miRNA Profiling

MicroRNAs (miRNAs) are ~22nt non-coding strands of expressed RNA that are used by the cell for gene regulation. While research in this area is still young, these molecules have been implicated in various forms of disease, which makes miRNA profiling a viable method for biomarker discovery.

miRNA profiling has traditionally been performed using microarrays, RT-PCR, and sRNA sequencing. These methods can suffer from tedious workflows and sample quality issues.  Learn more about the HTG EdgeSeq miRNA Whole Transcriptome Assay product.

Example

Profiling miR-205 with an HTG EdgeSeq system reliably differentiates between squamous and non-squamous lung carcinoma.

 

miR-205 expression is a highly specific marker for squamous cell carcinoma in lung cancer. The HTG EdgeSeq system differentiates nicely between Sq/non-Sq. let7a-5p expression is shown as a comparison. Data were normalized to all counts and plotted in R.

HTG has developed and commercialized the HTG EdgeSeq miRNA Whole Transcriptome Assay to enable tumor profile screening and discovery.

Learn More About HTG EdgeSeq Workflow And Chemistry

Performance

Specificity

 

Closely related synthetic miRNA pools from ABRF were split between pools. All possible probes were used to profile individual pools. 3-11% of NPA probes bound to off-target sequences with a 1-base difference (Figure 1A) while only 0.1-0.3% of NPA probes bound to off-target sequences with a 2-base difference (Figure 1B). In both examples, the on-target hybridization signal is at least 8X greater than off-target hybridization. Data was generated using the Illumina MiSeq v2 1x50 reagent kit.

Sensitivity

 

The HTG EdgeSeq miRNA Whole Transcriptome Assay comparison of matched FFPE vs Fresh Su-DHL6 B-cell lymphoma tissue was performed (Figure 2A). A matched sample correlation plot is shown demonstrating a Pearson Correlation (R) of >0.98. We also demonstrate little-to-no loss of information when using FFPE tissue compared to fresh frozen tissue.

To further demonstrate sensitivity, the dynamic range of 46 housekeeper genes was measured after 3 separately-barcoded sample replicates were profiled using the HTG EdgeSeq miRNA Whole Transcriptome Assay coupled sequencing on the Illumina HiSeq platform (Figure 2B). We demonstrate at least 4 logs of dynamic range with coefficients of variation at ~3%.

Sample Flexibility

 

The HTG EdgeSeq miRNA Whole Transcriptome Assay was run with Heart FFPE (Figure 3A) and plasma samples (Figure 3B). Technical replicate correlation plots are shown. Data were filtered for signals under 70 and log(2) transformed before plotting. We demonstrate that the HTG EdgeSeq miRNA Whole Transriptome Assay coupled with NGS produces robust profiling for many tissue sources.

Reproducibility

 

Resources

Automated high fidelity miRNA expression profiling using nuclease protection coupled with next generation sequencing

Ordering Information

HTG EdgeSeq miRNA Whole Transcriptome Assay is available to run on the HTG EdgeSeq system.

Catalog #

 Description 

Illumina Configurations
916-001-208 HTG EdgeSeq miRNA WTA (2x8)
916-001-008 HTG EdgeSeq miRNA WTA (4x8)
916-001-224 HTG EdgeSeq miRNA WTA (1x24)
916-001-024 HTG EdgeSeq miRNA WTA (4x24)
916-001-096 HTG EdgeSeq miRNA WTA (1x96)
Ion Torrent Configurations
916-001-308 HTG EdgeSeq miRNA WTA (2x8)
916-001-108 HTG EdgeSeq miRNA WTA (4x8)
916-001-324 HTG EdgeSeq miRNA WTA (1x24)
916-001-124 HTG EdgeSeq miRNA WTA (4x24)

orders@htgmolecular.com

 

For Research Use Only. Not for use in diagnostic procedures.

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Last updated: 12/28/2016 - 13:02