Contains the latest evidence-based genes involved in ovarian cancer research

Ovarian cancer is the leading cause of death from gynaecological cancers in the Western world¹. Next generation Sequencing (NGS) is quickly becoming a commonly used tool for analysis of mutations — both single nucleotide variants (SNVs) and indels — in genes associated with ovarian cancer.

The SureSeq Ovarian Cancer Panel has been developed with leading cancer experts and covers all coding exons of seven genes (Table 1). The panel allows detection of known and novel variants in tumour suppressor genes as well as genes involved in homologous repair to advance research into ovarian cancer treatment and for use in clinical trials to help the development of new targeted therapies.

Table 1: The SureSeq Ovarian Cancer Panel targets seven genes implicated in ovarian cancer.

Validated on FFPE and whole blood

Mutations in certain genes can predispose an individual to develop cancer at some point during their lifetime. Screening for germline mutations in such genes allows research into familial risk of developing breast and ovarian cancer. On the other hand, assessment of somatic mutations in tumour samples can help research into drug response and the development of new therapies.

Various new generation drugs are being trialled to replace classical chemotherapy with the promise of improved efficacy and reduced side effects. One approach to select the right patients for clinical trials may be to test for somatic mutations within the tumour.

The SureSeq Ovarian Cancer Panel has been validated on DNA derived from FFPE tissue and whole blood to allow investigation of both germline and somatic mutations in ovarian cancer research.

Hybridisation-based enrichment

Heterogeneous cancer samples pose significant challenges as alleles are likely to be present at a lower fraction than would be expected for standard germline variants. Samples typically contain a mixture of cancer and normal cells, moreover cancer can consist 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. Utilising hybridisation-based enrichment, the SureSeq Ovarian Cancer Panel delivers excellent run-to-run consistency and extremely uniform coverage across the whole region of interest to allow sensitive detection of variants present even at low minor allele fraction (MAF) (Table 2).

Table 2: 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.

Fast and easy workflow

Hybridisation-based enrichment is now well recognised as providing superior results over amplicon-based enrichment technology. To date, the protocol has required more DNA and the library preparation protocol has been longer and more complex. In combination with the OGT SureSeq Library Preparation Kit, these issues have been addressed. There are fewer hands-on steps, turnaround times have been significantly improved and the panel has been optimised to work with as little as 500 ng of DNA derived from FFPE (for samples passing QC criteria) or whole blood.

SureSeq Interpret Software — OGT’s powerful, standalone data analysis package — is provided free with the SureSeq Ovarian Cancer Panel and allows the conversion of FASTQ files into an intuitive interactive report. The user friendly report allows for easy filtering of the variants without the need for additional in-house bioinformatics resource (Figure 1).

Figure 1: The SureSeq Interpret Report enables simple and rapid identification of meaningful results. Variants are fully annotated with links to various databases (e.g. dbSNP, COSMIC, Genecards and OMIM) providing results in context.

Excellent uniformity of coverage across the whole panel

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 low-frequency variants, potentially lowering sequencing costs and increasing sample throughput.

Figure 2: BRCA1 Exon 15 (NM_007299) visualised in IGV from the Broad Institute. The whole region is uniformly covered ensuring detection of all — even rare variants — with confidence. The mean target coverage for the exon is 1744x.