NGS research applications

NGS technologies are transforming life science research and enabling scientists to gain a large wealth of information. Tecan’s proprietary technologies enable researchers to simplify their workflows and gain more information with each sequencing run thus saving time and money. Learn more about the research that is being done globally with Tecan’s NGS products.




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Tab 01 / Cancer
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Transforming disease:
Cancer research made simple

Next-generation sequencing (NGS) technologies are transforming the field of cancer, detection and diagnostic research due to the wealth of genetic information obtained through different sequencing approaches.

Targeted resequencing for mutation detection and RNA-Seq for gene fusion identification and detection are some of the areas where NGS methods have offered technology advantages.

Tecan’s broad portfolio of innovative DNA and RNA library preparation systems provides unique solutions for research into mutation detection and oncology.

Disease progression: Understanding different outcomes Disease progression: Understanding different outcomes

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.

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Exome approach: Identifying treatment targets Exome approach: Whole Exome Sequencing

Exome approach: Identifying treatment targets

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.  

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Tumor immunotherapy: Guidance by RNA-Seq Tumor immunotherapy: Guidance by RNA-Seq

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.

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Tab 02 / Infectious Disease
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Pushing the limits:
Highly sensitive pathogen detection

The field of medical microbiology has been rapidly adopting as well as leading the innovation of molecular diagnostics approaches to overcome the challenges of traditional pathogen detection workflows, such as limited sample and low viral copy number. 

Methods such as NGS are being used not only as diagnostic tools but also in leading edge research to deepen our understanding of host-pathogen interactions. NGS for virus detection is being used more frequently, particularly with hard-to-identify viral infections.

Tecan offers multiple solutions for pathogen detection and studying host-pathogen interactions, including Ovation® RNA-Seq System V2 + Ultralow Library Systems, which together provide robust amplification of cDNA from samples with very low levels of pathogen in the presence of a host genome or transcriptome and DimerFree technology to enable more sensitive detection of rare pathogen transcripts.

Uncovering the cause: Applying RNA-Seq for disease diagnostics Uncovering the cause: Applying RNA-Seq for disease diagnostics

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.

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Co-opting the host: New insights into host-virus interactions Co-opting the host: New insights into host-virus interactions

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.

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Protective correlations: Response to seroconversion Protective correlations: Response to seroconversion

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.

Read the paper

 




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Tab 03 / Liquid Biopsy
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Every drop counts:
Maximize biomarker discovery

Liquid biopsies are performed on a fluid sample such as blood, and typically monitor circulating tumor cells, cell-free DNA or cell-free RNA, or RNA from exosomes to find changes in genetic biomarkers. Such cell-free DNA or RNA tests can provide a less-expensive and less-invasive way to track cancer and when combined with next-generation sequencing technologies, enable researchers to screen thousands of biomarkers in one sample.

Tecan’s unique technologies enable highly efficient sample preparation of DNA or RNA from liquid biopsy samples to maximize biomarker research and discovery

Profiling biomarkers: Gene expression to predict tumors Profiling biomarkers: Gene expression to predict tumors

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.

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NGS analysis of blood samples: globin depletion NGS analysis of blood samples: Globin depletion

Cell-free approach: New NIPT test method

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.

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Methylated biomarkers: A new tool for liquid biopsy Methylated biomarkers: A new tool for liquid biopsy

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.

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Tab 04 / Agrigenomics
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Trait to table:
Solutions to advance agrigenomics

Agricultural researchers are increasingly adopting next-generation sequencing (NGS) technology as an essential research and development tool in plant and animal genomics.

As accessibility and affordability continue to improve, NGS is being used for marker-assisted selection (MAS) to accelerate plant breeding and selection, as well as in transcriptomics, plant or animal-pathogen interactions and epigenetics.

Tecan’s suite of NGS library systems, including customizable targeted genotyping-by-sequencing with Allegro® Targeted Genotyping and RNA-Seq solutions, are helping agricultural scientists exploit the power of next generation sequencing to further their research and realize the dream of improving nutrition across the globe.

Genotyping-by-Sequencing simplified Genotyping-by-Sequencing simplified

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.

View the webinar

 

A whole transcriptomics view to study drought resistance A whole transcriptomics view to study drought resistance

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.

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Epigenetics as a read-out for inherited traits Epigenetics as a read-out for inherited traits

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.

Read the interview

 




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Tab 05 / Microbiomics
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Communities revealed:
Complete microbiome solutions

Microbiome analysis is the study of microbial communities in a given ecological niche, providing a wealth of information about different environments and the changes occurring in those environments.

Recent research has shed light on the human microbiome and its role in health and disease. High profile collaborative projects such as the Human Microbiome project and MetaHIT have published multiple data sets using NGS as a foundational tool.

NGS addresses bottlenecks of traditional culture methods, such as gaining information about unculturable organisms, and provides higher throughput and cost savings, allowing for mainstream adoption of metagenomics studies to characterize the microbiota from various environments.

Modulating disease: A community effect on disease outcome Modulating disease: A community effect on disease outcome

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.

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Feasting on oil: Attack by the soil microbiome Feasting on oil: Attack by the soil microbiome

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.

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Super symbionts: Contribution of the microbiome to digestion and pathogen defense Super symbionts: Contribution of the microbiome to digestion and pathogen defense

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.

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Accessing Energy: Monitoring the microbiome in crop digesters Accessing Energy: Monitoring the microbiome in crop digesters

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.

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Join the resistance: Analyzing antibiotic genes across environments Join the resistance: Analyzing antibiotic genes across environments

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.

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Tracking pathogens: A metagenomic approach for quality control Tracking pathogens: A metagenomic approach for quality control

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.

Read the paper

 




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Tab 06 / Epigenetics
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On the mark:
Exploring our dynamic regulome

Epigenetics is the study of chemical modifications or physical structure changes to chromatin in the absence of DNA sequence alterations.

These modifications modulate gene expression to enable cell differentiation and identity. Disruption of the epigenome from environmental factors can have a significant impact on growth, development and disease.

Tecan solutions enable both the characterization of epigenetic changes in the DNA and the elucidation of the impact of those alterations on gene expression. Our Methyl-Seq Systems allow investigation of direct methylation of DNA via bisulfite sequencing while our Ovation® Ultralow Library Systems enable fast library construction for ChIP-Seq, FAIRE-Seq, Hi-C and more. Used in conjunction with our RNA-Seq library systems, researchers can probe both epigenetic modifications of interest and their associated gene expression changes.

Researchers have found evidence that suggests different cytosine modifications are functionally distinct and thus should be studied independently to better understand their biological impact. To distinguish cytosine DNA modifications, Tecan has partnered with CEGX to combine our Methyl-Seq NGS library prep kits with CEGX's TrueMethyl® to enable accurate quantification of 5mC and 5hmC in parallel at single-base resolution.

Learn more about distinguishing DNA modifications here.

Maintenance of parent-of-origin-specific gene expression by ZFP57 Maintenance of parent-of-origin-specific gene expression by ZFP57

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.

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Mapping Hydroxymethylation Patterns in Neurodegenerative Disease Mapping Hydroxymethylation Patterns in Neurodegenerative Disease

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.

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Dynamic changes in chromatin modifications observed during early mouse development Dynamic changes in chromatin modifications observed during early mouse development

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.

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Methylated Biomarkers: A new tool for liquid biopsy Methylated Biomarkers: A new tool for liquid biopsy

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.

Read the paper

 

Epigenetics as a read-out for inherited traits Epigenetics as a read-out for inherited traits

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.

Read the interview

 

ChIPping to an answer: Gene dysregulation in disease developmentChIPping to an answer: Gene dysregulation in disease development

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.

Read the paper