Liquid Biopsy Solutions

 
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Liquid Biopsy Solutions

Almac Diagnostic Services offer a range of comprehensive next-generation sequencing (NGS) Liquid Biopsy solutions, including large and mid-size panels, analysed using the Illumina NovaSeq6000 and NextSeq 500/550 sequencing platforms.

Our Liquid Biopsy solutions offer BioPharma clients a non-invasive approach, providing a rapid and precise translational research & biomarker discovery tool for early diagnosis screening, drug resistance and tumour heterogeneity in real-time. These include:

Liquid Biopsy Solutions Illumina Archer PGDx TSO-500 ctDNA Panel LIQUIDPlex™ elio™ plasma resolve panel
Liquid Biopsy Solutions Illumina Archer PGDx TSO-500 ctDNA Panel LIQUIDPlex™ elio™ plasma resolve panel

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

TruSight Oncology 500 ctDNA

TruSight Oncology 500 ctDNA (Research Use Only)

The Platform: The Illumina TruSight Oncology 500 circulating tumour DNA (ctDNA) assay is an NGS-based assay that enables comprehensive genomic profiling to assess multiple variant types in 523 cancer-related genes from cell-free DNA (cfDNA). This assay features the same DNA content as the TruSight Oncology 500 solid tumor assay for detection of single nucleotide variants (SNVs), indels, copy number variants (CNVs), DNA fusions, tumour mutational burden (TMB), and microsatellite instability (MSI) from plasma samples.

In addition, the DRAGEN Bio-IT Platform offers speed and accuracy to detect variants through its ultra-rapid variant calling algorithm.

Benefits
  • Enables comprehensive tumour cell profiling when tissue biopsy is not an option.
  • Targets multiple biomarkers and somatic variant types in a single assay with limited sample input requirements.
  • Allows monitoring of disease progression, response to treatment and acquired resistance.
Features
  • Coverage of current and emerging biomarkers including comprehensive coverage of key cancer-associated genes across multiple tumour types.
  • Immuno-oncology relevant biomarker readouts including blood TMB (bTMB) and blood MSI (bMSI).
  • Unique molecular barcode (UMI) technology, high raw coverage enabled by the NovaSeq 6000 system, and in silico error correction models improve variant calling and reduce artefacts.
  • Ultra-rapid variant calling powered and accelerated by DRAGEN Bio-IT Platform.
  • Robust variant calling performance demonstrated for low frequency (<0.5%) variants.
  • Hybrid capture enrichment library preparation coupled with comprehensive content enables novel variant and rearrangement detection without a priori knowledge.
  • Upstream cfDNA QC enables assessment of gDNA contamination in sample prior to library preparation and sequencing, enabling contextualisation of observed results.
  • Comprehensive variant annotation allows effective triage of clinically actionable variants.
Metric TSO-500 ctDNA Solution
Chemistry Illumina TruSight Oncology 500 ctDNA
System NovaSeq 6000™ System
Genes 523 genes. See Illumina Website under ‘Product Literature’ for (Full Gene List)
Panel Size 1.94 Mb DNA
Sample type Plasma
DNA input requirement 30ng
Standard Sequencing Specification Median Exon Coverage ≥1300X

≥80% of target exons covered at ≥1000X

Total assay turnaround time For batch retrospective testing – turnaround time agreed on a per project basis
Run time 44 hrs Sequencing run time (S4 flowcell)
Sample throughput 24 Libraries per run (S4 flowcell)
Variants SNVs and indels, DNA fusions, CNVs, MSI, TMB
Limit of detection (VAF) 0.5% VAF for small variants (as per Illumina’s manufacturing guidelines)
Data Analysis DRAGEN Server pipeline
Deliverables / Output files BCL
FASTQ
gVCF
Annotated Small Variant Report
Copy Number Variants Report
Fusion Report
Combined Variant Report
Metrics Report

LIQUIDPlex ™

Archer LIQUIDPlex ™ (Research Use only)

The Platform: The Archer LiquidPlex panel is a customisable NGS-based assay which allows profiling of cell-free DNA (cfDNA) samples to assess small variants across 28 key genes of interest across a variety of cancer types (additional genes can be added on request.

The assay enables the calling of small variants at low allelic fractions through the use of unique molecular barcodes and an Archer Analysis bioinformatics pipeline applying Almac-optimised parameters.

This results in highly sensitive variant calling, enabling somatic variant detection in this sample type, without sacrificing specificity. The smaller panel size and library preparation methodology allows for a rapid turnaround from sample acquisition to result and, reduces the need for large sequencing read budgets by focusing on key oncology driver genes.

Features & Benefits

Benefits
  • Low input to library preparation amenable to cfDNA yields obtainable from plasma samples.
  • Anchored multiplex PCR based library preparation method enables faster turnaround times from cfDNA sample to result.
  • Smaller panel size reduces sequencing read budget requirements.
  • Cloud based analysis platform allows scale up for large sample cohorts without impacting turnaround times.
Features
  • Archer Analysis variant calling pipeline applying Almac-optimised parameters ensures highly sensitive and specific variant calling.
  • Unique molecular barcodes enable consensus read generation to allow variant calling at allele frequencies below short read sequencer error rates.
  • Customisable gene content to suit your analysis application.
  • Filtering of germline polymorphisms enables a focus on key mutations of interest and discernment of underlying biology.
  • Custom variant annotation available on request.
Metric LIQUIDPlex™ Solution
Chemistry Archer LIQUIDPlex™
System Illumina NextSeq 550/500
Genes Customisable
Panel Size 28 Key Oncology Genes (Additional content can be added). See Archer Website for (More Information)
Sample type Plasma/ cfDNA
DNA input requirement 50ng minimum input recommended
Standard Sequencing Specification >5 Million 2x151bp reads per sample. Custom read budgets for more sensitive applications are also available
Total assay turnaround time For batch retrospective testing – turnaround time agreed on a per project basis
Sequencing Run time 29 Hours per run
Sample throughput Variable depending on flowcell type and required read budget
Variants Key hotspot mutations and de novo mutations covered across 28 genes
Minimum Theoretical Detectable Variant allele frequency (VAF) 0.1%
Data Analysis Archer Analysis ctDNA variant calling pipeline hosted on Archer Analysis Unlimited cloud platform (with Almac-optimised parameters)
Deliverables / Output files Raw unfiltered variant calls
Filtered and annotated variant calls files (custom filtering and/or annotation available on request)
BAM Files
FASTQ Files
Alignment Statistics QC Reports

PGDx elio™ plasma resolve

PGDx elio™ plasma resolve

The Platform: The Personal Genome Diagnostics PGDx elio™ plasma resolve panel is a broad multi-gene pan-cancer NGS-based assay that assesses 33 Full coding genes for Sequence Mutations in circulating cell-free DNA (cfDNA). This qualitative in vitro diagnostic assay uses targeted high throughput, parallel-sequencing technology to detect single nucleotide variants (SNVs), small insertions/deletions (indels), amplifications, rearrangements, and microsatellite instability (MSI) from plasma samples.

The Variant Dx™ Bioinformatics pipeline is an ensemble of approaches providing novel genetic analyses and proprietary data analysis algorithms.

Features & Benefits:
  • A comprehensive genomic profiling diagnostic panel that identifies key genomic alterations in 30+ genes including key immune-oncology biomarker microsatellite instability (MSI).
  • Utilises a robust automated Bioinformatics pipeline to offer fast, reliable and comprehensive results.
  • Faster turnaround time to reliable results, enabling the best and most informed treatment decisions

* The technical specification table for the PGDx elio™ plasma resolve panel is as per the PGDx website and guidelines. For further information visit: https://www.personalgenome.com/products

Metric PGDx elio™ Solution
Chemistry PGDx elio™ plasma resolve
System Illumina NextSeq
Genes 33 Full Coding Genes
Panel Size 0.24 Mb
Sample type Plasma
DNA input requirement 40ng
Standard Sequencing Specification Average Total Coverage 30,000x
Average Distinct Coverage 2,160x
Read length 2 x 150bp
Total assay turnaround time For batch retrospective testing – turnaround time agreed on a per project basis
Variants SNVs and indels, Amplifications, Rearrangements, MSI
Sensitivity 0.5% hotspots (1% all bases, AF as low as 0.125%)
Data Analysis Variant Dx™ Bioinformatics pipeline

Contact Us

Interested in partnering with Almac on your biomarker project using our (RUO) Liquid Biopsy Sequencing Solutions? Get in touch below:

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