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Genomics In The Journals: Mar 8, 2012

NEW YORK (GenomeWeb News) – In Nature Genetics, researchers from Japan report on two susceptibility loci for duodenal ulcer that have been found in that country.

The team did a genome-wide association study involving more than 7,000 Japanese individuals with duodenal ulcers and some 25,300 controls from the same population. The search led them to duodenal ulcer-associated sites: one involving a chromosome 8 variant near the PSCA gene that's been previously linked to lower gastric cancer risk and another in the ABO blood group locus on chromosome 9. Duodenal ulcer risk alleles at both loci appear to be present at lower-than-usual frequencies in the Japanese population compared to other populations sampled through HapMap, study authors note, potentially explaining the relatively low rates of duodenal ulcer compared to gastric ulcer in individuals of Japanese descent.

French researchers used RNA sequencing to find a gene fusion that seems to define a new bone sarcoma subtype in another Nature Genetics study. The investigators used paired-end sequencing with the SOLiD instrument to assess the transcriptomes in samples from four individuals who had bone tumors that resembled Ewing sarcoma but did not carry the characteristic EWSR1-ETS fusion.

The team found fusions in two of the four tumors. One involved the FUS and FEV genes, a fusion found in Ewing sarcoma in the past. But the other fusion was new, linking the X-chromosome genes BCOR and CCNB3. Analyses of another 594 sarcoma samples turned up two-dozen more cases involving the BCOR-CCNB3 fusion, researchers reported, and the presence of the fusion marked tumors that had gene expression and variant patterns unlike those seen in other sarcomas.

"Our results identify a distinct gene fusion, thereby shedding new light on the development of two tumor classes with similar phenotypes, Ewing sarcomas and Ewing-like tumors," Institut Curie researcher Olivier Delattre, the study's senior author, and colleagues explain. "[W]e can infer distinct mechanisms of oncogenesis for these subtypes, which may be of critical significance for diagnostics and, possibly, for therapeutic intervention in the coming age of personalized medicine."

Two Journal of the National Cancer Institute studies address the clinical relevance of cytochrome P450 2D6, or CYP2D6, gene polymorphisms for predicting tamoxifen treatment response and breast cancer recurrence.

In the first of these, members of the Breast International Group 1-98 Collaborative Group genotyped thousands of post-menopausal women with hormone receptor-positive breast cancer who had been treated with tamoxifen and/or letrozole between 1998 and 2003. Their goal was to see if cancer-free survival outcomes were linked to polymorphisms in CYP2D6, which codes for an enzyme that metabolizes tamoxifen into more potent metabolites.

The group did not find ties between CYP2D6 genotype and cancer free survival. Unexpectedly, though, variants linked to reduced tamoxifen metabolism coincided with an increase rather than a decrease in tamoxifen-related hot flushes, a side effect previously thought to be linked to effective drug metabolism.

"The results of this study do not support the using the presence or absence of hot flushes or the pharmacogenetic testing of CYP2D6 to determine whether to treat post-menopausal breast cancer patients with tamoxifen," authors of the study write.

A second JNCI study by a University of Michigan-led team found that CYP2D6 genotyping did not predict outcomes for post-menopausal women participating in the Arimidex Tamoxifen, Alone or in Combination (ATAC) trial.

Using data from around 1,200 women genotyped for variants in CYP2D6 and in UGT2B7, a gene whose product influences the activity of a tamoxifen metabolite called endoxifen. Again, researchers failed to find significant links between breast cancer recurrence rates over a median of 10 years of follow up and genotype patterns in CYP2D6 or UGT2B7 for women treated with tamoxifen or another drug, anastrazole, either alone or in combination.

An Oregon State University-led team used microsatellite genotyping and mitochondrial DNA data to measure the genetic diversity and geographic differentiation present in Antarctic blue whales — work that they describe in PLoS ONE. The researchers took biopsy samples from more than 200 Antarctic blue whales in the Southern Ocean over almost two decades, uncovering unexpectedly high haplotype diversity in the animals given the modest size of the Antarctic blue whale population, currently estimated at roughly 2,200 individuals, combined with their past population bottleneck.

"Fewer than 400 Antarctic blue whales were thought to have survived when this population was protected from commercial hunting in 1966," first author Angela Sremba, a researcher with Oregon State University's Marine Mammal Institute, said in a statement. "But the exploitation period, though intense, was brief in terms of years, so the whales' long lifespans and overlapping generations may have helped retain the diversity."

In Science, a team of researchers from the University of Illinois at Urbana-Champaign, Wellesley College, and Cornell University describe brain gene expression differences in honey bees that scout for food or nest sites compared to forager bees that don't scout. Among the genes showing differential expression by whole-genome microarray analyses of bee brain samples some related catecholamine hormone signaling and signaling involving the neurotransmitters glutamate and gamma aminobutyric acid. The team reported that treating bees with octopamine or glutamate made them more adventurous and apt to engage in scouting behavior while treatment that decreased dopamine interaction with its receptors curbed this behavior.

"Our results demonstrate intriguing parallels between honey bees and humans in novelty-seeking behavior," University of Illinois, Urbana-Champaign researcher Gene Robinson, the study's corresponding author, and colleagues note. "Although the molecular mechanisms that produce behavioral variation are similar, it is unknown whether both species inherited them from a common ancestor or evolved them independently."

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

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.