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NEW! Swift Amplicon HS Panels

Confident Detection of Low Frequency Variants in Liquid Biopsy Sequencing – Early access available now!

The NEW Swift Amplicon HS Panels enable ultra-low frequency variant detection at and below 1% MAF from 10-20 ng of cell-free DNA (cfDNA) for Illumina® sequencers. Nucleotide errors, normally introduced during PCR and sequencing, are removed through the implementation of unique molecular identifiers (MIDs or UMIs) that uniquely label target templates during amplification.

 

Swift Amplicon HS Panels enable variant calling at and below 1% frequency, with allele sensitivity dependent on the amount of input material available and the depth of sequencing.  Using 10 ng of input DNA, this assay consistently detects variants at 0.5% with a recommended sequencing depth of at least 60,000x (1M reads) prior to deduplication with MIDs and 0.25% from 20 ng of input DNA.

  • Oncology – liquid biopsy cfDNA and FFPE tissue
  • Genome/Host Detection – Graft vs. Host Disease and Fetal in Maternal cfDNA*
  • Custom targets*

* Please inquire

Detection of Low Frequency Cancer Mutations with Molecular IDs

The Swift Amplicon HS EGFR Panel consistently detected all expected variants from 10 ng SeraSeqTM ctDNA Reference Material v2 AF0.5% and 20 ng SeraSeq ctDNA Reference Material v2 AF0.25%.  Variants were called from an MID-based consensus sequence by LoFreq (Genome Institute of Singapore).

 

 

For additional data, please view the Data Sheet.

These panels are compatible with cell-free DNA (cfDNA and ctDNA), FFPE, whole blood, and high molecular weight genomic DNA.

We recommend a minimum of 10 ng input DNA. It is best to quantify input DNA using a qPCR-based assay since it reflects the amplifiable content of the sample. Please note that the input amount affects Limit of Detection – 0.5% from 10 ng and 0.25% from 20 ng.

The protocol takes approximately 3 hours from input DNA until finished library ready for quantification.

Swift Amplicon HS Panels enable variant calling at and below 1% frequency, with allele sensitivity dependent on the amount of input material available and the depth of sequencing.  Using 10 ng of input DNA, this assay consistently detects variants at 0.5% with a recommended sequencing depth of at least 60,000x (1M reads) prior to deduplication with MIDs and 0.25% from 20 ng of input DNA.

Currently, the Swift Amplicon HS EGFR Panel is available with early access pricing. Please view the bioinformatics files webpage for a target BED file and representative data.

If you are interested in a specific gene target list for interrogation with this technology, please fill out this form with your custom targets and submit to [email protected]. A Swift representative will be in contact with you to discuss your targets and the timeline for creating a custom panel.

There are a few key considerations when analyzing sequencing data generated from the Swift Amplicon HS Panels with MIDs:

  • The first 10 bases in front of Read 2 constitute an MID. Hence, trim (CROP) these first 10 bases from Read 2 to make an MID/UMI fastq file for use with MID pipeline using fgbio package from Fulcrum Genomics as MID (https://github.com/fulcrumgenomics/fgbio) using Trimmomatic.
  • In addition, prior to aligning the reads, make sure that the 10bp MID (which contains random bases) has been trimmed off from 5’ of Read 2. If additional informatics pipeline advice is needed to use these instructions, please contact Swift Technical Support at [email protected] or tel: 734.330.2568.

Please ensure that adapter trimming is enabled while setting up the sequencing run. Alternatively, adapter trimming may be performed bioinformatically prior to analysis. In addition, Swift Amplicon HS Panels are designed with overlapping amplicons to allow for contiguous regions of coverage in a single-tube format. Therefore, synthetic primer sequences will be encountered both at the beginning and end of some reads, which must be trimmed during the data analysis. This can be done using a publicly available tool called Primerclip (http://github.com/swiftbiosciences/primerclip). For more information, please consult our Bioinformatics Resources page at swiftbiosci.com/biofx. Download panel specific files through our website. A target BED file is provided with purchase of the Accel-Amplicon Panel.

Swift Amplicon HS Data Analysis on Genialis Platform

Sequencing data from all standard and custom Swift Amplicon HS panels can be analyzed through a web-based software solution supported by Genialis. This data analysis solution has been designed to integrate alignment, trimming, QC and variant calling into one simple pipeline. The Genialis App also automates an algorithm optimized for accurate variant detection, including low frequency variants. It is fast and easy to use, as it offers data visualization and annotated variants using direct links to publicly available databases such as COSMIC and NCBI.

Please visit genialis/swiftbio/ to learn more about this service.

 

Place Order

First, select a product and quantity:

Catalog No. Description Price QTY
HS-51024 Swift Amplicon HS EGFR Panel $1800.00

$1,800.00Add to cart

The below solution is included with your product. If you require extra, please add now:

Catalog No. Description Price QTY
90196  PEG NaCl Solution (96 rxns) $20.00

$20.00Add to cart

90296  Low EDTA TE (96 rxns) $20.00

$20.00Add to cart