Researchers led by Qiagen's Daniel Groelz write in Experimental and Molecular Pathology that the PAXgene Tissue System does not chemically alter RNA upon fixation and stabilization. They compared the RINs of FFPE, PAXgene-fixed, and fresh-frozen tissue samples and found that, in their model, "processing, which included embedding in low melting point paraffin, had only a minor effect on RNA integrity in PAXgene fixed/stabilized tissue but a moderate effect on RNA integrity in formalin-fixed tissue." Further, they report that RNA from FFPE samples was more likely to have chemical modifications than RNA from the PAXgene samples. "While RNA with acceptable RIN scores could be isolated from both FFPE and PFPE tissue, only RNA from PFPE tissue was comparable to RNA from fresh frozen tissue in real time RT PCR assays and for all amplifications of transcript sequences from 109 to 610 nt," the researchers write. PAXgene was developed by PreAnalytiX, which is a BD-Qiagen joint venture.

Also in Experimental and Molecular Pathology, Josef Wanninger from Regensburg University Hospital in Germany and his colleagues report on their lipidomic study of adiponectin deficient mice. As "adiponectin-deficient mice may compensate for adiponectin deficiency to a certain degree," they examined "the expression of lipogenic genes and lipid composition" in adiponectin-deficient mice. Adiponectin deficiency, Wanniger et al. write, is associated with different lipid classes in the liver and "lower levels of cholesteryl ester, stearate and eventually glucosylceramide may protect the liver from metabolic injury and may partly compensate for adiponectin deficiency."

Researchers in Vancouver report that their nine-gene panel could determine subtypes of endometrial carcinoma in the Journal of Pathology this week. The researchers sequenced the exons of ARID1A, PPP2R1A, PTEN, PIK3CA, KRAS, CTNNB1, TP53, BRAF, and PPP2R5C in 393 endometrial carcinomas from two large cohorts, and found that each subtype of the cancer had a different mutational profile: high-grade endometrioid cancers have different frequencies of PTEN and TP53 mutations than low-grade ones and serous carcinomas and high-grade endometrioid cancers have different mutational frequencies in PTEN, ARID1A, PPP2R1A, TP53, and CTNNB1. "Although endometrial carcinoma subtype diagnoses and grade are currently used in guiding patient management, mutational analysis is emerging as a realistic option in clinical practice," the researchers write. "In the future, we predict that the mutational classification of endometrial carcinomas will become an important tool in diagnosis, guiding mutation-based targeted treatment decisions."

Also in the Journal of Pathology researchers led by Portugal's Carla Oliveira show that deletions in miR-101 lead to its downregulation, overexpression of EZH2, and dysregulation of E-cadherin dysfunction in gastric cancer. "Our data reinforce the critical role of E-cadherin in GC and pinpoint EZH2 over-expression, as a consequence of miR-101 loci deletion and mature miR-101 down-regulation, as one of the missing mechanisms for E-cadherin inactivation in advanced intestinal GC," Oliveria and her colleagues write. "This strong association suggests that therapeutic intervention based on restoration of miR-101 or pharmacological inhibition of EZH2 may have clinical benefit in patients with intestinal-type GC."

Consumer genomics company 23andMe has submitted its first 510(k) application to the US Food and Drug Administration as part of a plan to seek clearance for its Personal Genome Service. The service provides health and ancestry information to users. In a post to the Spittoon blog, the company says "we believe personal genetic data will power a revolution in healthcare. But we also recognize that appropriate oversight of this industry can be a stepping stone on the path to realizing that revolution."

The Sample's sister publication Pharmacogenomics Reporter adds that although 23andMe is seeking FDA clearance, it still plans to offer its services directly to consumers. "23andMe has publicly expressed its willingness to meet FDA regulations, but has also insisted that the agency's oversight shouldn't necessarily preclude consumer access to genetic testing," Turna Ray reports, adding that "the FDA of course could still delineate certain portions of its service as prescription only."

Clinicians and government officials are working to set normal ranges for clinical tests performed on Chinese patients, reports Shanghai Daily. The paper adds the currently used ranges were developed for Westerners, and may differ for Chinese. "Each testing result means a life. So we must be accurate," says Pan Baishen, director of Shanghai's Zhongshan Hospital's Department of Clinical Laboratory.

A real-time PCR approach could help diagnose Helicobacter pylori infection in some patients with upper gastrointestinal bleeding, researchers led by Gloria Royo from the Hospital General Universitario de Elche in Spain report in the Journal of Clinical Microbiology. Drawing on samples from 158 patients, the researchers evaluated real-time PCR and conventional tests — such as the rapid urease test, culture studies, histological study, stool antigen test, or breath test — in diagnosing H. pylori infections in patients with bleeding peptic ulcers. "Our results suggest that our method has a good diagnostic capacity as compared with the classical gold standard in bleeding patients, and is slightly greater in antrum than in corpus," the researchers write. However, they note that the clinical significance of a small amount of microorganisms, which often gives a negative result in classical tests, must be examined as that could reflect a transient colonization.

Life Technologies has acquired Pinpoint Genomics and its test for early-stage non-small-cell lung cancer, Life Tech announced yesterday, continuing the company's push into the diagnostic arena. Pinpoint's qPCR-based assay can help clinicians determine which patients with early-stage disease are at high risk for progression to late-stage disease. "We see an opportunity in lung cancer to change the treatment paradigm with more effective diagnostics," says Greg Lucier, chairman and CEO of Life Technologies, in a statement. "As Life Technologies moves further into the diagnostics space, we will focus on tests that have strong clinical utility where there is a large unmet need."

Separately, as The Sample's sister publication GenomeWeb Daily News reports, Life Tech has entered into a partnership with diagnostics firm Quidel to develop and commercialize real-time PCR assays for an as-yet-unlaunched molecular instrument system.

Life Tech also recently acquired genetic testing firm Navigenics as part of its strategy to build its molecular diagnostics business.