SureSeq™ Solid Tumour Panel

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Fully validated on FFPE samples, the 60-gene NGS SureSeq Solid Tumour Panel allows discovery of novel and known variants in a range of solid tumours.

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For more information about any OGT product or service, please contact us.

Overview

The SureSeq Solid Tumour Panel delivers:

  • Highly accurate determination of allele frequency — Hybridisation-based enrichment allows the removal of PCR-based bias and duplications
  • Comprehensive variant detection — Targeting every codon of every exon in 60 key genes for mutation detection and discovery
  • Improved coverage uniformity — Sensitive and reproducible variant detection even in heterogeneous samples
  • Fully validated on FFPE samples — Unlock the potential of precious samples
  • Powerful variant analysis report included — Use OGT’s user-friendly interactive report or your own analysis pipeline for flexible data analysis

Special offer

Test the SureSeq Solid Tumour NGS Panel through OGT’s high-quality Genefficiency Services without disrupting your lab’s workflow. Get a 30% discount on the service and a 20% discount on your first product order. Find out more

Ordering Information

Product Contents Cat. No. Price
SureSeq Solid Tumour Panel (96 reactions) Enrichment baits sufficient for 96 samples; SureSeq Solid Tumour Report 600070 Get a quote
SureSeq Solid Tumour Panel (16 reactions) Enrichment baits sufficient for 16 samples; SureSeq Solid Tumour Report 600071 Get a quote


Genefficiency & SureSeq NGS Variant Analysis Report: For research use only; not for use in diagnostic procedures.

Details

Highly accurate determination of allele frequency

Next generation sequencing (NGS) has allowed the identification of a growing number of novel mutations in cancer samples, but many more mutations remain to be discovered. Furthermore, much research will be needed to determine which of these mutations are clinically relevant (driver mutations) and which can be targeted by new therapeutic agents. The SureSeq Solid Tumour Panel has been designed to deliver highly accurate detection of novel and known variants for clinical and translational research applications.

Utilising hybridisation-based enrichment, the SureSeq Solid Tumour Panel delivers greater run-to-run consistency and significantly less PCR bias (Figure 1) than amplicon-based assays. Run-to-run consistency is an important metric in determining confidence in NGS analysis — inconsistency indicates that duplicate or even triplicate sequencing may be necessary to ensure confidence in the assay result. Amplicon-based enrichment is susceptible to amplification bias, particularly in situations where there is limited sample or where the ability to detect minor allele frequencies is required (e.g.heterogeneous samples). Such bias may cause important variants to be missed or over-represented. For more information about assay bias, view our webinar.

SureSeq Figure1

 

 

 

 

 

 

 

 

 

 

 

 

 

Figure 1: The hybridisation-based SureSeq Solid Tumour Panel delivers consistent, reliable results. Replicates of 3 samples were individually enriched using the SureSeq Solid Tumour Panel and subsequently sequenced. Comparison of the allele frequencies of each run showed very high concordance, demonstrating the reproducibility of the assay.

After comparing three leading targeted enrichment platforms on matched fresh and FFPE genomic DNA, in terms of mutation detection, I would say OGT's SureSeq Solid Tumour Panel detected more of the mutations that we knew to be present compared to the other 2 platforms". Dr George Burghel, Scientist, St James' Hospital, Leeds, UK 

Comprehensive variant detection

The SureSeq Solid Tumour Panel targets selected key genes known to contain driver mutations for a range of cancer types including breast, prostate, ovarian, lung and colorectal (Table 1). The gene content has been defined by recognised cancer experts, including Cancer Research UK, Professor Mike Griffiths (West Midlands Regional Genetics Laboratory, UK) and Professor Nick Cross (National Genetics Reference Laboratory, Salisbury, UK). Targeting the entire coding regions of selected key genes, the SureSeq Solid Tumour Panel allows the discovery of novel variants as well as the analysis of known mutation hotspots. The SureSeq Solid Tumour Panel targets 327.5 kb of genomic sequence, including validated dbSNP positions — facilitating genome profiling and sample tracking.

AKT1 BRCA2 FGFR2 MAP2K1 NOTCH1 SMAD4
ALK CDH1 FGFR3 MED12 NRAS SMARCA4
APC CDKN1B FOXA1 MET PDGFRA SMARCB1
AR CDKN2A GNAS MLH1 PDGFRB SMO
ARID1A CHD1 HRAS KMT2A (MLL1) PIK3CA SPOP
ASXL1 CTNNB1 IDH1 KMT2C (MLL3) PTEN STK11
ATM DDR2 JAK2 KMT2D (MLL2) PTPN11 TP53
AXL EGFR JAK3 MTOR RB1 KDM6A (UTX)
BRAF ERBB2 KIT NF1 RET VHL
BRCA1 FGFR1 KRAS NKX3.1 ROS1 ZFHX3

 

Table 1: The SureSeq Solid Tumour Panel provides complete coverage of 60 key cancer genes selected by recognised cancer experts.

Fully validated on FFPE samples

The SureSeq Solid Tumour Panel has been validated using DNA extracted from FFPE samples for a range of solid tumours, including sarcomas and lung, pancreatic and head and neck cancers (Table 2). The panel has been optimised to work with as little as 100–500 ng of genomic DNA from formalin-fixed, paraffin-embedded (FFPE) samples, allowing you to unlock the potential of archived samples. The protocol incorporates several QC steps that determine the optimal processing workflow allowing difficult samples to be recovered whilst ensuring sufficient sequencing data for confident analysis. While we recommend starting with 500 ng or more of DNA from FFPE samples to limit the level of duplication, we have successfully sequenced DNA from FFPE samples where less than 100 ng of high integrity starting material was available. As the panel targets more than just mutation hotspots, novel variants can be detected, enhancing the discovery power of your translational medicine research projects.

SureSeq Table2

 

 

 

 

 

 

 

 

 

Table 2: Example mutations detected in FFPE samples from a range of solid tumours using the SureSeq Solid Tumour Panel. The ability to accurately detect minor allele frequencies (MAF) as low as 1.1% gives added confidence in the variants being called and facilitates the exploration of tumour heterogeneity.

Improved coverage uniformity

Enrichment assay optimisation is a crucial step in ensuring accuracy and sensitivity of targeted sequencing. Where regions are poorly enriched, they will generate fewer sequencing reads. If a variant falls into a region not covered at all, or covered by only a few reads, that variant is likely to be missed. OGT’s expert bait design ensures efficient and more uniform capture of all targeted regions, so that all variants present can be called with maximum confidence (Figure 2). Uniform enrichment also allows proportionately lower sequencing depth to be used to identify minor frequency variants — potentially lowering sequencing and analysis costs and increasing sample throughput.

SureSeq Figure2

 

 

 

 

 

 

 

 

 

 

Figure 2: OGT’s expert bait design delivers improved efficiency and uniformity of target sequence capture. A custom panel was designed using standard commercially available software (columns SSD1-SSD8) and OGT’s expert bait design algorithms (columns OGT1-OGT8). With OGT expert design, the percentage of bases sequenced to at least 20% of the mean target coverage depth increased from 73% to 98%.

Heterogeneous samples pose significant challenges as alleles are likely to be present at frequencies below what would be expected for standard germline variants. Solid tumour samples, for example, typically contain a mixture of tumour and normal cells. The tumour itself can be composed of several molecularly distinct clones. In order to detect alleles that contribute only a small percentage to the reads at any locus, a highly uniform and sensitive enrichment is required in order to avoid sequencing to excessive depths. The SureSeq Solid Tumour Panel has been shown to accurately call alleles present at a frequency of just 1.2%, at a read depth of 1000x (Table 3).

SureSeq Table3

 

 

 

 

 

 

Table 3: The SureSeq Solid Tumour Panel enables the accurate detection of low-frequency variants. A sample of known heterozygous genotype (A/G in MLH1 located on chromosome 3:37,057,568) was diluted with a second sample of known genotype (A/A). The SureSeq Solid Tumour Panel allowed accurate detection of the low-frequency variant at 1.2% contribution in the final 1:50 dilution of the heterozygous genotype. Sensitive detection of alleles occurring at these very low-frequencies is important when working with very small numbers of cancer cells within heterogeneous samples. 

Powerful variant analysis report included

OGT has validated a number of analysis pipelines, tailored to specific applications, from standard germline variant detection to high sensitivity somatic variant detection in a heterogeneous background. The unique SureSeq Solid Tumour Report incorporates these pipelines and provides researchers with the freedom to explore and retrospectively interrogate data with additional or new selection criteria, without the need for additional in-house bioinformatics resource (Figure 3). Using the report, data can be easily filtered by numerous parameters, including gene, depth of coverage, somatic variants and predicted effect on the protein. In addition, all variants are fully annotated with links to various databases (e.g. dbSNP, COSMIC, Genecards and OMIM) providing results in context.

SureSeq Figure3

 

 

 

 

 

 

 

 

Figure 3: The SureSeq Solid Tumour Report enables simple and rapid identification of meaningful results.

To find out how OGT's powerful SureSeq Solid Tumour Panel and complimentary SureSeq interpret software can make the analysis of solid tumour samples simple watch this short demonstration:

https://vimeo.com/120669881

For more information about the SureSeq Solid Tumour Panel or to discuss our custom panel services, please contact us.

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Ordering Information

Product Contents Cat. No. Price
SureSeq Solid Tumour Panel (96 reactions) Enrichment baits sufficient for 96 samples; SureSeq Solid Tumour Report 600070 Get a quote
SureSeq Solid Tumour Panel (16 reactions) Enrichment baits sufficient for 16 samples; SureSeq Solid Tumour Report 600071  Get a quote


Genefficiency & SureSeq NGS Variant Analysis Report: For research use only; not for use in diagnostic procedures.