Structural Multiplex cfDNA Reference Standard
The Structural Multiplex cfDNA Reference Standard provides biologically relevant quality control material, which can be used to assess the performance of NGS ctDNA assays that detect complex structural variants.
Structural variants including gene translocations, fusions, copy number variants (CNV) and large INDELs are commonly found in tumors, and can serve as clinical biomarkers to identify cancer, to monitor cancer treatment effectiveness and disease progression. CNVs such as amplification of MET in combination with mutations in EGFR (T790M) can lead to Gefitinib resistance in lung cancer1, 2. PCR-based assays3, 4 and NGS4 that better detect structural variants are constantly emerging. However, the detection of structural variants presents several challenges and bioinformatics pipelines are continuously evolving to improve confidence in structural variant detection. The Structural Multiplex cfDNA Reference Standard covers a wide range of mutations in a defined genomic context. This standard consists of DNA derived from human cell lines that is fragmented to an average size of 160 bp to closely resemble cfDNA extracted from human plasma. This product is designed to challenge your molecular and bioinformatic work flow by providing validated copy number variants/amplifications, translocations, and large insertions/deletions. Additionally, you may examine the genomic context of variants within regions of specific GC-content (high vs. low). The Structural Multiplex cfDNA Reference Standard includes 9 variants validated by ddPCR, with most of them centred at 5% allelic frequency. Highlight features of the Structural Multiplex include RET and ROS1 fusion variants, MYC-N and MET focal amplifications and a BRCA2 variant. The Structural Multiplex is also available in high molecular weight gDNA (HD753) and FFPE (HD789) format.
With this product you are able to:
- Evaluate the effect of genomic context on variant detection in ctDNA samples
- Analyze the robustness of your bioinformatics pipeline
- Optimize and validate new ctDNA workflows for structural variant detection
- Compare performance of fragmented to high molecular weight reference standards
Genes Covered: AKT1, BRAF, BRCA2, EGFR, FBXW7, FLT3, GNA11, KRAS, MET, MYC-N, NOTCH1, PIK3CA, RET, ROS1
Allelic Frequencies: 4.8-5.6% and 4.5 & 9.5 x amplification for the CNV
Buffer: Tris-EDTA (10mM Tris-HCl, 1mM EDTA), pH 8.0
Fragment Size: 160 bp
Unit Size: 350 ng per vial
Concentration: 20 ng/µl
|Gene||Variant (AA)||CDS mutation||GRCh38 co-ordinates||Legacy ID||Genomic mutation ID||Expected Allelic Frequency/copy number|
|EGFR||ΔE746 - A750||c.2235_2249del||7:55174771||COSM6223||COSV51765119||5.00%|
The gDNA format of this product (HD753) has been verified by whole exome sequencing. To download the full data set, in variant caller format (VCF), please visit our exome sequencing page. This data set provides information on variants in the parental cell lines which may be detected when performing NGS analysis of this product.
Expiry: See all product shelf life information
Fragmentation Size: D1000 DNA ScreenTape assay
Allelic Frequency: Droplet Digital™ PCR
Quantification: Qubit dsDNA BR Assay (post-fragmentation)
- Engelman JA, Zejnullahu K, Mitsudomi T, Song Y, Hyland C, Park JO, et al. MET amplification leads to gefitinib resistance in lung cancer by activating ERBB3 signaling. Science 2007,316:1039–43
- Bean J, Brennan C, Shih JY, Riely G, Viale A, Wang L, et al. MET amplification occurs with or without T790M mutations in EGFR mutant lung tumors with acquired resistance o gefitinib or erlotinib. Proc Natl Acad Sci.2007,104(52):20932–7
- Olsson, E.; Winter, C. et al. Serial monitoring of circulating tumor DNA in patients with primary breast cancer for detection of occult metastatic disease. EMBO Molec. Med. 2015, 7(12), 1034–47.
- Reinert, T.; Schøler, L.V. et al. Analysis of circulating tumor DNA to monitor disease burden following colorectal cancer surgery. Gut 2015, 0:1–10.
We accept orders using the following methods.
Our online catalog and ordering system can be used to search our full menu of available Reference Standards. Select your desired reference standards and add them to the shopping basket. Your order can be submitted instantly using credit card, telephone ordering or a purchase order number as the preferred payment method.
If you prefer to send us orders outside our online ordering system, please see the Contact Us page for telephone, fax, and email details in order to place an order. We recommend that you use our online system to identify the products you require and their respective “HD” product codes.
To order offline we will require the following information:
- Product code(s) of the item(s) you wish to order (e.g. "HD123")
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The Structural Multiplex cfDNA Reference Standard provides biologically relevant quality control material, which can be used to assess the performance of NGS ctDNA assays that detect complex structural variants
The Structural Multiplex FFPE Reference Standard is a highly-characterized, biologically-relevant quality control material, which can be used to assess the performance of NGS assays that detect structural, low-allelic somatic mutations