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.
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 |
Presence confirmed in parental cell line
| Gene | Variant (AA) | CDS mutation | GRCh38 co-ordinates | Legacy ID | Genomic mutation ID | Expected allelic frequency (%) | NGS allelic frequency (%) | NGS read depth |
|---|---|---|---|---|---|---|---|---|
| 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)
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