Accurate and Reliable Solid Tumour Profiling
Blog Jun 12, 2014
Oxford Gene Technology (OGT) recently launched its new SureSeq™ Solid Tumour Panel at the Association for Clinical Genetic Science (ACGS) meeting in Birmingham UK.
This new 60-gene next generation sequencing hybridisation-based enrichment panel offers researchers accurate and reliable solid tumour profiling for both known and novel variants.
To learn more the SureSeq Panel, its key features and how it was received at the ACGS meeting we spoke to Dr Stephen Archibald, Director of Communications at OGT.
AB: What benefits does the SureSeq Solid Tumour Panel provide?
Dr Stephen Archibald (SA): The SureSeq Solid Tumour Panel offers significant benefits over alternative NGS panels. The gene content for the panel has been selected by recognised cancer experts, including Cancer Research UK, West Midlands Regional Genetics Laboratory and National Genetics Reference Laboratory Wessex, to include 60 key genes known to contain driver mutations for a range of important cancer types. In addition, unlike amplicon-based panels that typically only analyse mutation hotspots, the SureSeq Solid Tumour Panel targets the entire coding region of each gene, allowing the discovery of novel variants as well as hotspot analysis.
OGT’s expertise in bait design ensures more uniform and efficient capture of all targeted regions, so that all the variants present can be called with maximum confidence. The high sensitivity of the assay also allows accurate analysis of heterogeneous samples — a common requirement when working with solid tumour samples.
The SureSeq Solid Tumour Panel has been optimised to work with as little as 100 ng of genomic DNA from formalin-fixed, paraffin-embedded (FFPE) samples, allowing researchers to unlock the potential of their archived samples.
AB: The recent news mentioned that SureSeq minimises PCR bias and duplications, why is this important?
SA: A key advantage of the SureSeq Solid Tumour Panel is that it utilises hybridisation-based enrichment, which provides the ability to accurately de-duplicate the data, meaning only data from unique, original DNA strands is analysed. This is especially important when analysing low-frequency alleles, such as those found in heterogeneous tumour samples. 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. Such bias may cause important variants to be missed or over-represented.
AB: The panel comes with your Variant Analysis Report, what information does this provide?
The unique SureSeq Solid Tumour Report 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. 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.
AB: How were peoples’ reactions to the panel at the recent Association for Clinical Genetic Science (ACGS) meeting?
SA: The SureSeq Solid Tumour Panel has been exceptionally well received since its launch. More and more researchers are identifying the benefits of hybridisation-based enrichment and, as such, demand for this comprehensive panel is growing rapidly. Dr Matthew Smith, Honorary Research Fellow, West Midlands Regional Genetics Service, gave a very well attended presentation on the development and validation of the SureSeq Solid Tumour Panel at the recent ACGS meeting, further highlighting the significant interest in this area.
For more information please visit www.ogt.com.