Structural Multiplex Reference Standard (FFPE)

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: 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