NGS Panels

Twist's probes for target enrichment are double-stranded DNA that target both strands for improved sensitivity. They can also be used to enrich targets from cDNA libraries made from RNA.

Yes, please contact customersupport@twistbioscience.com or your Account Manager for more information.

Yes, Twist can design panels using 80bp, 100bp, and 120bp probe lengths.  However, it is recommended you consult with your local Twist Account Manager for more information.

We do not make RNA probes. However, our DNA probes can be used to enrich targets from cDNA libraries made from RNA.

There are no size limitations on custom panel designs.

We are currently using a proprietary model to predict whether or not a probe will be difficult to detect by Illumina sequencing. The inputs to this model include GC content, global complexity (measured as the number of distinct kmers contained in a probe sequence), local complexity (measured as the number of distinct kmers within a limited region of a sequence), and the presence of homopolymers.

Generally, probes with GC content > 85%, homopolymers longer than 20 nt, or tandem repeats of di- or tri- nucleotides longer than 30 nt will be difficult to sequence.

Yes, in addition to designing panels for fusions and SNPs, Twist can also design panels for viruses, MSIs (microsatellite instabilities), structural variants, copy number variants (CNVs), and InDels (insertion/deletions).

Yes, Twist can design a custom panel for Targeted Methylation Sequencing. An application note can be found here.

You can select the transcript database (RefSeq, Gencode, CCDS), specify extra bases into introns, and choose regions to cover within each gene.

Select "Manual Input" and enter your requirements directly into the provided table. You can copy and paste from external sources.

Enter the chromosome, start, and stop positions in the provided table. You can also add optional annotations and specify tiling levels. Please ensure coordinates are 0-based.

Enter probe sequences directly in FASTA format, ensuring all probes are between 80bp and 120bp in length and of the same length.

Enter the chromosome, start, and stop positions, and optionally provide rsIDs. Specify tiling levels as needed. Please ensure coordinates are 0-based.

Ensure all submitted targets are correct and finalized. Make any necessary edits before proceeding to submission.

If your desired reference genome is not available, you can input a custom reference genome and provide a link for the design team to access. Please ensure the reference genome can be accessed.

Select "New Design" and provide a unique name for your panel.

Currently, the tool supports DNA designs. For RNA or Methylation designs, please use our White Glove Submission Sheet/Offline Submission. First, download one of our submission forms, fill your targets, and then provide your details along with the filled form. A member of the Twist team will then be in touch with you about your request.

Download the template file, fill it with your target details, and upload the completed file via the interface.

The standard probe length for a custom panel is 120 bp; however, we do offer custom probe lengths (80, 100, 120 bp, for example). All of the probes in a panel must be the same length.

In 0-based coordinate systems, the first position in a sequence is counted as 0, not 1. For example, in a 0-based system, the first nucleotide of a chromosome is at position 0, the second at position 1, and so on. This is different from 1-based coordinate systems, where the first nucleotide is at position 1. Many bioinformatics tools, including the UCSC Genome Browser, use 0-based coordinates for specifying genomic locations.

Advanced Features include options like repeat filtering, which are recommended for experienced users as they can affect panel performance.

Options include coding exons (default), all exons (coding + UTRs), the whole gene (exons + introns), or custom regions.

Provide a unique identifier for each probe and the probe sequence using only A, T, C, and G bases.

Enter genomic coordinates in BED format (chr, start, stop). SNPs can be entered as RSIDs or coordinates in BED format. Please ensure coordinates are 0-based.

Provide your contact details so our team can reach out if there are any questions about your design. Once completed, hit "Submit" to send your design request to our team.

At Twist, we have developed a filter to remove probes which have significant overlap with repetitive genomic elements (eg. SINE/LINE). Removal of these probes is necessary as they can negatively impact panel performance by capturing unwanted off-target regions. Repeat Filtering Stringency determines the filter's stringency for removing probes that overlap with highly repetitive genomic elements. Options include High, Medium (default), and Low stringency.  We advise users to stick with our default recommendation of Medium.

The Custom Panel Submission Tool allows you to create custom panels for hybridization based target enrichment. It supports designs targeting gene symbols, genomic coordinates, SNPs, and probe sequences.

Tiling specifies the overlap between probes. The default is 1X tiling (no overlap), but you can increase tiling for regions difficult to enrich.

Currently, the tool supports DNA designs. For RNA or Methylation designs, please use our White Glove Submission Sheet.

You can include gene symbols, genomic coordinates, SNPs, or probe sequences.

The TE number is included in the panel name of any previously designed panel (e.g., TE-91234567). The Online Submission ID is found in the confirmation email you received after submission (e.g., OTE-91234567).

If you need additional assistance, contact our support team through the provided link in the tool. You also have access to video walkthroughs and a tour guide to walk you through the submission process.

Your design request will be sent to our team of highly trained bioinformaticians to assess and design individually.

Twist's probes for target enrichment are double-stranded DNA that target both strands for improved sensitivity. They can also be used to enrich targets from cDNA libraries made from RNA.

This tool allows you to input your custom panel design requirements to the Twist team. Your design is not created within this tool.

Select the Quick tour hyperlink in the sidebar for the respective section of the tool you are in.

Select the How-to video hyperlink in the sidebar for the respective section of the tool you are in.

You can select the transcript database (RefSeq, Gencode, CCDS), specify extra bases into introns, and choose regions to cover within each gene.

Enter the chromosome, start, and stop positions in the provided table. You can also add optional annotations and specify tiling levels. Please ensure coordinates are 0-based.

Enter probe sequences directly in FASTA format, ensuring all probes are between 80bp and 120bp in length and of the same length.

Enter the chromosome, start, and stop positions, and optionally provide rsIDs. Specify tiling levels as needed. Please ensure coordinates are 0-based.

Ensure all submitted targets are correct and finalized. Make any necessary edits before proceeding to submission.

Select "New Design" and provide a unique name for your panel.

These complex targets require sophisticated probe placement strategies depending on the nature of the event. To best target these, please follow our offline submission process.

Select "Update Design", enter a new panel name, and provide your previous TE number or Online Submission ID and update instructions. Please note, the tool will not retrieve previous targets from your previous design.

Download the template/example file, fill it with your target details, and upload the completed file via the interface.

There are no limitations to the size of a Twist panel.

Use the Genes target option and use the gene specific settings to input your desired transcripts to be targeted.

Specific requirements, for example covering promoters or 5’ UTR’s for specific genes or transcripts can be specified by toggling the gene specific settings and filling the ‘Extras’ column.

If you have made a mistake or have forgotten to include a target in your design, please contact your Twist Account Manager or reach out to customersupport@twistbioscience.com with your Submission ID. You can then re-submit your design requirements through the submission tool.

To make edits to a previous submission, use the submission ID that was sent to you via email and select ‘Update Design’ within the tool. You will need to input the previous submission ID and specify the requested changes.

To assist with coverage of anchor SNPs to assist in alignment, a higher tiling of 4X can be requested for these targets. There is no guarantee that probes will be specific for your main gene of interest.

In this case, select ‘custom reference genome’ and provide a link to your genome of choice. Please ensure the reference genome can be accessed.

Targets that you know are difficult to capture, due to extremes in GC content or presence of pseudogenes for example can benefit from increased tiling. For these targets, specify a tiling of 4X.

In 0-based coordinate systems, the first position in a sequence is counted as 0, not 1. For example, in a 0-based system, the first nucleotide of a chromosome is at position 0, the second at position 1, and so on. This is different from 1-based coordinate systems, where the first nucleotide is at position 1. Many bioinformatics tools, including the UCSC Genome Browser, use 0-based coordinates for specifying genomic locations. You can find more information here.

Advanced features include options like repeat filtering, which are recommended for experienced users as they can affect panel performance.

Options include coding exons (default), all exons (coding + UTRs), the whole gene (exons + introns), or custom regions.

Provide a unique identifier for each probe and the probe sequence using only A, T, C, and G bases.

Provide your contact details so our team can reach out if there are any questions about your design. Once completed, hit "Submit" to send your design request to our team.

The Custom Panel Submission Tool allows you to create custom panels for hybridization based target enrichment. It supports designs targeting gene symbols, genomic coordinates, SNPs, and probe sequences.

Tiling specifies the number of different probes covering a given nucleotide in your submitted target. The default is 1X tiling which involves probes placed end to end with no overlap, ensuring each target nucleotide is covered by 1 probe. At 2X tiling, an overlap would be introduced between probes to ensure each nucleotide is covered by 2 probes. We suggest that you increase tiling for regions difficult to enrich.

Tiling specifies the number of different probes covering a given nucleotide in your submitted target. The default is 1X tiling which involves probes placed end to end with no overlap, ensuring each target nucleotide is covered by 1 probe. At 2X tiling, an overlap would be introduced between probes to ensure each nucleotide is covered by 2 probes. We suggest that you increase tiling for regions difficult to enrich.

Currently, the tool supports DNA designs. For RNA or Methylation designs, please use our White Glove Submission Sheet/Offline Submission. This can be found here.

You can include gene symbols/transcript accession IDs, genomic coordinates, SNPs, or probe sequences. Currently gene symbols are only supported for human reference genomes.

If you need additional assistance, contact our support team through the provided link in the tool. You also have access to video walkthroughs and a tour guide to walk you through the submission process.

We target all transcripts to ensure comprehensive coverage across all known variations of a gene. This approach captures all possible exons and splice variants, providing flexibility for downstream applications and reducing the risk of missing relevant regions. Targeting all transcripts is especially beneficial when the specific isoform of interest is unknown or when working with diverse sample types or research objectives.

Each database has unique annotations due to differences in gene models, transcript definitions or updates for specific genomes. By targeting all we ensure the most comprehensive and relevant coverage for your application.

Yes, the Exome 2.0 target .bed files for both hg38 and hg19 can be found on our Twist website in our Technical Resources, or click here.

In addition to providing custom panels, Twist also offers the following fixed panels:

1. Human Core Exome
   • 33 Mb in size
   • Covers 99% of ClinVar variants
2. Mouse Exome Panel
   • Based on Mouse Genome assembly mm10
   • 37.7 Mb in size
3. Human Comprehensive Exome
   • 36.8 Mb in size
   • Covers >99% of RefSeq, CCDS, and GENCODE databases
4. PanViral Panel
   • Contains over 600k probes
   • Targets >1,000 viral pathogens
5. SARS-CoV-2 Panel
   • Targets about 30 kb viral genome with approximately 1,000 probes
   • Can detect as little as 10 copies of the virus
6. Human RefSeq Panel
   • Adds 3.6 Mb of content to Core Exome Panel
7. Human Mito Panel
   • Covers 16,569 bp and 37 genes of the human mitochondrial genome
   • Can be used as a primary panel or as a spike-in
8. Twist Respiratory Virus Research Panel
   • Contains 41,047 probes covering viruses from 6 major viral clades
   • At least 4X tiling for each virus

Click here for more information.