This Week in the Journal of Molecular Diagnostics

Radboud University Nijmegen Medical Centre's Jeroen Dijkstra and colleagues report in the Journal of Molecular Diagnostics that formalin-fixed, paraffin-embedded samples sufficiently mimic clinical samples, and thus can be used to assess testing platforms. The researchers conducted a blind study across nine European laboratories to evaluate a novel synthetic control for FFPE tumor samples. "We demonstrate this control to be a valuable tool in the assessment of platforms used in testing for KRAS mutational status," they add.

Also in the Journal of Molecular Diagnostics, a team led by Duke University Medical Center's Michael Datto reports having found that genes with bimodal expression patterns define different subtypes of ovarian carcinomas. The researchers examined whether molecular switch genes exist in and are clinically relevant to epithelial ovarian cancer by applying a bimodal discovery algorithm to a publicly available ovarian cancer expression microarray data set. "Genes with robust bimodal expression patterns were identified across all ovarian tumor types and also within selected subtypes," the researchers say. They add that such genes are "ideal targets for translation into the clinical laboratory."

A New Leader for Quest

Stephen Rusckowski will be the new Quest Diagnostics CEO and president, reports The Wall Street Journal. This, the Journal notes, ends a six-month search for current CEO Surya Mohapatra's successor. Rusckowski has served as CEO of Philips Healthcare, which is part of Royal Philips. Under Rusckowski, Philips Healthcare's revenue increased by $11.8 billion, the Journal adds. Art Henderson, a healthcare analyst at Jefferies & Co. tells the Journal that Rusckowski "is obviously somebody who was pretty instrumental in the growth at Philips." Additionally, Daniel Stanzione will be Quest's new non-executive chairman.

This Week in Experimental and Molecular Pathology

Audrey Didelot from France's Inserm and her colleagues evaluate competitive allele-specific TaqMan PCR to determine the KRAS, BRAF, and EGFR genotypes of formalin-fixed, paraffin-embedded tumor samples. As they say in Experimental and Molecular Pathology, 60 of their 63 samples were typed correctly. Didelot and her team add that the missed mutations were EGFR exon 19 deletions that the assays did not recognize. "Clinical tests must be developed knowing that FFPE-DNA quality is unpredictable," Didelot et al. write, adding that "this technology is less laborious and requires less stringent precautions to prevent crossover of PCR products than methods that require amplified PCR product to be removed from the tube for analysis."

Researchers led by Rabab Gaafar at Cairo University looked into the roles a number of cell-cycle genes play in the development and progression of malignant pleural mesothelioma using immunohistochemical and PCR techniques. They also correlated aberrant expression to clinic-pathological factors, like overall and disease-free survival. From this, the researchers found that p14ARF, p16INK4A, Rb, and p27KIP1 appear to be involved in SV40-associated malignant pleural mesothelioma while mdm2, p53, and p21WAF are correlated with asbestos exposure. Malignant pleural mesothelioma "is a complex disease characterized by multiple genetic aberrations; some of them involve cell cycle regulatory genes," Gaafar's team concludes.

Not So Great

A new study published in Health Affairs by Georgetown University public policy professor Jean Mitchell shows that the practice of physician self-referral for imaging and pathology services is linked to increased utilization and higher spending, but lower rates of cancer detection, according to a release from the College of American Pathologists. "Self-referring urologists billed Medicare for nearly 75 percent more anatomic pathology specimens compared to non self-referring physicians," CAP says. "Furthermore … the [cancer] detection rate was 14 percent lower than that of non self-referring physicians." These findings should raise red flags about self-referral, says CAP President Stanley Robboy. "This analysis also supports the College's long-standing position that self-referral of anatomic pathology services needs to end by removing anatomic pathology from the exception in the Stark Law," CAP adds.

This Week in the Journal of Clinical Pathology

Reporting in the Journal of Clinical Pathology this week, researchers at the Shanghai Jiao Tong University School of Medicine in China discuss their immunohistochemistry-based investigation of pp120 protein expression patterns in samples from 68 patients with potentially malignant oral lesions. The researchers found that "there was high expression of pp120 in 35 of 68 (51.5 percent) of general potentially malignant oral lesions and 23 of 30 (76.7 percent) of OSCCs [oral squamous cell carcinomas] compared with expression in normal oral mucosa." Overall, the authors say that pp120 expression "may serve as a useful marker for the identification of a high risk of potentially malignant oral lesions progressing to OSCC."

Elsewhere in the publication, Adelino Leite-Moreira and his colleagues at the University of Porto in Portugal describe their attempt to evaluate the expression of TLR2, TLR4, TLR5, and related molecules in various human colonic lesions using real-time reverse transcription PCR and immunohistochemistry. Leite-Moreira et al. found that "persistently positive TLR expression and lower expression of TLR inhibitors was associated with higher TLR protein levels throughout the spectrum of lesions of colon carcinogenesis," they write.

This Week in Modern Pathology

In Modern Pathology, Oslo University Hospital's David Warren and his colleagues report that the molecular markers DDIT3, STT3A, ARG2 and FAM129A are not useful for diagnosing thyroid follicular tumors. The markers had previously been shown to be able to distinguish follicular carcinoma and follicular adenoma, and Warren and his team aimed to verify the predictive accuracy of these makers. To do so, they conducted a retrospective study of protein expression of those follicular carcinomas, follicular adenomas, and controls. "Regrettably, using both immunohistochemistry and western blotting, we demonstrate that these markers are not useful for this purpose," Warren and his team write. "The reasons for the discordance between our results and those of Cerutti et al are, at present, and despite considerable focus on quality assurance of all steps, unknown."

Also in Modern Pathology, the National Cancer Institute's Sinchita Roy Chowdhuri and colleagues examine the use of laser capture microdissection to isolate tumor cells from primary or metastatic lung adenocarcinoma, to detect EGFR and KRAS mutations in formalin-fixed, paraffin-embedded tissues. Chowdhuri et al. found that "laser capture microdissection-enabled mutation detection on cytologic material provides highly accurate and reproducible data comparable or superior to standard methods, and could be invaluable particularly when the tumor sample is limited."

GenMark and Advanced Liquid Logic to Work on IVD Platform

GenMark Diagnostics has entered into an agreement with Advanced Liquid Logic to combine GenMark's electrochemical detection method with Advance Liquid Logic's electrowetting technology, reports MedCity News. With both technologies, the companies plan to "to develop an all-electronic, fully integrated in-vitro diagnostic platform," according to a GenMark press release. "Our initial focus on multiplex molecular testing will be followed by efforts in other areas of diagnostics including protein detection and point-of-care testing, as we redefine industry standards for performance, reliability and ease of use with even the most complex of assays," says Hany Massarany, the president and CEO of GenMark, in a statement.

This Week in Clinical Chemistry

Researchers led by Keio University School of Medicine's Yuhei Koyama report in Clinical Chemistry on their two-step biochemical method to differentially diagnose classic 21-hydroxylase deficiency and cytochrome P450 oxidoreductase deficiency, both of which are marked by high concentrations of 17α-hydroxyprogesterone in the blood. The researchers examined 29 infants' urinary steroid profile using GC/MS,and found that a specific ratio of pregnanetriolone to cortisol metabolites 5α- and 5β-tetrahydrocortisone could distinguish 21-hydroxylase deficiency and cytochrome P450 oxidoreductase deficiency from 17α-hydroxyprogesteronemia. In addition, a cut off for 11β-hydroxyandrosterone could differentiate classic 21-hydroxylase deficiency from P450 oxidoreductase deficiency.

As they report in an online early article at Clinical Chemistry, University of Utah School of Medicine's Kathy Swoboda and colleagues developed a screening assay to test newborns for spinal muscular atrophy. The assay takes advantage of the different melt profiles between wild type SMN1 regions and those with homozygous exon 7 deletions. The researchers report that they could detect all samples with homozygous deletions without any false positives in their test set. "A prospective SMA-screening pilot project to be initiated in 2012 will assess 400,000 newborns," the researchers add. "In the course of that project, we will accurately determine sensitivity, specificity, positive predictive value, and negative predictive value."

Practice Makes Perfect

A new report from the US Centers for Disease Control and Prevention aims to clarify CLIA requirements regarding biochemical genetic testing and newborn screening, and recommends quality assurance practices beyond those required by CLIA. "The recommended practices address the benefits of using a quality management system approach, factors to consider before introducing new tests, establishment and verification of test performance specifications, the total laboratory testing process (which consists of the preanalytic, analytic, and postanalytic phases), confidentiality of patient information and test results, and personnel qualifications and responsibilities for laboratory testing for inherited metabolic diseases," the authors write in Morbidity and Mortality Weekly Report.

For example. the authors note that laboratory personnel should consider a number of factors before introducing new tests, including the benefits and validity of the test as well as its demand, any reimbursement issues, and any training requirements. "Recommendations described in this report should be considered, in addition to appropriate professional guidelines and recommendations, when planning and preparing for the introduction of biochemical genetic testing or offering new biochemical genetic tests," the authors add.

This Week in the Journal of Molecular Diagnostics

In the Journal of Molecular Diagnostics, researchers from Brown University report a novel method for detecting nucleic acid targets using a ligation step and an isothermal, exponential amplification step. "We use an engineered ssDNA with two variable regions on the ends, allowing us to design the probe for optimal reaction kinetics and primer binding," the authors write. "This two-part probe is ligated by T4 DNA ligase only when both parts bind adjacently to the target. The assay demonstrates that the expected 72-nt RNA product appears only when the synthetic target, T4 ligase, and both probe fragments are present during the ligation step." The team also found 40 mmol/L KCl in the final amplification mix to be optimal, and that increasing P5 in excess of P3 reduced the amount of extraneous 38-nt RNA product. "We believe that this method can be used effectively for a number of diagnostic assays," they add.

Also in the Journal of Molecular Diagnostics, a team of researchers from South Korea has developed a DNA methylation marker panel for the diagnosis of extrahepatic cholangiocarcinoma in bile fluids. The team investigated the methylation status of 59 DNA methylation markers in 20 EHC and 20 non-neoplastic gallbladder tissue samples, and selected a panel of markers that showed a sensitivity of 60 percent or more, and a specificity of 100 percent. "Using bile fluids, a methylation assay consisting of a five-gene panel may be useful for detecting EHC and in helping to increase the sensitivity of preoperative diagnoses," they write.

This Week in Experimental and Molecular Pathology

Researchers from Italy's National Cancer Center report in Experimental and Molecular Pathology that NHERF1 is a potential new biomarker for advanced colorectal cancer. The study examined protein expression levels of NHERF1, HIF-1α, and TWIST1 in distant normal mucosa, adjacent normal mucosa, tumor, lymph node metastasis, and liver metastasis, and correlated it to histological grade. "Overall, nuclear NHERF1 expression was associated with poorer differentiation grade and with higher expression both of HIF-1α in lymphatic metastasis and TWIST1 in invasive front of tumor," the researchers write. "Our results support the oncogenic role of NHERF1 and promote nuclear NHERF1 as a potential new biomarker of advanced CRC."

Nobuhisa Yamamura and Takashi Kishimoto from Chiba University Graduate School of Medicine in Japan report their examination of the epigenetic regulation of GATA4 in AFP-producing adenocarcinoma, a highly malignant form of the disease. They found that GATA4 expression is epigenetically regulated through histone modification. "[Our] results indicated that histone deacetylation is a silencing mechanism for GATA4 expression in AFP-producing gastric cancer cells," Yamamura and Kishimoto write.

Colon Cancer Risk Test Approved in New York

New York State has approved the use of ColonSentry, a colon cancer risk assessment test developed by GeneNews, reports General Surgery News. ColonSentry measures seven RNA biomarkers in blood to assess risk and patients found to have a higher risk of colon cancer could be recommended to have a colonoscopy. However, Memorial Sloan-Kettering Cancer Center's Sidney Winawer tells General Surgery News that the test is not ready for the clinic. "We have [been] down this road before with blood-based markers," Winawer says. "A screening test needs to be shown to detect early curable cancers to be effective. Detecting late-stage cancers is of no benefit."

David Goldberg, the interim president of Enzo Clinical Labs, says that ColonSentry is actually not a screening test, but assesses risk. "What ColonSentry is designed for is to give primary care physicians a tool [with] which to help assure compliance with regular colonoscopy screening," Goldberg tells General Surgery News.

This Week in the Journal of Clinical Pathology

In the Journal of Clinical Pathology this week, a team led by investigators at Università di Napoli Federico II in Naples, Italy, reports its comparison of different molecular techniques to detect EGFR mutations in liquid-based cytology, or LBC, samples from non-small cell lung cancer. Overall, the team found that laser capture microdissection coupled with direct sequencing "may be replaced by more sensitive non-sequencing methods directly performed on CytoLyt-derived DNA, an easier and faster approach to improve epidermal growth factor receptor testing standardization on LBCs."

In another paper recently published online in advance, researchers at Miraca Life Sciences, Brigham and Women's Hospital, and Caris Life Sciences report their KRAS mutational analysis of biopsy and corresponding subsequent surgical resection specimens from 30 colorectal cancer patients. The public-private team says its study showed a 100 percent correlation between biopsy and resection specimens with the presence or absence of KRAS mutations, suggesting that "biopsy material is adequate for KRAS mutational analysis in CRC [colorectal cancer] patients."