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Genomics in the Journals: Apr 24, 2014

NEW YORK (GenomeWeb) – In Nature Genetics, a French- and German-led team described findings from an exome sequencing analysis of epileptic encephalopathy that turned up de novo mutations in a HCN1 — a gene coding for a cationic channel component suspected to have a role in epilepsy based on animal studies.

The researchers started by doing exome sequencing on 39 individuals with early infantile epileptic encephalopathy and each of their unaffected parents. Within these parent-child trios, they saw de novo HCN1 mutations in one affected child from France and another from Italy.

Through targeted HCN1 sequencing in 95 more individuals with fever-sensitive early infantile epileptic encephalopathy, the team uncovered heterozygous de novo HCN1 alterations in three more affected individuals from France. HCN1 was also among the genes screened in dozens more Dutch cases, where yet another de novo glitch in HCN1 was detected.

From their follow-up experiments, the study's authors determined that early infantile epileptic encephalopathy cases involving de novo HCN1 mutations tend to include clinical symptoms similar to those found in an epileptic condition called Dravet syndrome, with affected individuals taking on autistic features and intellectual disability over time.

The Max Planck Institute for Evolutionary Anthropology's Svante Pääbo led an international team that scrutinized protein-coding variation in the exome sequences of Neanderthals from Spain, Croatia, and southern Siberia.

As they reported online in the Proceedings of the National Academy of Sciences, the researchers relied on a hybridization enrichment scheme to capture protein-coding sequences from DNA isolated from the Spanish and Croatian Neanderthals. After sequencing those exomes, they went on to compare them with those of a Neanderthal individual from Siberia sequenced for a prior study.

The analysis indicated that genetic diversity in Neanderthals was far lower than that detected in current human populations in Africa, Europe, and Asia — a pattern that investigators attributed to small, relatively isolated Neanderthal populations in Eurasia.

Despite the relatively low diversity in Neanderthal coding sequences, though, the team narrowed in on an over-representation of sequence changes expected to alter the resulting amino acid sequence of Neanderthal proteins.

Compared to human exomes, those non-synonymous changes were particularly common in genes contributing to skeletal features in the Neanderthal lineage. In contrast, results of the study suggest that behavior and pigmentation-related genes have been more prone to change in the lineage leading to modern humans.

In an effort to understand the evolution of the bacteria behind whooping cough, researchers from Radboud Hospital, the Centre for Infectious Diseases Research in the Netherlands, the Wellcome Trust Sanger Institute, and elsewhere used comparative genomics and phylogeny to characterize 343 Bordetella pertussis isolates collected in 19 countries between 1920 and 2010.

Results of their analysis, reported in mBio, suggest that the B. pertussis isolates behind most modern-day whooping cough cases belong to a lineage that emerged roughly 500 years ago. That strain appears to have spread quickly across the globe since the first whooping cough cases were described in 16th century Europe.

By bringing together data on the large collection of B. pertussis isolates, the team got a more refined look at mutation rates in the pathogen and identified new alterations that may have arisen as a bacterial response to the introduction of vaccines targeting B. pertussis — information that's expected to aid future vaccine development methods.

"The mutation rate we were working with is probably two orders of magnitude out," the Sanger Institute's Julian Parkhill, corresponding author on the study, said in a statement, "so we thought the last common ancestor of these modern B. pertussis strains was tens of thousands of years old when, in fact, it is much younger than that."

A Science study suggests Stone Age hunter-gatherers in Sweden had lower genomic diversity than their farming counterparts, while Stone Age agriculturalists carried signs of admixture from the foraging population.

Members of an international team led by investigators in Sweden generated low-coverage genome sequences using DNA from the 5,000-year-old remains of half a dozen Neolithic hunter-gatherers belonging to the so-called Pitted Ware Culture in Sweden.

They also sequenced four members of a Neolithic farming culture known as the Funnel Beaker culture living in Sweden at around the same time and from a single hunter-gatherer individual who had lived during an earlier stage of the Stone Age some 7,500 years ago.

The team found that foraging individuals did not carry sequences that would point to past introgression from farming populations. On the other hand, data from the farming individuals suggest that that population did experienced admixture with hunter-gatherers.

The available sequence data suggested that there was more genetic differentiation between the Neolithic hunter-gatherers and farmers than is typically detected in individuals from dozens of present-day Western European populations, with neither of the ancient groups showing particularly close genetic ties to current Swedish populations.

Overall, the Stone Age hunter-gatherers had lower genetic diversity than members of the farming culture living in around the same time, perhaps due to their low population numbers, the study authors noted.

"Stone-Age hunter-gatherers had much lower genetic diversity than farmers," co-corresponding author Mattias Jakobsson, an evolutionary biology researcher at Uppsala University, said in a statement. "This suggests that Stone Age foraging groups were in low numbers compared to farmers."

"The asymmetric gene-flow shows that the farming groups assimilated hunter-gatherer groups, at least partly," Jakobsson added.