Sponsor: EMD Millipore
On-demand recording is available here.
In Modern Pathology, Daniel Baumhoer from University Hospital Basel in Switzerland and his colleagues report that expression of CXCL12, a ligand for the chemokine receptors CXCR4 and CXCR7, is associated with positive osteosarcoma outcomes. Baumhoer and his colleagues examined the expression of those chemokines in 223 osteosarcoma samples, and found that CXCL12 and CXCR4 expression correlates with better outcomes and fewer metastases. Further, the researchers say that their "findings suggest a distinct role of CXCR4/CXCR7/CXCL12 signaling in the tumors of bone, as has also been previously described in acute leukemia," Baumhoer et al. write, adding that "the disruption of CXCR4/CXCR7/CXCL12 signaling could therefore be crucial in OSs [osteosarcomas] for the migration of tumor cells from bone into circulation and for developing systemic disease."
Also in Modern Pathology, the Mayo Clinic's Jennifer Boland and her colleagues examine whether p16 protein expression in adenoid cystic carcinoma of the head and neck is linked to HPV expression. From their study of 27 cases of adenoid cystic carcinoma of the head and neck, the researchers found that p16 protein expression is found in a subset of the cases, though appears to be unrelated to HPV infection. "Nevertheless, HPV positivity should not be used to exclude the possibility of high-grade adenoid cystic carcinoma when the differential diagnosis includes squamous cell carcinoma," Boland et al. conclude. "Moreover, although p16 overexpression is often used as a surrogate marker for HPV in squamous cell carcinoma, it cannot be used in this manner in high-grade adenoid cystic carcinoma."
In Clinical Laboratory News, Genna Rollins says that while next-generation sequencing is not quite routine practice for clinical labs, lab workers should learn what they can about it. "I don't think anybody should be on the sidelines waiting," Baylor College of Medicine's Michael Metzker tells Rollins. Ryan Kim from the UC Davis Genome Center adds that knowledgeable lab workers can be a resource for clinicians as they begin to figure out sequencing data.
In Clinical Chemistry, Gert Matthijs from the University of Leuven in Belgium and his colleagues discuss their combination of a microfluidic amplification system with sequencing to search for genes associated with familial hypercholesterolemia. Matthijs and his colleagues used Fluidigm's Access Array System to amplify three genes — LDLR, APOB, and PCSK9 — associated with familial hypercholesterolemia, that were then sequenced using Roche 454's GS FLX Titanium system. Of the 38 amplicons, the researchers report that 37 were amplified successfully, and they found pathogenic mutations in 29 percent of the patient samples. "Our study demonstrated that all point mutations and small deletions and insertions can be detected if a well-considered minimal coverage threshold is set. For large rearrangements, the use of an additional detection method like MLPA is still obligatory," the researchers write.
Nesher Technologies' Seok Yim and colleagues report in Clinical Chemistry on their adaptation of microsecond-scale alternating-laser excitation, or ALEX, to use four colors. "This method introduces additional laser excitation source(s) to probe the fluorescent acceptor (A) in a direct, fluorescence resonance energy transfer (FRET)-independent fashion, and it obtains both donor (D)-excitation-based and A-excitation-based observables for each single molecule," Yim et al. write. The researchers then used this approach to detect a number of different markers from a single well. "This improved methodology is well suited for diagnostics applications in which rapid simultaneous and accurate quantification of several DNA-, RNA-, or protein-based targets in limited amounts of complex clinical matrices is of vital importance but is not achieved cost-effectively with current technologies," Yim and colleagues add.
Researchers from the University of Helsinki have developed a DNA microarray-based test to detect and genotype 15 high-risk and two low-risk human papillomavirus types, as they report in PLoS One. "The method is based on multiplex PCR amplification of the viral L1 region using an improved set of type-specific PGMY primers and subsequent ligation detection reaction. Further, we establish an objective criterion for HPV type presence by statistical comparison to a background distribution," the researchers say. They add that their preliminary results indicate that their test could be used in the clinic. "In [the] future, HPV genotyping is likely to be launched to clinical use for the management and follow-up of patients with cervical epithelial abnormalities requiring accurate and economical high-throughput testing," the Helsinki team adds.
Researchers led by Jinfeng Liu from the State Key Lab of Seedling Bioengineering in Yinchuan, China, describe in the Journal of Molecular Diagnostics their method to determine gene copy number. First, the researchers amplified a target and a control gene using PCR, which were quantified before being mixed at different molar ratios. Then, using real-time PCR, the researchers measured the quantification cycle value of the mixture. "A standard curve was constructed to correlate the differences between the Cq values and the logarithmic ratios of the target gene to the internal control gene," the researchers say, adding that "this method was validated by a set of internal control genes and a foreign gene in transgenic alfalfa, demonstrating the utility of this method in the determination of gene copy number for various applications."
Also in the Journal of Molecular Diagnostics, Manchester Cancer Research Centre's John Radford and his colleagues report that archival FFPE samples are useful for a number of microarray experiments, including molecular classification projects. Radford and his team compared fresh-frozen archival diffuse large B-cell lymphoma biopsy samples for use in such experiments. "Enrichment for NF-κB genes was appropriately seen in ABC-DLBCL FFPE tissues," the researchers report. "The top discriminatory genes expressed in FFPE separated cases with high statistical significance and contained novel biology with potential therapeutic insights, warranting further investigation."
In a policy statement issued at its annual meeting being held in Charlotte, NC, the American College of Medical Genetics says that genomic data should be used in conjunction with patient's medical and family history to guide decision-making. Among the indications for considering whole-genome or whole-exome sequencing as a diagnostic test are when the patient appears to have a heterogeneous genetic disorder and when the results of specific gene tests are inconclusive. Further, ACMG says that each step of the test should be performed under the direction of a "board-certified individual with appropriate and broad medical genetics and genomics training." Clinical labs should also have protocols in place for reporting secondary or incidental findings, and ACMG encourages labs to share data in public databases.
"The transition from traditional targeted gene testing to genome-wide analysis constitutes a genuine sea change in medicine, offering vastly enhanced diagnostic power along with unprecedented challenges in test interpretation and reporting," says Wayne Grody, ACMG president, in a press release.
Molecular diagnostics company Vermillion reported revenue increases for both the fourth quarter of 2011 and full year 2011. The company's fourth quarter total revenue increased by 152 percent to $868,000 from $345,000 for the same time period in 2010, Vermillion says in a statement. That revenue includes $755,000 from sales of its ovarian cancer diagnostic OVA1. Vermillion also has a licensing deal with Quest Diagnostics, under which Quest pays $50 per OVA1 test performed, plus royalty fees.
The company's total 2011 revenue increased by 64 percent to $1.9 million from $1.2 million in 2010. Our sister publication GenomeWeb Daily News adds that "highlights for 2011 included expanded payer coverage for OVA1."
"Since improving payer coverage and reimbursement for OVA1 remains our key strategic initiative in 2012, we are continuing to work closely with our partner, Quest Diagnostics, and our territory development managers to both engage with physician offices during the claims process and as well as better educate payers," says Gail Page, president and CEO of Vermillion, in a statement.
Researchers led by Tatjana Crnogorac-Jurcevic from Queen Mary University of London report in the Journal of Pathology their comparison of the proteomes of pancreatic ductal adenocarcinoma and lymph node metastases. By using MudPIT to examine laser capture microdissected FFPE specimens, Crnogorac-Jurcevic and her colleagues report that 115 out of 854 proteins were differentially expressed between the primary tumors and metastases. The researchers then focused on 14-3-3 sigma and S100P as they were both associated with pancreatic ductal adenocarcinomas, and found that both proteins were up-regulated in metastases as compared to primary tumors, and even more so when compared to normal tissue. "We have shown that comparative proteomic analysis of FFPE tissue is a valid approach for the investigation of pancreatic malignancy," the researchers write. "In addition to establishing the first proteome of primary PDAC and matched LN metastases, our study has identified S100P and 14-3-3 sigma as two proteins that may represent viable epithelial-specific targets for the treatment of both primary and metastatic disease."
Also in the Journal of Pathology, University College Dublin's Fiona Furlong and colleagues report that low expression levels of MAD2 are associated with resistance of epithelial ovarian cancer cells to paclitaxel treatment. Furlong et al. examined MAD2 protein expression levels in high-grade serous epithelial ovarian cancer samples, and found that "paclitaxel can no longer induce cell cycle arrest or apoptosis in ovarian cells devoid of MAD2." In addition, the researchers report that microRNA-433 down-regulates MAD2. "We propose that miR-433 expression becomes deregulated in ovarian cancer resulting in the down-regulation of MAD2 expression," the authors write. "We hypothesize that this contributes to a poorer chemoresponse in EOC as paclitaxel responses are attenuated in pre-miR-433 transfected cells as a result of MAD2 protein down-regulation."
As they report in the Journal of Clinical Pathology, researchers led by Shanghai Jiao Tong University School of Medicine's Wei-Wen Jiang performed a retrospective study of phosphorylated p120 catenin expression and its predictive power for oral cancer progression. They found that just over 50 percent of the potentially malignant oral lesions they studied had high levels of pp120 and that more than three-quarters of the oral squamous cell carcinoma cells had high levels of pp120, as compared to normal oral mucosa cells. "Pp120 may serve as a useful marker for the identification of a high risk of potentially malignant oral lesions progressing to OSCC," Jiang and his colleagues write.
The University of Udine's Nadia Passon and her colleagues studied the expression and localization of Dicer and Drosha, which are involved in microRNA formation, in triple-negative breast cancer. From their examination of 31 triple-negative breast cancers and a number of cell lines, Passon et al. report that Drosha mRNA and protein levels were higher in triple-negative breast cancers than normal breast tissue, and that Dicer was found in the nucleus of breast cancer cells while it is usually found in the cytoplasm of normal cells. The researchers say their "findings indicate that Dicer and Drosha expression is deregulated in triple-negative breast cancers."
The Queens, NY, hospital that was closed down by the state health department due to a number of problems with its clinical lab is shutting down permanently, reports the Queens Chronicle. The health department had found 59 issues, including storing blood platelets at improper temperatures, poor maintenance of instruments, and limited staff supervision and training. "The state did not say when it expects the hospital to close, though hospital workers said they have been told it could happen as early as Friday," the Queens Chronicle reports, adding that the area will now be served by one hospital.
A study conducted by the Medco Research Institute and Quest Diagnostics found that patients who are told their gene test results are more likely to stay on their cholesterol medication. The Additional KIF6 Risk Offers Better Adherence to Statins, or AKROBATS, study looked at 1,294 people who were newly prescribed statins, half of whom were told their KIF6 gene variant. Those told their KIF6 status were nearly two times as likely to adhere to their medication regimen, Medco says. "This is the first prospective study to show that genetic testing, and subsequently providing patients their test results, has clinical utility through improving adherence to a specific drug therapy — a finding that could open-up a whole new way of thinking about the benefits of pharmacogenetic testing," says Medco's Scott Charland in a statement. The study was presented at the American College of Cardiology meeting.
Our sister publication Pharmacogenomics Reporter has more on the study and its implications here.
In Modern Pathology, researchers from Charité-Universitätsmedizin in Berlin report that expression of p16INK4a and p14ARF mRNA in Pap smears is related to age. Using real-time PCR, the German researchers examined p16INK4a and p14ARF mRNA expression levels in normal, HPV-negative women and high-risk, HPV-positive, or HSIL, women. "As expected, we found that relative p16INK4a and p14ARF transcript frequencies increased significantly in samples of patients with HSIL diagnoses," the researchers write. "We also found a significant correlation between the patient age and the increased expression of p16INK4a and p14ARF that interfered with HPV-induced upregulation." These findings, the researchers add, "support wariness in interpretation of p16INK4a and p14ARF mRNA expression results from older patients."
In an online early article at Modern Pathology, researchers led by Washington University in St. Louis's John Pfeifer find that targeted next-generation sequencing can be applied in the clinic to identify DNA mutations. Pfeifer and his colleagues conducted a proof-of-concept study using a hybrid-capture enrichment approach coupled to next-gene sequencing to detect genes associated with leukemia outcomes. "Using DNA from cell lines with previously characterized findings, we identified all published mutations occurring within genes on the capture panel, without false positives," the researchers write. "We further identified translocations in three of three cell lines and in one patient sample (one of one) by analyzing both paired-end and single-end read data."
Andrew Baker, the former CEO of Unilab, filed a whistleblower lawsuit against Quest Diagnostics in 2005 and one against Laboratory Corporation of America Holdings in 2007, accusing them of Medicare fraud, reports Bloomberg. Baker tells The Dark Report that the companies — Quest bought Unilab in 2003 — allegedly offered insurance companies discounts on lab tests if the insurance plans recommended that their network doctors send patients to their labs, Bloomberg says. In addition, Baker's suit claims that the labs then charged Medicare and Medicaid higher prices. Quest tells Bloomberg that the company has "complied with Medicare and Medicaid pricing requirements," and LabCorp did not respond to Bloomberg's request for comment.
Sponsor: EMD Millipore
On-demand recording is available here.
Sponsor: New England Biolabs
Library preparation methods continue to be challenged by the requirement for faster and more efficient protocols, using lower input amounts. In this online seminar, recorded Feb. 7, 2013, experts discuss new approaches to tackle these challenges, particularly for bacterial and exome sequencing.
National Heart, Lung, and Blood Institute
There can be a bit of a chasm between dry lab work and wet lab work. But NHLBI's Andrew Johnson aims to close that gap. "A lot of things that I attempt in terms of projects try to bridge those barriers between the dry lab, computational side of things and wet lab experiments that are two different worlds," he says.
Currently, Johnson's work focuses on developing tools. During the early days of genome-wide association studies, he noticed that it was difficult for researchers to compare results generated across various array platforms. In conjunction with scientists at the Broad Institute, he developed a tool called SNAP to do just that. "[It] was pretty successful in terms of allowing people to rapidly query for proxy markers, but also just to do basic annotation of SNPs, like chromosome position, gene, and also to do plotting for regional genetic association plots," he says.
David Agus calls for legislative action to prevent monopolies, such as Myriad's around BRCA 1 and BRCA 2 genes, that have life and death implications.
Slate discusses the issue of nonpaternity and personal genome scans.
The California Institute for Regenerative Medicine discloses a conflict of interest violation involving Lee Hood.
FASEB makes case for the role of NIH and NSF in medical, economic, and scientific gains.
High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates
Dugar, Herbig, et al. PLOS Genetics
The University of Würzburg's Cynthia Sharma and colleagues undertook a transcriptomics-based analysis of the gastroenteritis-causing bacterial species Campylobacter jejuni. The team used its so-called differential RNA sequencing strategy to sequence and compare the transcriptomes of four C. jejuni isolates (three from humans and one from a chicken), applying a new method to automatically annotate transcription start sites in each. "Overall," they write, "our study provides new insights into strain-specific transcriptome organization and [small RNAs], and reveals genes that could modulate phenotypic variation among strains despite high conservation at the DNA level."
Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts
Hacquard, Kracher, et al. Proceedings of the National Academy of Sciences
The barley powdery mildew (Blumeria graminis f. sp. hordei) pathogen genome is comprised of chunks of sequence that are particularly rich or replete in polymorphisms, according to a study by researchers from the Max Planck Institute for Plant Breeding Research. The team sequenced the genomes of two Bgh isolates from Europe, comparing each to the barley powdery mildew reference genome. The newly sequenced isolates each contained distinct combinations of sequence blocks with high or low SNP concentrations — isolate-specific mosaic genomes that point to "exceptionally large standing genetic variation in the Bgh population," study authors say. Meanwhile, their transcriptome sequencing experiments offered a look at genes used by Bgh during attempted infiltration of barley or immunocompromised Arabidopsis.
Kevin Hrusovsky is resigning his post at PerkinElmer as senior VP and president of the Life Science and Technology division. Hrusovsky will serve as a consultant to the company for up to one year, beginning in June. He joined PerkinElmer through the company's acquisition of Caliper Life Sciences, where he was CEO and president.
Hologic has appointed former Beckman Coulter head Scott Garrett to its board of directors, where he will serve on the corporate development committee.
Garrett currently is an operating partner with Water Street Healthcare Partners, a private equity firm. Garrett spent 10 years at Beckman Coulter, where he was chairman, president, and CEO.
Gina Costa is now senior director of genomic applications at Illumina. She joins Illumina from Life Technologies, where she was senior director of genetic analysis, working on development of the Ion Torrent and SOLiD sequencing technologies. She has also held positions at Agencourt Bioscience and Roche's 454 Life Sciences.
Bioinformatics firm Golden Helix has hired Andreas Scherer to be its new president and CEO. Scherer has managed large global software services businesses, and he started his executive career at AOL/Netscape. He will replace Former CEO Christophe Lambert, who will take on the new role of company chairman.