Accel-Amplicon™ Custom NGS Panels
Let’s Design Your Targeted Sequencing Assays
Accel-Amplicon Custom NGS Panels offer a completely curated, targeted NGS workflow to rapidly and precisely interrogate genomic targets relevant to your research. This approach is ideal as a follow-up to whole genome or exome sequencing studies, as well as diving deep into specific biological pathways.
Our Accel-Amplicon Custom NGS Panels generate highly multiplexed, targeted PCR libraries that are compatible with both Illumina® and Ion Torrent™ sequencing platforms. The unique single-tube design is also compatible with most sample types, including limited or degraded samples such as FFPE and cfDNA samples.
Tailored to meet your specific needs, Accel-Amplicon Custom NGS Panels can be customized to include coverage of both clinically-relevant hotspot loci and regions of contiguous coverage, as well as Sample_ID targets spiked-in at a low percentage (2-4% of reads). This allows for somatic mutation detection using high depth of coverage and sample identification using low coverage depth of germline targets.
- Flexible, intelligent assay design
- Simple and scalable
- Enables discovery, characterization, and screening of SNPs and small indels (< 15 bp).
- Provides comprehensive coverage of critical hotspot SNVs, indels, and contiguous tiled regions in coding regions and intron-exon boundaries.
- Tailors your assay at the size that works best for you — from a small panel of just 15 amplicons up to 1,500 — all in a single-tube multiplexed reaction.
- Generates complete libraries in under 2 hours with a fast, easy workflow.
- Delivers highly reproducible performance from only 10-25 ng input DNA, including fragmented or degraded samples.
- Produces highly specific, exceptional target coverage uniformity to make your sequencing reads work for you.
At Swift, we firmly believe in the power of scientific collaboration to drive novel discoveries. Our world-class bioinformatics and support team partners with you along the way to design, implement, and utilize our Accel-Amplicon NGS Panels. Visit our Design Guide page to learn more about the process.
The Accel-Amplicon workflow provides a fast, single-tube approach resulting in a < 2-hour start-to-finish procedure, including hands-on time.
The single-tube workflow includes two brief incubations to generate the multiplex amplicon targets and add a unique combination of Illumina-compatible indexed adapters, creating up to 96 uniquely-indexed libraries for multiplexing on a single sequencing run.
Eliminate the Variant Calling Bottleneck
In partnership with Genialis, Swift provides basic and clinical researchers’ with a streamlined data analysis solution that integrates alignment, primer trimming, QC and variant calling into one, simple pipeline.
Your Partner Through Every Step – from Design to Data
*As quantified by qPCR. For sample types with more consistent high quality DNA including whole blood, fresh frozen samples, and cultured cells, quantification by Qubit® is also a reliable indicator of amplifiable content.
The University of Texas MD Anderson Cancer Center needed a custom targeted NGS panel to profile causative mutations in a type of endometrial cancer known as endometrial endometrioid adenocarcinoma (EEA). This study required an assay that would both be compatible with small quantities of circulating, cfDNA from blood plasma and also work with matching tumor samples preserved as FFPE tissue. Bolivar, Ana et al. from Dr. Russell Broaddus’ group in the Department of Pathology, recently published their results in the journal Cancer Genetics (Bolivar, Ana et al. Cancer Genetics , Volume 214 , 34 – 35).
The study sought to design and evaluate a cfDNA-based assay for EEA — an incurable cancer with no current methods for early detection. A Swift Accel-Amplicon Custom NGS Panel was developed based on four genes previously shown to have mutations in 98% of EEA: CTNNB1, KRAS, PTEN, and PIK3CA. Sequencing was done by NGS (Illumina MiSeq®) on plasma/tumor pairs from 33 early stage EEA patients.
The team found that 11 (1/3) of the patients showed EEA-associated mutations in both plasma and tumor, and these samples were re-sequenced deeply to 20,000X for confirmation. The remaining 22 (2/3) patients exhibited mutations in the FFPE tumor but not in cfDNA. Tumors from the cohort with mutations in both cfDNA and tumor were, on average, almost 3X larger (10.4 cm vs. 3.6 cm) than those with mutations only in the tumor.
Let’s work together to design your assay.
There are several paths to design your Accel-Amplicon panel. Pick the route that fits your needs.
1.) Already know your targets?
There’s no need to learn how to use a complicated online design tool: just email [email protected] and we’ll do the work.
Visit our Accel-Amplicon Custom Panel Design Guide if you would like some guidance ahead of time, or simply contact us today.
Download our Submission Form and submit to [email protected] and we will contact you to start a complimentary design consultation.DOWNLOAD FORM
2.) Need assistance selecting your targets?
We can help you identify the most informative disease-specific genes/variants for your panel. Swift Biosciences and Genomenon have partnered to provide you a fast and comprehensive way to design Accel-Amplicon™ panels.
How it works:
- First, Genomenon identifies biomarker targets associated with diseases by applying automated machine learning algorithms to its Mastermind Genomic Search Engine to objectively correlate genes and genetic variants with the quality and frequency of citations from the scientific literature.
- Now you’re ready to design your panel. Go to step 1 above to submit your targets to Swift. We’ll design and validate a highly informative Accel-Amplicon Custom NGS Panels to deeply sequence your targeted gene regions.
Protocols and Tools
- Download Protocol
- Accel-Amplicon Custom NGS Panel Design Guide
- Accel-Amplicon Custom NGS Panel Target Submission Form
- Input DNA Quantification Assay
- Accel-Amplicon Master Mixing Volume Calculator
Optimal coverage uniformity, sensitivity, and specificity are achieved with qPCR-verified DNA input amounts in the 10-25 ng range. Between 25-100 ng, coverage uniformity may be mildly reduced while sensitivity and specificity are preserved. Using less than 10 ng may reduce specificity of the assay and affect variant calling for low frequency alleles due to low copy number.
Accel-Amplicon panels perform best within the 10-25 ng input range, so it is important to have an accurate understanding of the input material. Quantification by a fluorometric assay such as Qubit is satisfactory for high quality DNA from whole blood, fresh frozen, or cultured cells. However, this method may significantly overestimate the amplifiable content of a more fragmented sample, such as FFPE or cfDNA, because it reflects double-stranded content regardless of molecule size. A qPCR-based assay can be designed such that the primers will only produce amplicons from fragments larger than a given size, which is a better indicator for how well they will amplify in typically compromised samples such as FFPE and cfDNA. The table below illustrates the variability that can be expected across 10 different FFPE samples when quantified with three common methods, including the absorbance-based NanoDrop, the fluorescence-based Qubit, and a qPCR assay. Please note that the Input DNA Quantification Assay provides full details for the published ALU115-qPCR assay and there are also commercial options for qPCR input quantification available.
The level of multiplexing is directly correlated to the size of the specific Accel-Amplicon Panel and the flow cell chemistry utilized for sequencing of the libraries. The table below provides an example of the number of libraries from the Accel-Amplicon Comprehensive TP53 and 56G Oncology Panels which can be multiplexed on a single MiSeq® flow cell. Accel-Amplicon panels currently include up to 96 indexing combinations and are consistently increasing.
*Please inquire by email to Tech Support if you require more than 96 unique indices.
Lower than expected yields most likely relate to the quality and quantity of the sample, as well as how it was quantified. If possible, for severely compromised samples including FFPE, use 25 ng of qPCR-quantified input and extend the incubation time for the Indexing Step from 20 minutes to 60 minutes to improve yields. It is very important to quantify cfDNA or FFPE with qPCR as opposed to Qubit or NanoDrop to ensure there is a minimum of 10 ng of amplifiable content in the sample.
It is not recommended to use a Bioanalyzer or Qubit for quantifying libraries because there is no PCR enrichment of the library following the Indexing Step, so the Bioanalyzer or Qubit will not accurately quantify fully adapted library vs. other DNA. In addition, the Accel-Amplicon library adapters have secondary structure which exhibit migration artifacts on the Bioanalyzer.
Low cluster density is typically related to an error in library quantification. If the final library is quantified by methods other than qPCR, this will lead to determining an inaccurate value for library concentration. It is not recommended to use a Bioanalyzer or Qubit for quantifying libraries because there is no PCR enrichment of the library following the Indexing Step, so the Bioanalyzer or Qubit will not accurately quantify fully adapted library vs. other DNA.
In addition, the Accel-Amplicon library adapters have secondary structure which exhibit migration artifacts on the Bioanalyzer. When diluting the library for loading the flow cell and sequencing, if the dilution is based off an erroneous quantification the cluster density will not be optimal.
Swift is pleased to accept custom Accel-Amplicon Panel requests. We will use a custom design pipeline to generate the primer pools and provide a functionally-tested pilot kit, with pricing decided on a case-by-case basis dependent on reaction volumes and assay complexity. Please contact us by email at [email protected] and specify:
- Number of genes to cover, with gene symbols
- Hotspot (i.e., SNP) or whole-gene coverage requirements
- Sample type(s) to be used with the custom panel such as FFPE, cfDNA, or high quality gDNA
- Expected number of reactions required for the custom panel
There are multiple factors which determine the LOD, the most important being the number of copies of the variant-containing DNA actually present in the sample and the depth of sequencing performed.
There is also some variation in the reasonable LOD depending on the variant of interest. In general, the Accel-Amplicon technology is capable of a LOD down to 1% for most base substitution variants when working with 10-25 ng input DNA as quantified by a qPCR input assay.
It is very important to quantify cfDNA or FFPE with qPCR as opposed to Qubit or Nanodrop to ensure there is a minimum of 10 ng of amplifiable content in the sample for this LOD to be achieved, since for 10 ng this will be represented by ~30 mutant copies detected in ~3000 total copies.
It is also critical to achieve adequate sequencing depth to obtain sufficient mutant copy number detection. The table below illustrates observable allele frequencies for Accel-Amplicon libraries at 10 ng and 1 ng input amounts.
Please note that Swift Biosciences currently supports inputs down to 10 ng.
For maximal (lowest) LOD, increasing the input amount to 25 ng, if possible, will provide more confidence due to increased copy number ( > 6000 total copies and therefore > 60 copies of a 1% variant).
It is also important to note that the LOD inherent in Illumina technology can be discussed in terms of bases rated at Q30. Most bases are read with a rate of 1 error in 1000, or 0.1%. Some bases have a lower quality score and therefore the background false positive noise level is between 0.1-0.6%.
Using a base quality filter during the variant calling steps is one way to address this issue.
Swift does not currently offer a proprietary data analysis software package. Please view our technical note “Accel-Amplicon Panels: Bioinformatics Guidelines“, which includes a tutorial for using open-source Linux-based tools to perform the required primer trimming step, as well as general recommendations for the alignment and variant calling analysis.
While this can be caused by multiple factors, one of the most common explanations is that the Sample Sheet was not set to automatically trim the Illumina adapter sequences when generating the FASTQs prior to the primer trimming requirement of Accel-Amplicon Panels.
Make sure that the “Use adapter trimming” and “Use adapter trimming Read 2” are selected during the sample sheet setup. It is possible to re-run this analysis even after the sequencing run has been performed if these selections were not made during the initial sample sheet setup.