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Table 1 Alignment result of the HLA gene sequence and genotype in the HLA homozygous cell lines

From: Phase-defined complete sequencing of the HLA genes by next-generation sequencing

Cell line Gene Allele Average depth False heterozygous SNVs Coverage* Closest HLA genotype Note
AKIBA A 24:02 219.5 0 100 A*24:02:01:01  
  C 12:02:02 655.5 0 100 C*12:02:02  
  B 52:01 74.0 0 100 B*52:01:01:02  
  DRB1 15:02 346.9 0 100 DRB1*15:02:01  
  DQB1 06:01:01 33.2 0 100 DQB1*06:01:01  
  DPB1 09:01 604.9 0 100 DPB1*09:01  
AMAI A 68:02 35.2 0 100 A*68:02:01:01  
  C 04:01 159.3 0 100 C*04:01:01:01  
  B 53:01 52.2 0 100 B*53:01:01  
  DRB1 15:03 92.6 0 100 DRB1*15:03:01 2bp (TG) deletion
  DQB1 06:02 133.6 0 100 DQB1*06:02:01  
  DPB1 04:02 94.9 0 100 DPB1*105:01 different from ECACC
ARBO A 03:01 133.5 0 100 A*03:01:01:01  
  C 06:02 208.8 0 100 C*06:02:02:01  
  B 58:02 108.2 0 100 B*58:02  
  DRB1 15:03 43.4 - 86.6 not determined  
  DQB1 06:02 40.0 - 71.5 not determined  
  DPB1 04:02 100.6 0 99.2 not determined  
BM15 A 01:01 79.3 0 100 A*01:01:01:01  
  C 07:01 198.7 0 100 C*07:01:01  
  B 49:01 34.0 0 100 B*49:01:01  
  DRB1 11:02 90.9 0 98.3 not determined  
  DQB1 03:01 14.2 0 100 DQB1*03:01:01:01 2 intronic and 1 nonsynonymous novel variants
  DPB1 03:01 132.0 0 100 DPB1*03:01:01 24 intronic novel variants
BM16 A 02:01 28.6 0 100 A*02:01:01:01  
  C 07:01 249.0 0 100 C*07:01:01:01  
  B 18:01 183.3 0 100 B*18:01:01 3 intronic novel variants
  DRB1 12:01 55.4 0 100 DRB1*12:01:01 43 intronic novel variants
  DQB1 03:01 36.3 0 100 DQB1*03:01:01:01 1 intronic novel variant
  DPB1 02:01:02 58.3 0 100 DPB1*02:01:02 4bp (GGAA) insertion
BM21 A 01:01 61.0 0 100 A*01:01:01:01  
  C 17:01 233.0 0 100 C*17:01:01:02  
  B 41:01 176.3 0 100 B*41:01  
  DRB1 11:01 80.0 0 100 DRB1*11:01:01  
  DQB1 03:01 17.8 9 99.7 DQB1*03:01:01:01  
  DPB1 10:01 103.8 0 100 DPB1*10:01  
BM92 A 25:01:01 24.1 0 100 A*25:01:01  
  C 01:02 458.0 0 100 C*01:02:01  
  B 51:01:01 218.0 0 100 B*51:01:01  
  DRB1 04:04 2.9 - 32.9 not determined  
  DQB1 03:01 1.1 - 0 not determined  
  DPB1 04:02 115.6 0 100 DPB1*04:02:01  
Boleth A 02:01:01:01 25.7 1 100 A*02:01:01:01  
  C 03:04 273.3 0 100 C*03:04:01:01  
  B 15:01 260.2 0 100 B*15:01:01:01  
  DRB1 04:01:01 27.1 0 98.4 not determined  
  DQB1 03:02:01 67.2 0 100 DQB1*03:02:01  
  DPB1 04:01:01 99.1 0 100 DPB1*04:01:01  
BSM A 02:01 56.9 0 100 A*02:01:01:01  
  C 03:04 238.6 0 100 C*03:04:01:01  
  B 15:01 204.3 0 100 B*15:01:01:01  
  DRB1 04:01 18.3 0 98.4 not determined  
  DQB1 03:02 91.1 0 100 DQB1*03:02:01  
  DPB1 02:01:02 57.6 0 100 DPB1*02:01:02  
Carogero A 02:01 28.2 0 100 A*02:01:01:01  
  C 20:22 22.8 0 100 C*02:02:02  
  B 40:02 6.1 - 91 not determined  
  DRB1 - 16.8 0 100 DRB1*16:01:02  
  DQB1 - 27.5 0 100 DQB1*05:02:01  
  DPB1 04:01 18.8 0 99.7 not determined  
COX A 01:01:01:01 99.1 0 100 A*01:01:01:01  
  C 07:01:01 322.2 0 100 C*07:01:01  
  B 08:01:01 123.5 0 100 B*08:01:01  
  DRB1 03:01 284.9 0 100 DRB1*03:01:01  
  DQB1 02:01 367.3 0 100 DQB1*02:01:01  
  DPB1 03:01 270.5 0 100 DPB1*03:01:01  
DBB A 02:01 454.2 0 100 A*02:01:01  
  C 06:02 636.8 0 100 C*06:02:01:01  
  B 57:01 142.5 0 100 B*57:01:01  
  DRB1 07:01 14.3 - 90.7 not determined  
  DQB1 30:32 1.9 - 70.8 not determined  
  DPB1 04:01 568.0 0 100 DPB1*04:01:01:01  
DHI A 31:01 2.2 - 12.9 not determined  
  C 12:03 292.9 0 100 C*12:03:01:01  
  B 38:01 250.1 0 100 B*38:01:01  
  DRB1 11:01 57.2 0 100 DRB1*11:01:01  
  DQB1 03:01 140.1 0 100 DQB1*03:01:01:03  
  DPB1 04:01 302.2 0 100 DPB1*04:01:01:01  
DKB A 24:02 358.6 0 100 A*24:02:01 1 intronic novel variant
  C 03:04 502.8 0 100 C*03:04:01:01  
  B 40:01 634.1 0 100 B*40:01:02  
  DRB1 90:12 61.4 - 65 not determined  
  DQB1 30:32 310.1 0 100 DQB1*03:03:02:02  
  DPB1 04:01 259.2 0 100 DPB1*04:01:01:01  
HARA A 24:02:01:01 122.6 0 100 A*30:01:01 different from ECACC
  C 12:02 214.3 0 100 C*12:02:02  
  B 52:01:01 189.1 0 100 B*52:01:01:02  
  DRB1 15:02:01 4.5 0 97.5 not determined  
  DQB1 06:01 124.6 0 100 DQB1*06:01:01  
  DPB1 09:01 52.9 - 97.6 not determined  
HHK A 03:01 265.9 0 100 A*03:01:01:01  
  C 07:02 84.6 0 100 C*07:02:01:03  
  B 07:02 11.5 0 100 B*07:02:01  
  DRB1 13:01 47.7 0 100 DRB1*13:01:01  
  DQB1 06:03 103.3 0 100 DQB1*06:03:01  
  DPB1 04:01 65.1 0 100 DPB1*04:01:01:01  
HOKKAIDO A - 8.0 0 100 A*24:02:01:01  
  C - 42.8 0 100 C*03:04:01:02  
  B - 99.0 0 100 B*54:01:01  
  DRB1 04:05 8.2 - 11.6 not determined  
  DQB1 04:01 48.4 - 57.4 not determined  
  DPB1 05:01 70.4 0 100 DPB1*05:01:01  
JBUSH A 32:01 10.9 1 100 A*32:01:01  
  C 12:03 128.8 0 100 C*12:03:01:01  
  B 38:01 298.3 0 100 B*38:01:01  
  DRB1 11:01 23.7 0 100 DRB1*11:01:03  
  DQB1 03:01 80.1 0 100 DQB1*03:01:01  
  DPB1 04:01 86.7 0 100 DPB1*04:01:01:01  
JEST A 02:01 11.3 0 100 A*02:01:01  
  C 01:02 80.3 0 100 C*01:02:01  
  B 27:05:02 76.8 0 100 B*27:05:02 1 intronic novel variant
  DRB1 01:01 16.3 0 100 DRB1*01:01:01  
  DQB1 05:01 87.5 0 100 DQB1*05:01:01 1 intronic novel variant
  DPB1 04:01 69.1 0 100 DPB1*04:01:01:01  
K265 A - 127.1 0 100 A*03:01:01:01  
  C 12:02 163.7 0 100 C*07:02:01:03  
  B - 54.3 0 100 B*07:02:01  
  DRB1 15:02 92.7 0 100 DRB1*15:01:01  
  DQB1 - 257.5 0 100 DQB1*06:02:01  
  DPB1 - 107.8 0 100 DPB1*04:01:01:01  
LBUF A 30:01:01 26.9 0 100 A*30:01:01  
  C 06:02 326.3 0 100 C*06:02:01:01  
  B 13:02:01 249.1 0 100 B*13:02:01  
  DRB1 07:01:01 16.6 0 100 DRB1*07:01:02  
  DQB1 02:02 2.9 - 18.9 not determined  
  DPB1 17:01 177.9 0 100 DPB1*17:01  
LKT3 A 24:02 86.9 0 100 A*24:02:01  
  C 01:02 213.3 0 100 C*01:02:01  
  B 54:01 48.7 0 100 B*54:01:01  
  DRB1 08:01 23.4 - 55.4 not determined  
  DQB1 04:01 1.1 - 0 not determined  
  DPB1 05:01 227.8 0 100 DPB1*05:01:01  
MADULA A 02:01 86.8 0 100 A*02:01:01  
  C 03:04 206.9 0 100 C*03:04:01  
  B 40:01 223.8 0 100 B*40:01:02  
  DRB1 08:01 42.6 0 100 DRB1*08:01:03  
  DQB1 04:02 123.9 - 86.3 not determined  
  DPB1 04:01 215.6 0 100 DPB1*04:01:01  
PITOUT A 29:02 91.5 0 100 A*29:02:01  
  C 16:01 51.8 0 100 C*16:01:01  
  B 44:03:01 74.6 0 99.4 not determined  
  DRB1 07:01 3.2   40.4 not determined  
  DQB1 02:01 38.3 0 100 DQB1*02:02 different from ECACC
  DPB1 04:01 340.7 0 100 DPB1*04:01:01  
RMAL A 02:04 75.8 0 100 A*02:04  
  C 15:02 68.6 0 100 C*15:02:01  
  B 51:01 21.9 0 100 B*51:01:01  
  DRB1 16:02 63.5 0 100 DRB1*16:02:02 3 intronic novel variants
  DQB1 03:01 16.2 0 100 DQB1*03:01:01  
  DPB1 04:02 66.8 0 100 DPB1*04:02:01  
SAVC A 03:01 99.4 0 100 A*03:01:01:01  
  C 07:02 140.3 0 100 C*07:02:01  
  B 07:02 45.3 0 100 B*07:02:01  
  DRB1 04:01 2.4 - 50.3 not determined  
  DQB1 03:02 1.2 - 12.9 not determined  
  DPB1 10:01 129.2 0 100 DPB1*10:01  
SRACH A 31:01 14.5 - 1.5 not determined  
  C 01:02 388.3 0 100 C*01:02:01  
  B 15:01 688.5 0 100 B*15:01:0101  
  DRB1 08:02:01 61.5 0 100 DRB1*08:02:01  
  DQB1 04:02 174.0 - 91 not determined  
  DPB1 04:02 207.0 0 100 DPB1*04:02:01  
T182 A 24:02 12.4 0 100 A*24:02:01:01  
  C 12:02:02 113.5 0 100 C*12:02:02  
  B 52:01 106.0 0 100 B*52:01:01:02  
  DRB1 15:02 4.9 - 0 not determined  
  DQB1 06:01 72.2 0 100 DQB1*06:01:01  
  DPB1 09:01 69.2 0 98.3 not determined  
TAB089 A 02:07 13.3 0 98.3 not determined  
  C 01:02 101.9 0 100 C*01:02:01  
  B 46:01 36.9 0 100 B*46:01:01  
  DRB1 02:02 2.7 - 91.1 not determined  
  DQB1 06:01 49.1 1 100 DQB1*06:01:01  
  DPB1 02:02 39.2 0 100 DPB1*02:02 9 intronic novel variants
TOK A 24:02 286.2 0 100 A*24:02:01:01  
  C 12:02:02 241.5 0 100 C*12:02:02  
  B 52:01 127.9 0 100 B*52:01:01:02  
  DRB1 15:02 163.7 0 100 DRB1*15:02:01  
  DQB1 06:01 243.1 0 100 DQB1*06:01:01  
  DPB1 09:01 175.2 0 100 DPB1*09:01  
VAVY A 01:01 36.1 0 100 A*01:01:01:01  
  C 07:01 141.6 0 100 C*07:01:01  
  B 08:01 535.1 0 100 B*08:01:01  
  DRB1 03:01 43.4 0 100 DRB1*03:01:01  
  DQB1 02:01 126.4 0 100 DQB1*02:01:01:01  
  DPB1 01:01 57.0 0 100 DPB1*01:01:01  
WT100 A 11:01 66.4 0 100 A*11:01:01  
  C 04:01 112.9 0 100 C*04:01:01:02  
  B 35:01 15.9 0 100 B*35:01:01  
  DRB1 01:01 143.5 0 100 DRB1*01:01:01  
  DQB1 05:01 136.4 0 100 DQB1*05:01:01 1 intronic novel variant
  DPB1 01:01 122.0 0 100 DPB1*01:01:01  
WT47 A 32:01 56.5 0 100 A*32:01:01  
  C 05:01 192.5 0 100 C*05:01:01  
  B 44:02 47.8 0 100 B*44:02:01  
  DRB1 13:02 116.1 0 100 DRB1*13:02:01 4 intronic novel variants
  DQB1 06:04 807.8 0 100 DQB1*06:04:01  
  DPB1 16:01 172.2 0 100 DPB1*16:01  
  1. * Percentage of the HLA gene covered by reads that passed the Q20 threshold for nucleotide quality.
  2. Confirmed by sanger sequence.