OGT enhances NGS results from FFPE samples

Wednesday 8 June 2016

Oxford Gene Technology (OGT), The Molecular Genetics Company, has introduced its SureSeq™ FFPE DNA Repair Mix — optimised to repair a broad range of damage in formalin-fixed, paraffin-embedded (FFPE) derived DNA. The mix effectively repairs DNA damage, improving library yields, on-target rates and mean target coverage, while removing fixation and storage artefacts and reducing the amount of starting material required.

Having sufficient quality and quantity of FFPE samples for sequencing is a common problem in clinical research. Fixation processes significantly damage nucleic acids and long storage times can produce problematic artefacts. In addition, many FFPE samples are often irreplaceable and there is a real need to reduce DNA input for NGS. Consequently low-starting material amplicon-based NGS methods are frequently favoured, however, resulting PCR bias and lower complexity from smaller inputs mean these methods are not well suited to detect low-frequency mutations in heterogeneous tumour samples. Hybridisation-based approaches on the other hand eliminate PCR bias — providing much more reliable data — but require higher DNA inputs.

Available with OGT’s SureSeq panels, the FFPE DNA Repair Mix increases success and accuracy of hybridisation-based NGS for FFPE samples by repairing damage such as nicks and gaps, oxidised bases, blocked 3’ ends and deamination of cytosine to uracil. Repairing the damage in this way enables a reduction of the amount of required starting material down to as little as 100 ng while delivering excellent sequencing data for the utmost confidence in variant calling.

The new SureSeq FFPE DNA Repair Mix highlights OGT’s strong commitment to continuous optimisation of its products and workflows. This commitment is further demonstrated in a recent application note on the use of enzymatic DNA digestion rather than mechanical shearing when preparing DNA samples for NGS. Enzymatic digestion was found to offer a more streamlined protocol saving up to two hours of time while lowering the amount of input DNA required and removing the requirement for expensive mechanical shearing equipment.

David Cook, Senior Product Manager at OGT commented, ‘We’re very excited about the new SureSeq FFPE DNA Repair Mix — it’s going to make a big difference to anybody sequencing from FFPE samples. Products like this and the vast amount of research OGT undertakes on product and workflow optimisation demonstrates our commitment to delivering the best, most innovative tools to our customers’.

To find out more, visit the SureSeq FFPE DNA Repair Mix product page.

For further information, please contact:

Oxford Gene Technology, Begbroke Science Park, Begbroke Hill, Woodstock Road, Begbroke, Oxfordshire, OX5 1PF, U.K.

T: +44 (0) 1865 856826 ; F: +44 (0) 1865 848684

E: contact@ogt.com ; W: www.ogt.com ; Twitter: @OxfordGeneTech


Notes for editors:

About Oxford Gene Technology

Oxford Gene Technology (OGT) provides world-class genetics research solutions to leading clinical and academic research institutions. Founded by Professor Sir Edwin Southern, and with customers in over 60 countries worldwide, OGT has a strong reputation and increasing share in the large and growing genomic medicine market. The Company’s Cytocell®, CytoSure™ and SureSeq™ range of fluorescence in situ hybridisation (FISH), microarray and next generation sequencing (NGS) products deliver high-quality genetic analysis, enabling accurate identification and confirmation of the causative variation underlying genetic disease.

For more information on the Company, please visit our website at www.ogt.com

CytoSure™, SureSeq™ and Genefficiency™: For Research Use Only; Not for Use in Diagnostic Procedures. Cytocell®: Some products may not be available in the US.

CytoSure: This product is provided under an agreement between Agilent Technologies, Inc., and OGT. The manufacture, use, sale or import of this product may be subject to one or more of U.S. patents, pending applications, and corresponding international equivalents, owned by Agilent Technologies, Inc. The purchaser has the non-transferable right to use and consume the product for RESEARCH USE ONLY AND NOT for DIAGNOSTICS PROCEDURES. It is not intended for use, and should not be used, for the diagnosis, prevention, monitoring, treatment or alleviation of any disease or condition, or for the investigation of any physiological process, in any identifiable human, or for any other medical purpose.

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