DNA-Sequencing Solutions

 
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DNA-Sequencing Solutions

Background Information

Almac Diagnostic Services has implemented a range of comprehensive next-generation sequencing (NGS) solutions including large panels, mid-size panels and bespoke single gene assays.  These multiple solutions are analysed using the Illumina MiSeq, NextSeq500, NextSeq550 and NovaSeq6000 sequencing platforms.  Our DNA-Sequencing solutions support novel biomarker discovery through to prospective clinical trial use, supported by Almac innovative proprietary bioinformatics solutions. These include:

RUO Illumina TSO-500 Panel Agilent WES DNA-Sequencing Solutions CTA Illumina Almac TST-170 Panel TP53 Single Gene Assay
RUO Illumina TSO-500 Panel Agilent WES DNA-Sequencing Solutions CTA Illumina Almac TST-170 Panel TP53 Single Gene Assay

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

TruSight™ Oncology 500

TruSight™ Oncology 500

The Platform:  The TSO-500 panel targets DNA and RNA variants for assessment of 523 genes, including RNA fusions from 55 genes, in the same solid tumour sample.  In addition, it accurately measures the key immunotherapy biomarkers: tumour mutation burden (TMB) and microsatellite instability (MSI).

Features & Benefits:

  • Pan-cancer content aligned with key guidelines and clinical trials
  • Tumour-only workflow for simplicity and efficiency
  • TMB calling performance similar to whole-exome sequencing (WES) panels
  • Large 1.94 Mb panel and sophisticated algorithm for accurate TMB score
  • A solution that can be kit-able in future to support multiple CDx tests
Metric TSO-500 Solution
Chemistry Illumina TruSight™ Oncology 500
Tissue Type FF and 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 tissue guidelines will be provided on a per-project basis
Recommended DNA Input Recommended sample input 120 ng, minimum 40 ng
Standard Sequencing Specification Minimum 200X coverage
Deliverables FASTQ, VCF, TMB & MSI Scores and QC Report as standard. BAM files available on request

Whole Exome Sequencing

The Platform: Almac optimised solution for comprehensive Whole Exome Sequencing (WES) from multiple sample types, including more challenging Formalin Fixed Paraffin Embedded (FFPE) material. The platform covers 99.7% of coding exons with readily interpretable raw sequencing data for use in biomarker discovery and retrospective clinical investigation.

Features & Benefits:

  • A comprehensive variant detection platform, covering 213,994 coding exons
  • QC guarantee of 100X mean target coverage across sample cohort ensured comprehensive downstream analysis and data interpretation
  • Machine-learning based bait design of SureSelect Human All Exon V7 maximises coverage with minimal sequencing
  • Interactive QC report enables rapid and comprehensive sample quality interrogation across cohort
  • Raw sequence data delivered in FASTQ format and compatible with the majority of bioinformatics pipelines
Metric WES Solution
Chemistry Agilent Human All Exon V7
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 >1mm3 and high tumour content >10% viable cells
Specific guidelines will be provided on a per-project basis
Recommended DNA Input Recommended Minimum 100 ng from FF
Recommended Minimum 100 ng of amplifiable DNA from FFPE
Standard Sequencing Specification On average 100X coverage
Other Sequencing specifications available on request
Deliverables FASTQ, VCF and interactive QC Report as standard. BAM available files on request

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TruSight™ Tumor 170 Clinical Trial Assay

Almac TruSight™ Tumor 170 Clinical Trial Assay

The Platform:  Almac has validated the Illumina TST-170 cancer mutation panel for prospective clinical trial use, within Europe and the US. The TST-170 panel targets DNA and RNA variants for assessment of 170 genes including 55 genes for fusions and splice variants, 148 for SNVs and Indels and 59 genes for CNV (CNV – Illumina RUO Assay Only).

Features & Benefits:

  • Pan-cancer content aligned with key guidelines and clinical trials
  • Analytically validated for use in prospective clinical trials
  • High levels of accuracy and precision from FFPE suitable for clinical trial use
  • Bespoke Almac bioinformatics pipelines providing enhanced variant call reproducibility, accuracy and data quality control (QC)
  • A solution that can be kit-able in future to support multiple CDx
Metric Almac TST-170 Solution
Chemistry Illumina TruSight™ Tumor 170
Tissue Type Validated for FFPE solid tumour tissue
(compatible with other sample types on request for RUO testing)
Recommended Tissue Requirements 1 mmTissue ∞ (If FFPE, tissue should be macrodissected)
Specific guidelines provided on a per-project basis
Recommended Input 120 ng DNA
85 ng RNA*
Standard Sequencing Specification Minimum coverage of 95% of reportable range ≥259X
Deliverables FASTQ, VCF, QC Report as standard with Customised Reporting. BAM files available on request
Estimated TAT Approx. 9 days § for prospective testing
(From sample receipt, inclusive of pathology review)

For RUO testing, timelines advised on a per-project basis

*Ability of TST-170 to analyse RNA allows for detection of expressed fusion genes resulting from both chromosomal abnormalities and posttranscriptional events and thus detects gene fusions that DNA sequencing panels would not recognize
∞ Variable across tissue type; Melanoma would require more tissue; Tissue fixation has greatest influence upon sample QC and assay performance
§ From sample receipt, inclusive of pathology review

 

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TP53 Clinical Trial Assay

Almac TP53 Clinical Trial Assay

The Platform: A bespoke single gene assay targeting the TP53 tumour suppressor gene. This assay is intended to detect genomic germline and somatic DNA aberrations (SNVs and indels) enabling determination of molecular eligibility to facilitate clinical trial enrolment.

Features & Benefits:

  • Comprehensive coverage of the full coding sequence
  • Dual amplicon workflow and individual base QC ensure high-confidence ‘Mutation Detected’ & ‘Not Detected’ status
  • High levels of accuracy and precision from FFPE suitable for clinical trial use
  • Rapid turnaround time with powerful reporting and interpretation services
Metric  Almac TP53 Solution
Chemistry Illumina TruSeq™ Custom Amplicon Dx
Tissue Type Validated for FFPE solid tumour tissue
(compatible with other sample types on request for RUO testing)
Recommended Tissue Requirements 1 mmTumor Tissue (macrodissected)
10% viable tumour cells within marked tumour area
Specific guidelines will be provided on a per-project basis
Recommended Input Input for FFPE is determined based on sample quality from qPCR amplifiability assessment and comparison to high-quality genomic DNA control
100 ng input for RUO testing of FF tissue, blood, BMA etc
Standard Sequencing Specification Minimum coverage of 99% of reportable range ≥ 1000X
Deliverables FASTQ, VCF, QC Report as standard with Customised Reporting. BAM files available on request
Estimated TAT Approx. 7 days § for prospective testing
(From sample receipt, inclusive of pathology review)
For RUO testing, timelines advised on a per-project basis
§ From sample receipt, inclusive of pathology review

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Custom DNA Sequencing Solutions

Custom DNA Sequencing Solutions

We offer the development of custom RUO DNA sequencing solutions for retrospective use tailored to clients exact requirements.

When a biomarker assay is required for trial enrichment, or a patient treatment decision will be made based on the result, assays must be run under CLIA / GLP. Not all biomarker assays that take place in the clinical trial setting will result in patient treatment decisions; those that are pharmacodynamic (PD) biomarkers or assays for research use only purposes (RUO) do not require the same level of validation and are typically run retrospectively in batches as the trial progresses.

Although the validation requirements are less stringent, we develop and process these assays under the same quality management system and with the same processes and protocols for robust delivery.

Almac Additional Benefits for DNA Sequencing Solutions

Flexible Extraction Protocols: Almac offer both high-quality single DNA extractions and a dual RNA / DNA extraction protocol for our DNA-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.

 

DNA-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 DNA Sequencing Solutions? Get in touch below: 

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