GRASPER predicts HLA-DR types (DR34, DR33, DR3X, DR44, DR4X and DRXX) based on a minimum subset of SNPS:
- rs3104413 G/C, rs6931277 A/T, rs2187668 A/G, rs9273327 C/A
- rs2854275 A/C, rs3129716 G/A, rs2856674 G/A, rs7454108 G/A
To have an optimal prediction, any of the following two SNPs can be used:
- rs2854275 rs3104413
- rs6931277 rs9273327
- rs2854275 rs6931277
- rs3104413 rs9273327
- rs6931277 rs3129716
- rs3104413 rs3129716
- rs3104413 rs2856674
- rs3104413 rs2187668
- rs6931277 rs2856674
- rs7454108 rs2187668
GRASPER can also predict DR34-DQ8 and/or DR4-DQ7 and DR4-DQ8 if one additional SNP is provided from the followings:
- rs9273363, rs9275184, rs9275495, s9275532, rs9275334
Input data should be in the following format:
- Header is in the 1st line: id,snp1,snp2,...
- Data is from the 2nd line, one sample per line.
- Columns are separated by comma, tab or space.
- Missing values are NA, ? or 0.
- See example