RNA-Sequencing Solutions

Background Information

Almac Diagnostic Services has a proven ability to discover, develop and validate high quality, innovative RNA-based biomarkers with an extensive track record in establishing assays across key regulatory standards. We currently offer multiple Research Use Only (RUO) RNA-Sequencing solutions analyzed using the Illumina NextSeq500, NextSeq550 and NovaSeq6000 sequencing platforms.  All our RNA-Sequencing solutions support novel biomarker discovery and translational research, supported by Almac innovative proprietary bioinformatics solutions. These include:

 

RNA-Sequencing Solutions Illumina RNA Exome Roche Total RNASeq Illumina mRNA Stranded ClaraT Total mRNA Report

RNA-Sequencing Solutions Illumina RNA Exome Roche Total RNASeq Illumina mRNA Stranded ClaraT Total mRNA Report

 

 

To find out more information on each Almac solution, click the appropriate drop-down below:

RNA Exome Sequencing

RNA Exome Sequencing

The Platform: RNA Exome is a probe-based target capture approach for sequencing of coding regions.  An Almac optimized solution recommended for gene expression from poor quality and formalin-fixed paraffin embedded (FFPE) samples.

Features & Benefits:

  • Comprehensive panel covering >21,000 genes from the RefSeq Exome (99%)
  • Almac optimized process and workflow maximizing on pass rates and sequencing data quality from challenging sample types
  • Produces highly repeatable and reproducible gene expression data in comparison to other RNA expression platforms
  • Almac have analytically validated a selection of gene expression signatures demonstrating RNA Exome as a potential platform suitable for CTA delivery
Metric RNA Exome Solution
Chemistry Illumina TruSeq™ RNA Exome
Tissue Type Optimized for FFPE (compatible with other sample types on request)
Recommended Tissue Requirements

For FFPE, tissue should be macrodissected
10 x 5 µm FFPE sections with a tissue area >1cm2 and high tumor content >10% viable cells
Specific guidelines will be provided on a per-project basis

Recommended RNA Input

Recommended Minimum 100 ng
(100-500 ng dependent on quality based on DV200 and
Almac Proprietary qPCR assay – RNASeq-ability™)

Standard Sequencing Specification

25M PE reads (50M Total Reads)
Other Sequencing specifications available on request

Deliverables FASTQ, FPKM Expression Matrix, Count Matrix and QC Report as standard.  BAM files on request
NOTE: Optimal sample number ≥24 samples

Find out more

Total RNA-Sequencing

Total RNA-Sequencing

The Platform: Total RNA-Seq is a ribosomal depletion approach for sequencing of both coding and non-coding regions.  A total assessment specifically suitable for including an evaluation of non-coding regions in either fresh frozen (FF) or FFPE samples. Also includes in-built globin depletion for analysis of whole blood samples.

Features & Benefits:

  • Complete workflow with efficient ribosomal RNA (rRNA) depletion steps in-built
  • Lower duplication rates observed in samples resulting in increased sequencing success
  • Additional downstream applications by targeting non-coding RNA
Metric Total RNA-Seq Solution
Chemistry Roche KAPA HyperPrep Kit with RiboErase (HMR)
Tissue Type FF or FFPE (compatible with other sample types on request)
Recommended Tissue Requirements

For FFPE, tissue should be macrodissected
10 x 5 µm FFPE sections with a tissue area >1cm2 and high tumor content >10% viable cells
Specific guidelines will be provided on a per-project basis

Recommended RNA Input Recommended Minimum 100 ng
Standard Sequencing Specification

50M PE reads (100M Total Reads) for all applications
Other Sequencing specifications available on request

Deliverables FASTQ, FPKM Expression Matrix, Count Matrix and QC Report as standard.  BAM files on request
NOTE: Optimal sample number ≥24 samples

mRNA Stranded Sequencing

mRNA Stranded Sequencing

The Platform: mRNA Stranded Sequencing is a polyA stranded capture approach for transcriptome sequencing including antisense analysis of good quality FF samples only.

Features & Benefits:

  • Captures a complete overview of the coding transcriptome with strand information
  • A broad dynamic range to enable accurate gene expression changes in good quality samples
  • Provides an understanding of both known and novel RNA fusions in FF samples
Metric mRNA Stranded Solution
Chemistry Illumina TruSeq™ Stranded mRNA
Tissue Type FF only
Recommended Tissue Requirements

Specific tissue guidelines will be provided on a per-project basis

Recommended RNA Input Recommended Minimum 100 ng
Standard Sequencing Specification 30M SE reads (30M Total Reads)
Deliverables FASTQ, FPKM Expression Matrix, Count Matrix and QC Report as standard.  BAM files on request.
NOTE: Optimal sample number ≥24 samples

Almac Additional Benefits for RNA Sequencing Solutions

Flexible Extraction Protocols: Almac offer both high quality single RNA extractions and a dual RNA/DNA extraction protocol for our RNA-Sequencing solutions. Dual extraction facilitates simultaneous generation of RNA-Seq data and DNA-Seq data from a single sample, conserving valuable sample material.

Customisable Analysis & Reporting: Data analysis and reporting is performed using Almac customized bioinformatics pipelines implemented on DNAnexus, a global leader in biomedical informatics and data management. DNAnexus is a cloud-based NGS solution which ensures scalability and security of project data. A significant benefit of utilizing DNAnexus within this offering is the flexibility of workflow optimzation and the ability to customize bespoke pipelines for quality control, alignment & expression estimation.

claraTclaraT – Unique gene expression report: claraT classifies multiple publicly available gene expression signatures and single gene targets linked to multiple key biologies, alongside Almac’s own proprietary assays, according to the well-established 10 Hallmarks of Cancer. The claraT report is a pan-cancer solution generated from raw gene expression data, utilizing Almac’s RNA-Sequencing Services. 

RNA-Sequencing Resources

To view additional resources such as whitepapers, technical factsheets, webinars and other information, click here.

Contact Us

Interested in partnering with Almac on your biomarker project using our RNA Sequencing Solutions? Get in touch below