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.

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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: GNA11, AKT1, EGFR,PIK3CA , MET, MYC-N, 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: 

Gene Variant (AA) CDS mutation GRCh38 co-ordinates Expected Allelic Frequency/copy number
GNA11 Q209L c.626A>T 19:3118944 4.40%
AKT1 E17K c.49G>A 14:104780214 3.50%
PIK3CA E545K c.1633G>A 3:179218303 4.50%
EGFR A767_V769dup c.2300_2308dup 7:55181317 4.40%
EGFR ΔE746 - A750 c.2235_2249del 7:55174771 4.40%
ROS1 SLC34A2/ROS1 fusion N/A  N/A 9.70%
RET CCDC6/RET fusion N/A  N/A 4.60%
MET amplification N/A  N/A 4.5 copies
MYC-N amplification N/A  N/A 8.5 copies

The gDNA format of this product (HD753) has been verified by whole exome sequencing.

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

Expiration: 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