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Product Support

Delivering expedient assistance to address all your needs.

We understand that our customers may occasionally encounter difficulties when ordering or using our products. We take these issues seriously and will make them our top priority to ensure your satisfaction. In order to assist you in the most efficient way possible, please select the support topic below that best describes your situation:

Most issues are quickly resolved through our Frequently Asked Questions (FAQs). Please review the following list of FAQs first to see if your question is addressed here:

Domestic shipments within the United States are expected to arrive within 1 business day of scheduled ship date. Most international shipments are expected to arrive within 3 business days of scheduled ship date.

Yes. On the day of shipment, you will be sent an email containing tracking information for your order. We encourage customers to proactively track their shipments in order to avoid delays, as our Terms and Conditions indicate the customer is responsible for the order once it leaves Swift Biosciences.

Swift Biosciences ships all orders through FedEx, unless otherwise requested by the customer. If you would like to use another shipping carrier, please contact Order Support and provide your account number for that carrier, if you prefer to have the shipment processed through your account. We will do our best to accommodate your preference, however a $25 handling fee may apply for non-FedEx shipments.

Domestic shipments are packaged with ice packs to keep the contents frozen. Most international shipments are packaged with ice packs. For international shipments that are expected to take longer than 3 business days to arrive, dry ice may be included in the shipment. Please place kits in the freezer immediately upon arrival to prevent spoilage of the reagents.

We partner with distributors in many countries around the world. For a complete list of our distributors, please see our Distributors Page. If you do not find a distributor in your country, please contact Order Support for information on direct shipment.

International shipments and domestic shipments within the state of Michigan are subject to tax. Please contact Order Support with any tax emption documents when placing your order to ensure exemption from taxes.

If you are experiencing an issue that is not answered by the above, please fill out the following form and a customer service specialist will respond to you within 48 business hours:

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Most issues are quickly resolved through our Frequently Asked Questions (FAQs). Please review the following list of FAQs first to see if your question is addressed here:

Accel-Amplicon™ Panels

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

Accel-NGS® 1S Plus DNA Library Kits

The Accel-NGS 1S Plus technology uses a simultaneous end repair, tailing, and adapter ligation reaction called Adaptase™ to add an adapter oligonucleotide onto the 3′ end of single-stranded DNA in a template-independent manner. The 5′ adapter ligation is then facilitated by priming off this 3′ adapter, extending through the insert, and creating a compatible end for the 5′ ligation. This technology is very unique in the NGS library market and also forms the basis for Swift’s Accel-NGS Methyl-Seq DNA Library Kit and Accel-NGS DNA Library Kit for Ion Torrent™.

In some cases, with extremely degraded DNA that has been heavily nicked or denatured as a result of decrosslinking or other high temperature steps, this kit can produce the highest recovery and conversion rates of input DNA. However, for standard FFPE samples, we recommend using the Accel-NGS 2S Plus DNA Library Kit to achieve a 2-3 fold increase in yields versus competing kits and is usually superior to that obtained with the Accel-NGS 1S Plus DNA Library Kit.

Yes. Many users are attracted to this technology because it can convert the short, single-stranded fragments common in ancient DNA into NGS library molecules. Please contact us at Tech Support for recommended modifications to the standard protocol.

No. The polymerase used in the 1S Plus kit does not exhibit uracil tolerance. Therefore, for methyl-seq and other applications requiring tolerance to uracil-containing sequences, we recommend the Accel-NGS Methyl-Seq DNA Library Kit.

Yes. First you must isolate the RNA and remove rRNA by ribodepletion or enrich eukaryotic mRNA by polyA enrichment, followed by fragmenting the mRNA and determining its size distribution. First-strand cDNA should then be generated by an RT reaction, purified and quantified. From the purified first-strand cDNA, you may proceed to Accel-NGS 1S Plus library preparation. Please contact us at Tech Support for further recommendations.

Accel-NGS® 2S Plus DNA Library Kits

The Accel-NGS 2S kits are used for whole genome sequencing, de novo sequencing, whole exome sequencing, hybridization capture enrichment, metagenomics and ChIP-Seq applications.

Yes, we recommend using a qPCR-based assay to quantify starting material with amplicons that are sized to indicate the amplifiable content of the sample. There are several commercially-available qPCR-based input quantification kits available.

Yes, cfDNA recommendations are specified in the protocol, and include a modified Repair I Thermocycler program (to minimize chimera formation) and modified SPRI™ Cleanup Step bead and PEG NaCl volumes (for 2S PCR-Free and 2S Plus Kits only; to ensure capture of the relatively short cfDNA fragments).

The shelf life of the Accel-NGS 2S Plus, Accel-NGS 2S Hyb and Accel-NGS 2S PCR-free DNA Library kits is 6 months, when stored at -20C.

The sequences of the adapters in Accel-NGS 2S libraries are identical to Illumina TruSeq® LT adapters (Single Indexing) or Illumina TruSeq HT adapters (Dual Indexing), but are constructed in a proprietary manner. The adapters and indices are supplied directly from Swift Biosciences in a 2S Indexing Kit.

Oligonucleotide sequences © 2016 Illumina, Inc. All rights reserved.

No, the unique chemistry of the Accel-NGS 2S Kits maintains a low rate of adapter dimer formation without the need to titrate adapters.

Accel-NGS 2S adapters are constructed in a proprietary manner and must be purchased from Swift. The adapters and indices are supplied directly from Swift Biosciences.

Yes, for customers who prefer to use their own polymerase, we recommend the Accel-NGS 2S PCR-free DNA Library Kit. This kit contains amplification primers, but does not include a polymerase.

Enzymatic and sonication methods (Covaris) are supported for DNA fragmentation prior to library creation. For more information, refer to our Enzymatic Fragmentation with Accel-NGS 2S technical note.

The Accel-NGS 2S kits have been validated with 165 bp (cfDNA), 200 bp (gDNA), 350 bp (gDNA), and 450 bp (gDNA) fragments. If working with fragments of another size, please contact Tech Support for recommendations.

The minimal input for creating PCR-free libraries is 100ng of high quality DNA, 10ng of cfDNA, or 5ng when pooling samples. Please refer to our PCR-Free Libraries from 10 ng Input with the Accel-NGS 2S PCR-Free DNA Library Kit technical note for more details.

The input ranges for Accel-NGS 2S kits are 10pg – 250ng. Please consider genome complexity and sample quality when choosing input DNA quantity. Although libraries may be successfully prepared from ultra-low inputs, reduced representation of genome complexity may occur.

Accel-NGS 2S Kits construct high complexity libraries from dsDNA input through two dedicated repair steps and sequential ligation of adapters. Repair I dephosphorylates 5’ termini of input dsDNA to prevent chimera formation. Repair II performs 3’ end repair and polishing. Ligation I performs 3’ ligation of the P7 adapter, and Ligation II performs 5’ ligation of the P5 adapter. These separate, sequential ligation steps prevent formation of adapter dimers and enable independent optimization of each adapter attachment to each terminus. Following Ligation II, an Optional PCR Step can be performed to amplify the library, if necessary.

Repair I dephosphorylates 5’ termini of input dsDNA to prevent chimera formation. Chimeric library molecules can affect alignment metrics, as they are composed of fragments that will be read as a single library molecule, but will align to different genomic locations. Repair II performs 3’ end repair and polishing, which is critical to efficient ligation of adapters.

These separate, sequential ligation steps prevent formation of adapter dimers. As adapter dimers will take up space on the flow cell without providing meaningful sequencing data, minimizing adapter dimer formation during library preparation results in more efficient sample sequencing. Additionally, sequential ligation steps enable independent optimization of each adapter attachment to each terminus, which maximizes efficiency of library construction.

Yes, for customers that have not yet prepared the Ligation I master mix, we recommend pausing the library preparation following the Post-Repair II Step. We recommend re-suspending the SPRI beads in 10 µl of Low EDTA TE following the Post-Repair II SPRI Step, and storing the samples at 4°C. When you are ready to resume the library preparation, adjust the Ligation I master mix to include only 10 µl of Low EDTA TE rather than 20 µl. This will account for the 10 µl of Low EDTA TE that the beads have been stored in, so that the final volume of the Ligation I reaction remains the same. Proceed to run the samples with the Ligation I Thermocycler Program.

For customers that have already prepared the Ligation I master mix who desire a safe stopping point prior to the Post-Ligation II SPRI Step, please contact Tech Support for recommendations.

The Accel-NGS 2S Kits have been validated with SPRIselect beads. However, AMPure XP beads prove to exhibit equivalent performance and are an acceptable alternative.

Following the standard SPRI Cleanup steps that are specified in the protocol will result in left side size selection (removal of small DNA only). For customers with samples that contain large fragments (>600 bp), we recommend removal of these prior to library quantification as these large library molecules will contribute to the library concentration, but will not cluster well on the flow cell. For information on performing a right side size selection (removal of large DNA only) or double size selection (removal of both small and large DNA), please see the SPRIselect User Guide published by Beckman Coulter.

For high quality, fragmented gDNA, the Accel-NGS 2S Kits exhibit a conversion efficiency of 20-70%.* For circulating, cell-free DNA (cfDNA), higher conversion efficiencies are observed (up to 90%). This increase can be attributed to the relatively undamaged ends of cfDNA resulting from enzymatic cleavage in the blood and the narrow size distribution of cfDNA. For low quality DNA samples, such as those from FFPE, conversion rates can be lower due to unrepairable damage on the ends of DNA.

*Conversion efficiency calculations compare PCR-free yield (in nM) to the theoretical maximum yield (in nM). This calculation accounts for the added weight of NGS adapters, which can artificially inflate conversion efficiency.

Lower than expected yields can usually be attributed to inaccurate quantification of input DNA or inefficient recovery of DNA during the bead-based clean-up steps. While NanoDrop® or Qubit® may be acceptable for high quality DNA samples, quantification by a qPCR-based method is recommended to ensure accuracy of input DNA.

For damaged DNA samples, please be aware that small fragments (< 100 bp) will be excluded by the standard SPRI bead ratios indicated in the protocol.

There are two common causes for abnormal migration of Accel-NGS 2S library molecules.

The first cause applies to PCR-free libraries only. The secondary structure of sequencing adapters in PCR-free Accel-NGS 2S libraries results in abnormal migration and overestimation of library size. On the Agilent High Sensitivity Chip, it is normal and expected to observe 200 bp insert PCR-free libraries to migrate to a ~500 bp peak, and for 350 bp insert PCR-free libraries to migrate to a ~800 bp peak. Performing a few cycles of PCR on the library resolves the adapter secondary structure and results in library molecules that migrate true to size.

The second cause applies to libraries that have been over-amplified. Too many cycles of PCR can deplete primer concentration in the reaction, resulting in the formation of library molecule heteroduplex structures that will migrate abnormally. Denaturation of these heteroduplex structures – with a denaturing gel, for example – will result in library molecules that migrate true to size. Over-amplified libraries can still be sequenced, as they will be denatured just prior to loading on the flow cell, but customers should aim to perform the minimum number of PCR cycles necessary to avoid undesirable PCR duplicates.

96 different indices are currently available for Accel-NGS 2S products. Please consider your sample type, desired depth of sequencing, and sequencing instrument capabilities when determining your level of multiplexing.

Yes, Accel-NGS 2S kits are readily compatible with automation instruments. Scripts are in the process of being written for the Beckman Coulter Biomek® FXP and NXP, the PerkinElmer SciClone® and SciClone Janus®, the TECAN Fluent™, the Hamilton Microlab® STAR™, and the Eppendorf epMotion®.

Please contact Tech Support for more details.

The Accel-NGS 2S libraries are only compatible with Illumina platforms. However, Swift’s Accel-NGS DNA Library Kit for Ion Torrent will construct libraries compatible with Ion Torrent instrumentation.

Accel-NGS® Methyl-Seq DNA Library Kits

The Accel-NGS Methyl-Seq Kit has been validated with the EZ DNA Methylation-Gold™ Kit (Zymo Research). While other bisulfite conversion kits may be compatible with the Swift kit, it is not recommended to use Accel-NGS Methyl-Seq with bisulfite conversion kits that utilize a single stranded nucleic acid carrier, as this carrier may act as substrate and result in creation of artifactual library molecules.

Yes. The unique chemistry of Accel-NGS Methyl-Seq easily works in an RRBS workflow. The process differs slightly from traditional methods, as illustrated below. To capture the fraction of DNA fragments that are enriched for CpG islands, RRBS protocols require that size selection of inserts occurs after MspI DNA digestion, but prior to bisulfite conversion. As Accel-NGS Methyl-Seq performs bisulfite conversion prior to library preparation, size selection must be performed on the DNA fragments immediately following MspI digestion (rather than on library molecules, in the traditional workflow).

Methyl-Seq RRBS Workflow

It is not recommended. Fragmentation solely by bisulfite treatment results in a broad size distribution of larger DNA fragments. Such fragments may be converted into library molecules, however the wide distribution of library molecules will cluster poorly on the flow cell. If skipping fragmentation is unavoidable, we recommend examining the size of library molecules prior to library quantification, and, if necessary, performing a right side size selection to remove very large library molecules to improve clustering on the flow cell. This scenario will result in reduced complexity of sample representation. Please contact us at Tech Support for recommended modifications if relying on bisulfite treatment for fragmentation.

In addition to converting unmethylated cytosines, bisulfite treatment also results in damage which fragments DNA. Therefore, it is normal to observe bisulfite-converted libraries that are slightly smaller in size than their unconverted control libraries, as illustrated by the Bioanalyzer profile below.

MSeq_Bioanalyzer

The Accel-NGS Methyl-Seq Kit constructs libraries that are readily compatible with NimbleGen™ SeqCap™ Epi Target Enrichment Systems. Sequencing data from capture with the SeqCap Epi CpGiant panel can be found on the Accel-NGS Methyl-Seq Product Page. The Accel-NGS Methyl-Seq Kit is not compatible with the Agilent SureSelectXT Human Methyl-Seq Enrichment Systems, as this technology uses capture probes that are not compatible with bisulfite converted DNA.
The Accel-NGS 2S Hyb DNA Library Kit creates libraries that are readily compatible with SureSelectXT Human Methyl-Seq Enrichment. However, because this approach to targeted methylation sequencing results in decreased sample complexity and increased input requirements compared to the Methyl-Seq workflow, this is only recommended if the Methyl-Seq workflow cannot be performed. Please contact us at Tech Support for more information.

Yes. Many users are attracted to this technology because it can convert the short, single-stranded fragments common in ancient DNA into NGS library molecules. Additionally, Accel-NGS Methyl-Seq is capable of preserving uracil-containing DNA resulting from the damage inflicted on ancient DNA samples. Please contact us at Tech Support for recommended changes to the standard protocol.

If you are experiencing an issue that is not answered by the above, please fill out the following form and a customer service specialist will respond to you within 48 business hours:

* Required

Most issues are quickly resolved through our Frequently Asked Questions (FAQs). Please review the following list of FAQs first to see if your question is addressed here:

Accel-Amplicon™ Panels

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.

Accel-NGS® 1S Plus DNA Library Kits

In most cases there is no effect. Please view our technical note titled Accel-NGS 1S Plus and Methyl-Seq: Tail Trimming for Better Data for more details on the tail and how to trim if necessary.

Accel-NGS® Methyl-Seq DNA Library Kits

Bisulfite treatment results in a low complexity library, which requires a high complexity spike-in to avoid low Q-scores, issues with cluster recognition and demultiplexing ability. The Accel-NGS Methyl-Seq Kit has been validated on a MiSeq and HiSeq 2500 with a 10% spike-in of a PhiX library. Please contact Illumina for questions concerning sequencing bisulfite converted samples on other instruments.

Yes. Bases added to the 3’ termini of DNA fragments during the Adaptase reaction may contain unmethylated cytosines, which adds both artifactual sequence and methylation information to the dataset. Therefore, trimming of Methyl-Seq libraries is required to obtain accurate mapping efficiency and precise methylation information. Please view our technical note titled Accel-NGS 1S Plus and Methyl-Seq: Tail Trimming for Better Data for more details on the tail and how to trim it.

If you are experiencing an issue that is not answered by the above, please fill out the following form and a customer service specialist will respond to you within 48 business hours:

* Required