Structural Multiplex cfDNA Reference Standard

Format
cfDNA

Description

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.

With this product you can:
• 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

Catalog ID
Qty
Unit Price
HD786
$505.00
Bulk order discount
  • Buy 3 for $430.00 each and save 15%
  • Buy 5 for $404.00 each and save 21%

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Technical Information

Structural variants including gene translocations, fusions, copy number variants (CNV) and large INDELs are commonly found in tumours, 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 cancer 1, 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 - coming soon) format.

References:

  1. 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
  2. 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
  3. 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.
  4. Reinert, T.; Schøler, L.V. et al. Analysis of circulating tumour DNA to monitor disease burden following colorectal cancer surgery. Gut 2015, 0:1–10.


Technical Data

Genes Covered
AKT1, BRCA2, EGFR, FBXW7, FLT3, GNA11, KRAS, MET, MYC, NOTCH1, PIK3CA, RET, ROS1
Cosmics
1,500+
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

Product Information

Fragment Size
160 bp
Unit Size
350 ng per vial
Concentration
40 ng/µl
Verified Mutations
Variant TypeChromosome NumberGeneVariantExpected Allelic Frequency, %
SNV High GC chr.19GNA11Q209L5.6
SNV High GC chr.14AKT1E17K5.0
SNV Low GC chr.3PIK3CAE545K5.6
Long Insertion chr.7EGFRV769_D770insASV5.6
Long Deletionchr.7EGFR∆E746 - A7505.3
Fusion chr.4:chr.6ROS1SLC34A2/ROS1 fusion5.6
Fusion chr.10RETCCDC6/RET fusion5.0
CNV chr.7METamplification4.5 copies
CNV chr.2MYC-Namplification9.5 copies
Presence confirmed in parental cell line
Variant TypeChromosome NumberGeneVariantExpected Allelic Frequency, %
SNV Low GCchr.12KRASG13D5.6
SNV High GC chr.9NOTCH1P668S5.0
Short Deletion chr.7METV237fs2.5
Short Deletion chr.13FLT3S985fs5.6
Short Deletion chr.13BRCA2A1689fs5.6
Short Deletionchr.4FBXW7G667fs5.6
SNVchr.7EGFRG719S5.3
SNVchr.7BRAFV600E18.2
SNVchr.3PIK3CAH1047R16.7

General Information

Storage
4°C
Expiry
12 months from the date of manufacture
Cell Line Background

Please contact for more information

Quality Control

Fragmentation Size
D1000 DNA ScreenTape assay
Allelic Frequency
Droplet Digital™ PCR
Quantification
Qubit dsDNA BR Assay (post-fragmentation)
Protocols & Documents

Please browse our collection of downloads below.

If you need any support, advice or additional documentation then don't hesitate to contact us here.

Certificate of Analysis

Batch ID: 18046
PDF Download
Batch ID: 23888
PDF Download
Batch ID: 27590
PDF Download

Documents & Related Literature

Product Insert
PDF Download
Product Specification
PDF Download
Safety Data Sheet
PDF Download
Order & Delivery Information

Please see our terms and conditions of ordering.

If you need any support, advice or additional documentation then don't hesitate to contact us here.

Order Information

We accept orders using the following methods:

Online: 

Our online catalog and ordering system can be used to search our full menu of available HDx™ 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.

Offline:

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")
  • Your name, email address, title and organization
  • Shipping address and billing address with contact names
  • Purchase Order number if you have one
  • Telephone number
  • VAT Number (European Countries only)

Shipping Information

We aim to ship your order direct within 5 business days of receipt of your order and we will notify you of your expected delivery date. We ship direct to the following territories:

TerritoryPrice (Room Temperature)Price (4°C)Service

US & Canada

$25.00

$45.00

FEDEX International Priority

EU Countries
(Excluding Italy)

€20.00

€36.00

FEDEX International Priority

UK

£18.00

£32.40

Royal Mail Recorded Signed For™

Rest of the World
(Excluding Japan, Israel, Hong Kong) 

 

$25.00 - $80.00

 

$45.00 - $120.00

 

FEDEX International Priority

 

We have selected Room Temperature as the most appropriate shipping condition to ensure the stability of our HDx DNA and FFPE Reference Standards and 4°C for our HDx FISH Reference Standards during transit.

It is possible to use your own FEDEX account for shipment of goods and we will apply a small fee ($5.00 / £5.00 / €5.00) to cover packaging costs for Room Temperature Shipments and ($25.00 / €20.00 / £18.00) for Dry Ice Shipments. 

If you’re having trouble ordering or finding what you’re looking for, or if you require something we don’t yet offer, please see below for more information: 

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