The SeqLL Sequencing Services Laboratory is expanding its capacity in DRS to meet increasing demand.

DRS is an important step forward in the RNA Sequencing world. Researchers can explore the RNA transcriptome directly as it exists in vivo with minimal upfront manipulation.

True Single Molecule Sequencing (tSMSTM) relies on no library preparation and minimal sample preparation to ensure true information related to the samples used in investigations. The DRS utility success and strength is presented in peer-reviewed articles that span the last 7 years. The results from some studies were only possible through tSMS DRS protocols as indicated in these publications.

A more accurate data set is created by eliminating the biases and sample loss that occurs through the multiple ribosomal RNA depletion and sample preparation steps required by other platforms. Significant cost reduction is also achieved through SeqLL’s streamlined process. With DRS, directly capture and sequence polyadenylated RNA without conversion to cDNA.

tSMS Sample Prep is more streamlined in comparison with standard Library Construction approaches, reducing the hands-on time, as well as overall turnaround time (TAT). DRS has a 1-3 step Sample Prep protocol which does not involve PCR at any stage, thus avoiding the sample bias and loss of diversity that can occur during PCR amplification.

DRS provides a new tool for a wide range of applications.

Sample preparation can be completed in as few as 3 steps and typically no more than 4. No amplification is required and custom chemistry flow cells are possible to address very specific questions or needs.

Direct RNA Sequencing is very useful when investigating the basic features and functions of gene expression and encoding - transcriptome or epitranscriptome studies. This can include such areas as –

• The impact of mRNA methylation on gene expression
• Potential expression changes and related effects created by modifications to ribosomal RNA, transfer RNA and small nuclear RNA
• Modulating gene coding
• The impact of changes to polyadenylation to disease risk or a change in disease risk
• How RNA environmental challenges or changes affect expression and the related impact of change
• Transcription or expression initiation change
• Biomarker discovery related to rare transcription change events
• Pharmocogenomics studies

Sequencer Beta Test Program Expanded

The Early Access Program for SeqLL’s new sequencing platform has been expanded. Due to the favorable response received from the sequencing community, all the initial systems placed into the program have been assigned.

The institutions that will participate include biotechnology and biopharmaceutical companies as well as leading academic and medical research centers.

The most common reasons for participation include:

1. The need for increased sensitivity (detection of expression level changes as low at 1.3-1.5 fold)
2. Higher accuracy by sequencing original transcripts and not adding bias through amplification
3. Consistent performance
4. Elimination of sample library preparation and direct RNA sequencing capability
5. Greater flexibility across sample types (such as FFPE treated samples and cell free nucleic acids)
6. Seeking a viable and proven alternative to the sequencing technology they currently use

The Early Access Program will run through mid-2017. SeqLL is now seeking to expand the number of collaborators agreeing to field test beta versions of the new tSMS sequencing system. Data generated from the Early Access Program will be used to optimize the ease of use and training materials in support of the 2017 commercial launch of the tSMS Benchtop System. Priority will be given to collaborators with a near term research project that would benefit from the unique capabilities of the tSMS platform to generate superior and/or complimentary results to other sequencing approaches.

Bioinformatics Services

SeqLL’s Sequencing Services Laboratory offers a full range of bioinformatics services from Basic to Advanced to Custom analyses. SeqLL provides basic bioinformatics analysis as part of its standard sequencing service and also offers a menu of stand-alone bioinformatics services for data generated at other sites, including a variety of sequencing platforms.

We recognize that the value of your NGS data is dependent on the quality of the analysis. Increasingly complex analysis is becoming routine as researchers strive to leverage the most they can from sequencing runs. Combining these issues with shorter and shorter timelines has raised unique issues for many research labs.

SeqLL offers a wide variety of bioinformatic packages, allowing the researcher to customize the analysis to fit the needs of a given project. SeqLL bioinformatic specialists will work with your team to define your project requirements and develop an analysis package that meets the specific needs of your program. Balancing cost, timing and level of analysis assures that you will receive a cost effective program, on time, and with the details that you require.

Sequencing Metrics are evaluated and delivered with the raw data in every project. Users select the file format that best suits their needs. This includes quality scores, evaluation of raw and filtered reads and where applicable aligned reads.

Basic Biometric interpretation is designed to provide intuitive visual evaluation of the data presented. The format will vary depending on the needs of the laboratory but will typically include quality control metrics, box plots, bar graphs and distribution plots of detected genes.

Advanced Biometrics analysis are used to provide additional insight into the sample and data obtained. The basic biometric analysis is typically expanded to include gene ontology; Differentially Expressed Gene (DEG) and pathway analysis.

Custom Biometrics involves the SeqLL team working with your laboratory in a partnering mode. This allows a combination of your molecule or target expertise with our analysis experience to gain non-intuitive insight into your data. Many projects involve re-evaluating existing data for additional correlation and enhanced discovery.

Address a Wide Variety of Sample Types with tSMS

The Development of a Blood Test for Coronary Artery Disease

Patients who develop coronary artery disease exhibit specific changes in gene expression in whole blood RNA that are not present in patients without coronary artery disease. To identify diagnostic biomarkers of CAD, whole blood RNA was analyzed by advanced single molecule sequencing (tSMS) of RNA (RNAseq), to identify transcripts associated with CAD (TRACs).

These studies potentially provide a clinic-ready diagnostic test for the presence of CAD in chest pain patients. In the future, this test could be expanded for use in diagnosing CAD in asymptomatic patients, which could potentially prevent unexpected MI and provide physicians the chance for early intervention, with simple, proven therapies such as aspirin, statins, and lifestyle changes.