As non-invasive prenatal tests for genetic abnormalities are adopted in the clinic, the Wall Street Journal says that there may be confusion among doctors and patients regarding what the results of those tests mean. In fact, the Journal points out, the American College of Genetics and Genomics is working on a statement urging such tests to be called "screens" to emphasize that they predict risk rather than give definitive results. Four US companies, Ariosa Diagnostics, Natera, Sequenom, and Verinata Health, which is part of llumina, offer such tests.

Non-invasive screens appeal to many pregnant women as they avoid the small miscarriage risk associated with amniocentesis. Jeff Chapa, the head of obstetrics and maternal-fetal medicine at the Cleveland Clinic, tells the Journal that doctors there perform half as many invasive tests.

"All patients want to hear that you don't need to have something invasive," says Laura Limone, genetic-counseling supervisor New Jersey Perinatal Associates in Livingston and a member of Sequenom's speakers bureau. "Those who understand the technology find it very promising, but we also know it isn't perfect yet."

Indeed, the screens can yield false-positive or false-negative results, and positive results should be followed up on with invasive procedures, the Journal says. Athena Cherry, who heads the cytogenetics lab at Stanford University Medical Center, tells the Journal that case studies like one of a patient who terminated a pregnancy after only the screening — and the fetus was subsequently found to be normal — indicate that the message to follow up on positive results may not be "driven home enough."

False-negative results also may occur, as one instance was recounted at the ACMG annual meeting last month, as our sister publication GenomeWeb Daily News reported. The test, from Verinata, indicated that the fetus did not have Down syndrome but an amniocentesis performed after unusual ultrasound findings found that the fetus did have Down syndrome — the company's test had boasted a 100 percent sensitivity for detecting the syndrome; it now indicates a sensitivity greater than 99.9 percent, the Journal adds.

"Noninvasive prenatal [testing] as a whole has the potential to someday replace invasive procedures," says Jonathan Sheena, Natera's chief technology, adding that "the field has taken a giant leap forward … but we believe it is important to understand they don't replace invasive tests yet."

PubMed Central draws readers away from scientific journals, weakening community ties, says Philip Davis, from Phil Davis Consulting based in Ithaca, NY, in a forum article in The FASEB Journal. Davis examined 13,223 articles published in 14 research journals — spanning the fields of nutrition, experimental biology, physiology, and radiology — published by academic societies between February 2008 and January 2011. The articles were available only to subscribers for a year, and then they were available to all at the journals' websites. Forty-five percent of the articles were funded in part by the US National Institutes of Health, and they were, as policy requires, also deposited into PubMed Central after a year.

Davis found that there is 21.4 percent decline in HTML downloads and 13.8 percent decrease in PDF downloads of articles from the journals' websites after the articles become available at PubMed Central, as compared to articles that were not deposited into PMC. "Whereas PMC may be providing access to readers traditionally underserved by scientific journals, the loss of readership from journal websites may have negative consequences for readers," Davis argues. "As PMC draws readership away from the journal, the journal editor loses the opportunity to direct readers to related articles, editorials, letters and commentary surrounding the article of interest."

"Traditionally, scientific societies published the scholarly research of their members in their own journals. This collegial nexus has been extended — some say disrupted — by the centralization of research reports in PubMed Central," says Gerald Weissmann, the editor in chief of The FASEB Journal, according to Science 2.0.

In this week's Nature Genetics, a team from Washington University publishes the sequence and analysis of the platyfish genome, representing the first genome sequence of a poeciliid fish. The researchers found that genes associated with viviparity show signatures of positive selection, "identifying new putative functional domains and rare cases of parallel evolution." They also discovered that genes implicated in cognition show an "unexpectedly high rate of duplicate gene retention after the teleost genome duplication event, suggesting a hypothesis for the evolution of the behavioral complexity in fish, which exceeds that found in amphibians and reptiles."

Daily Scan sister publication GenomeWeb Daily News has more on the platyfish here.

Meanwhile, in Nature Methods, a team from the J. Craig Venter Institute describe a new method for the transfer of genomes into yeast, a process that aids genome engineering for genetically intractable organisms, but that has been hampered by need to isolate intact genomes before transfer. The new process allows involves direct cell-to-cell transfer of bacterial genomes as large as 1.8 megabases into yeast under conditions that promote cell fusion. Removal of restriction endonucleases from donor bacteria was also found to enhance genome transfer.

The Canadian federal information commissioner is investigating complaints that media access to government scientists has been restricted, reports the Vancouver Sun. Both the University of Victoria Environmental Law Clinic and Democracy Watch, a non-profit organization, filed a complaint with Suzanne Legault, the information commissioner, arguing that government media policies violated the Access to Information Act, the Nature News Blog adds.

"There are few issues more fundamental to democracy than the ability of the public to access scientific information produced by government scientists … Yet the attached report shows that the federal government is preventing the media and the Canadian public from speaking to government scientists for news stories," the groups say in their letter, referencing a report they generated called "Muzzling Civil Servants: A Threat to Democracy?" The letter adds that the "muzzling" especially affects researchers whose work "runs counter to current Government policies on matters such as environmental protection, oil sands development, and climate change."

The office of the information commissioner has notified seven agencies that it plans to investigate such complaints, the Vancouver Sun adds.

In the advance access edition of Nucleic Acids Research, National Institutes of Health researchers summarize findings from genomic studies on archaea and bacteria, focusing in particular on defense strategies uncovered in the prokaryotic microbes via comparative genomics. Such data have helped in delineating the types of defense systems that are sprinkled across the archaeal and bacterial phylogenies, the team says, highlighting the propensity for defense genes to cluster, for instance, and revealing ties between genes contributing to immune system function and those in place to prompt dormancy or cell suicide.

A Japanese team presents a new statistical method for calling somatic mutations in cancer genomes using high-throughput sequence data. The strategy — known as empirical Bayesian mutation calling, or EBCall — relies on a Bayesian statistical model to help find situations in which allele frequencies don't match patterns predicted from known sequencing error profiles, the researchers say. In addition to describing the rationale behind their approach, authors of the study demonstrate the utility of EBCall, using whole-exome sequence data on paired tumor-normal samples to call mutations stretching into the low frequency range in coding regions of the tumors.

A study by researchers from Wayne State University and elsewhere highlights the variety of RNA molecules found in sperm cells and that apparently contribute to the function of these reproductive cells. The group used RNA sequencing to follow shifts in coding and non-coding RNA representatives present in human sperm during development, looking also at factors influencing this collection. The population of RNA in sperm as revealed by RNA-seq provides a window into the developmental history, functional viability, and potential elements present by sperm that may serve a role in the final stages of spermiogenesis or at fertilization," the study authors say.