shiels, the study's first author, said in a statement.

A genetic study in the European Journal of Wildlife Research suggests that compact, dark-maned lions at a zoo in Addis Ababa that are descended from animals captured in Ethiopia's southwest differ from other lions in more than their physical appearance.

An international group led by investigators at the Max Planck Institute for Evolutionary Anthropology and Imperial College London looked at variation over a set of 10 microsatellite markers in 15 lions from the Addis Ababa zoo. When they compared these patterns to those found in lions from six wild populations, the researchers found that the Addis Ababa lions fell into a distinct genetic cluster — findings supported by a similar comparison of mitochondrial cytochrome B gene sequence data. The genetic diversity appears to have been fairly maintained in the zoo animals, they noted, indicating that the genetic differences detected are not simply a consequence of inbreeding.

"We hope field surveys will identify wild relatives of the unique Addis Ababa Zoo lions in the future," the study's first author Susann Bruche said in a statement, "but conserving the captive population is a crucial first step."

"Our results show that these zoo lions harbor sufficient genetic diversity to warrant a captive breeding program," added Bruche, who performed the research at the Max Planck Institute for Evolutionary Anthropology and is now based at the Imperial College London.

Two papers appearing online in Lancet Oncology look at blood-based transcriptional patterns associated with prostate cancer prognoses.

For the first of these studies, a Mount Sinai School of Medicine-led team assessed blood-based expression profiles for 168 candidate genes known for their roles in inflammation, immune, or prostate-related processes, using blood samples from 62 men with castration-resistant prostate cancer who were classified in high- or low-risk groups based on their survival times expression levels. Expression patterns for half a dozen genes identified in that discovery stage were subsequently linked to prostate cancer prognoses in a validation group comprised of 140 more castration-resistant prostate cancer patients.

An international group led by investigators in the UK tracked down four distinct prostate cancer-related expression profiles when they did array-based analyses of blood gene expression patterns in 94 patients with castration-resistant prostate cancer or with prostate cancer under active surveillance. Examples of castration-resistant cancer cases turned up in all four of the gene expression groups described. But castration-resistant prostate cancer patients falling in one of the expression groups — defined using a nine-gene expression signature — had worse survival outcomes.

"Our results suggest that whole-blood gene profiling could identify gene expression signatures that stratify patients with castration-resistant prostate cancer into distinct prognostic groups," senior author Johann de Bono, a researcher with the Institute of Cancer Research and the Royal Marsden NHS Foundation Trust, both in Sutton, UK, and his colleagues wrote.

A PLoS ONE study by researchers at the Translational Genomics Research Institute, the May Clinic in Scottsdale, Ariz., and other centers in Arizona looks at the mutations present in pancreatic cancer.

The TGen and Mayo Clinic-led team did whole-genome sequencing on matched tumor biopsy and normal samples from three individuals with pancreatic adenocarcinoma, the most commonly diagnosed pancreatic cancer subtype. Within the tumor genomes, the investigators uncovered 142 suspicious somatic point mutations, small insertions/deletions, or copy number alterations. Among them were genetic glitches in genes implicated in pancreatic cancer in the past, such as KRAS, TP53, BRCA2, and MYC. But previously unappreciated genes and pathways also popped up, as did new kinds of mutations to known genes. For two patients whose tumors were also tested by transciptome sequencing, study authors found mutations and copy number shifts that they believe might make useful treatment targets.

"As we continue to sequence patients, we will acquire a better understanding of the compendium of events that have a role in the disease, and strengthen our knowledge base for identifying and developing improved therapeutics," co-first author Winnie Liang, assistant director of the collaborative sequencing center at TGen, said in a statement.

A gene-focused meta-analysis by researchers in the UK, US, the Netherlands and elsewhere has uncovered 21 genes that appear to influence lipid levels in the blood.

As they report online in the American Journal of Human Genetics, almost 200 International IBC Lipid Genetics consortium members analyzed data for individuals tested using Illumina's ITMAT-Broad-CARe, or "Cardiochip" — an array designed to assess 50,000 or so variants within 2,000 genes suspected of influencing cardiovascular traits, inflammation, and/or metabolic profiles. Based on data for more than 66,200 individuals tested through nearly three-dozen prior studies, the investigators identified 21 lipid-associated loci within genes, which they went on to verify either through testing on nearly 25,000 more individuals or using data generated as part of a project by the Global Lipid Genetic Consortium.

"While each of the genetic variants has a small effect on the specific lipid trait, their cumulative effect can significantly add up to put people at risk for disease," University College London researcher Fotios Drenos, co-senior author on the study, said in a statement.

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

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