IPD-IMGT/HLA

Answers

I'm submitting a genomic extension of a partial allele, but I cannot use that allele in my description?

The closest allele used in the sequence description is used to cross reference the polymorphisms described to the sequence in the submission. If you are submitting a full length sequence, you must include a full length allele in your description. Any allele can be used in the description, and this does not impact the allele designation. If you are submitting a genomic extension of an existing allele that only has coding sequence you must still describe your sequence against a full length allele to ensure you have described any polymorphisms in the introns. You may also include the allele you are extending as a comment in your description.

How do I become a bulk submitter?

Bulk submissions to the database are available to high-throughput organisations that can submit dozens or hundreds of sequence per month. We have recently developed an Application Program Interface (API) to allow for programmtic submissions to the database, suitable for high volumes of submissions. To use the submission API, you must first seek approval from IPD-IMGT/HLA. Approval requires that you have completed a small number of submissions using the standard HLA Submission Tool to a high standard. For information on the use of the submission API please see our Submission API help page. To become and approved API submitter please contact ipdsubs@anthonynolan.org.

What should I use for a cell ID?

The cell ID is a unique identifier for the cell being submitted. It should be a unique and not contain identifying information about the individual the cell was derived from, or additional information about the sample or sequence being submitted. If multiple sequences are submitted from the same cell, the same cell ID should be used for each sequence. The cell ID can be any string of characters, but must be between 6 and 75 characters. We recommend using a combination of letters and numbers to ensure uniqueness. Many submitters use a combination of their lab name or initials and a unique number, e.g. AN300120 is a cell submitted from Anthony Nolan.

How can I get an INSDC accession number?

It is a requirement of submitting to the IPD-IMGT/HLA Database that all sequences also be represented in a public sequence repository such as GenBank, ENA or DDBJ. These databases are part of the International Nucleotide Sequence Database Collaboration (INSDC) and share accession numbers. You can submit your sequences to any of these databases using their respective submission tools. Once your sequence has been accessioned you will be provided with an accession number which can then be included in your submission to IPD-IMGT/HLA.

Alternatively you can now submit your sequences to the IPD-IMGT/HLA Database and we will submit them to ENA on your behalf. In order to do this you will need to register an ENA Study Accession and provide this in your submission and indicate your approval for IPD-IMGT/HLA to broker with ENA on your behalf.

What is an ENA study accession number?

An ENA study accession number is a unique identifier for a study in the European Nucleotide Archive (ENA). All sequences submitted to ENA must be associated with a study. You can register a study using the ENA Study Registration Tool. Once you have registered your study you will be provided with a study accession number which can then be included in your submission to IPD-IMGT/HLA. A study can contain multiple sequences, so if you are submitting multiple sequences you can use the same study accession number for each sequence.

For more information on registering an ENA study please see our ENA Study Registration help page.

What allele should I used for my description?

The sequence description should provide a human readable description of the sequence which we use to cross reference the sequence that has been submitted with the polymorphisms described. It's purpose it to ensure that the sequence we have receied matches that you were intending to submit, and that all polymorphisms included have been considered as correct by the submitter. Any allele can be used in the description, and this does not impact the allele designation. A good allele to include in your description is one that covers the complete region of the submission and has a low number of mismatches. Our only requirement is that full length sequences are compared to full length alleles. This ensures that the submitter is aware of polymorphisms in intron sequences which will not be described against a CDS only allele.

Can I submit partial genomic sequence?

We encourage all submitters, wherever possible, to submit complete genomic sequences. However, we are aware that some regions, such as HLA-DRB1 intron 1, continue to be difficult to fully sequence even with NGS technology. Unfortunately, if you are submitting an intronic variant with partial sequence we will be unable to process your submission, as we require full length sequences (all exons and introns) for inclusion in our genomic alignments, and will not name a polymorphism which we cannot represent to the community. However, if you have a coding polymorphism in a partial genomic sequence we will be able to process this, however the intron sequence will not be represented in the database.

When can I expect to receive my allele designation?

The IPD-IMGT/HLA Database does our best to curate every submission within a month of the submission date. However, incomplete or inaccurate information in the submission can result in delays. If your submission has been delayed you will be contacted by our curators to clarify any issues regarding your submission. If you have not had any contact from IPD-IMGT/HLA after 40 days please contact ipdsubs@anthonynolan.org to get an update on it's processing status.