Ancestry Tool Help Page
The ancestry qualifier is used to describe the ancestry and geographical location of the cell donor. This can be used in population genetics studies of the HLA alleles. The origin of the cell donor can be used to infer which alleles are found in particular ancestral groups, and the geographical spread of HLA alleles.
Description of Ancestry Qualifier
The databases uses a tree structure to allow a more consistent method of recording the origin of an individual and to improve the query options available. The basic structure of the qualifier is show below:
Ancestry Category - Tribe or Local Area, Country, Region
The first part of the qualifier represents the general ancestry/ethnic group of the cell donor. This splits all entries into groups, providing a general classification of the major ancestry of the cell. These broad groups are based on the Hancestro Ancestry Categories and these groups, as well as brief descriptions based on the Hancestro Catalogue are included here:
| Ancestry | Description |
|---|---|
| Aboriginal Australian | Includes individuals who either self-report or have been described by authors as Australian Aboriginal |
| Admixed | Ancestry which is an admixture of more than one defined ancestral population |
| African | Includes individuals that either self-report or have been described as African, but there was not sufficient information to allow classification as African American, Afro Caribbean or Sub-Saharan African |
| African - Sub-Saharan African | Includes individuals who either self-report or have been described by authors as Sub-Saharan African or one of the subpopulations from this region |
| African descent | Includes individuals who either self-report or have been described by authors as African descent and have geographic qualifiers outside of Africa but are not known to be assigned to African American or Afro-Caribbean. |
| African descent - African American | Includes individuals who either self-report or have been described by authors as African American |
| African descent - Afro-Caribbean | Includes individuals who either self-report or have been described by authors as Afro-Caribbean |
| Asian | Includes individuals that either self-report or have been described as Asian but there was not sufficient information to allow classification as East Asian, Central Asian, South Asian or South-East Asian.. |
| Asian - Central Asia | Includes individuals who either self-report or have been described by authors as Central Asian. |
| Asian - East Asian | Includes individuals who either self-report or have been described by authors as East Asian or one of the sub-populations from this region (e.g Chinese). |
| Asian - South Asian | Includes individuals who either self-report or have been described by authors as South Asian or one of the sub-populations from this region (e.g Indian). |
| Asian - South East Asian | Includes individuals who either self-report or have been described by authors as South East Asian or one of the sub-populations from this region (e.g Vietnamese). |
| European | Includes individuals who either self-report or have been described by authors as European, Caucasian, White or one of the sub-populations from this region (e.g Dutch). |
| Greater Middle Eastern | Includes individuals who self-report or were described by authors as Middle Eastern, North African, Persian or one of the subpopulations from this region (e.g. Saudi Arabian). |
| Hispanic or Latin American | Includes individuals who either self-report or are described by authors as Hispanic, Latino, Latin American or one of the sub-populations from this region. This category includes individuals with known admixture of primarily European, African and Native American ancestries, though some may have also a degree of Asian ancestry (e.g. Peru). |
| Native American | Includes indigenous individuals of North, Central and South America, descended from the original human migration into the Americas from Siberia. |
| Oceanian | Includes individuals that either self-report or have been described by authors as Oceanian or one of the sub-populations from this region (e.g. Native Hawaiian). |
| Undefined | Population for which insufficient information is available to allocate it to a specific ancestral group or which contain individuals from a range of known ancestry categories (e.g. American). |
These broader groupings allow more general queries on the field. The second part of the qualifier details the regional information including local area or tribal group, country and geographic region. This second set of qualifiers permits a more specialised query on particular groups or tribes, and on particular countries or continents. The geographic data is encoded in line wiht the UN geographic definitions as defined here: https://unstats.un.org/unsd/methodology/m49/overview/
Further examples are shown below.
- Terena Indians, Brazil would be listed as Native American - Terena, Brazil, South America
- Italian would be listed as European - Italy, Europe
- Luo Tribe, Kenya would be listed as African - Sub-Sahran African - Luo, Kenya, East Africa
Querying the Ancestry Qualifier
Due to structure of the qualifier it is possible to query the database at a number of levels. The user can make general queries on the ancestral group or more specialised queries on a particular country or region. The structure of all entries means that the query can easily be constructed as all entries follow a standard format. Once the user is used to the simple structure they can begin to construct more advanced queries. Examples of queries are shown below.
| Search Parameters | Query Entered |
|---|---|
| Cells of a particular ethnic group e.g. European | European |
| Cells from a particular tribe or region e.g. Jaidukama | Jaidukama |
| Cells from a particular country e.g. Nigeria | Nigeria |
| Cells from a particular region e.g. Europe | Europe |
Recoding of IPD Ethnicities
The IPD-IMGT/HLA and IPD-KIR Sequence Databases have long maintained information on the source material each allele is derived from. This meta-data includes a description of the ethnicity, race or ancestry of the individual. The descriptive terms used were originally developed over 20 years, and whilst all efforts were made to make sure the terms listed were acceptable, we realise that society has changed and the descriptions used have become out-dated. For this reason, all terminology used in the IPD project has been reviewed and updated to utilise the Human Ancestry Ontology published in Genome Biology (https://rdcu.be/c6ZVu) and available at https://www.ebi.ac.uk/ols/ontologies/hancestro. From Release 3.52.0 of the IPD-IMGT/HLA Database onwards all descriptions will align with the Hancestro ontology. Previous designations will only be available from the Release archives held within our Git Hub Repositories. The IPD-KIR Database will be updated shortly after IPD-IMGT/HLA and prior to the release of Release 2.13 of the database.
References:
- Morales, J., Welter, D., Bowler, E.H. et al.
A standardized framework for representation of ancestry data in genomics studies, with application to the NHGRI-EBI GWAS Catalog
Genome Biol (2018) 19:21.