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Cancer panels enable sequencing of difficult genes

27th April 2017

Posted By Paul Boughton


Excellent uniformity of coverage of the CEBPA gene averaging ~3000x coverage. Depth of coverage per base (grey). Targeted region (green). Gene coding region (blue). GC percentage (red). Repeat regions and GC-rich regions (pink)

Oxford Gene Technology (OGT) has expanded its SureSeq myPanel NGS Custom Cancer Panel content.

The expansion comes in response to NGS becoming ever more important for research into an increasing number of cancer types, and a need to obtain reliable data for difficult-to-sequence genes and mutations.

The expanded content now covers more than 70 genes, with many more available in the near future, optimised for haematology and solid tumours including breast, colorectal, lung, ovarian and prostate cancer, glioma, melanoma, sarcoma, leukaemias, myeloproliferative neoplasms and myelodysplastic syndrome.

The strength of OGT’s hybridisation-based bait design coupled with its unique expertise delivers excellent whole gene coverage, unparalleled uniformity and the ability to sequence even the most difficult of regions.

This yields reproducible and meaningful data, enabling researchers to be confident in sequencing results and analyses.

Some of the most difficult cancer-associated genes to sequence are those that have high levels of GC-rich content, such as the tumour suppressor gene CEBPA in acute myeloid leukaemia, and TP53, which is frequently mutated in many cancer types including breast cancer.

In addition, genes that contain internal tandem duplications are challenging to target due to their repetitive nature and length.

Panels available from other suppliers can experience problems with data variability, coverage drop-out or masked mutations in these regions.

In contrast, OGT’s innovative bait design uniquely overcomes these issues, delivering the high levels of uniform coverage required, and reducing the need for supplementary fill-in by Sanger sequencing.

This design allows researchers to detect low frequency variants consistently down to 1% VAF (variant allele frequency) at a read depth of >1000x.

The panels are fully customisable—researchers can select the gene, exonic or intronic content needed to create an NGS cancer panel that meets their exact requirements. All the content is fully pre-optimised, removing the need for lengthy in-house optimisation, reducing assay development time.





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