Total HED-all

Total HED-all

HLA Evolutionary Divergence across eight classical loci:
HLA-A, -B, -C, -DRB1, -DQB1, -DPB1, -DQA1, -DPA1. About

Single sample: allele selection

Start typing to search alleles, suggestions appear from the catalogue. You can also type any allele directly (e.g. A*02:01). Leave a locus blank to skip it.

Class I
Class I
Class I
Class II α
Class II β
Class II α
Class II β
Class II β
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▸ Supported formats

cHED / extended format (comma-separated):

ID,A_1,A_2,B_1,B_2,C_1,C_2,DRB1_1,DRB1_2,DQB1_1,DQB1_2,DPB1_1,DPB1_2,DQA1_1,DQA1_2,DPA1_1,DPA1_2

HLA-HED format (tab-separated):

Sample	A1	A2	B1	B2	C1	C2

T1K single-sample TSV (auto-detected, one file per sample):

HLA-A	...	A*01:01	...	...	A*02:01

T1K multi-sample long format (extracted batch CSV):

Sample_ID,Gene,...,Allele_1,Allele_2,...
sample1,HLA-A,...,HLA-A*01:01,...,HLA-A*02:01,...

Class II columns are optional. Missing alleles: blank, ., or NA. Single alleles give HED = 0.

▸ Allele coverage
Locus Full mode sequence ABS-only mode sequence Source (full) Full alleles ABS-only alleles
HLA-A Exon 2+3 (181 AA) ABS only (32 AA) Lenz CWD + IMGT 3.64.0 5820 228
HLA-B Exon 2+3 (181 AA) ABS only (32 AA) Lenz CWD + IMGT 3.64.0 6978 345
HLA-C Exon 2+3 (181 AA) ABS only (32 AA) Lenz CWD + IMGT 3.64.0 5554 129
HLA-DPA1 Full exon 2 (90 AA) ABS only (9 AA) IMGT 3.64.0 458 458
HLA-DPB1 Full exon 2 (84 AA) ABS only (17 AA) IMGT 3.64.0 1918 1918
HLA-DQA1 Full exon 2 (90 AA) ABS only (10 AA) IMGT 3.64.0 535 535
HLA-DQB1 Full exon 2 (89 AA) ABS only (24 AA) Lenz CWD + IMGT 3.64.0 1939 26
HLA-DRB1 Full exon 2 (89 AA) ABS only (24 AA) Lenz CWD + IMGT 3.64.0 2717 211

Full mode: A/B/C, DRB1, DQB1 use Lenz CWD as the primary source; IMGT/HLA 3.64.0 provides fallback coverage for alleles absent from the CWD catalogue. DPB1, DQA1, DPA1 use IMGT 3.64.0 directly (no Lenz FASTA exists for these loci).
ABS-only mode: A/B/C, DRB1, DQB1 are restricted to the Lenz CWD catalogue (no IMGT fallback — matches original Pierini & Lenz 2018 / Chowell 2019 methodology). DPB1 (17 positions) and DPA1 (9 positions) use ABS positions derived from the HLA-DP crystal structures (Dai 2010, Klobuch 2022); DQA1 (10 positions) from the HLA-DQ2 structures (Kim 2004, Nguyen 2017). Alleles not in catalogue return NA.

▸ Key references
  1. Bjorkman et al. 1987 — HLA-A2 crystal structure; class I ABS positions
    Bjorkman PJ, Saper MA, Samraoui B, Bennett WS, Strominger JL, Wiley DC.
    Nature. 1987;329(6139):506–512.
    DOI: 10.1038/329506a0
  2. Brown et al. 1988 — class II ABS model; source of the DRB1/DQB1 ABS positions used by Lenz
    Brown JH, Jardetzky T, Saper MA, Samraoui B, Bjorkman PJ, Wiley DC.
    Nature. 1988;332(6167):845–850.
    DOI: 10.1038/332845a0
    A modelling paper, not a crystal structure. The experimental HLA-DR1 structure appeared five years later: Brown JH, Jardetzky TS, Gorga JC, Stern LJ, Urban RG, Strominger JL, Wiley DC. Nature. 1993;364(6432):33–39, DOI: 10.1038/364033a0
  3. Chowell et al. 2019 — HED applied to cancer immunotherapy; defines the Original Lenz methodology in clinical context
    Chowell D, Krishna C, Pierini F, Makarov V, Rizvi NA, Kuo F, Morris LGT, Riaz N, Lenz TL, Chan TA.
    Nat Med. 2019;25(11):1715–1720.
    DOI: 10.1038/s41591-019-0639-4
  4. Dai et al. 2010 — first HLA-DP crystal structure (DPB1*02:01); source of DPB1 ABS pocket residues
    Dai S, Murphy GA, Crawford F, Mack DG, Falta MT, Marrack P, Kappler JW, Fontenot AP.
    Proc Natl Acad Sci USA. 2010;107(16):7425–7430.
    DOI: 10.1073/pnas.1001772107  |  PDB: 3LQZ
  5. Klobuch et al. 2022 — HLA-DP1 crystal structure (DPB1*01:01); reverse peptide binding; detailed P1/P6/P9 contacts
    Klobuch S, Lim JJ, van Balen P, Kester MGD, de Klerk W, de Ru AH, Pothast CR, Jedema I, Drijfhout JW, Rossjohn J, Reid HH, van Veelen PA, Falkenburg JHFF, Heemskerk MHM.
    Proc Natl Acad Sci USA. 2022;119(49):e2214331119.
    DOI: 10.1073/pnas.2214331119  |  PDB: 7T6I
  6. Kim et al. 2004 — HLA-DQ2 crystal structure (DQA1*05:01); α-chain peptide contacts and the α53 deletion
    Kim CY, Quarsten H, Bergseng E, Khosla C, Sollid LM.
    Proc Natl Acad Sci USA. 2004;101(12):4175–4179.
    DOI: 10.1073/pnas.0306885101  |  PDB: 1S9V
  7. Nguyen et al. 2017 — HLA-DQ2.5·CLIP structures; the α9–α22–α24–α31 hydrogen bond network
    Nguyen T-B, Jayaraman P, Bergseng E, Madhusudhan MS, Kim C-Y, Sollid LM.
    J Biol Chem. 2017;292(22):9218–9228.
    DOI: 10.1074/jbc.M117.785139  |  PDB: 5KSU / 5KSV
  8. Grantham 1974 — the amino acid distance matrix
    Grantham R. Amino acid difference formula to help explain protein evolution.
    Science. 1974;185(4154):862–864.
    DOI: 10.1126/science.185.4154.862
  9. Pierini & Lenz 2018 — divergent allele advantage; the HED method itself
    Pierini F, Lenz TL.
    Mol Biol Evol. 2018;35(9):2145–2158.
    DOI: 10.1093/molbev/msy116

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