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Structural Multiplex Reference Standard (FFPE)

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.

The Structural Multiplex Reference Standard covers a wide range of mutations in defined genomic context. This standard is designed to challenge your molecular and bioinformatics workflow 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 FFPE DNA Reference Standard includes 9 digital PCR-validated variants with allelic frequencies ranging from 3.5% to 9.7% and CNVs at 4.5x and 8.5x amplification.

Highlight features of this control material include RET and ROS1 fusion variants, MYC-N and MET focal amplifications and a BRCA2 variant.

The Structural Multiplex Reference Standard is also available in high molecular weight gDNA (HD753) and cfDNA (HD786) format.

Download Product Information

With this product you are able to:

  • Evaluate workflow integrity from pre-analytical DNA extraction to post-analytical bioinformatics
  • Optimize and validate the sensitivity of your workflow for structural variant detection
  • Optimize and validate new cancer panels and routinely monitor the performance of your assay

 

Product Information

Product Description: Structural Multiplex Reference Standard

Catalog Number: HD789

Format: FFPE

Genes Covered: AKT1, BRAF, BRCA2, EGFR, FBXW7, FLT3, GNA11, KRAS, MET, MYC-N, NOTCH2, PIK3CA, RET, ROS1

Fixation Method: 4% PFA (w/v)

Section Size: 15 µm

Cell Density: 3 x 108 cells per block. Approx. 3.5 x 105 cells per section

Expected DNA Yield: ≥ 400 ng DNA per section using Promega Maxwell RSC Plus FFPE DNA Extraction kit

Verified Mutations: 

Variant Type Chromosome Number Gene Variant Expected Allelic Frequency, %
SNV High GC chr.19 GNA11 Q209L 4.4
SNV High GC chr.14 AKT1 E17K 3.5
SNV Low GC chr.3 PIK3CA E545K 4.5
Long Insertion chr.7 EGFR V769_D770insASV 4.4
Long Deletion chr.7 EGFR ΔE746 - A750 4.4
Fusion chr.4:chr.6 ROS1 SLC34A2/ROS1 fusion 9.7
Fusion chr.10 RET CCDC6/RET fusion 4.6
CNV chr.7 MET amplification 4.5 copies
CNV chr.2 MYC-N amplification 8.5 copies

Presence confirmed in parental cell line

Variant Type Chromosome Number Gene< Variant
SNV Low GC chr.12 KRAS G13D
SNV High GC chr.9 NOTCh2 P668S
Short Deletion chr.7 MET V237fs
Short Deletion chr.13 FLT3 S985fs
Short Deletion chr.13 BRCA2 A1689fs
Short Deletion chr.4 FBXW7 G667fs
SNV chr.7 EGFR G719S
SNV chr.7 BRAF V600E
SNV chr.3 PIK3CA H1047R

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.

Unit Size: 1 FFPE Curl

Extractable DNA: ≥ 400 ng DNA per section using Promega Maxwell RSC Plus FFPE DNA Extraction kit

Intended Use: Research Use Only

 

General Information

Allelic Frequency: 3.5%-9.7% and 4.5 and 8.5 copies for the CNVs

Storage: 4˚C

Shipping: Ambient

Expiry: See all product shelf life information

 

Quality Control

Genotype and Allelic Frequency: Droplet Digital™ PCR

DNA Integrity: Agarose gel electrophoresis

Quantification: Quantifluor™

Manufacturing Quality: ISO 13485:2016