Custom Panel Submission Tool

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.

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.

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

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.

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

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.

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

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

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

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

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.

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

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

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

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.

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

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.

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

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

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

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.

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

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.

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

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

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.

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

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

In 0-based coordinate systems, the start of 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.

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.

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.

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.

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.

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.

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

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.

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

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.

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

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

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

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

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.

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

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

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

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.

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

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.

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

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

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

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.

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

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.

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

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

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.

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

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

In 0-based coordinate systems, the start of 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.

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.

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.

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.