NGS Custom
Ovarian Cancer
panelFeatures
Contains the latest evidence-based genes
involved in ovarian cancer research• Gain insight into homologous repair
deficiencies and cell cycle dysregulation
Validated for research on FFPE and wholeblood• Detect germline mutations in DNA derived
from blood as well as both germline andsomatic mutations in DNA derived fromFFPE tissue
Fast and easy workflow• Streamlined library preparation, short 4-hourhybridisation and intuitive software
Excellent uniformity of coverage across thewhole panel• Detect low-frequency variants withconfidence, even in heterogeneous cancer
samplesNGS Custom OvarianCancer panel

Introduction
A hybridisation-based NGS enrichment panel with complimentary Interpret NGS Analysis Software thatdelivers accurate and easy identification of variants. Validated for research use on FFPE samples andwhole 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
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 allcoding 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.

BRCA1

BRCA2

TP53PTENATMATR

NF1

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 theirlifetime. 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 canhelp 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 bloodto allow investigation of both germline and somatic mutations in ovarian cancer research.

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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 mixtureof cancer and normal cells, moreover cancer can consist of several molecularly distinct clones. In orderto detect alleles that contribute only a small percentage to the reads at any locus, a highly uniform andsensitive enrichment is required. Utilising hybridisationbased enrichment, the SureSeq Ovarian Cancer
Panel delivers excellent run-to-run consistency and extremely uniform coverage across the wholeregion of interest to allow sensitive detection of variants present even at low variant allele fraction (VAF)(Table 2).

Gene

Variant detected

Type of variant

Mean target coverage% VAF detected

BRCA1c.3424G>C (p.Ala1142Pro)

SNV

881

11.92%

BRCA2

c.556G>C (p.Ala186Pro)

SNV

728

1.92%

TP53

c.1129A>C (p.Thr377Pro)

SNV

1024

3.03%

ATR

c.7274G>A (p.Arg2425Gln)

SNV

1579

38.63%

NF1

c.8137_8138insG (p.Phe2714ValfsTer16)

Insertion

683

1.45%

NF1

c.3354delT (p.Ser1118ArgfsTer24)

Deletion621

1.13%

ATR

c. 4154delC (p.Thr1385MetfsTer3)

Deletion

506

1.61%

Table 2: Example mutations detected in FFPE clinical research samples using the SureSeq Ovarian Cancer Panel. The ability to detect VAFs 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.

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Fast and easy workflow
Hybridisation-based enrichment is now well recognised as providing superior results over ampliconbased 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 beensignificantly improved and the panel has been optimised to work with as little as 500 ng of DNA derived
from FFPE* or whole blood.
Interpret — OGT’s powerful, standalone NGS data analysis package — is complimentary with theSureSeq Ovarian Cancer Panel and allows the conversion of FASTQ NGS 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.
*For samples passing QC citeria.

GeneChr

Start

End

Alt

Ref

HGVSc
(Gene Symbol)

Zygosity

Total
Depth

Ref
Depth

Alt
Depth

AlleleFrequency

Genotype

TypeATR3

142178144

142178144

CT

BRCA1:c.1067A>GHeterozygous

530

27327548.49%

0/1snpATR11108183167

108183167

AG

BRCA1:c.1067A>G

Heterozygous

546

0546

100%

1/1

snp

BRCA2

1332907420

32907421

GAG

BRCA1:c.1067A>G

Heterozygous

502

26922945.98%

0/1

delBRCA21332911888

32911888

AG

BRCA1:c.1067A>G

Heterozygous

588

261

327

55.61%

0/1

snp

BRCA2

1332913055

32913055

AG

BRCA1:c.1067A>G

Heterozygous

574

1572

100%

1/1

snp

BRCA2

1332915005

32915005

GC

BRCA1:c.1067A>G

Heterozygous

593

0593

100%

1/1

snp

BRCA21332929387

32929387

TC

BRCA1:c.1067A>G

Heterozygous

616

599

17

2.76%0/0

snp

BRCA2

1341246481

41246481

TC

BRCA1:c.1067A>G

Heterozygous

567

0565

100%

1/1

snp

TP53

177579472

7579472

GC

BRCA1:c.1067A>G

Heterozygous

514

0514

100%

1/1

snp

NF1

1729705947

29705947

TC

BRCA1:c.1067A>G

Heterozygous

534

19515

96.44%

1/1

snp

BRCA1

1741246481

41246481

TC

BRCA1:c.1067A>G

Heterozygous

542

287

254

46.95%

0/1

snp

Figure 1: An example batch analysis report in Interpret, enabling simple and rapid identification of result. Let OGT customise your report to meet yourexact requirements.

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NGS Custom Ovarian
Cancer panel

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 lowfrequency variants, potentiallylowering 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 — evenrare variants — with confidence. The mean target coverage for the exon is 1744x.

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NGS Custom OvarianCancer panel

Ordering information
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US +1 914 467 5285
contact@ogt.com
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ProductContents

Cat. No.

SureSeq Ovarian Cancer Panel(16 reactions)

Enrichment baits sufficient for 16 samples; Interpret Software

600073

SureSeq Ovarian Cancer Panel(96 reactions)

Enrichment baits sufficient for 96 samples; Interpret Software

600074

SureSeq NGS Library Preparation
Complete Solution (16)Bundle of 1x SureSeq NGS Library Preparation Kit (16), containingadaptors, PCR primers and enzymes, 1x SureSeq NGS Index Kit –Collection A, 1x SureSeq NGS Hyb & Wash Kit (16), 1x Dynabeads
M270 Streptavidin (2ml) and 1x AMPure XP beads (10ml). Sufficientfor 16 samples

500084

SureSeq NGS Library Preparation
Complete Solution (48)

Bundle of 1x SureSeq NGS Library Preparation Kit (48), containingadaptors, PCR primers and enzymes, 1x SureSeq NGS Index Kit –Collection B, 3x SureSeq NGS Hyb & Wash Kit (16), 3x Dynabeads
M270 Streptavidin (2ml) and 3x AMPure XP beads (10ml). Sufficientfor 48 samples500085

References
1.

Helleman J. et al., (2006) Molecular profiling of platinum resistant ovarian cancer. Int J Cancer 118(8):1963-71.

Oxford Gene Technology Ltd., Begbroke Science Park, Woodstock Road, Begbroke, Oxfordshire, OX5 1PF, UKSureSeq: For research use only, not for diagnostic procedures. This document and its contents are © Oxford Gene Technology IP Limited –2021. All rights reserved. OGT™ and SureSeq™ are trademarks of Oxford Gene Technology IP Limited. The SureSeq NGS Library Preparation Kit
was jointly developed between Oxford Gene Technology and Bioline Reagents Limited. Dynabeads is a trademark of Thermo Fisher Scientificand AMPure® is a registered trademark of Beckman Coulter Inc.

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