CytoSure™ Comprehensive FH Panel
OGT is offering an optimised NGS panel which has selected the most relevant genes and SNPs implicated in FH, for your research needs.
Familial Hypercholesterolaemia (FH) is a genetic condition which results in a high cholesterol level and subsequently leads to a higher risk of early heart disease. It affects approximately 1 in 250 people with around 34 million cases worldwide1.
Together with the complimentary Interpret analytical software, the CytoSure Comprehensive FH NGS platform provides the optimal solution for FH research.
We were previously using another custom panel but found OGT’s custom FH Panel much easier and more cost-effective to work with. From the start we worked very closely with OGT on the design of the panel and were impressed by the support especially with bioinformatics. The ability to call CNV from the NGS data as well as point mutations is also extremely valuable to us. The fact that the panel is pre-optimised has reduced the need for in-house optimisation and decreased our assay development time. Dr Mafalda Bourbon, Head of the Cardiovascular Research Group at the National Health Institute Doutor Ricardo Jorge, Lisbon, Portugal
The Panel Features:
- Detection of CNVs as well as SNVs with a single assay – enabled by the exon resolution of the targeted genes
- Pre-optimised content that meets your technical requirements – no more laborious in-house optimisation, decreasing assay development time
- Bespoke panel content – sequence only what’s relevant for your research
- Interpret, OGT’s complimentary analysis software – designed to give unparalleled CNV and SNV calling.
Genes at Exon-Level Resolution
SNPs Associated With FH
|rs10401969 SUGP1 Intron Variant
||rs2479409 PCSK9 : 2KB Upstream Variant
|rs10455872 LPA Intron Variant
||rs3757354 MYLIP : 2KB Upstream Variant
|rs11220462 ST3GAL4 intron variant
||rs3798220 LPA : Missense Variant
|rs121909548 SERPINC1 : Missense Variant
||rs3846663 HMGCR : Intron Variant
|rs12740374 CELSR2 UTR variant
||rs4149015 SLCO1B1 : 2KB Upstream Variant
|rs1346268 GATM : Intron Variant||rs4149056 SLCO1B1 : Missense Variant|
|rs1367117 APOB : Missense Variant||rs428785 ADAMTS1 : Missense Variant|
|rs1501908||rs429358 APOE : Missense Variant|
|rs1564348 SLC22A1 : Intron Variant||rs4299376 ABCG8 : Intron Variant|
|rs1719247||rs4693075 COQ2 : Intron Variant|
|rs17244841 HMGCR : Intron Variant||rs515135|
|rs1799768 SERPINE1 : 2KB Upstream Variant||rs6025 F5 : Missense Variant|
|rs1799963 F2 : 3 Prime UTR Variant||rs6102059 LOC102724968 : Intron Variant|
|rs1800562 HFE : Missense Variant, LOC108783645 : 2KB Upstream Variant||rs629301 CELSR2 : 3 Prime UTR Variant|
|rs1801131 MTHFR : Missense Variant||rs6511720 LDLR : Intron Variant, LDLR-AS1 : 2KB Upstream Variant|
|rs1801133 MTHFR : Missense Variant
||rs6544713 ABCG8 : Intron Variant
|rs2032582 ABCB1 : Missense Variant||rs7412 APOE : Missense Variant|
|rs2231142 ABCG2 : Missense Variant||rs8017377 NYNRIN : Missense Variant|
|rs2306283 SLCO1B1 : Missense Variant|
*Some genes/SNPs may not be available in your region - contact us for more details
CNV and SNV from a single assay
The hybridisation enrichment methodology, combined with our bait design expertise, allows generation of panels with outstanding completeness and coverage uniformity. Together, this allows the areas of CNV to be easily identified within each sample using our proprietary algorithm — delivering an increased understanding of the sample without an increase in cost or time.
Figure 1 (below): CNV in LDLR gene shown using IGV from the Broad Institute [A].
[A] Red bars indicate areas of CNV (data from aCGH), purple bars represent deleted exons (data from NGS): 5 samples are shown, each with at least one area of CNV. There is complete concordance between the aCGH and NGS data. Note the evenness of the NGS coverage (even peak height) across each exon, allowing the areas of CNV to be easily identified. The data from the custom CytoSure aCGH array, confirms the deletions in LDLR.
[B] A 2 exon deletion corresponding to sample 3 in [A].
[C] A deletion of 2 exons and 4 exons, corresponding to sample 5 in [A] respectively.
The Interpret software has been designed to easily visualise CNVs and SNVs, with an intuitive interface to switch between different sets of results. Interpret also has simple to use protocols and filtering options, to easily target the results of interest.
The CytoSure Comprehensive FH NGS panel has the ability to detect CNVs in whole genes, at exon resolution (Figures 2-3) and can target select SNPs that have been implicated in FH (Figure 4). The CytoSure Comprehensive FH panel can also detect SNVs and Indels within genes, as demonstrated by Figure 5.
Figure 2: Double deletion on the LDLR gene, as visualised by Interpret software.
Figure 3: Duplication on the LDLR gene, as visualised by Interpret software.
Figure 4: Deletion on the SLOCO1B1 gene, as visualised by Interpret software.
Figure 5: Missense variant on the APOB gene, as visualised by Interpret software
|CNV Resolution||Exon Level|
|SNVs and Indels||Targeted Genes (8)|
|Mean Target Coverage||>300x|
|Recommended DNA Input||>500 ng high quality DNA|
|Samples per MiSeq® v2 run||16|
|CytoSure Comprehensive FH Panel (16 reactions)||Enrichment baits; Interpret Software||601004-16||Get a quote
|SureSeq NGS Library Preparation Complete Solution (16)||Bundle of 1x SureSeq library preparation kit (16), containing adaptors, PCR primers and enzymes, 1x SureSeq NGS Index Kit – Collection A, 1x SureSeq Hyb & Wash Kit (16), 1x Dynabeads M270 Streptavidin (2ml) and 1x AMPure XP beads (10ml). Sufficient for 16 samples||500084||Get a quote|
|SureSeq NGS Library Preparation and Hyb & Wash Kit (16)||Bundle of 1x SureSeq NGS Library Preparation Kit (16), containing adaptors, PCR primers and enzymes, 1x SureSeq NGS Index Kit – Collection A and 1x SureSeq Hyb & Wash Kit (16). Sufficient for 16 samples||500082||Get a quote|
- Goldberg AC, and Gidding, SS. Knowing the Prevalence of Familial Hypercholesterolemia Matters. Circulation, 2016; 133 (11).
CytoSure and SureSeq: For research use only; not for use in diagnostic procedures. This webpage and its contents are © Oxford Gene Technology IP Limited – 2020. All rights reserved. OGT™, CytoSure™ 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.
An approach for determination of copy number variation using short-read next-generation sequencing
Presented at ESHG 2017, this poster outlines how OGT’s combined bioinformatics and focused panel approach offers the ability to analyse both germline copy number variation (CNV) and single nucleotide variation (SNV) using a single assay.
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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