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Genomics in the Journals: Feb 14, 2013

NEW YORK (GenomeWeb News) – In BMC Evolutionary Biology, a research duo from Uppsala University and the Swedish University of Agricultural Sciences described how they used phylogenetic information to retrace single nucleotide changes contributing to two forms of color vision in birds.

Using sequence data for an opsin gene called SWS1 from 40 birds belonging to 21 orders, investigators cobbled together a molecular phylogeny that spells out nucleotide substitutions linked to ultraviolet sensitive-to-violet sensitive vision swaps and vice versa in birds. Their analyses suggested such color vision changes have happened 14 times or more in the avian lineage, most probably starting from a violet-sensitive ancestor common to all birds.

Because the study hints that the genetics of avian color vision are not as clear cut and conserved as once suspected, study authors cautioned that "inferences of spectral sensitivities from closely related taxa should be used with caution."


Early onset prostate cancer tumors tend to have a propensity for containing balanced structural rearrangements, particularly involving genes regulated by the androgen hormone, according to a study in Cancer Cell. As part of the International Cancer Genome Project's Early-Onset Prostate Cancer project, researchers from Germany and the UK performed whole-genome sequencing on tumor and matched normal samples from 11 individuals who were surgically treated for prostate cancer at a median age of 47 years old. The tumors were also subjected to transcriptome and methylome sequencing.

When they compared sequences from these tumors with sequences from a previously described set of samples taken from seven individuals diagnosed with prostate cancer at around 65 years of age, investigators saw a rise in gene fusion-producing structural changes in the early onset samples.

Those fusions often affected ETS family genes and other genes prone to androgen-related regulation, researchers reported. In contrast, tumors from individuals whose prostate cancer appeared later in life were more apt to contain structural rearrangements affecting genes without any androgen ties.

Follow-up tests using samples from more than 10,000 other patients seemed to support this link between age at prostate cancer diagnosis and androgen receptor rearrangement, study authors said, pointing to a distinct, androgen-driven "pathomechanism" in early-onset forms of the disease.


Within the Canadian Healthy Infant Longitudinal Development study, a research team characterized the development of gut microbe communities in healthy infants during their first four months of life, looking in particular at ways in which this gut microbiome varied relative to the method by which the babies had been delivered and what they were fed.

As described in the Canadian Medical Association Journal, the researchers performed 16S ribosomal RNA gene sequencing on fecal samples from two dozen infants. Of these, six babies had been born by cesarean section and 10 were exclusively breastfed. Five of the infants had received a combination of breast milk and formula in the months leading up to sampling, while nine had not been breastfed.

From this data, investigators identified differences in gut microbiome composition that correlated with both birth and feeding methods. For instance, they reported an apparent dip in microbial diversity in samples from babies born by elective cesarean section. On the other hand, gut microbiomes of formula-fed babies typically had higher-than-usual species richness, including elevated levels of Clostridium difficile.

"We want parents (and physicians) to realize that their decisions regarding c-section and breastfeeding can impact their infant's gut microbiome," the study's first author Meghan Azad, a post-doctoral researcher at the University of Alberta, said in a statement, "and this can have potentially lifelong effects on the child's health."


An international team took a look at genome sequences generated by the 1000 Genomes Project in search of clues about recent adaptive human traits and their genetic underpinnings. The researchers used a genome-wide version of their "composite of multiple signals," or CMS, test to find new regions suspected of containing variants under positive natural selection, before fine-mapping 412 candidate regions by standard CMS. Together with functional, epigenetic, protein structure, and association data, that analysis revealed promising causal variant candidates within parts of the genome that show signs of selection.

In particular, the team catalogued almost three dozen apparently adaptive non-synonymous variants as well as 59 adaptation-related variants that seem to coincide with neighboring gene or long intergenic non-coding RNA expression. Many more SNPs coming out of the analysis are suspected of influencing infectious disease risk and other traits.

For that study, appearing online in Cell, the group more fully characterized the adaptive effects of one SNP — a non-synonymous variant in a Toll-like receptor gene that mediates certain cell signaling pathways in response to a protein in bacteria's tail-like flagella.

Meanwhile, an accompanying paper in the same journal explored the evolution — and effects of — a specific variant within a gene called EDAR. Using mouse models and other experiments, authors of that study found that a variant in EDAR that's been under positive selection in East Asian populations is associated with everything from thicker hair to changes in mammary gland features and the density of certain sweat glands.

"The two studies have uncovered two intriguing human adaptive traits," Broad Institute and Harvard University researcher Pardis Sabeti, a senior author on both studies, said in a statement, "and demonstrate the ability to go from an unbiased genome scan to a novel hypothesis of human evolution."


Also in Cell, another Massachusetts-led research group outlines clonal evolution patterns in chronic lymphocytic leukemia. The researchers started from whole-exome sequence data on tumor and matched normal samples from 160 individuals with CLL. For samples from 149 of the patients, including 18 individuals whose tumors were assessed at more than one time point, they had enough information to discern mutations profiles and copy number changes within sub-populations of tumor cells.

Together, such data made it possible to get a glimpse at how CLL sub-populations change over the course of tumor evolution. For instance, the team uncovered situations in which driver mutation-containing sub-clones expanded over time, corresponding with CLL progression following treatments intended to staunch its advance.

"It's been clear for some time that tumors are collections of different subgroups of cells, each with a particular set of gene mutations, and that, over time, some of these subgroups become more prevalent and some less," said co-senior author Catherine Wu in a statement.

"So the tumor that you initially treat can be quite different, from a genetic standpoint, from the tumor that recurs later on," added Wu, who is affiliated with the Dana-Farber Cancer Institute and Harvard Medical School.


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

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