An integrated approach to tumour profiling

Thursday 10 December 2015
Applications:

Want to download this as a PDF? Download now

Changing the way we look at cancer

Classifying tumours by genetic make-up, rather than by which organ is affected, is changing the approach to cancer. The determination of mutation type — including single point mutations, translocations, copy number variations (CNV) or loss of heterozygosity (LOH) — can guide research into diagnostic and prognostic applications, and allow for truly personalised treatment options. This genetic information is the basis for the rapidly developing field of precision medicine.

Integrated technologies for accurate mutation detection

Various technologies are available to study the mutations that cause cancer, but none is capable of accurate detection of all types of genetic aberrations. By combining information from multiple technologies, researchers can analyse complex cancer samples and get the most complete overview of disease-driving mutations.

Oxford Gene Technology (OGT) offers an integrated portfolio of products providing clinical researchers with the most advanced tools available to study cancer. Our products are backed by deep technical expertise and dedicated customer support. We partner with leading clinical researchers to advance discoveries by providing proven, high-quality solutions. Custom product capabilities are also available.

  • Fluorescence in situ hybridisation (FISH) — Cytocell FISH Probes
  • Next generation sequencing (NGS) — SureSeq Products
  • Microarrays — CytoSure Cancer +SNP Arrays

OGT offers high-quality integrated technologies that detect the complete range of genetic aberrationsFigure 1. OGT offers high-quality integrated technologies that detect the complete range of genetic aberrations.

Cytocell Pathology and Haematopathology FISH Probes

 

 

 

 

Cytocell® Pathology and Haematopathology FISH Probes

Fluorescence in situ hybridisation (FISH) provides cost-effective and accurate detection of a range of genetic aberrations. FISH probes are particularly useful when the gene of interest is strongly suspected and for the detection of balanced translocations, which cannot be easily detected using arrays or NGS. FISH probes are also often used to confirm the findings of other higher throughput techniques.

OGT’s comprehensive Cytocell range of high-quality FISH probes delivers reliable, tight, bright signals (Figure 2) which can significantly reduce scoring times, improve efficiency and reduce running costs. Cytocell offers one of the largest portfolios of FISH products with over 400 catalogue probes and provides custom FISH probes through our myProbes® service.

The HER2 amplification probe consists of a 347kb probe labelled in red, spanning the HER2 (ERBB2) gene and neighbouring regions, and a green probe for the chromosome 17 centromere.Figure 2. Cytocell probes deliver strong signals for fast and accurate scoring. The HER2 amplification probe consists of a 347kb probe labelled in red, spanning the HER2 (ERBB2) gene and neighbouring regions, and a green probe for the chromosome 17 centromere.

Cytocell FISH probes deliver:

  • 50% cost savings compared with some alternative FISH probe suppliers*
  • Bright signals with minimal background for fast and accurate scoring with low retest rates
  • Cost-effective formats to suit your throughput requirements
  • Excellent customer service and support in over 60 countries worldwide
  • Convenient, directly-labelled products premixed in hybridisation solution

*Savings calculated by comparing the average list price for Cytocell FISH probes with the average list price for equivalent probes from an alternative leading supplier.

Catalogue FISH probes

Cytocell Pathology FISH ProbesTable 1: A selection of high-quality Cytocell Pathology FISH probes

Cytocell Haematopatholgy FISH ProbesTable 2: A selection of high-quality Cytocell Haematopathology FISH probes

View our full range of pathology FISH probes or view our full range of haematopathology FISH probes

Custom probes to accelerate research

myProbes® custom probes utilise Cytocell’s proprietary BAC clone collection to produce fully quality-assured custom FISH probes. Options include a simple modification such as a change in fluorophore label through to the custom production of a truly unique, quality-assured product.

Optimised buffers and reagents for excellent results

Correct pretreatment of formalin-fixed, paraffin-embedded (FFPE) tissue sections is essential for high-quality and reproducible FISH results. The Cytocell Tissue Pretreatment Kit utilises a streamlined two-step process to increase permeabilisation of cell membranes and facilitate penetration of desired FISH probes to target DNA.

It was very important for us to have more consistent results with our probes — easy-to-read bright signals and a range of vial sizes, which is much more costeffective. It also was critical to upgrade our pretreatment kit to expedite the analysis of FFPE samples. We can now complete the process in about 90 minutes. Janet M. Cowan, PhD, Director of the Cytogenetics Laboratory, Tufts Medicial Center

For more information on our range of FISH probes visit our Cytocell website

SureSeq NGS products

 

 

 

 

 

SureSeq™ NGS Products

NGS is a powerful technique for accurately analysing nucleotide-level aberrations. The advent of targeted sequencing approaches, with its associated cost, time and analysis advantages, is further increasing the adoption of NGS to the clinical research lab. Utilising hybridisationbased enrichment, SureSeq NGS Cancer Panels deliver greater run-torun consistency and allow for detection and removal of PCR bias, which is not easily achievable when using amplicon-based assays. This is particularly important when using heterogeneous samples, where the ability to detect low allele fractions is required.

OGT offers an expanding portfolio of high-quality NGS products, including targeted sequencing panels aimed at specific cancer types and library preparation reagents to streamline your workflow.

All SureSeq NGS panels for solid tumours deliver:

  • Highly accurate determination of allele frequency — Hybridisation-based enrichment allows the removal of PCR bias and duplications
  • Excellent coverage uniformity — Sensitive and reproducible variant detection even in heterogeneous cancer samples
  • Fully validated on FFPE samples — Unlock the potential of precious samples
  • Powerful and intuitive variant analysis software included (Figure 3)

SureSeq Interpret SoftwareFigure 3: SureSeq Interpret Software is provided free of charge with all SureSeq NGS Panel purchases and enables simple and rapid identification of meaningful variants, without the requirement for additional bioinformatic support.

A growing range of NGS cancer panels

SureSeq Solid Tumour Panel

The SureSeq Solid Tumour Panel is designed in collaboration with recognised cancer experts and fully validated on FFPE samples. The 60-gene panel allows discovery of novel and known variants in a range of solid tumours — including breast, prostate, ovarian, lung and colorectal cancer (Table 2).

Example mutations detected in FFPE samples from a range of solid tumours using the SureSeq Solid Tumour PanelTable 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 fractions (MAF) as low as 1.0% gives added confidence in the variants being called and facilitates the exploration of tumour heterogeneity

SureSeq Ovarian Cancer Panel

The SureSeq Ovarian Cancer Panel contains the latest evidence-based genes involved in ovarian cancer research. This panel accurately detects germline mutations in blood-derived DNA, as well as germline and somatic mutations in DNA derived from FFPE tissues (Table 3).

This panel provides comprehensive variant detection, including all coding exons of the following seven genes: BRCA1, BRCA2, TP53, PTEN, ATM, ATR, NF1.

Example mutations detected in FFPE clinical research samples using the SureSeq Ovarian Cancer PanelTable 3: Example mutations detected in FFPE clinical research samples using the SureSeq Ovarian Cancer Panel. The ability to detect MAFs as low as 1.13% gives added confidence in the variants being called and facilitates the exploration of tumour heterogeneity. Rows 1–4: low-frequency SNVs; rows 5–7: low-frequency indels. Samples kindly provided by Biopathology Department of Gustave Roussy, Villejuif, France.

Streamlined library preparation

With fewer hands-on steps, the SureSeq Library Preparation Kit saves an entire day from the typical library preparation workflow and reduces the potential for handling errors. Extensive optimisation of enzymes and buffers has enabled the number of steps to be reduced over standard methods, while still delivering libraries of the highest quality.

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, Clinical Scientist at Manchester Centre for Genomic Medicine, UK

View our complete range of SureSeq NGS products

CytoSure Array Products

 

 

 

 

 

CytoSure™ Cancer +SNP Arrays

Copy number variation (CNV) has been implicated in predisposition to and progression of a wide range of cancers. While next generation sequencing holds some promise for CNV detection, array comparative genomic hybridisation (aCGH) is still regarded as the superior technique for detection of copy number changes.

OGT’s CytoSure Cancer +SNP arrays combine long oligo aCGH probes for superior copy number detection with fully research-validated single nucleotide polymorphism (SNP) content for accurate identification of loss of heterozygosity (LOH) without concurrent changes in gene copy number (Table 4). Two array designs are available, each targeting specific regions known to be important for researching disease progression.

CytoSure Cancer +SNP arrays selection guideTable 4: CytoSure Cancer +SNP arrays selection guide.

OGT’s CytoSure Cancer +SNP arrays deliver:

  • Confident detection of CNV and LOH on a single array
  • High signal to noise ratios
  • Increased specificity and sensitivity compared to BAC arrays
  • Flexible choice of reference sample allowing comparison of matched cancer and “normal” samples
  • Exclusive CytoSure Interpret Software to translate data into meaningful results (Figure 4)

CytoSure Interpret Software enables easy and accurate detection of aberrations and breakpoints.

Figure 4: CytoSure Interpret Software enables easy and accurate detection of aberrations and breakpoints. Shown here using the CytoSure Cancer +SNP array is a complex bladder cancer sample with multiple copy number (CN) changes and LOH. Sample kindly provided by Cancer Cytogenetic Unit in Lausanne University Hospital, Switzerland.

Complete solutions for clinical genetics research

The CytoSure Cancer +SNP array targets regions of importance for both haematological malignancies and solid tumours. Designed in collaboration with Dr. Jacqueline Schoumans, Head of the Cancer Cytogenetic Unit at Lausanne University Hospital, the array focuses on 1500 known cancer-associated genes which have been handcurated from current literature.

The CytoSure Consortium Cancer +SNP array focuses on the content recommended by the Cancer Genomics Consortium (CGC). The targeted design covers over 500 cancer genes and 130 cancer-associated genomic regions for haematological malignancies and solid tumours.

The major advantage of the OGT array…is that it enables one to use a matched reference. This enables the detection of the acquired abnormalities, copy number aberrations as well as copy neutral loss of heterozygosity, and allows [one] to distinguish it from benign germline aberrations. This is very important information when interpreting the results. With all other platforms, two hybridizations would be needed to get this result, which doubles the costs and the workload. Professor Jacqueline Schoumans, Head of the Cancer Cytogenetic Unit in Lausanne University Hospital, Switzerland

View our CytoSure Cancer +SNP arrays or view full range of CytoSure products

CytoSure™, SureSeq™ and myProbes®: For research use only. Not for use in diagnostic procedures. Cytocell®: Some products may not be available in the US.

Request a technical consultation

Do you have a question about what you've just read? Contact us today and one of our technical specialists will be happy to answer any questions you may have.

Request a technical consultation

 

 

Download literature

Download a PDF of this literature.

Download Literature