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Amplicon Sequencing

Amplicon sequencing has emerged as a reliable and cost-effective method for ultra-deep targeted sequencing. This highly adaptable approach is utilized in various fields ranging from agriculture and metagenomics to oncology, becoming a standard method of interrogating several targets in multiple samples in a single run. This unique molecular biology approach provides powerful solutions for detecting genetic variations and screening clinically-relevant somatic and germline mutations in low input DNA, as well as other challenging sample types such as FFPE and cfDNA. Amplicon sequencing provides an accurate yet economical alternative to whole genome or whole exome sequencing, allowing researchers to focus on genes of interest without the burden of high cost and cumbersome data analysis.

Swift Biosciences’ advanced technology offers amplicon panels with the ability to generate multiple amplicons in a single tube using a rapid 2-hour workflow. Our Accel-Amplicon™ technology offers several off-the-shelf panels, optimized for multiple sequencing platforms, designed for germline and somatic variant detection of clinically-relevant genes. Alternatively, we offer an option to design custom panels to meet our customers’ unique requirements. A fast and easy single-tube workflow produces the best-in-class performance for on-target percentage and coverage uniformity, enabling low frequency variant discovery and confirmation.

SWIFT PRODUCT LINES COMPATIBLE WITH AMPLICON SEQUENCING:

Accel-Amplicon™ Panels

The Swift advantage:
  • Single-tube assay provides easy and consistent processing.
  • Ready-to-sequence libraries in 2 hours.
  • 10 ng of input DNA required.
  • Average amplicon size of 138-149 bp is compatible with FFPE and cfDNA.
  • Contiguous coverage provides complete coverage of desired regions.
  • Coverage uniformity > 95%.
  • On target > 95%.
High Coverage Uniformity Across Sample Types

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The Accel-Amplicon 56G Oncology Panel was used to prepare libraries from 10 ng of input DNA from a variety of sample types. The coverage uniformity, as the percentage of the bases covered at least 20%, 30%, 40%, or 50% of the average depth, was determined across four sample types. The percentage of reads on target was > 95% for all sample types.
Reproducible Variant Calling from Q-Seq HDx™ Quantitative Standards

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The Accel-Amplicon 56G Oncology Panel consistently detected validated variants at the expected frequency in replicates from 10 ng of the Horizon Diagnostics Quantitative Multiplex DNA Reference Standards HD701. The variants were called by LoFreq 2.1.1 (Genome Institute of Singapore) and GATK HaplotypeCaller (Broad Institute). When examining uncommon variants between the 10 replicates, the majority of background variants were present at less than 0.6%. No sporadic variants greater than 0.6% were detected.
Robust Yields and Performance from Clinical Oncology Research Samples

Endometrial study by John Martignetti and Peter Dottino, Icahn School of Medicine at Mount Sinai, for analysis of somatic mutations in 56 oncology-related genes from over 200 samples.

AP_Amp Seq_Table_Edometrial Study

The Accel-Amplicon 56G Oncology Panel was used to assess the germline variant profile of 39 normal samples and 162 tumor samples of varying quality. Following qPCR input quantification using the ALU115 assay, 10 ng of input DNA was used per sample and libraries were sequenced using MiSeq® v2 chemistry. Tumor samples were sequenced to a target depth of 5000X for somatic variant detection while normal samples were sequenced to a target depth of 500X for establishment of a background variant profile for subtraction during variant calling. Bases on target is the percentage of aligned bases on target and coverage uniformity is the percentage of amplicons covered greater than 20% of the mean.