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Accel-Amplicon™ BRCA1 and BRCA2 Panel

Targeted Sequencing for Breast Cancer Genes

All-in-One Amplicon Solution

The Accel-Amplicon BRCA1 and BRCA2 Panel offers comprehensive coverage of the entire coding sequence of BRCA1 and BRCA2 genes. Utilizing 246 amplicons with average size of 148 bp, this panel generates targeted libraries compatible with Illumina® and Ion Torrent sequencing platforms. The unique design of the Accel-Amplicon BRCA1 and BRCA2 Panel enables compatibility with FFPE and cfDNA samples. This product is a complete kit that includes all components necessary for generating ready-to-sequence libraries, including primer pairs and indexed sequencing adapters.

Features:

  • Single-tube assay
  • Ready-to-sequence libraries in 2 hours
  • Inputs as low as 10 ng

Benefits:

  • Average amplicon size of 148 bp for compatibility with FFPE and cfDNA
  • Limit of detection as low as 1-5% for somatic mutations
  • On-target specificity and coverage uniformity > 95%
  • Leverages the high fidelity performance of the Illumina platform
  • Complete library generation in a single kit

The Accel-Amplicon workflow uses a fast, single-tube approach consisting of a 90-minute target enrichment amplification step and a 10-minute adapter ligation step, yielding a 2-hour start-to-finish procedure.

amplicon-workflow-100416

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.

Decrease Input, Not Sensitivity

Like the Accel-Amplicon BRCA1, BRCA2, and PALB2 Panel, the Accel-Amplicon BRCA1 and BRCA2 Panel offers high sensitivity variant detection from input amounts from 10-25 ng. The kit utilizes Illumina-compatible dual-indexed adapter sequences and has been validated on the MiSeq® and MiniSeq® platforms. Barcoded adaptors for sequencing on Ion Torrent platforms are also available (please inquire).

Product Specifications

amplicon_brca1_2_table_specs

*As quantified by qPCR. Qubit® represents amplifiable DNA content more accurately than NanoDrop®, however is still not as accurate as the qPCR assay. For sample types with more consistent high quality DNA including whole blood, fresh frozen samples, and cultured cells, quantification by Qubit is a reliable indicator of amplifiable content.
Comprehensive Coverage of Coding Sequences of BRCA1

amplicon_brca1_comp-coverage

Coverage of all coding exons of the BRCA1 gene by Accel-Amplicon BRCA1 and BRCA2 Panel are represented in a Sashimi plot (IGV; Broad Institute).
Comprehensive Coverage of Coding Sequences of BRCA2

amplicon_brca2_comp-coverage

Coverage of all coding exons of the BRCA2 gene by Accel-Amplicon BRCA1 and BRCA2 Panel are represented in a Sashimi plot (IGV; Broad Institute).

 Performance on the Illumina Platform

The data below demonstrate the performance of the Accel-Amplicon BRCA1 and BRCA2 Panel on a variety of sample types.

amplicon_table_brca1_2_performance

The Accel-Amplicon BRCA1 and BRCA2 Panel was used to prepare libraries from 10 ng inputs of high quality Coriell (NA12878, NA24143,NA24695, and NA19240) gDNA, Horizon Diagnostics Quantitative Multiplex DNA Reference Standards HD701 and FFPE samples subjected to 6, 24, or 48 hours of fixation. Sequencing was performed using MiniSeq® Reagents.
Variant Calling by Accel-Amplicon BRCA1 and BRCA2 Panel

amplicon_table_brca1_2_variant-calling

The Accel-Amplicon BRCA1 and BRCA2 Panel consistently detected validated variants at the expected allele frequency (AF) in replicates from 10 ng of the Horizon Diagnostics Quantitative Multiplex DNA Reference Standards HD701 and Coriell (NA14684, NA14805 and NA14788). The variants were called by GATK HaplotypeCaller (Broad Institute).

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.

Amplicon_Table_Level of Multiplexing

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 Tech Support 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.

Amplicon_Table_Allele Frequencies

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.

Place Order

First, select a product and quantity:

Catalog No. Description Price QTY
AL-52048 Accel-Amplicon BRCA1 and BRCA2 Panel (48 rxns) $3600.00

$3,600.00 Add to cart

And, add optional components:

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

$20.00 Add to cart