Submission field descriptions
The following table contains detailed information regarding the different data fields required for submission to the IPD-IMGT/HLA Database, including descriptions.
Submission Metadata
Information regarding the submission itself, including submitter ID, email and local name of the sequence.
| Field | Description | |
|---|---|---|
| Submitter ID | Your IPD-IMGT/HLA Submitter ID | |
| Email associated with submission | ||
| Local Name | Local designation of the sequence in your lab. Should not resemble official nomenclature | |
| INSDC Database | All submissions to the database must be included in an public sequence database such as GenBank/ENA/DDBJ. IPD-IMGT/HLA can now broker submissions to ENA on your behalf | |
| INSDC Accession | If already submitted to INSDC, a sequence accession number can be included in submission to IPD-IMGT/HLA | |
| ENA Study Accession | If you wish IPD-IMGT/HLA to broker sequences to ENA on your behalf a registered ENA study accession can be provided | |
Sequence Information
Information regarding the sequence being submitted, including locus, closest named allele, nucleotide sequence and feature annotation.
| Field | Description |
|---|---|
| Locus | The HLA or HLA related locus to be submitted (e.g. HLA-A, HLA-B, HLA-DRB1, MICA) |
| Sequence Type | The level of the sequence (coding/genomic) used to annotate feature coordinates |
| Closest Named Allele | An existing allele in the IPD-IMGT/HLA Database for use in describing the submitted sequence. If a genomic sequence is being submitted a full length closest allele must be provided. For more information on closest named alleles please see our Submission FAQs. |
| Description | A human readable description of the submitted sequence compared to the Closest Named Allele, including all polymorphisms in all regions covered by the submission. The Closest Named Allele must be included in the sequence description. We do not require descriptions in a particular format, however suggest reading HGVS Recommendations for the Description of Sequence Variants for guidance. |
| Nucleotide Sequence | The nucleotide sequence to be submitted as plain text. Please read our submission guidelines for more information. |
| Sequence Features | Automatic exon/intron feature annotation through our web tool is provided by the Sequence Feature Annotation Tool. For API submitters please refer to the SFAT API documentation for more information. |
Cell Information
Information regarding the cell source of the sequence, including ancestry, cell owner and HLA typing, as well as methodology used to generate the sequence.
Any sequence identified in a patient with a malignant disease must be confirmed in the germ line before submitting to the IPD-IMGT/HLA Database.
| Field | Description | |
|---|---|---|
| Cell Name | A unique identifier for the cell source of the submitted sequence. This must not contain any personally identifiable information. | |
| Alias | Any other names the cell has been known by. This is particularly useful of the sequence comes from an established cell line. | |
| Ancestry | Information on the ancestry of the cell source, our ancestry identifiers are taken from the Human Ancestry Ontology. | |
| Broad Ancestry | Broad ancestral group (e.g. African, Asian, European) | |
| Local Designation | Specific population an individual belongs to, or multiple populations for an admixed individual | |
| Country | The country of origin of the individual | |
| Region | The global region of origin of the individual, if the country is not known | |
| Sex | The biological sex of the individual | |
| Consanguineous | Whether the individual is consanguineous | |
| Homozygous | Whether the individual is homozygous for the HLA region | |
| Cell Owner | Information on the original laboratory that isolated the cell | |
| Lab of origin | The name of the laboratory where the cell was originally isolated | |
| Lab Contact | A named individual to contact regarding the cell | |
| Material Avaiable | If and what material of this cell is available for resequencing | |
| Cell Bank | If and what cell bank can this cell be obtained from | |
| IHIW Cell | Is this cell from the collection developedd by the International Histocompatibility and Immunogenetics Workshops | |
| HLA Typing | The HLA typing for the cell source. Minimum HLA typing requirements include both alleles for HLA-A, -B, -DRB1, and the submitted locus | |
Methodology Information
Information regarding the methodology used to generate the sequence, including sequencing method, target enrichment and any secondary methods used to confirm polymorphisms.
| Field | Description |
|---|---|
| Sequencing Method | Sequencing method or platform used to generate the nucleotide sequence |
| Target Enrichment | Method used to amplify the gene for sequencing |
| Secondary Methods | A polymorphism may also be confirmed using a secondary method such as PCR-SSO, PCR-SSP |