SureSeq™ Ovarian Cancer Panel
A hybridisation-based NGS enrichment panel with complimentary SureSeq Interpret Software that delivers accurate and easy identification of variants.
Validated for research use on FFPE samples and whole blood, this panel covers all coding exons of seven key genes and allows the analysis of variants associated with ovarian cancer and research into therapeutic response.
- Contains the latest evidence-based genes involved in ovarian cancer research — gain insight into homologous repair deficiencies and cell cycle dysregulation
- Validated for research use on FFPE and whole blood — detect germline mutations in DNA derived from blood as well as both germline and somatic mutations in DNA derived from FFPE tissue
- Hybridisation-based enrichment — sensitive and reproducible detection of low-frequency variants, even in heterogeneous cancer samples
- Fast and easy workflow — streamlined library preparation, short 4-hour hybridisation and intuitive software allowing easy variant analysis
- Excellent uniformity of coverage across the whole panel — over 99% of targeted regions are covered to at least 20% of mean target coverage
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.
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).
|Gene||Variant detected||Type of variant||Mean target coverage||% MAF detected|
|NF1||c.8137_8138insG (p.Phe2714Valfs Ter16)||Insertion||683||1.45%|
|NF1||c.3354delT (p.Ser1118Argfs Ter24)||Deletion||621||1.13%|
|ATR||c. 4154delC (p.Thr1385Metfs Ter3)||Deletion||506||1.61%
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.
|SureSeq Ovarian Cancer Panel (96 reactions)||Enrichment baits sufficient for 96 samples; SureSeq Interpret Software||600074||Get a quote|
|SureSeq Ovarian Cancer Panel (16 reactions)||Enrichment baits sufficient for 16 samples; SureSeq Interpret Software||600073||Get a quote|
|SureSeq NGS Library Preparation Kit (16)||Bundle of 1 x library preparation kit (16) containing adaptors, PCR primers and enzymes sufficient for 16 samples and 1 x SureSeq NGS Index Kit – Collection A||500070||Get a quote|
|SureSeq NGS Library Preparation Kit (48)||Bundle of 3 x library preparation kit (16), containing adaptors, PCR primers and enzymes sufficient for 48 samples and 1 x SureSeq NGS Index Kit – Collection B||500073||Get a quote|
|SureSeq NGS Index Kit - Collection A (16)||16 different indexes, each sufficient for 4 samples [included with SureSeq NGS Library Preparation Kit (16)]||500071||Get a quote|
|SureSeq NGS Index Kit - Collection B (48)||48 different indexes, each sufficient for 4 samples [included with SureSeq NGS Library Preparation Kit (48)]||500072||Get a quote|
|Dynabeads™ M270 Streptavidin, 2ml||Sample capture beads, sufficient for 20 samples||500080*||Get a quote|
|AMPure® XP beads, 10ml||Sample purification beads, sufficient for 16 samples||500081*||Get a quote|
* Only for use with SureSeq NGS panels
SureSeq myPanel™ NGS Custom Cancer Panels Full Gene List
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Evaluation of enzymatic DNA digestion as an alternative to mechanical DNA fragmentation (sonication) for targeted NGS using the SureSeq™ Myeloid Panel
DNA fragmentation is a crucial first step in the preparation of libraries for NGS. In this application note, Oxford Gene Technology has evaluated an alternative method of fragmentation using the NEBNext® dsDNA Fragmentase®.
Improving experimental reproducibility through automated hybridisation-based NGS library preparation
In this application note, an Agilent Bravo A Automated Liquid Handling Platform was configured to run the SureSeq NGS library preparation protocol. The results demonstrate marked improvement not only in hands-on-time, but also a number of quality metrics
Selecting the best NGS enrichment assay for your needs
With NGS now in routine use for a broad range of research and clinical applications, this application note details the value of making the correct choice for the initial sequence enrichment step.
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The importance of enrichment assay choice and optimisation for confident variant detection
This white paper discusses the main strategies employed to optimise the enrichment step, depending on the type of assay chosen.
The role of NGS in stratified cancer medicine
In this white paper, two Clinical Scientists, Dr Matthew Smith and Dr George Burghel, share their views on the use of NGS in cancer genomics and its integration into the laboratory.
Understanding myeloid disorders with next-generation sequencing
How OGT’s SureSeq™ Myeloid Panel helps researchers identify and decipher the complex genetic origins of myeloproliferative disorders
Optimised, 1-day hybridisation-based NGS protocol yields 1% variant detection in MPN samples, as quickly and cost-effectively as multiplex PCR
Presented at AMP 2016, this poster outlines how the SureSeq™ Core MPN Panel can accurately detect alleles down to 1% variant allele fraction (VAF) in JAK2 (V617F) at a read depth of >1000x, facilitating reliable detection.
The accurate detection by next-generation sequencing (NGS) of difficult to sequence genes (CALR, CEBPA, FLT3) associated with myeloid disorders using a hybridisation-based enrichment approach
Presented at CGC 2017, this poster highlights the excellent uniformity of coverage obtained from the hybridisation-based enrichment using the SureSeq myPanel NGS Custom AML Panel.
The Analysis of FFPE Samples by Next-Generation Sequencing (NGS) of Key Genes for Research into Breast and Ovarian Cancer
Presented at AMP Europe 2018, this poster illustrates the confident detection of germline and somatic variants in key cancer-related genes including BRCA1 and TP53.
The analysis of myeloproliferative neoplasm samples using a rapid (30 minute) hybridisation-based enrichment protocol for next-generation sequencing (NGS)
Presented at the CGC 2017 annual summer meeting in Denver, USA, this poster illustrates the excellent quality data generated by the OGT 1-day hybridisation-based SureSeq LPK protocol in combination with the SureSeq Core MPN Panel.
The application of a hybridisation-based next-generation sequencing (NGS) enrichment panel for the analysis of key genes involved in ovarian and breast tumours using DNA from FFPE samples
The application of a hybridisation-based NGS enrichment panel for the analysis of somatic variants in tumour samples and reference standards
Presented at AGT 2017, this poster outlines the application of a hybridisation-based NGS enrichment panel for the analysis of solid tumour somatic variants, demonstrating 100% concordance in variant detection in both genomic and formalin-compromised DNA.
The application of a one-day hybridisation-based enrichment protocol for NGS incorporating a rapid (30 minute) hybridisation step
Presented at AGT 2017, this poster outlines how OGT has optimised a one-day hybridisation-based enrichment protocol for NGS incorporating a rapid 30 hybridisation step.
The use of a hybridisation-based NGS enrichment panel for the confident identification of a broad range of low frequency variants from as little as 50ng of challenging clinical research FFPE samples
Presented at AMP 2016, this poster outlines how the SureSeq FFPE DNA Repair Mix significantly improves NGS library yields, with an increase of mean target coverage (increased by >2.2 fold), resulting in more meaningful data.
SureSeq myPanel™ NGS Custom Breast Cancer panel
SureSeq myPanel™ NGS Custom Cancer Panels
SureSeq™ NGS Library Preparation Kit
SureSeq™ Ovarian Cancer Panel