The Allele Frequency Net Database (AFND) is a free online resource that compiles known allele frequencies from different polymorphic areas of the human genome into one searchable database.
The online database currently holds information from over 1,600 population studies with frequencies from more than 10.5 million individuals. Frequencies are included from several immune genes, including:
- 136,000+ Human Leukocyte Antigens (HLA)
- 6,000+ Killer-cell Immunoglobulin-like Receptors (KIR)
- 4,000+ cytokine polymorphisms
- 800+ Major Histocompatibility Class I Chain-related (MIC) genes
I use AFND to predict the allele frequencies I can expect from particular populations, especially those that are not as common in the U.S. Up until recently, we were only testing HLA at low resolution. AFND was useful to predict the suballele that was most likely present. Now, I still find it to be a helpful resource for understanding the frequency of alleles when a customer is looking for something specific.
4 Ways to Use AlleleFrequencies.net
1. Find the Frequency of an Allele Worldwide
We are asked for cells from donors with certain alleles, such as HLA-A*02:01, almost every day while others are only requested from time to time. Limiting research to only HLA-A*02:01 individuals is a very “Euro-centric” approach to immunology, so I encourage researchers to include other alleles in their studies where appropriate.
If you are looking for a more uncommon allele, AFND is a great place to start. Navigate to the HLA Allele Frequency (Classic) tool under HLA on the left hand side of the homepage. Here you can enter your search criteria, including information about your allele, population, region, or sample of interest.
As an example, entering A*02:01 results in a list of populations by country. The map view provides a more interesting look at the data. Simply click the globe icon in any row of the table to view the map. For this particular search, you will notice a cluster of A*02:01 in Europe and a lower frequency in other regions of the world.
If you follow the same process to search for A*11, you will see that this allele is most frequent in China and South Asia. See both examples below.
2. Find the Frequency of an Allele in a Particular Country
If you don’t care about where you allele of interest is found but would rather know how often is is found in a particular country, you can use the same search tool as above, but also specify a country.
As an example, see all of the A*11 frequencies in populations in China. Drill down to see studies reported and suballele frequencies.
3. Discover Drug Interactions with HLA Type
Drug interactions with HLA alleles is intriguing to us immunologists, making this part of the database particularly interesting. Navigate to the HLA and Adverse Drug Reactions tool under HLA on the left side of the homepage.
Query the database by drug name to find the HLA alleles associated with adverse reactions or protection from the adverse reaction.
In addition to offering important information to physicians, these drug-HLA interactions provide researchers with a window into immune system malfunctions.
4. Explore KIR and Cytokine Type
These two tools in AFND, both accessible from the left side of the homepage, offer several ways to explore the frequencies of KIR genotypes and SNP in various cytokine genes.
If you know more about KIR than I do — which most of you do 🙂 — then this area of AFND is perfect for you.
The data sets here are more limited than those available for HLA, but I’m sure the data will become more robust over time. Here are the search and database options for KIR and Cytokines:
- KIR Allele/Gene Frequency Search
- KIR Frequency Maps
- KIR Genotypes
- KIR Linkage Disequilibrium
- IHWC Cell-Lines and CEPH Families
- KIR and Disease Associations
- KIR and HLA Ligands
- KIR Breakdowns
- Cytokine Frequency Search
- Cytokine Breakdowns