RNA-Sequencing Solutions
RNA-Sequencing Solutions
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 analysed using the Illumina NextSeq500, NextSeq550, NovaSeq6000 and NovaSeq X Plus sequencing platforms. All our RNA-Sequencing solutions support novel biomarker discovery and translational research, supported by Almac innovative proprietary bioinformatics solutions. These include:
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 optimised 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 optimised process and workflow maximising 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 | Optimised 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 tumour 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) |
| 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
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 |
| Recommended RNA Input | Recommended Minimum 100 ng |
| Standard Sequencing Specification |
50M PE reads (100M Total Reads) for all applications |
| 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 customised 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 utilising DNAnexus within this offering is the flexibility of workflow optimisation and the ability to customise bespoke pipelines for quality control, alignment & expression estimation.
claraT – 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, utilising 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: