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Disease progression: Understanding different outcomes
Dr. Shain and coworkers take an evolutionary look at order of occurrence of pathogenic mutations in melanoma. Their research looks at 37 FFPE samples and 293 cancer relevant genes with DNA prepared using the Ovation® Ultralow Library System. Their work characterizes the series of genetic alternations that occur during melanoma progression to define the trajectory of different melanoma subtypes.
Exome approach: Whole Exome Sequencing
Whole exome sequencing (wgs) only covers protein-coding genes, approximately 3 % of the whole genome. However, it is these protein-coding genes that harbor the majority of genetic variations associated with human diseases. Thus, exome sequencing provides many of the benefits of wgs, while greatly reducing sequencing costs and time. Combining Celero™ EZ DNA-Seq library prep with exome enrichment provides several key advantages – including a single bead cleanup step – simplifying the workflow and saving cost and time.
Tumor immunotherapy: Guidance by RNA-Seq
In this publication, Koyama, Akbay, and Li et. al. study the development of resistance to tumor immunotherapy using mouse models of lung adenocarcinoma and define biomarkers associated with adaptive resistance to PD-1 blockade. The team use the Ovation® Universal RNA-Seq System to further their research in T cells and immunotherapy-resistant and untreated tumors.
Uncovering the cause: Applying RNA-Seq for disease diagnostics
Dr. Wilson and team identify a rare form of encephalitis caused by an amoeba, Balamuthia mandrallis, using Tecan’s Ovation RNA-Seq System V2 to help detect B. mandrallis transcripts in cerebrospinal fluid samples.
Co-opting the host: New insights into host-virus interactions
Dr. Abrisch and co-workers investigate how genome-bound Pol II levels change in response to Herpes Simplex Virus I infection using Ovation Ultralow System V2 to prepare ChIP-seq libraries. Their work provides new insights into virus-induced changes in host regulation of gene expression.
Protective correlations: Response to seroconversion
Laughlin et. al. utilize Ovation RNA-Seq System V2 and Tecan Library Systems to study the underlying genetic events preceding protective seroconversion in cattle and sheep vaccinated against Rift Valley Fever. Their study identifies time-dependent gene expression changes related to vaccine-induced immune response and regulation.
Profiling biomarkers: Gene expression to predict tumors
Dr. Moshayoff and coworkers utilized the Ovation® PicoSL WTA System to further their research into the characterization profile of early-stage colorectal cancer (CRC) and advanced adenomas (AA). Combining current molecular knowledge with whole-transcriptome profiling of cell-free RNA, the team defines a panel of markers to further CRC and AA research.
NGS analysis of blood samples: Globin depletion
Transcriptome analysis from whole blood using NGS is an unbiased approach for biomarker research and discovery. However, one of the major challenges when performing whole blood mRNA-Seq is the presence of significant amounts of globin mRNA (up to 80 %) that usurps sequencing space without providing useful biological information. The paper describes a streamlined workflow for mRNA-Seq from whole blood using the Universal Plus mRNA-Seq library prep kit with Human Globin AnyDeplete.
Methylated biomarkers: A new tool for liquid biopsy
Legendre and Gooden et. al. analyze cell free DNA in breast cancer patients and healthy individuals. Using the Ovation® Ultralow Methyl-Seq Library System, the authors research tumor-specific signatures and identify 21 hypermethylation hotspots associated with metastatic breast cancer.
Genotyping-by-Sequencing simplified
Dr. Davide Scaglione from IGA Technology Services uses Allegro Targeted Genotyping to simultaneously interrogate thousands of samples for thousands of SNPs.
A whole transcriptomics view to study drought resistance
Rodrigues et. al. use the Ovation® Universal RNA-Seq System to study the whole transcriptome profile of soybean, one of the most important commercial crops, to identify strains less susceptible to drought conditions.
Epigenetics as a read-out for inherited traits
Dr. Moreno-Romero's studies focus on the identification of epigenetic modifications that occur during early stages of endosperm development. Methyl-seq libraries were prepared using the Ovation Ultralow Methyl-Seq Library System and ChIP-seq libraries were prepared with Ovation Ultralow Library System V2 using very small amounts of starting material.
Modulating disease: A community effect on disease outcome
Perlejewski et. al. characterized the microbiome composition in patients with multiple sclerosis, a chronic demyelinating disease of the central nervous system, using Tecan’s Ovation® RNA-Seq System V2.
Feasting on oil: Attack by the soil microbiome
Dr. Bell and co-workers study modifications to soil microbiome composition and its impact on degradation of crude oil using Ovation Ultralow Library System V2.
Super symbionts: Contribution of the microbiome to digestion and pathogen defense
Peterson and Scharf present a metatranscriptomic analysis of the bacterial and protist symbionts of the eastern subterranean termite in the presence and absence of a fungal pathogen. The authors used Tecan’s Ovation Complete Prokaryotic RNA-Seq System in combination with custom targeted depletion oligos for termite, protists, and the fungal pathogen to maximize informative sequencing reads in their data.
Accessing Energy: Monitoring the microbiome in crop digesters
Weithmann, Weig, and Freitag present a characterization of the microbial communities in an agricultural energy crop digester. The authors used the Ovation Rapid Library System to prepare 16S amplicons for sequencing, tracking species spatially and temporally as a new biogas production plant is established.
Join the resistance: Analyzing antibiotic genes across environments
Versluis et. al. investigate the microbiota across a range of species to detect antibiotic resistance genes. The Ovation RNA-Seq System V2 was utilized with bacterial enriched samples to characterize the genes found in a variety of ecological niches.
Tracking pathogens: A metagenomic approach for quality control
Dr. Yang and co-workers developed a metagenomic workflow to monitor presence of foodborne pathogens in environmental samples at different longitudinal steps of a beef production chain. In this study, Tecan’s Ovation Ultralow DR Multiplex System was used to enable sequencing of limited input microbiome samples.
Maintenance of parent-of-origin-specific gene expression by ZFP57
Genetic imprinting is a phenomenon by which the maternal or paternal allele is 'marked' epigenetically to control gene expression. Riso, et al., describe the role of ZFP57 in the maintenance of these epigenetic markers in mouse stem cells using Ovation Ultralow System V2 and Ovation Ultralow Methyl-Seq. The authors conclude that ZFP57 plays a key role in maintaining the methylation state of Imprinting control regions that regulate imprinted gene expression.
Mapping Hydroxymethylation Patterns in Neurodegenerative Disease
Dr. Mill is a Professor of Epigenetics at the University of Exeter Medical School in the United Kingdom where he is interested in understanding the causes and consequences of genomic variation in the brain, and the role this plays in neuropsychiatric and neurodegenerative disease. To better understand how DNA methylation and hydroxymethylation play a role in neurobiology, Dr. Mill's research has taken advantage of the TrueMethyl oxBS technology to quantify the 'true' levels of these DNA modifications and to better determine how gene regulation is affected in specific neural cell populations.
Dynamic changes in chromatin modifications observed during early mouse development
Development is very dynamic process that is intimately regulated by changes in chromatin modifications. In this study, Zylicz and colleagues investigated how epigenetics influences the genome during early embryonic development. Zylicz, et al. performed a comprehensive analysis utilizing Ovation RNA-Seq System V2, Ovation Rapid Library System, Ovation Ultralow Library System, and Ovation Ultralow Methyl-Seq Library System to understand how epigenetics influences transcriptional regulation and chromosomal modifications. Their findings identify two enzymes (EZH2 and G9a) that dramatically affect histone methylation and thus impact cell fate decisions during development.
Methylated Biomarkers: A new tool for liquid biopsy
Legendre and Gooden et. al. analyze cell free DNA in breast cancer patients and healthy individuals. Using the Ovation Ultralow Methyl-Seq Library System, the authors define tumor-specific signatures by identifying 21 hypermethylation hotspots associated with metastatic breast cancer.
Epigenetics as a read-out for inherited traits
Dr. Moreno-Romero's studies focus on the identification of epigenetic modifications that occur during early stages of endosperm development. Methyl-seq libraries were prepared using the Ovation Ultralow Methyl-Seq Library System and ChIP-seq libraries were prepared with Ovation Ultralow Library System V2 using very small amounts of starting material.
ChIPping to an answer: Gene dysregulation in disease development
Dr. Mannini and co-workers investigate the role of the cohesion complex in gene transcription. The scientists use multiple orthogonal methods including ChIP-sequencing with the Ovation Ultralow Library System V2 to uncover the impact of gene dysregulation as an underlying mechanism for Cornelia de Lange syndrome.