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Genomics in the Journals: Sep 11, 2014

NEW YORK (GenomeWeb) — In Nature Genetics, a team from the US and China described three loci showing ties to a rare laryngeal cancer called laryngeal squamous cell carcinoma in individuals from China.

Starting from a genome-wide association study that involved 993 Chinese individuals with LSCC and nearly 2,000 unaffected controls from the same population, the researchers narrowed in on SNPs from 18 haplotype blocks that appeared to be over-represented in those with the disease.

Of those, variants at three loci — falling on chromosomes 6, 11, and 12 — remained associated with the disease in the team's replication tests, done with samples from thousands more LSCC cases and controls.

"These findings should advance understanding of the genetic etiology of this malignancy," the study's authors wrote. "The newly identified susceptibility loci warrant additional follow-up studies involving fine mapping and functional characterization."


A Nature Communications study by investigators at the Wellcome Trust Sanger Institute, the University of Oxford, and other international centers focused on a form of the malaria-causing Plasmodium parasite found in chimpanzees.

The team began by producing a 24-million-base reference genome for the chimp parasite P. reichenowi, which contained an estimated 5,731 protein-coding genes, partial genes, or pseudogenes.

All but a handful of those overlapped with genes described in the human malaria parasite P. falciparum, the researchers reported, and the human parasite contained pseudogenized forms of some genes present in P. reichenowi.

Despite the overall conservation in genome structure and sequence between the two parasites, though, their analysis identified some significant sequence differences in genes coding for proteins that help invade host red blood cells.

Likewise, the suite of genes expressed on host blood cells following infection differed in number, consistent with the notion that there has been enhanced selective pressure on features affecting the parasites' ability to overrun red blood cells — patterns the study's authors saw in other aspects of their analysis as well.

"Researchers have identified surface proteins as promising vaccine candidates already," the study's first author Thomas Otto, with the Sanger Institute, said in a statement.

"[O]ur finding adds more support," he said, "showing that it is the difference in the parasites' surface proteins that determine which host it will infect."


The University of California, San Francisco's Joseph DeRisi and colleagues from centers across the US used genome sequencing to identify and characterize a new nidovirus that appears to cause a dangerous respiratory condition in captive ball python snakes — work that they outlined in mBio.

After using transmission electron microscopy to identify what appeared to be viral particles in lung tissues from affected snakes, the investigators applied metagenomic sequencing on samples from eight snakes to narrow in on the pathogen behind the mysterious and sometimes deadly disease, first recognized in ball pythons in the late 1990s.

The search led to sequences that resembled viruses in the order Nidovirales. The team was able to put together a 33,500-base genome assembly for the newly detected pathogen, a single-stranded RNA virus. That sequence was not only compared to those of related species described in the past, but also used to predict the protein-coding potential of the new python pathogen.

RNA coinciding with the nidovirus was subsequently found in samples from all of the ball pythons with the respiratory disease, but not in samples from dozens of unaffected snake controls.

It remains to be seen how widespread the ball python nidovirus is in these animals, the study's authors noted, and work is needed to explore its potential modes of transmission and host range.

"[U]p to this point there have been no known viruses of this type in reptiles," DeRisi said in a statement.

"Our work suggests there may be very large reservoirs of genetic diversity of viral families that can cause human disease in understudied organisms, like reptiles," he said, adding that "[w]e would do well to look broadly across all species."


A PLOS Genetics study uncovered new genetic culprits to an inherited and progressive muscle weakening condition called Emery-Dreifuss muscular dystrophy, or EDMD, which can ultimately lead to muscle wasting, joint stiffening, and heart problems.

An international team led by investigators at the University of Leicester focused on EDMD cases that did not involve alterations in the half dozen genes implicated in the condition in the past.

In the process, it uncovered previously unknown changes to nuclear membrane protein-coding genes called SUN1 and SUN2, which seem to cause a subset of the EDMD cases not attributed to those previously described gene mutations.

"Our research has shown that the mutated SUN1 and SUN2 proteins interfere with connections between the nucleus and the rest of the cell and that this results in abnormal positioning of the nuclei within the muscle cells," senior author Sue Shackleton, a biochemistry researcher at the University of Leicester, said in a statement.

"We therefore believe that incorrect positioning of muscle nuclei may contribute to causing the symptoms of EDMD," Shackleton noted. "Further research is now needed to investigate this new potential disease mechanism and to increase our understanding of how nuclei are positioned in normal muscle cells, but our findings offer the possibility for a novel drug target for the treatment of this disease in the future."

The Scan

Omicron's Emergence

The World Health Organization has called Omicron a SARS-CoV-2 "variant of concern," the Los Angeles Times writes.

Not as Much

Merck's pill to treat COVID-19 reduces the risk of hospitalization and death among COVID-19 patients by less than previously reported, the New York Times says.

Bats That Hang Together

Discover magazine writes that researchers have found a social microbiome among vampire bats.

PLOS Papers on CEWAS, Simian Varicella Virus Transcriptome, Dermatomyositis Markers

In PLOS this week: multi-omic approach to home in on genetic risk variants, transcriptomic analysis of the simian varicella virus, and more.