xGen™ Exome Sequencing Kit Trinity™ for Element
Target enrichment research reagents for the Trinity™ workflow on the Element Biosciences AVITI™ sequencing platform.
A streamlined workflow through on-sequencer target enrichment providing a seamless transition from capture to sequencing.
xGen NGS—made for efficiency.
Ordering
- xGen Exome Sequencing Kit Trinity™ for Element utilizes IDT chemistry with Trinity simplicity for target enrichment 97% target coverage at 20X for 24 samples
- Streamlined workflow with fewer steps and no need for conversion or circularization. Automate the Trinity workflow on the Element AVITI system for better efficiency
- Up to a 4 hour reduction in hands-on time
Product details
Trinity workflow compared to a traditional hybridization capture workflow
Figure 1. The Trinity™ workflow on the Element Biosciences AVITI™ sequencing platform offers a simplified library prep process.
xGen DNA Library EZ UNI Kit
The xGen DNA Library EZ UNI Kit supports an indexing by ligation workflow for optional PCR amplification or PCR-free workflow, amplification primers are included in the kit. Indexed adapters are supplied separately.
Includes an enzymatic fragmentation module, a high efficiency ligase, and a PCR Master Mix that can generate library yields sufficient for Element Trinity hybridization-based enrichment workflow and direct sequencing. Workflows compatible with high throughput applications.
Table 1. Supported applications.
| Research applications | xGen DNA Library EZ UNI Kit |
|---|---|
| Whole genome sequencing | ✓ |
| Whole exome sequencing | ✓ |
| Variant detection | Germline + somatic |
| Genotyping | ✓ |
| CNV detection | ✓ |
Table 2. Specifications.
| Features | Specifications |
|---|---|
| Sample types | Fresh frozen tissue, genomic DNA, PCR amplicons, high quality FFPE* |
| Range of input concentrations | 0.1–1000 ng |
| Indexing compatibility | xGen Stubby Adapter-UDI Primers for Element |
| System compatibility and multiplexing format | Manual and automated. Please inquire for a list of compatible liquid handling robots and scripts. |
*Optimization of the enzymatic fragmentation step may be required.
xGen Deceleration Module enables additional control over fragment length with the xGen DNA Library EZ Kits.
The xGen Deceleration Module generates an average library insert size of 550 bp offers flexible fragmentation times on automation platforms.
xGen Stubby Adapter-UDI Primers for Element
Barcodes designed with edit distance in mind to minimize any sequence errors from PCR or sequencing that might impact demultiplexing.
Stubby adapter and unique dual-index primer pairs for TA-ligation library preparation workflows where indexing by PCR is preferred. Available as single-use plates containing either 16 or 96 primer pairs, and a separate tube of stubby adapters with a matching number of reactions. The resulting libraries are intended for sequencing on an Element Biosciences sequencer.
xGen Stubby Adapter for Element is loaded in a multi-use tube and the xGen UDI Primers for Element are loaded into a single-use, 96-well plate containing a pierceable seal. The unique dual index (UDI) has a barcode length of 9 nucleotides. Each well contains one specific index pair for indexing one sample.
Sample multiplexing:
- 4 plex = wells A1-D1
- 8 plex = any column except column 6
- 12 plex = any row
- 16 plex = columns 1 & 2
xGen Exome Hyb Panel v2
- Shown to have higher on-target rate than leading array based competitors since each probe is individually synthesized and then added to the panel
- Consistency across lots as each probe was synthesized on a large scale prior to panel creation
- High end-to-end coverage of the RefSeq genes even in areas of high GC content
Our xGen Exome Hyb Panel v2 consists of 5' biotin–modified oligonucleotide probes that are individually synthesized and analyzed by electrospray ionization-mass spectrometry (ESI-MS) and optical density (OD) measurement. The probes are normalized before pooling to ensure that each probe is represented in the panel at the correct concentration. Probes that fail quality control are resynthesized. This manufacturing process gives the xGen Exome Hyb Panel v2 a unique advantage over array-derived pools in which missing or truncated probes cannot be identified before sequencing. IDT proprietary synthesis methods enable challenging probes—such as those with high GC and AT content—to be appropriately represented in the panel. The individual probes are synthesized on a larger scale than is used for array manufacturing, allowing IDT to produce a single, large lot of material that is aliquoted over time, providing consistent content from one aliquot to the next.
The xGen Exome Hyb Panel v2 consists of 415,115 probes that spans a 34 Mb target region (19,435 genes) of the human genome and 39 Mb of probe space—the genomic regions covered by probes. Our probes are designed using a new “capture-aware” algorithm and assessed with proprietary off-target analysis. All probes in the panel are manufactured under ISO 9001 standards, and then, mass spectrometry and dual quantification measurements of each probe are performed before they are pooled into the xGen Exome Hyb Panel v2. These measures ensure the quality of the probe and its appropriate representation in the final panel.
xGen Hyb components
The xGen Hyb Capture Kit Trinity™ for Element reagents are designed for use with xGen Exome Sequencing Kit Trinity™ for Element workflow. This kit consists of three components: xGen Hyb Buffer Enhancer (16 rxn), xGen 2X Hybridization Buffer (16 rxn), and Human Cot DNA (150 µl aliquot); and is designed for the hybridization capture workflow on the Element Biosciences's AVITI sequencer using the Trinity flowcell.
- Trinity simplifies exome sequencing without compromising to flexibility or performance.
- Trinity eliminates the need for specialized equipment or methods for any scale of work.
- Trinity includes more flexible scaling, providing cancer researchers with a powerful suite of fully integrated genomics tools in a single platform.
- All the options you need to run a complete array of research assays including flexible scaling, high standard accuracy, and now integrated exome capture.
Product data
No need to sacrifice performance for speed. The paired IDT chemistry and Element’s novel Trinity workflow has demonstrated exceptional specificity across samples that it is highly reproducible across runs (Figure 2).
Figure 2. Consistent flanked on-target percentage and selected bases across samples and runs. Libraries generated using the xGen Exome Sequencing Kit Trinity™ for Element were consistent in flanked on-target percentage (A–B); and present selected bases (C–D). Libraries were constructed from 100 ng input of Coriell NA12878 genomic DNA (gDNA) using the xGen DNA EZ UNI Library Prep Kit per the manufacturer’s instructions. Samples were then hybridized using an xGen Exome v2 Hybridization Panel following the xGen Exome Sequencing Kit Trinity™ for Element AVITI System Protocol. Hybridized libraries were sequencing using a Trinity 2 x 150 Sequencing Kit on an Element Biosciences AVITI™ Sequencing System. Following sequencing, samples were downsampled to 40 million reads before analysis using Picard (n = 24 per run).
High on-target coverage and uniformity with low duplicate read and drop out rates demonstrates you can achieve high efficiency exome sequencing, in less time, with consistent results across experiments to extract maximum insights from your samples (Figure 3).
Figure 3. High on-target coverage and uniformity with low duplicate read and drop out rates. (A) A high degree of target bases showed > 20X Coverage between and among runs. (B) Fold-80 base penalty shows consistent uniformity between and among runs. (C) Zero target coverage percentage shows limited probe drop-outs between and among runs. (D) Low duplication rate shows a high rate of unique molecule detection between and among runs. Libraries were constructed from 100 ng input of Coriell NA12878 genomic DNA (gDNA) using the xGen DNA EZ UNI Library Prep Kit per the manufacturer’s instructions. Samples were then hybridized using an xGen Exome v2 Hybridization Panel following the xGen Exome Sequencing Kit Trinity™ for Element AVITI System Protocol. Hybridized libraries were sequencing using a Trinity™ 2 x 150 Sequencing Kit on an Element Biosciences AVITI™ Sequencing System. Following sequencing, samples were downsampled to 40 million reads before analysis using Picard (n = 24 per run).
xGen Hybridization Capture for Trinity™ on the Element Biosciences AVITI™ simplifies exome sequencing unlike any previously available workflow. This workflow moves time consuming steps from the benchtop to your AVITI™ System, saving up to 4 hours of hands-on time without compromising performance.
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Frequently asked questions
Why do the xGen™ Exome Sequencing Kit Trinity™ for Element workflow solution components recommendations default to different reaction sizes when ordering?
How will my xGen™ Exome Sequencing Kit Trinity™ for Element be delivered?
What is the shelf life and recommended storage conditions for the xGen™ Exome Sequencing Kit Trinity™ for Element?
The xGen™ Exome Sequencing Kit Trinity™ for Element has a guaranteed minimum shelf life of 90 days when stored at -20°C and handled according to the protocol.