QIAGEN’s bioinformatics portfolio was greatly enhanced in January 2017 with our acquisition of OmicSoft, which added a powerful multi-omics data management solution and highly curated data sets to our roster. We thought it was time to look at how OmicSoft is serving the scientific community by reviewing some recent citations in the literature.
The July issue of Gynecologic Oncology included a study about endometrial tumors, which caused more than 8,000 deaths in the U.S. in 2016. The team looked at the expression landscape of immune regulatory molecules in a group of endometrial tumors, finding elevated protein levels of both PD-L1 and B7-H4. They used OmicSoft’s proprietary data normalization and expression analysis pipeline to prepare raw sequence data and to compute gene expression values. This study concluded that targeting combination immunotherapies on checkpoint proteins might hold promise for treating endometrial cancers.
The July 2017 issue of Hepatology Communications included reports from a Japanese team that researched mice with liver cirrhosis and circadian rhythm disturbances. Such disturbances contribute to carcinogenesis, osteoporosis, hypertension, and diabetes, among other conditions. Knowing that liver damage upsets circadian rhythms, the team analyzed the relationship by evaluating differences in liver metabolic products every six hours, comparing healthy and affected mice. They used OmicSoft’s ArrayStudio metabolomic and statistical analyses and posited that their study might help develop a solution for circadian rhythm upsets in the face of liver damage.
A group of German researchers studied the retinas of rats with diabetes, looking at gene expression patterns related to hyperglycemia and hyperinsulinemia, a common microvascular complication of the disease. They isolated RNA from the rats’ eyes, using OmicSoft’s ArrayStudio for data processing and statistical analysis, including the processing of probe-level data (CEL files). Their findings, published in PLoS One, determined that systemic hyperglycemia significantly contributes to the initiation and progression of experimental diabetic retinopathy.
The British Journal of Nutrition recently published the results of an English team that used zebrafish to determine the effect on the general metabolism of high dietary arachidonic acid (ARA) levels when compared with low dietary ARA levels. They found that high ARA levels contributed to a significant shift in lipid metabolism, pointing to the possibility that physiological functions might be affected. The team used OmicSoft’s ArrayStudio for statistical analysis, applying Welch’s two-sample t test to compare metabolites between the groups. This is the first study to use metabolomics to look at the metabolic impact of high dietary ARA levels, which can greatly change physiologic outcomes.
A list of adapters collected by OmicSoft contributed to short-read quality control in a recent study published in BMC Genomics. The California-based team focused on the well-annotated Strongylocentrotus purpuratus (purple sea urchin) genome to evaluate and identify the genes that experience diversifying selection and to confirm the widespread action of positive selection. They used whole-genome sequencing data from nine sea urchin species and identified promising targets for future research into the selective agents responsible for their adaptive diversification and contribution to speciation.
We are thrilled to add OmicSoft to our regular roster of blog posts that recap our customers’ contributions to research around the world. If you’d like to request a trial, please contact us. If you’re an OmicSoft user or are interested in learning more about OmicSoft and the breadth of QIAGEN’s bioinformatics portfolio, please consider attending our second annual OmicSoft User Group Meeting, to be held in Cambridge, MA, USA on Sept. 19-20, 2017. Registration is free and the agenda is packed, but space is limited, so register now to book your spot. We look forward to seeing you there!
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