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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
Technical Data

Format

FFPE

Genes Covered

AKT1, BRAF, BRCA2, EGFR, FBXW7, FLT3, GNA11, KRAS, MET, MYC-N, NOTCh2, PIK3CA, RET, ROS1

Fixation Method

4% Formalin

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 LEV Plus FFPE DNA Extraction kit

Product Information

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

Unit Size

1 FFPE Curl

Extractable DNA

≥ 400 ng DNA per section using Promega Maxwell LEV Plus FFPE DNA Extraction kit

Intended Use

For routine performance monitoring (Research Use Only)

General Information

Allelic Frequency

3.5%-9.7% and 4.5x and 8.5x amplification for the CNVs

Storage

4˚C

Expiry

See all product shelf life information

Quality Control

Allelic Frequency

Droplet Digital™ PCR

Genotype

Droplet Digital™ PCR

Quality

Agarose gel electrophoresis

Quantification

Quantifluor™