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Structural Multiplex Reference Standard (gDNA)

The Structural gDNA Multiplex Reference Standard provides biologically relevant quality control material, which can be used to assess the performance of NGS assays that detect complex structural variants.

Next generation sequencing (NGS) platforms give researchers much greater power when profiling the complex human genome. However, the use of NGS presents challenges surrounding sample variability, platform bias, and potential failure to detect biomarkers. Horizon’s standards are appropriate for any NGS library preparation including whole-genome, whole-exome, custom capture and targeted amplicon panels. Horizon has developed this NGS Reference Standard range to support the development and continued validation of Next Generation Sequencing platforms. The Structural Multiplex Reference Standard covers a wide range of mutations in defined genomic context. This standard 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 includes 9 ddPCR-validated mutations, with most of them centered 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 cfDNA (HD786) and FFPE (HD789) format.

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With this product you are able to:

  • Evaluate the effect of genomic context on variant detection
  • Analyze the robustness of your bioinformatics pipeline
  • Optimize and validate new cancer panels and routinely monitor the performance of your assay

 

Technical Data

Format: Genomic DNA

Genes Covered: AKT1, BRCA2, EGFR, FBXW7, FLT3, GNA11, KRAS, MET, MYC-N, 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 8.1

 

Product Information

Verified Mutations: The Structural Multiplex Reference Standard has been manufactured using multiple engineered cell lines and mixed to generate multiple Allelic Frequencies in multiplex. This product has been verified by whole exome sequencing. The NGS determined allelic frequency and read depths are reported in the table below. To download the full data set, in variant caller format (VCF), please visit our exome sequencing page.

Gene Variant (AA) CDS mutation GRCh38 co-ordinates Legacy ID Genomic mutation ID Expected allelic frequency (%) NGS allelic frequency (%) NGS read depth
GNA11 Q209L c.626A>T 19:3118944 COSM52969 COSV50017277 5.60% 3.04% 362
AKT1 E17K c.49G>A 14:104780214 COSM33765 COSV62571334 5.00% 4.26% 329
PIK3CA E545K c.1633G>A 3:179218303 COSM763 COSV55873239 5.60% 4.46% 1122
EGFR V769_D770insASV c.2300_2308dup 7:55181305 COSM12376 COSV51766549 5.60% 3.87% 1369
EGFR ΔE746 - A750 c.2235_2249del 7:55174771 COSM6223 COSV51765119 5.30% 4.60% 543
ROS1 SLC34A2/ROS1 fusion N/A  N/A N/A COSF1196 5.60% b b
RET CCDC6/RET fusion N/A  N/A N/A COSF1271 5.00% b b
MET amplification N/A  N/A N/A N/A 4.5 copies b b
MYC-N amplification N/A  N/A N/A N/A 9.5 copies b b
BRAF V600E c.1799T>A 7:140753336 COSM476 COSV56056643 18.2 13.92% 697
BRCA2 K1691Nfs*15 c.5073del 13:32339421 COSM6048456 COSV66451438 5.6 6.00% 900
EGFR G719S c.2155G>A 7:55174014 COSM6252 COSV51767289 5.3 5.20% 635
FBXW7 S668Vfs*39 c.2001del 4:152323003 COSM1427624 COSV55893496 5.6 5.93% 1163
FLT3 P986Afs*27 c.2955_2956del 13:28004077 COSM1366185 COSV54042810 5.6 6.73% 758
KRAS G13D c.38G>A 12:25245347 COSM532 COSV55497388 5.6 4.00% 600
MET L238Yfs*25 c.713del 7:116699793 COSM1579080 COSV59256400 2.5 2.65% 1964
NOTCH1 P668S c.2002C>T 9:136515302 COSM3216059 COSV53100753 5 3.51% 541
PIK3CA H1047R c.3140A>G 3:179234297 COSM775 COSV55873195 16.7 15.64% 927

b – Variant type not called by DRAGEN (large insertion, CN variant, fusion, indel)

Exome sequencing data: Download additional information on variants present in the parental cell lines

Unit Size: 1 µg

Concentration: 50 ng/µl

 

General Information

Storage: 4˚C

Expiry: See all product shelf life information

 

Quality Control

Allelic Frequency: Droplet Digital PCR™

Genotype: Sanger sequencing of locus specific PCR

Quality: Agarose gel electrophoresis

Quantification: Spectrophotometry (A260)