Targeted DNA panels to detect CNVs, SNVs, indels by NGS

The Archer® VariantPlex® Assay system generates target-enriched libraries for next-generation sequencing (NGS) from DNA inputs. VariantPlex assays enable accurate and comprehensive detection of copy number variations (CNVs), single-nucleotide variants (SNVs) and insertions and deletions (indels) from low-input FFPE and other clinical sample types.

Archer's convenient VariantPlex Kit format

All VariantPlex kits include gene-targeting primers, easy-to-handle lyophilized enzymes, Illumina® platform-specific reagents to generate targeted sequencing libraries and an Archer PreSeq DNA QC Assay to confirm your input material quality prior to library generation.

Archer MBCs are also required, but provided separate for customizable multiplexing and indexing flexibility.

Choose your VariantPlex Kit

Archer VariantPlex Solid Tumor Kit Solid Tumor Kit

Characterize SNVs, CNVs and indels in 67 genes associated with solid tumors

Archer VariantPlex Comprehensive Lung Thyroid Kit CTL Kit

NGS target-enrichment assay to detect CNVs, SNVs and indels in 31 thyroid and lung cancer-implicated genes

Archer VariantPlex Custom Kits Custom Kits

Customize a catalogue VariantPlex kit or create a kit that fits your exact target specifications

Archer VariantPlex Core AML Kit Core AML Kit

Uncover mutations in 10 genes implicated in AML, in addition to FLT3 ITD detection

Archer VariantPlex Core Myeloid Kit Core Myeloid Kit

Identify mutations in 37 AML, MPN and MDS markers

Archer VariantPlex Myeloid Kit Myeloid Kit

Detect mutations in 72 genes associated with AML, MPN, MDS and lymphoid malignancies.

Archer VariantPlex p53 Kit p53 Kit

Capture all variants of the p53 tumor supressor with this full-coverage panel

Archer VariantPlex BRCA 1/2 Kit BRCA 1/2 Kit

Detect and characterize all known germline mutations in BRCA1 and BRCA2 with full exon coverage

Archer VariantPlex CFTR Kit CFTR Kit

Capture large deletions and pan-ethnic polymorphisms of this cystic fibrosis-associated gene

3 reasons to use VariantPlex for variant detection:
Chemistry, Workflow and Analysis

AMP™ Chemistry

Archer VariantPlex Assays are powered by powerful Anchored MultiPlex PCR (AMP) technology, which is uniquely suited for variant detection from FFPE samples.


Single-Primer Flexibility

Ligating half-functional adaptors to input DNA fragment ends enables single-direction priming and amplification into the adapter. Unidirectional priming is superior over opposing primer techniques because of the following:

Unique start sites

VariantPlex assays use unique start sites

Because each fragment has a unique start site opposing the gene-specific primer, the molecular complexity of the sample is maintained through amplification and sequencing. With amplicon-based techniques, small, degraded fragments common in FFPE samples can fail to extend to both primers and are lost. Fragments that are of sufficient length to amplify become indistinguishable from one another. Resultant data fails to represent the sample complexity and has less accuracy in detecting low allelic frequency variants. Anchored Multiplex PCR, however, enriches fragments of all sizes, resulting in greater target recovery and complex libraries containing unique barcoded fragments.

Superior coverage

VariantPlex assays offer superior target coverage

AMP enrichment is unrestrained by opposing primers, allowing larger genomic regions to be amplified and sequenced. AMP-enabled long-range enrichment can cover more relevant variants without using multiple tubes and the additional cost, time and sample requirements associated with it.

Primer design flexibility

VariantPlex assays offer primer design flexibility

Longer regions of enrichment and strand specificity provide the flexibility to design primers that are optimized for coverage across challenging regions of the genome (e.g., GC-rich regions). Designs also include intronic buffers, so primers do not cover any portions of the target exon.

Dual independent coverage

VariantPlex assays use dual independent coverage

Allele dropout due to primers blocking SNVs can reduce confidence in mutation calling. AMP’s strand-specific priming, however, facilitates dual independent coverage across target regions to ensure that some reads are retained when one primer drops out, thus reducing inconclusive results.

Molecular Barcodes

AMP attaches a unique tag to each input molecule prior to amplification. After sequencing, PCR duplicates, artifacts and sequencing errors can be identified and corrected. De-duplication and identification of unique reads enables robust, quantitative data that can be used for accurate variant calling and sensitive, concurrent CNV detection.

Sensitive and specific variant calling

VariantPlex assays use molecular barcodes that provide sensitive and specific variant calling

Deduplication and error correction that accounts for PCR bias deliver a more accurate measure of allelic frequency and thus more accurate variant calls. In addition, false-negative variant calls due to low allelic frequency are reduced, because sample-specific sensitivity can be accurately measured by powerful MBC-enabled metrics. When used in conjunction with the PreSeq DNA QC Assay, sample-specific sensitivity can be predicted prior to library preparation and verified in Archer Analysis post-sequencing.

Robust CNV calling

VariantPlex assays use molecular barcodes that provide robust CNV calling

By counting molecular barcodes within target regions and normalizing across the other targets or to a tumor normal sample, Archer Analysis reports relevant copy number variations present in the sample. CNV calls from Archer Analysis are sensitive, picking up fold changes below 2x that are highly correlated to qPCR and aCGH results. Learn more about AMP-enabled CNV detection in clinical sample types.

Simple lyophilized workflow

The VariantPlex kit provides all the reagents and accessories necessary for targeted library preparation. The kit is completely lyophilized, includes color coded tubes and only requires about a day's work. The tech-friendly protocol is a simple series of liquid transfers and eases reproducibility and contamination concerns.

VariantPlex assays use a simple, lyophilized workflow

Comprehensive Analysis

Archer Analysis is a complementary software suite that provides in-depth sequencing data analysis and interpretation. Features of Archer Analysis include:

  • Point-and-click interface
  • CNV, SNV and indel detection
  • CNV visualization
  • Variant effect prediction
  • Read statistics on library quality
  • Customizable PDF reports
  • Cloud-based or local installation
Archer Analysis provides comprehensive mutation reporting
Learn more about
Archer Analysis Software

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All content © 2018 ArcherDX, Inc.

For Research Use Only. Not for use in diagnostic procedures. For Research Use Only. Not for use in diagnostic procedures.