Technical Note: PreSeq™ RNA QC Assay predicts high-confidence libraries

Abstract

RNA derived from formalin-fixed, paraffin-embedded (FFPE) tissue can be of variable quality due to chemical modification incurred during the fixation process as well as during pre-fixation handling. While many different methods are available for measuring RNA mass and fragment length, we have developed the Archer™ PreSeq™ RNA QC Assay, a qPCR-based transcript analysis assay that is highly predictive of sequencing success using Archer FusionPlex™ Assays. PreSeq is superior to alternative RNA analytical methods because the assay is in-line with the Archer Universal RNA library production protocol and gives a quantitative readout that assesses all aspects of RNA input quality that determine suitability for NGS library generation.

PreSeq is a SYBR®-based qPCR assay designed to assess the suitability of an RNA input for FusionPlex library generation based on the quantification of chemically available fragments greater than 100bp in length. Positive PreSeq results are predictive of successful FusionPlex library sequencing results and of passing the Archer Analysis software quality filter. While the observed PreSeq Cq value of a given sample can vary depending on the instrument and master mix used, routinely performing this assay during FusionPlex library creation can help establish a baseline pass/fail metric to predict library quality prior to sequencing and aid in determining the cause of failure after sequencing.

Key points from the PreSeq RNA technical note

Input mass does not predict library quality

Input mass does not predict library quality

PreSeq measures the quantity of amplifiable RNA fragments in an input sample

PreSeq measures the quantity of amplifiable RNA fragments in an input sample

PreSeq integrates into the FusionPlex workflow.

PreSeq integrates into the FusionPlex workflow

PreSeq is sensitive to RNA quantity and quality.

PreSeq is sensitive to RNA quantity and quality

Archer Analysis predicts high-quality RNA libraries.

Archer Analysis predicts high-quality RNA libraries

PreSeq predicts high-confidence libraries

PreSeq predicts high-confidence libraries

For more information, visit the
PreSeq RNA QC Assay page

Subscribe to stay in the loop







How to contact us

Address

2477 55th Street, Suite 202

Boulder, CO 80301

Phone

Phone: (877) 771 1093

Phone: (303) 357 9001

All content © 2017 ArcherDX, Inc.

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