T cells recognize a complex between a specific major histocompatibility complex (MHC) molecule and a particular pathogen-derived epitope. A given epitope will elicit a response only in individuals that express an MHC molecule capable of binding that particular epitope. This phenomenon is known as denominated MHC restriction of T cell responses. MHC molecules are extremely polymorphic and over a thousand different human MHC (HLA) alleles are known. Selecting multiple peptides with different HLA binding specificities will afford increased coverage of the patient population targeted by peptide-based vaccines or diagnostics. The issue of population coverage in relation to MHC polymorphism is further complicated by the fact that different HLA types are expressed at dramatically different frequencies in different ethnicities. Thus, without careful consideration, a vaccine or diagnostic with ethnically biased population coverage could result.

To address the issue, this tool is implemented to calculate the fraction of individuals predicted to respond to a given epitope set on the basis of HLA genotypic frequencies and on the basis of MHC binding and/or T cell restriction data ( Bui et al. 2005). HLA allele genotypic frequencies were obtained from Allele Frequency database (http://www.allelefrequencies.net/). At present, Allele Frequency database provides allele frequencies for 115 countries and 21 different ethnicities grouped into 16 different geographical areas. In addition, the program also accepts custom populations with allele frequencies defined by users. Multiple population coverages can be simultaneously calculated and an average population coverage is generated. Since MHC class I and MHC class II restricted T cell epitopes elicit immune responses from two different T cell populations (CTL and HTL, respectively), the program provides three calculation options to accommodate different coverage modes: (1) class I separate, (2) class II separate, and (3) class I and class II combined. For each population coverage, the tool computes the following: (1) projected population coverage, (2) average number of epitope hits / HLA combinations recognized by the population, and (3) minimum number of epitope hits / HLA combinations recognized by 90% of the population (PC90).

The file must contain data in tab delimited columns. The first line is a required header line. The first three columns are required and their headings are "MHC class", "MHC locus" and "MHC allele." The following column headings are population names. The first column specifies MHC class (I or II). The second column specifies HLA locus (HLA-A, HLA-B, ...). The third column specifies HLA allele ( HLA-A*01:01, HLA-A*02:01, ...). The following columns specify genotypic frequencies (ranging from 0 to 1) of the allele for different populations.
Example:

File should be in simple text format. It should have only one epitope-allele combination per line. Each line should contain a tab-separated epitope name and comma-separated allele names (example given below).
Example:

1. Enter number of epitopes
2. Enter epitope / MHC restriction data
3. Select population(s)
4. Select calculation option(s)
5. Click submit

Note: If you want to add "user population(s)", this should be done before step 1.

The HLA allele frequencies for each of the population categories were estimated as follows: The HLA allele frequencies and associated data for different individual populations from studies around the world were provided by allelefrequencies.net database. The populations were organized into a hierarchy based upon geographical area, country, and ethnicity and the allele frequencies for each merged population were estimated by combining the data from individual populations in each group. The frequencies were estimated for alleles with resolution of 2 sets of digits (e.g. HLA-A*01:01). For this, the data for alleles with resolution of less than 2 sets of digits were excluded (e.g. HLA-A*07, HLA-A*09 etc. which has resolution of only one set of digits) and that for alleles with resolution of more than 2 sets of digits were combined to 2 sets of digits (e.g. HLA-A*02:01:01, HLA-A*02:01:02, HLA-A*02:01:02:01, HLA-A*02:01:02:03 etc. were combined to HLA-A*02:01). The allele frequencies were calculated by estimating the total number of copies of alleles (a) and the number of subjects (n) in each group of populations and using the formula, AF = a/2n. The final set contains frequencies of 3,245 alleles (including class I and class II) for the world, 16 geographical areas, 21 ethnicities, 115 countries and ethnicities by country.