Custom Panels

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.

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

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

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.

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

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

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., TE-91234567).

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.

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

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

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.

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.

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.

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.

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.

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

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.

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

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.

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

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

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

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.

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.

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.

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).

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

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).

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.

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

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

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.

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

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

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., TE-91234567).

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.

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

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

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.

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.

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.

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.

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.

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

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.

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

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.

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

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

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

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.

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.

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.

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).

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

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).