MiDAS_vignette.RmdMiDAS is a comprehensive R package for immunogenetic data manipulation and statistical analysis. MiDAS recodes input data in the form of HLA alleles and KIR types into biologically meaningful variables, allowing HLA amino acid fine mapping, analyses of HLA evolutionary divergence as well as validated HLA-KIR interactions. Further, it allows comprehensive statistical association analysis workflows with phenotypes of diverse measurement scales. MiDAS thus closes the gap between the inference of immunogenetic variation and its efficient utilization to make relevant discoveries related to T cell, Natural Killer cell, and disease biology.
MiDAS includes functions to read HLA and KIR typing
data, checking for the correct format and adherence to the right
nomenclature. HLA calls can be reduced to a desired resolution when
importing it, e.g. from 6-digit to 4-digit. Phenotypic observations can
be read e.g. using the read.table function (make sure to
include stringsAsFactors = FALSE argument).
pheno_file <- system.file("extdata", "MiDAS_tut_pheno.txt", package = "midasHLA")
pheno <- read.table(pheno_file, header = TRUE, stringsAsFactors = FALSE)| ID | disease | lab_value | outcome |
|---|---|---|---|
| P001 | 1 | -0.85 | 1 |
| P002 | 1 | -1.60 | 1 |
| P003 | 1 | -1.04 | 0 |
| P004 | 1 | -0.92 | 0 |
| P005 | 1 | -0.42 | 1 |
| P006 | 1 | -1.53 | 0 |
| P007 | 1 | 0.48 | 1 |
| P008 | 1 | -1.88 | 0 |
| P009 | 1 | 0.88 | 0 |
| P010 | 1 | -0.68 | 0 |
# HLA calls can be loaded using the readHlaCalls function with the desired resolution
hla_calls_file <- system.file("extdata", "MiDAS_tut_HLA.txt", package = "midasHLA")
hla_calls <- readHlaCalls(hla_calls_file, resolution = 4)| ID | A_1 | A_2 | B_1 | B_2 | C_1 | C_2 | DPA1_1 | DPA1_2 | DPB1_1 | DPB1_2 | DQA1_1 | DQA1_2 | DQB1_1 | DQB1_2 | DRA_1 | DRA_2 | DRB1_1 | DRB1_2 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| C001 | A*25:01 | A*26:01 | B*07:02 | B*18:01 | C*12:03 | C*07:02 | DPA1*01:03 | DPA1*01:03 | DPB1*02:01 | DPB1*04:01 | DQA1*05:05 | DQA1*01:02 | DQB1*06:02 | DQB1*03:01 | DRA*01:02 | DRA*01:02 | DRB1*15:01 | DRB1*12:01 |
| C002 | A*02:01 | A*02:324 | B*50:01 | B*18:01 | C*06:02 | C*12:03 | DPA1*01:03 | DPA1*01:03 | DPB1*04:02 | DPB1*04:02 | DQA1*02:01 | DQA1*05:05 | DQB1*02:02 | DQB1*03:01 | DRA*01:01 | DRA*01:01 | DRB1*07:01 | DRB1*11:04 |
| C003 | A*24:02 | A*24:04 | B*46:01 | B*40:06 | C*01:03 | C*15:02 | DPA1*02:02 | DPA1*02:01 | DPB1*05:01 | DPB1*14:01 | DQA1*01:04 | DQA1*01:03 | DQB1*06:01 | DQB1*05:02 | DRA*01:02 | DRA*01:01 | DRB1*14:07 | DRB1*08:03 |
| C004 | A*01:01 | A*24:02 | B*08:01 | B*15:01 | C*07:01 | C*03:03 | DPA1*01:03 | DPA1*01:03 | DPB1*04:01 | DPB1*03:01 | DQA1*01:03 | DQA1*01:02 | DQB1*06:04 | DQB1*06:03 | DRA*01:02 | DRA*01:01 | DRB1*13:01 | DRB1*13:02 |
| C005 | A*01:01 | A*25:01 | B*18:01 | B*08:01 | C*12:03 | C*07:01 | DPA1*01:03 | DPA1*01:03 | DPB1*04:01 | DPB1*23:01 | DQA1*05:01 | DQA1*01:02 | DQB1*02:01 | DQB1*06:02 | DRA*01:02 | DRA*01:02 | DRB1*03:01 | DRB1*15:01 |
| C006 | A*03:01 | A*01:01 | B*07:02 | B*08:01 | C*07:01 | C*07:02 | DPA1*01:03 | DPA1*01:03 | DPB1*57:01 | DPB1*271:01 | DQA1*01:02 | DQA1*01:01 | DQB1*06:04 | DQB1*05:01 | DRA*01:01 | DRA*01:02 | DRB1*13:02 | DRB1*01:02 |
| C007 | A*01:01 | A*02:01 | B*15:01 | B*08:01 | C*07:01 | C*03:03 | DPA1*02:01 | DPA1*01:03 | DPB1*04:02 | DPB1*13:01 | DQA1*05:01 | DQA1*03:01 | DQB1*02:01 | DQB1*03:02 | DRA*01:01 | DRA*01:02 | DRB1*03:01 | DRB1*04:01 |
| C008 | A*11:01 | A*02:01 | B*35:01 | B*27:05 | C*03:04 | C*04:01 | DPA1*01:03 | DPA1*01:03 | DPB1*04:01 | DPB1*04:01 | DQA1*03:03 | DQA1*01:02 | DQB1*06:04 | DQB1*03:01 | DRA*01:02 | DRA*01:01 | DRB1*13:02 | DRB1*04:01 |
| C009 | A*23:01 | A*01:01 | B*13:02 | B*18:01 | C*07:01 | C*07:02 | DPA1*02:01 | DPA1*01:03 | DPB1*01:01 | DPB1*04:02 | DQA1*05:05 | DQA1*03:01 | DQB1*03:01 | DQB1*03:02 | DRA*01:01 | DRA*01:01 | DRB1*11:04 | DRB1*04:03 |
| C010 | A*31:01 | A*02:06 | B*15:01 | B*56:01 | C*04:01 | C*03:03 | DPA1*02:02 | DPA1*02:02 | DPB1*05:01 | DPB1*05:01 | DQA1*03:02 | DQA1*03:02 | DQB1*03:03 | DQB1*03:96 | DRA*01:01 | DRA*01:01 | DRB1*09:01 | DRB1*09:01 |
# KIR calls (currently presence/absence calls, no allele-level resolution) can be loaded using the readKirCalls function
kir_calls_file <- system.file("extdata", "MiDAS_tut_KIR.txt", package = "midasHLA")
kir_calls <- readKirCalls(kir_calls_file)| ID | KIR3DL3 | KIR2DS2 | KIR2DL2 | KIR2DL3 | KIR2DP1 | KIR2DL1 | KIR3DP1 | KIR2DL4 | KIR3DL1 | KIR3DS1 | KIR2DL5 | KIR2DS3 | KIR2DS5 | KIR2DS4 | KIR2DS1 | KIR3DL2 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| C001 | 1 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 1 |
| C002 | 1 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 1 |
| C003 | 1 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | 1 | 0 | 1 | 1 |
| C004 | 1 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | 1 | 0 | 1 | 1 |
| C005 | 1 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 |
| C006 | 1 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 1 |
| C007 | 1 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 1 |
| C008 | 1 | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 1 |
| C009 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 0 | 1 | 1 |
| C010 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 0 | 1 | 0 | 1 | 1 |
For convenience, we will here use test data shipped with the package.
HLA <- reduceHlaCalls(MiDAS_tut_HLA, resolution = 4)
KIR <- MiDAS_tut_KIR
pheno <- MiDAS_tut_phenoMiDAS provides the prepareMiDAS function to
combine genetic and phenotypic data for subsequent analysis. In this
step, it is also possible to infer amino acid level information from HLA
calls, encode HLA-KIR interactions, or calculate HLA evolutionary
divergence (experiment argument).
midas <- prepareMiDAS(
hla_calls = HLA,
kir_calls = KIR,
colData = pheno,
experiment = c("hla_alleles", "hla_aa")
)A MiDAS object contains our input data as well as defined
transformations. This is an extension of a
MultiAssayExperiment and can be handled as such.
MiDAS provides some functions to interact with
MiDAS objects (check ?MiDAS-class for a full
list).
For example, we can explore the HLA alleles frequencies, compare them with published frequencies from the allelefrequencies.net database, and filter out low frequency alleles.
freq <- getFrequencies(
object = midas,
carrier_frequency = FALSE,
experiment = "hla_alleles",
compare = TRUE
)| term | Counts | Freq | USA NMDP African American pop 2 | USA NMDP Chinese | USA NMDP European Caucasian | USA NMDP Hispanic South or Central American | USA NMDP Japanese | USA NMDP North American Amerindian | USA NMDP South Asian Indian |
|---|---|---|---|---|---|---|---|---|---|
| A*01:01 | 236 | 0.1180 | 0.046700 | 0.014500 | 0.1646000 | 0.072600 | 0.01000 | 0.12020 | 0.154500 |
| A*01:02 | 2 | 0.0010 | 0.004200 | NA | 0.0001000 | 0.001400 | NA | 0.00020 | 0.000005 |
| A*01:234 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| A*01:237 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| A*01:274 | 4 | 0.0020 | NA | NA | NA | NA | NA | NA | NA |
| A*01:43 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | 0.000008 |
| A*01:98 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| A*02:01 | 486 | 0.2430 | 0.123500 | 0.094600 | 0.2755000 | 0.209500 | 0.14800 | 0.27760 | 0.049200 |
| A*02:02 | 2 | 0.0010 | 0.041400 | 0.000100 | 0.0009000 | 0.007600 | 0.00004 | 0.00140 | 0.000200 |
| A*02:03 | 7 | 0.0035 | 0.000200 | 0.077400 | 0.0000193 | 0.000200 | 0.00140 | 0.00003 | 0.011000 |
| A*02:05 | 17 | 0.0085 | 0.014900 | 0.001400 | 0.0097000 | 0.014800 | 0.00060 | 0.00720 | 0.010000 |
| A*02:06 | 22 | 0.0110 | 0.000700 | 0.034900 | 0.0018000 | 0.019800 | 0.07480 | 0.02750 | 0.017500 |
| A*02:07 | 7 | 0.0035 | 0.000017 | 0.094800 | 0.0000392 | 0.000055 | 0.02000 | 0.00003 | 0.000600 |
| A*02:08 | 2 | 0.0010 | 0.000001 | 0.000005 | 0.0000121 | 0.000007 | NA | NA | 0.000200 |
| A*02:10 | 3 | 0.0015 | NA | 0.001100 | NA | NA | NA | NA | 0.000026 |
| A*02:211 | 1 | 0.0005 | NA | NA | NA | 0.000007 | NA | 0.00001 | NA |
| A*02:22 | 1 | 0.0005 | 0.000079 | 0.000030 | 0.0000640 | 0.005600 | NA | 0.00008 | 0.000013 |
| A*02:324 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| A*02:60 | 1 | 0.0005 | 0.000500 | NA | 0.0000012 | 0.000017 | NA | NA | NA |
| A*02:614 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| A*02:642 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| A*02:686 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| A*02:753 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| A*02:763 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| A*03:01 | 199 | 0.0995 | 0.083900 | 0.014000 | 0.1399000 | 0.073800 | 0.00900 | 0.10440 | 0.063600 |
| A*03:02 | 13 | 0.0065 | 0.000400 | 0.000600 | 0.0024000 | 0.002500 | 0.00100 | 0.00150 | 0.008600 |
| A*03:205 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| A*03:24 | 1 | 0.0005 | 0.000005 | NA | NA | NA | NA | NA | NA |
| A*03:312 | 3 | 0.0015 | NA | NA | NA | NA | NA | NA | NA |
| A*03:72 | 2 | 0.0010 | NA | NA | NA | NA | NA | NA | NA |
| A*11:01 | 114 | 0.0570 | 0.014200 | 0.275200 | 0.0609000 | 0.045600 | 0.08740 | 0.04880 | 0.139600 |
| A*11:02 | 1 | 0.0005 | 0.000005 | 0.026300 | 0.0000056 | 0.000014 | NA | NA | 0.000100 |
| A*11:03 | 1 | 0.0005 | 0.000008 | 0.000065 | NA | 0.000007 | NA | 0.00001 | 0.000400 |
| A*11:12 | 1 | 0.0005 | NA | 0.000010 | 0.0000080 | 0.000007 | NA | NA | 0.000003 |
| A*11:306 | 3 | 0.0015 | NA | NA | NA | NA | NA | NA | NA |
| A*11:43 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| A*11:50Q | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| A*11:88 | 3 | 0.0015 | NA | NA | NA | NA | NA | NA | NA |
| A*23:01 | 47 | 0.0235 | 0.109900 | 0.002100 | 0.0197000 | 0.036800 | 0.00110 | 0.01810 | 0.006600 |
| A*23:17 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| A*23:18 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| A*24:02 | 228 | 0.1140 | 0.024500 | 0.151900 | 0.0846000 | 0.131600 | 0.35300 | 0.12920 | 0.136200 |
| A*24:03 | 2 | 0.0010 | 0.000400 | 0.001400 | 0.0019000 | 0.004900 | 0.00010 | 0.00480 | 0.006000 |
| A*24:04 | 1 | 0.0005 | NA | 0.000100 | NA | NA | NA | NA | 0.000038 |
| A*24:07 | 2 | 0.0010 | 0.000500 | 0.004500 | 0.0000690 | 0.000300 | 0.00070 | 0.00010 | 0.011200 |
| A*24:104 | 2 | 0.0010 | NA | NA | NA | NA | NA | NA | NA |
| A*24:20 | 4 | 0.0020 | 0.000004 | 0.001400 | 0.0000004 | NA | NA | NA | 0.000043 |
| A*24:50 | 4 | 0.0020 | NA | NA | NA | NA | NA | NA | NA |
| A*24:95 | 1 | 0.0005 | NA | NA | 0.0000004 | 0.000007 | NA | NA | NA |
| A*25:01 | 52 | 0.0260 | 0.003400 | 0.000200 | 0.0210000 | 0.010100 | 0.00070 | 0.01480 | 0.000100 |
| A*25:09 | 2 | 0.0010 | NA | NA | NA | NA | NA | NA | NA |
| A*25:25 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| A*26:01 | 90 | 0.0450 | 0.014600 | 0.023700 | 0.0309000 | 0.029500 | 0.07980 | 0.01990 | 0.041800 |
| A*26:02 | 4 | 0.0020 | 0.000005 | 0.000100 | 0.0000068 | 0.000024 | NA | NA | 0.000025 |
| A*26:03 | 2 | 0.0010 | 0.000010 | 0.000100 | 0.0000036 | 0.000034 | 0.02330 | 0.00001 | 0.000014 |
| A*26:08 | 3 | 0.0015 | 0.000100 | 0.000003 | 0.0010000 | 0.000900 | NA | 0.00090 | NA |
| A*26:16 | 1 | 0.0005 | NA | NA | 0.0000002 | 0.000002 | NA | NA | NA |
| A*29:01 | 6 | 0.0030 | 0.000300 | 0.007600 | 0.0027000 | 0.002100 | 0.00030 | 0.00170 | 0.013200 |
| A*29:02 | 45 | 0.0225 | 0.031800 | 0.001000 | 0.0353000 | 0.044100 | 0.00180 | 0.02740 | 0.001300 |
| A*29:119 | 3 | 0.0015 | NA | NA | NA | NA | NA | NA | NA |
| A*30:01 | 37 | 0.0185 | 0.068500 | 0.027400 | 0.0130000 | 0.019900 | 0.00190 | 0.01090 | 0.017300 |
| A*30:02 | 44 | 0.0220 | 0.066700 | 0.000300 | 0.0090000 | 0.027300 | 0.00060 | 0.01160 | 0.002400 |
| A*30:04 | 3 | 0.0015 | 0.002200 | 0.000200 | 0.0015000 | 0.002500 | 0.00030 | 0.00110 | 0.000200 |
| A*31:01 | 58 | 0.0290 | 0.010000 | 0.024200 | 0.0270000 | 0.043900 | 0.08490 | 0.07370 | 0.033100 |
| A*31:08 | 1 | 0.0005 | NA | NA | 0.0000101 | NA | NA | NA | NA |
| A*31:21 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| A*32:01 | 58 | 0.0290 | 0.015000 | 0.006200 | 0.0355000 | 0.026100 | 0.00170 | 0.02540 | 0.038600 |
| A*32:02 | 1 | 0.0005 | NA | NA | 0.0000028 | 0.000007 | NA | NA | 0.000003 |
| A*32:116 | 4 | 0.0020 | NA | NA | NA | NA | NA | NA | NA |
| A*33:01 | 20 | 0.0100 | 0.020600 | 0.000500 | 0.0081000 | 0.021800 | 0.00020 | 0.00660 | 0.001200 |
| A*33:03 | 16 | 0.0080 | 0.051800 | 0.101100 | 0.0032000 | 0.008200 | 0.06480 | 0.00390 | 0.099200 |
| A*33:05 | 2 | 0.0010 | 0.000013 | NA | 0.0000986 | 0.000020 | NA | 0.00001 | NA |
| A*33:125 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| A*33:163 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| A*33:51 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| A*34:01 | 1 | 0.0005 | 0.000077 | 0.001100 | 0.0000398 | 0.000200 | 0.00060 | 0.00020 | 0.000100 |
| A*34:02 | 6 | 0.0030 | 0.033500 | 0.000016 | 0.0009000 | 0.004600 | NA | 0.00190 | 0.000040 |
| A*66:01 | 10 | 0.0050 | 0.014100 | 0.000200 | 0.0041000 | 0.006400 | 0.00010 | 0.00320 | 0.000300 |
| A*68:01 | 53 | 0.0265 | 0.039500 | 0.004000 | 0.0319000 | 0.048000 | 0.00170 | 0.03810 | 0.067600 |
| A*68:02 | 21 | 0.0105 | 0.060300 | 0.000100 | 0.0084000 | 0.024800 | 0.00030 | 0.00790 | 0.000300 |
| A*68:04 | 1 | 0.0005 | 0.000001 | NA | NA | 0.000003 | NA | NA | 0.000003 |
| A*68:16 | 1 | 0.0005 | NA | NA | NA | 0.000037 | NA | NA | 0.000001 |
| A*68:164 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| A*68:17 | 1 | 0.0005 | 0.000011 | 0.000002 | 0.0000012 | 0.000100 | NA | NA | NA |
| A*68:23 | 1 | 0.0005 | NA | NA | 0.0000008 | 0.000017 | NA | NA | NA |
| A*68:66 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| A*69:01 | 6 | 0.0030 | 0.000200 | 0.001000 | 0.0014000 | 0.002800 | 0.00008 | 0.00070 | 0.000600 |
| A*74:01 | 2 | 0.0010 | 0.054600 | 0.001400 | 0.0004000 | 0.007300 | 0.00010 | 0.00230 | 0.001500 |
| B*07:02 | 152 | 0.0760 | 0.072900 | 0.007900 | 0.1306000 | 0.058400 | 0.05880 | 0.10050 | 0.044000 |
| B*07:04 | 1 | 0.0005 | 0.000008 | 0.000005 | 0.0003000 | 0.000017 | 0.00002 | 0.00010 | NA |
| B*07:05 | 5 | 0.0025 | 0.008200 | 0.008300 | 0.0030000 | 0.005200 | 0.00070 | 0.00210 | 0.025000 |
| B*07:06 | 5 | 0.0025 | NA | NA | NA | NA | NA | NA | NA |
| B*07:10 | 1 | 0.0005 | 0.000022 | NA | 0.0000616 | 0.000007 | NA | NA | 0.000003 |
| B*07:14 | 1 | 0.0005 | 0.000007 | 0.000005 | 0.0000286 | 0.000092 | NA | NA | NA |
| B*07:22 | 1 | 0.0005 | 0.000002 | NA | 0.0000052 | NA | NA | NA | NA |
| B*07:47 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| B*08:01 | 128 | 0.0640 | 0.037600 | 0.004600 | 0.1144000 | 0.039000 | 0.00510 | 0.08220 | 0.036600 |
| B*08:156 | 2 | 0.0010 | NA | NA | NA | NA | NA | NA | NA |
| B*08:94 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| B*13:01 | 5 | 0.0025 | 0.000097 | 0.063500 | 0.0000961 | 0.000200 | 0.01110 | 0.00020 | 0.013600 |
| B*13:02 | 74 | 0.0370 | 0.007800 | 0.029100 | 0.0239000 | 0.012800 | 0.00370 | 0.01640 | 0.018400 |
| B*13:117 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| B*14:01 | 22 | 0.0110 | 0.007900 | 0.000200 | 0.0102000 | 0.008900 | 0.00070 | 0.00790 | 0.000200 |
| B*14:02 | 40 | 0.0200 | 0.021600 | 0.001000 | 0.0286000 | 0.044100 | 0.00120 | 0.02040 | 0.001700 |
| B*14:28 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| B*15:01 | 86 | 0.0430 | 0.010800 | 0.030000 | 0.0606000 | 0.027100 | 0.07690 | 0.06160 | 0.016100 |
| B*15:02 | 6 | 0.0030 | 0.000300 | 0.064700 | 0.0000410 | 0.000300 | 0.00060 | 0.00020 | 0.025600 |
| B*15:03 | 8 | 0.0040 | 0.064000 | 0.000700 | 0.0014000 | 0.012900 | 0.00010 | 0.00320 | 0.000200 |
| B*15:07 | 2 | 0.0010 | 0.000100 | 0.001600 | 0.0006000 | 0.000400 | 0.00470 | 0.00690 | 0.000051 |
| B*15:09 | 2 | 0.0010 | 0.000064 | 0.000010 | 0.0002000 | 0.000700 | 0.00002 | 0.00010 | 0.000200 |
| B*15:10 | 4 | 0.0020 | 0.034600 | 0.000100 | 0.0004000 | 0.005500 | 0.00020 | 0.00130 | 0.000200 |
| B*15:11 | 3 | 0.0015 | 0.000011 | 0.009100 | 0.0000084 | 0.000017 | NA | NA | 0.000064 |
| B*15:12 | 1 | 0.0005 | 0.000001 | 0.002800 | 0.0000008 | 0.000010 | NA | NA | 0.000076 |
| B*15:15 | 1 | 0.0005 | NA | 0.000015 | 0.0000125 | 0.004300 | 0.00008 | 0.00006 | 0.000003 |
| B*15:17 | 10 | 0.0050 | 0.004500 | 0.000800 | 0.0036000 | 0.006800 | 0.00020 | 0.00220 | 0.014300 |
| B*15:18 | 3 | 0.0015 | 0.001500 | 0.009300 | 0.0026000 | 0.002100 | 0.01540 | 0.00250 | 0.013500 |
| B*15:20 | 1 | 0.0005 | 0.000004 | 0.000005 | 0.0000004 | 0.000200 | NA | NA | NA |
| B*15:212 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| B*15:220 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| B*15:25 | 3 | 0.0015 | 0.000100 | 0.007400 | 0.0000072 | 0.000092 | 0.00020 | 0.00006 | 0.005100 |
| B*15:256 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| B*15:27 | 1 | 0.0005 | NA | 0.011200 | 0.0000036 | 0.000003 | 0.00100 | 0.00003 | 0.000024 |
| B*15:39 | 1 | 0.0005 | 0.000018 | 0.000035 | 0.0000929 | 0.000700 | NA | 0.00010 | 0.000032 |
| B*15:63 | 1 | 0.0005 | NA | 0.000005 | 0.0000020 | 0.000027 | 0.00004 | 0.00040 | NA |
| B*18:01 | 129 | 0.0645 | 0.032000 | 0.002600 | 0.0443000 | 0.041100 | 0.00210 | 0.03230 | 0.025200 |
| B*18:02 | 1 | 0.0005 | 0.000010 | 0.001500 | 0.0000016 | 0.000010 | NA | 0.00001 | 0.000086 |
| B*18:03 | 1 | 0.0005 | 0.000020 | 0.000005 | 0.0001000 | 0.000031 | NA | 0.00002 | NA |
| B*18:07 | 1 | 0.0005 | 0.000001 | NA | 0.0000141 | 0.000002 | NA | NA | 0.000001 |
| B*27:02 | 9 | 0.0045 | 0.000400 | 0.000070 | 0.0039000 | 0.001900 | 0.00020 | 0.00280 | 0.000800 |
| B*27:03 | 3 | 0.0015 | 0.003300 | NA | 0.0000680 | 0.000500 | NA | NA | 0.000019 |
| B*27:04 | 2 | 0.0010 | 0.000018 | 0.019100 | 0.0000064 | 0.000027 | 0.00200 | 0.00010 | 0.002000 |
| B*27:05 | 59 | 0.0295 | 0.008400 | 0.003500 | 0.0373000 | 0.016000 | 0.00230 | 0.05450 | 0.008300 |
| B*27:06 | 1 | 0.0005 | 0.000300 | 0.001000 | 0.0000056 | 0.000089 | 0.00006 | 0.00001 | 0.000093 |
| B*27:127 | 2 | 0.0010 | NA | NA | NA | NA | NA | NA | NA |
| B*27:14 | 1 | 0.0005 | 0.000032 | 0.000005 | 0.0000909 | 0.000003 | NA | 0.00040 | NA |
| B*35:01 | 84 | 0.0420 | 0.068900 | 0.022300 | 0.0560000 | 0.071300 | 0.08690 | 0.09790 | 0.062200 |
| B*35:02 | 14 | 0.0070 | 0.000800 | 0.000700 | 0.0102000 | 0.012900 | 0.00040 | 0.00450 | 0.007300 |
| B*35:03 | 39 | 0.0195 | 0.002000 | 0.007900 | 0.0162000 | 0.014700 | 0.00050 | 0.00950 | 0.072000 |
| B*35:05 | 2 | 0.0010 | 0.000400 | 0.005400 | 0.0000378 | 0.005600 | 0.00050 | 0.00010 | 0.000600 |
| B*35:08 | 15 | 0.0075 | 0.000400 | 0.000500 | 0.0043000 | 0.006000 | 0.00010 | 0.00150 | 0.002000 |
| B*35:09 | 1 | 0.0005 | NA | NA | 0.0000012 | 0.000400 | NA | NA | 0.000001 |
| B*35:17 | 1 | 0.0005 | 0.000017 | 0.000010 | 0.0000595 | 0.005100 | 0.00001 | 0.00030 | 0.000008 |
| B*35:194 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| B*35:41 | 1 | 0.0005 | 0.000008 | NA | 0.0000616 | 0.000003 | NA | 0.00001 | NA |
| B*35:42 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| B*35:43 | 1 | 0.0005 | 0.000092 | 0.000005 | 0.0000394 | 0.018500 | NA | 0.00020 | 0.000011 |
| B*35:60 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| B*35:67 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| B*35:71 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| B*37:01 | 25 | 0.0125 | 0.005500 | 0.006000 | 0.0144000 | 0.007500 | 0.00480 | 0.01080 | 0.034100 |
| B*37:68 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| B*38:01 | 53 | 0.0265 | 0.002200 | 0.004100 | 0.0209000 | 0.019900 | 0.00100 | 0.01020 | 0.002800 |
| B*38:02 | 5 | 0.0025 | 0.000073 | 0.040000 | 0.0000378 | 0.000200 | 0.00330 | 0.00030 | 0.006900 |
| B*39:01 | 29 | 0.0145 | 0.003200 | 0.019300 | 0.0112000 | 0.007300 | 0.03030 | 0.03390 | 0.005500 |
| B*39:05 | 1 | 0.0005 | 0.000200 | 0.002000 | 0.0001000 | 0.023300 | 0.00008 | 0.00090 | 0.000019 |
| B*39:06 | 10 | 0.0050 | 0.001400 | 0.000095 | 0.0064000 | 0.014600 | 0.00020 | 0.01760 | 0.001100 |
| B*39:09 | 1 | 0.0005 | 0.000012 | 0.000900 | 0.0000125 | 0.002100 | 0.00004 | 0.00006 | 0.000200 |
| B*40:01 | 58 | 0.0290 | 0.012800 | 0.153800 | 0.0528000 | 0.014400 | 0.06030 | 0.05180 | 0.022100 |
| B*40:02 | 28 | 0.0140 | 0.003300 | 0.017300 | 0.0126000 | 0.047800 | 0.07660 | 0.03100 | 0.003000 |
| B*40:06 | 17 | 0.0085 | 0.000400 | 0.017200 | 0.0003000 | 0.001300 | 0.04450 | 0.00060 | 0.091400 |
| B*40:117 | 1 | 0.0005 | NA | 0.000005 | NA | NA | NA | NA | NA |
| B*40:21 | 1 | 0.0005 | NA | 0.000002 | NA | NA | NA | NA | NA |
| B*40:32 | 1 | 0.0005 | NA | NA | 0.0000097 | NA | NA | NA | NA |
| B*40:353 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| B*40:49 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| B*41:01 | 9 | 0.0045 | 0.003000 | 0.000400 | 0.0043000 | 0.010100 | 0.00040 | 0.00280 | 0.003500 |
| B*41:02 | 9 | 0.0045 | 0.005600 | 0.000055 | 0.0050000 | 0.005200 | 0.00010 | 0.00310 | 0.000600 |
| B*42:01 | 5 | 0.0025 | 0.053100 | 0.000070 | 0.0003000 | 0.006800 | 0.00006 | 0.00170 | 0.000100 |
| B*42:02 | 2 | 0.0010 | 0.007300 | 0.000025 | 0.0001000 | 0.001900 | NA | 0.00020 | 0.000016 |
| B*44:02 | 169 | 0.0845 | 0.020800 | 0.003800 | 0.0952000 | 0.040300 | 0.00750 | 0.07440 | 0.008200 |
| B*44:03 | 87 | 0.0435 | 0.045900 | 0.014000 | 0.0467000 | 0.055200 | 0.06050 | 0.03780 | 0.074000 |
| B*44:04 | 1 | 0.0005 | 0.000100 | 0.000005 | 0.0006000 | 0.000300 | 0.00002 | 0.00040 | 0.000001 |
| B*44:05 | 5 | 0.0025 | 0.000300 | 0.000045 | 0.0029000 | 0.001300 | 0.00010 | 0.00140 | 0.000040 |
| B*44:06 | 1 | 0.0005 | 0.000001 | NA | 0.0000398 | 0.000041 | NA | NA | 0.000300 |
| B*44:27 | 10 | 0.0050 | NA | NA | NA | NA | NA | NA | NA |
| B*44:270 | 2 | 0.0010 | NA | NA | NA | NA | NA | NA | NA |
| B*44:37 | 1 | 0.0005 | NA | NA | 0.0000004 | NA | NA | NA | 0.000005 |
| B*44:55 | 1 | 0.0005 | NA | NA | 0.0000004 | NA | NA | NA | NA |
| B*45:01 | 15 | 0.0075 | 0.049500 | 0.002000 | 0.0059000 | 0.017100 | 0.00040 | 0.00630 | 0.000900 |
| B*46:01 | 11 | 0.0055 | 0.000072 | 0.134300 | 0.0000752 | 0.000200 | 0.04100 | 0.00010 | 0.001000 |
| B*47:01 | 6 | 0.0030 | 0.001000 | 0.000070 | 0.0027000 | 0.001800 | 0.00006 | 0.00180 | 0.000600 |
| B*47:04 | 2 | 0.0010 | NA | 0.000005 | NA | NA | NA | NA | NA |
| B*48:01 | 11 | 0.0055 | 0.000500 | 0.013100 | 0.0007000 | 0.014200 | 0.02710 | 0.01820 | 0.003700 |
| B*49:01 | 43 | 0.0215 | 0.027900 | 0.000600 | 0.0158000 | 0.025700 | 0.00050 | 0.01450 | 0.006100 |
| B*50:01 | 31 | 0.0155 | 0.008900 | 0.002700 | 0.0105000 | 0.015000 | 0.00050 | 0.00790 | 0.017200 |
| B*50:02 | 1 | 0.0005 | 0.000100 | 0.000005 | 0.0004000 | 0.002000 | 0.00008 | 0.00040 | 0.000008 |
| B*51:01 | 132 | 0.0660 | 0.021700 | 0.045700 | 0.0473000 | 0.060500 | 0.08900 | 0.06780 | 0.074700 |
| B*51:02 | 1 | 0.0005 | 0.000800 | 0.012200 | 0.0000696 | 0.002400 | 0.00260 | 0.00760 | 0.000200 |
| B*51:05 | 1 | 0.0005 | 0.000014 | NA | 0.0002000 | 0.000051 | 0.00002 | 0.00004 | 0.000011 |
| B*51:07 | 4 | 0.0020 | 0.000068 | 0.000800 | 0.0005000 | 0.000900 | 0.00010 | 0.00030 | 0.001400 |
| B*51:08 | 6 | 0.0030 | 0.000100 | 0.000100 | 0.0012000 | 0.001800 | 0.00002 | 0.00070 | 0.000900 |
| B*51:09 | 1 | 0.0005 | 0.000700 | 0.000018 | 0.0005000 | 0.000200 | 0.00007 | 0.00130 | 0.000046 |
| B*51:173Q | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| B*51:203 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| B*51:230 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| B*52:01 | 43 | 0.0215 | 0.015400 | 0.013400 | 0.0089000 | 0.020500 | 0.09900 | 0.00660 | 0.074500 |
| B*53:01 | 8 | 0.0040 | 0.117800 | 0.000300 | 0.0034000 | 0.019500 | 0.00030 | 0.00730 | 0.001300 |
| B*54:01 | 12 | 0.0060 | 0.000030 | 0.030400 | 0.0000382 | 0.000092 | NA | NA | 0.000300 |
| B*55:01 | 32 | 0.0160 | 0.004000 | 0.000800 | 0.0186000 | 0.009100 | 0.00100 | 0.01430 | 0.020300 |
| B*55:02 | 8 | 0.0040 | 0.000066 | 0.027600 | 0.0000342 | 0.000089 | 0.02720 | 0.00004 | 0.000500 |
| B*56:01 | 17 | 0.0085 | 0.002300 | 0.006100 | 0.0064000 | 0.003400 | 0.00930 | 0.00440 | 0.006100 |
| B*56:03 | 1 | 0.0005 | 0.000004 | 0.001800 | 0.0000012 | 0.000003 | NA | NA | 0.000016 |
| B*56:09 | 1 | 0.0005 | NA | 0.000002 | NA | NA | NA | NA | NA |
| B*57:01 | 81 | 0.0405 | 0.007100 | 0.005100 | 0.0365000 | 0.015200 | 0.00130 | 0.02680 | 0.067600 |
| B*57:02 | 7 | 0.0035 | 0.003800 | 0.000015 | 0.0003000 | 0.000700 | 0.00002 | 0.00020 | 0.000024 |
| B*57:03 | 6 | 0.0030 | 0.031800 | 0.000065 | 0.0007000 | 0.006200 | 0.00002 | 0.00100 | 0.000200 |
| B*58:01 | 22 | 0.0110 | 0.037800 | 0.087400 | 0.0073000 | 0.014200 | 0.00760 | 0.00700 | 0.042000 |
| B*58:02 | 5 | 0.0025 | 0.042200 | 0.000035 | 0.0001000 | 0.003700 | NA | 0.00180 | 0.000057 |
| B*59:01 | 2 | 0.0010 | 0.000007 | 0.000600 | 0.0000028 | 0.000003 | 0.02240 | 0.00004 | 0.000019 |
| B*67:01 | 1 | 0.0005 | 0.000100 | 0.004100 | 0.0000652 | 0.000100 | 0.00910 | 0.00010 | 0.000040 |
| B*73:01 | 2 | 0.0010 | 0.000200 | 0.000070 | 0.0004000 | 0.000700 | NA | 0.00008 | 0.000200 |
| C*01:02 | 100 | 0.0500 | 0.007800 | 0.191500 | 0.0341000 | 0.054400 | 0.17320 | 0.04920 | 0.035100 |
| C*01:03 | 2 | 0.0010 | NA | 0.001400 | 0.0000063 | NA | NA | NA | 0.000034 |
| C*01:103 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| C*01:22 | 1 | 0.0005 | NA | NA | NA | 0.000005 | NA | NA | NA |
| C*01:51 | 1 | 0.0005 | NA | NA | 0.0000012 | NA | NA | NA | NA |
| C*02:02 | 88 | 0.0440 | 0.089000 | 0.003600 | 0.0435000 | 0.036700 | 0.00150 | 0.05540 | 0.009300 |
| C*02:06 | 1 | 0.0005 | 0.000006 | NA | 0.0000140 | NA | NA | 0.00010 | NA |
| C*02:10 | 8 | 0.0040 | NA | NA | NA | NA | NA | NA | NA |
| C*02:20 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| C*03:02 | 13 | 0.0065 | 0.018500 | 0.087400 | 0.0022000 | 0.004900 | 0.00760 | 0.00230 | 0.041900 |
| C*03:03 | 82 | 0.0410 | 0.012900 | 0.047300 | 0.0534000 | 0.029800 | 0.14850 | 0.04170 | 0.015200 |
| C*03:04 | 86 | 0.0430 | 0.056500 | 0.116500 | 0.0749000 | 0.060200 | 0.12690 | 0.10160 | 0.016200 |
| C*03:05 | 1 | 0.0005 | 0.000042 | NA | 0.0000211 | 0.019700 | NA | 0.00005 | NA |
| C*03:06 | 1 | 0.0005 | 0.000004 | NA | 0.0000143 | 0.002600 | NA | 0.00010 | NA |
| C*03:344 | 4 | 0.0020 | NA | NA | NA | NA | NA | NA | NA |
| C*03:39 | 3 | 0.0015 | NA | 0.000020 | NA | NA | NA | NA | NA |
| C*03:85 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| C*04:01 | 247 | 0.1235 | 0.203700 | 0.043400 | 0.1059000 | 0.175600 | 0.04040 | 0.13120 | 0.136400 |
| C*04:03 | 3 | 0.0015 | 0.000100 | 0.011200 | 0.0000748 | 0.000300 | 0.00030 | 0.00030 | 0.013800 |
| C*04:277 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| C*05:01 | 159 | 0.0795 | 0.033600 | 0.003600 | 0.0939000 | 0.057900 | 0.00720 | 0.07610 | 0.008400 |
| C*05:05 | 1 | 0.0005 | 0.000003 | NA | 0.0000167 | NA | NA | NA | NA |
| C*05:37 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| C*06:02 | 195 | 0.0975 | 0.086500 | 0.044700 | 0.0932000 | 0.061400 | 0.01050 | 0.06970 | 0.139100 |
| C*06:09 | 1 | 0.0005 | 0.000051 | NA | NA | 0.000007 | NA | 0.00004 | NA |
| C*07:01 | 243 | 0.1215 | 0.117000 | 0.010100 | 0.1600000 | 0.102000 | 0.00730 | 0.11720 | 0.103900 |
| C*07:02 | 219 | 0.1095 | 0.071300 | 0.194400 | 0.1413000 | 0.121400 | 0.12180 | 0.15100 | 0.107800 |
| C*07:04 | 34 | 0.0170 | 0.007200 | 0.006400 | 0.0154000 | 0.005500 | 0.00940 | 0.01160 | 0.015500 |
| C*07:18 | 10 | 0.0050 | NA | NA | NA | NA | NA | NA | NA |
| C*07:204 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| C*07:51 | 2 | 0.0010 | 0.000004 | NA | 0.0000012 | NA | NA | NA | 0.000006 |
| C*07:578 | 7 | 0.0035 | NA | NA | NA | NA | NA | NA | NA |
| C*07:615 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| C*07:696 | 2 | 0.0010 | NA | NA | NA | NA | NA | NA | NA |
| C*08:01 | 22 | 0.0110 | 0.001100 | 0.104300 | 0.0004000 | 0.014900 | 0.06820 | 0.02220 | 0.028300 |
| C*08:02 | 72 | 0.0360 | 0.034000 | 0.001200 | 0.0385000 | 0.052600 | 0.00190 | 0.02860 | 0.001900 |
| C*08:03 | 9 | 0.0045 | 0.000070 | 0.004000 | 0.0004000 | 0.003300 | 0.01290 | 0.00440 | 0.001800 |
| C*12:02 | 43 | 0.0215 | 0.001100 | 0.030700 | 0.0087000 | 0.011600 | 0.10000 | 0.00480 | 0.081300 |
| C*12:03 | 142 | 0.0710 | 0.014900 | 0.017600 | 0.0486000 | 0.041500 | 0.00190 | 0.02650 | 0.049100 |
| C*12:132 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| C*12:167 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| C*12:28 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| C*14:02 | 29 | 0.0145 | 0.016500 | 0.040600 | 0.0127000 | 0.015400 | 0.07810 | 0.01350 | 0.033600 |
| C*14:03 | 5 | 0.0025 | 0.001500 | 0.004200 | 0.0000629 | 0.000200 | 0.05760 | 0.00010 | 0.000077 |
| C*15:02 | 47 | 0.0235 | 0.005400 | 0.025600 | 0.0223000 | 0.039300 | 0.01960 | 0.04350 | 0.107700 |
| C*15:05 | 12 | 0.0060 | 0.013000 | 0.007400 | 0.0035000 | 0.006100 | 0.00050 | 0.00200 | 0.011500 |
| C*15:07 | 1 | 0.0005 | 0.000006 | NA | 0.0000034 | 0.000013 | NA | NA | 0.000200 |
| C*15:09 | 1 | 0.0005 | 0.000004 | NA | 0.0000133 | 0.001900 | NA | 0.00020 | 0.000010 |
| C*16:01 | 49 | 0.0245 | 0.096900 | 0.000200 | 0.0338000 | 0.050300 | 0.00160 | 0.02810 | 0.000700 |
| C*16:02 | 16 | 0.0080 | 0.000200 | 0.000700 | 0.0027000 | 0.003900 | 0.00010 | 0.00100 | 0.027900 |
| C*16:04 | 4 | 0.0020 | 0.000043 | 0.000200 | 0.0006000 | 0.000300 | NA | 0.00020 | 0.000300 |
| C*17:01 | 11 | 0.0055 | 0.068100 | 0.000500 | 0.0088000 | 0.020000 | 0.00070 | 0.00820 | 0.003900 |
| C*17:03 | 10 | 0.0050 | NA | NA | NA | NA | NA | NA | NA |
| C*18:02 | 3 | 0.0015 | NA | NA | NA | NA | NA | NA | NA |
| DPA1*01:03 | 1522 | 0.7610 | NA | NA | NA | NA | NA | NA | NA |
| DPA1*01:04 | 12 | 0.0060 | NA | NA | NA | NA | NA | NA | NA |
| DPA1*01:05 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPA1*01:11 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPA1*02:01 | 308 | 0.1540 | NA | NA | NA | NA | NA | NA | NA |
| DPA1*02:02 | 125 | 0.0625 | NA | NA | NA | NA | NA | NA | NA |
| DPA1*02:06 | 9 | 0.0045 | NA | NA | NA | NA | NA | NA | NA |
| DPA1*02:07 | 13 | 0.0065 | NA | NA | NA | NA | NA | NA | NA |
| DPA1*03:01 | 8 | 0.0040 | NA | NA | NA | NA | NA | NA | NA |
| DPA1*04:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*01:01 | 74 | 0.0370 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*02:01 | 304 | 0.1520 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*02:02 | 30 | 0.0150 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*03:01 | 137 | 0.0685 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*04:01 | 685 | 0.3425 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*04:02 | 202 | 0.1010 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*05:01 | 107 | 0.0535 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*06:01 | 19 | 0.0095 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*09:01 | 20 | 0.0100 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*10:01 | 25 | 0.0125 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*104:01 | 48 | 0.0240 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*105:01 | 14 | 0.0070 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*107:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*11:01 | 40 | 0.0200 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*113:01 | 2 | 0.0010 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*124:01 | 12 | 0.0060 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*126:01 | 7 | 0.0035 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*13:01 | 51 | 0.0255 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*131:01 | 2 | 0.0010 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*133:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*135:01 | 6 | 0.0030 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*138:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*14:01 | 39 | 0.0195 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*15:01 | 13 | 0.0065 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*150:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*158:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*16:01 | 10 | 0.0050 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*162:01 | 5 | 0.0025 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*17:01 | 49 | 0.0245 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*18:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*19:01 | 7 | 0.0035 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*20:01 | 7 | 0.0035 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*21:01 | 4 | 0.0020 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*22:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*23:01 | 15 | 0.0075 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*234:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*259:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*271:01 | 4 | 0.0020 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*294:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*33:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*350:01 | 7 | 0.0035 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*351:01 | 3 | 0.0015 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*36:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*38:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*398:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*40:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*41:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*414:01 | 7 | 0.0035 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*45:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*461:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*462:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*463:01 | 4 | 0.0020 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*47:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*51:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*519:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*547:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*57:01 | 3 | 0.0015 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*651:01 | 4 | 0.0020 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*702:01 | 7 | 0.0035 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*744:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*80:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*88:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DPB1*92:01 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DQA1*01:01 | 192 | 0.0960 | NA | NA | NA | NA | NA | NA | NA |
| DQA1*01:02 | 358 | 0.1790 | NA | NA | NA | NA | NA | NA | NA |
| DQA1*01:03 | 150 | 0.0750 | NA | NA | NA | NA | NA | NA | NA |
| DQA1*01:04 | 52 | 0.0260 | NA | NA | NA | NA | NA | NA | NA |
| DQA1*01:05 | 25 | 0.0125 | NA | NA | NA | NA | NA | NA | NA |
| DQA1*01:06 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DQA1*01:10 | 2 | 0.0010 | NA | NA | NA | NA | NA | NA | NA |
| DQA1*02:01 | 256 | 0.1280 | NA | NA | NA | NA | NA | NA | NA |
| DQA1*03:01 | 163 | 0.0815 | NA | NA | NA | NA | NA | NA | NA |
| DQA1*03:02 | 31 | 0.0155 | NA | NA | NA | NA | NA | NA | NA |
| DQA1*03:03 | 132 | 0.0660 | NA | NA | NA | NA | NA | NA | NA |
| DQA1*04:01 | 58 | 0.0290 | NA | NA | NA | NA | NA | NA | NA |
| DQA1*04:02 | 2 | 0.0010 | NA | NA | NA | NA | NA | NA | NA |
| DQA1*05:01 | 222 | 0.1110 | NA | NA | NA | NA | NA | NA | NA |
| DQA1*05:03 | 20 | 0.0100 | NA | NA | NA | NA | NA | NA | NA |
| DQA1*05:05 | 305 | 0.1525 | NA | NA | NA | NA | NA | NA | NA |
| DQA1*05:06 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DQA1*05:07 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DQA1*05:08 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DQA1*05:09 | 6 | 0.0030 | NA | NA | NA | NA | NA | NA | NA |
| DQA1*06:01 | 22 | 0.0110 | NA | NA | NA | NA | NA | NA | NA |
| DQB1*02:01 | 218 | 0.1090 | NA | NA | NA | 0.178000 | NA | NA | NA |
| DQB1*02:02 | 201 | 0.1005 | NA | NA | NA | NA | NA | NA | NA |
| DQB1*02:10 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DQB1*03:01 | 403 | 0.2015 | NA | NA | NA | 0.192700 | NA | NA | NA |
| DQB1*03:02 | 169 | 0.0845 | NA | NA | NA | 0.194400 | NA | NA | NA |
| DQB1*03:03 | 78 | 0.0390 | NA | NA | NA | 0.021600 | NA | NA | NA |
| DQB1*03:04 | 7 | 0.0035 | NA | NA | NA | 0.001400 | NA | NA | NA |
| DQB1*03:05 | 3 | 0.0015 | NA | NA | NA | 0.000200 | NA | NA | NA |
| DQB1*03:19 | 11 | 0.0055 | NA | NA | NA | NA | NA | NA | NA |
| DQB1*03:22 | 22 | 0.0110 | NA | NA | NA | NA | NA | NA | NA |
| DQB1*03:251 | 2 | 0.0010 | NA | NA | NA | NA | NA | NA | NA |
| DQB1*03:96 | 5 | 0.0025 | NA | NA | NA | NA | NA | NA | NA |
| DQB1*04:01 | 26 | 0.0130 | NA | NA | NA | NA | NA | NA | NA |
| DQB1*04:02 | 58 | 0.0290 | NA | NA | NA | 0.090300 | NA | NA | NA |
| DQB1*04:23 | 3 | 0.0015 | NA | NA | NA | NA | NA | NA | NA |
| DQB1*05:01 | 206 | 0.1030 | NA | NA | NA | 0.112200 | NA | NA | NA |
| DQB1*05:02 | 68 | 0.0340 | NA | NA | NA | 0.014000 | NA | NA | NA |
| DQB1*05:03 | 48 | 0.0240 | NA | NA | NA | 0.019600 | NA | NA | NA |
| DQB1*05:04 | 4 | 0.0020 | NA | NA | NA | 0.000300 | NA | NA | NA |
| DQB1*05:107 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DQB1*06:01 | 49 | 0.0245 | NA | NA | NA | 0.011200 | NA | NA | NA |
| DQB1*06:02 | 215 | 0.1075 | NA | NA | NA | 0.074800 | NA | NA | NA |
| DQB1*06:03 | 113 | 0.0565 | NA | NA | NA | 0.049200 | NA | NA | NA |
| DQB1*06:04 | 70 | 0.0350 | NA | NA | NA | 0.030300 | NA | NA | NA |
| DQB1*06:07 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DQB1*06:09 | 18 | 0.0090 | NA | NA | NA | 0.009300 | NA | NA | NA |
| DRA*01:01 | 1289 | 0.6445 | NA | NA | NA | NA | NA | NA | NA |
| DRA*01:02 | 711 | 0.3555 | NA | NA | NA | NA | NA | NA | NA |
| DRB1*01:01 | 130 | 0.0650 | 0.026500 | 0.009300 | 0.0860000 | 0.044400 | 0.05840 | 0.07030 | 0.032100 |
| DRB1*01:02 | 38 | 0.0190 | 0.039200 | 0.000700 | 0.0138000 | 0.035800 | 0.00060 | 0.00950 | 0.001300 |
| DRB1*01:03 | 9 | 0.0045 | 0.002600 | 0.000070 | 0.0123000 | 0.007900 | 0.00070 | 0.01000 | 0.000049 |
| DRB1*03:01 | 215 | 0.1075 | 0.069900 | 0.068100 | 0.1216000 | 0.069500 | 0.00680 | 0.08970 | 0.074600 |
| DRB1*03:02 | 4 | 0.0020 | 0.063100 | 0.000035 | 0.0003000 | 0.010300 | 0.00008 | 0.00210 | 0.000086 |
| DRB1*03:07 | 1 | 0.0005 | 0.000023 | NA | 0.0000072 | 0.000034 | NA | NA | 0.000003 |
| DRB1*04:01 | 101 | 0.0505 | 0.020200 | 0.005100 | 0.0878000 | 0.015000 | 0.01150 | 0.06580 | 0.009000 |
| DRB1*04:02 | 20 | 0.0100 | 0.000800 | 0.000500 | 0.0106000 | 0.014300 | 0.00050 | 0.00380 | 0.006400 |
| DRB1*04:03 | 36 | 0.0180 | 0.001700 | 0.023100 | 0.0079000 | 0.017400 | 0.02440 | 0.01130 | 0.052700 |
| DRB1*04:04 | 48 | 0.0240 | 0.008200 | 0.008800 | 0.0388000 | 0.042100 | 0.00320 | 0.05120 | 0.020100 |
| DRB1*04:05 | 49 | 0.0245 | 0.015300 | 0.061200 | 0.0067000 | 0.024300 | 0.14720 | 0.00980 | 0.007500 |
| DRB1*04:06 | 8 | 0.0040 | 0.000200 | 0.024800 | 0.0004000 | 0.001300 | 0.02480 | 0.00020 | 0.001500 |
| DRB1*04:07 | 16 | 0.0080 | 0.003900 | 0.000800 | 0.0112000 | 0.074800 | 0.00640 | 0.04860 | 0.001300 |
| DRB1*04:08 | 7 | 0.0035 | 0.000600 | 0.000300 | 0.0039000 | 0.001600 | 0.00006 | 0.00250 | 0.002300 |
| DRB1*04:10 | 2 | 0.0010 | 0.000100 | 0.001500 | 0.0000591 | 0.003500 | 0.01820 | 0.00160 | 0.001500 |
| DRB1*04:13 | 1 | 0.0005 | NA | 0.000005 | 0.0000153 | 0.000003 | NA | NA | 0.000200 |
| DRB1*04:92 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DRB1*07:01 | 249 | 0.1245 | 0.101100 | 0.053100 | 0.1342000 | 0.109000 | 0.00940 | 0.10060 | 0.169500 |
| DRB1*08:01 | 32 | 0.0160 | 0.003700 | 0.000200 | 0.0232000 | 0.012000 | 0.00080 | 0.01560 | 0.003200 |
| DRB1*08:02 | 14 | 0.0070 | 0.000900 | 0.005500 | 0.0008000 | 0.055600 | 0.04340 | 0.01580 | 0.005100 |
| DRB1*08:03 | 18 | 0.0090 | 0.000400 | 0.068000 | 0.0024000 | 0.001800 | 0.07440 | 0.00170 | 0.007100 |
| DRB1*08:04 | 9 | 0.0045 | 0.054200 | 0.000100 | 0.0020000 | 0.009400 | 0.00020 | 0.03070 | 0.000800 |
| DRB1*08:06 | 2 | 0.0010 | 0.005400 | 0.000010 | 0.0002000 | 0.000800 | NA | 0.00020 | NA |
| DRB1*08:11 | 1 | 0.0005 | 0.000800 | 0.000002 | 0.0001000 | 0.000007 | NA | 0.00700 | NA |
| DRB1*08:18 | 1 | 0.0005 | NA | NA | 0.0000024 | 0.000024 | NA | NA | 0.000011 |
| DRB1*08:40 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DRB1*08:77 | 7 | 0.0035 | NA | NA | NA | NA | NA | NA | NA |
| DRB1*09:01 | 32 | 0.0160 | 0.029700 | 0.155400 | 0.0103000 | 0.017600 | 0.13870 | 0.02720 | 0.009400 |
| DRB1*10:01 | 22 | 0.0110 | 0.019200 | 0.013400 | 0.0085000 | 0.018100 | 0.00400 | 0.00690 | 0.062800 |
| DRB1*11:01 | 137 | 0.0685 | 0.085400 | 0.062600 | 0.0556000 | 0.044300 | 0.02580 | 0.04350 | 0.059800 |
| DRB1*11:02 | 8 | 0.0040 | 0.038800 | 0.000060 | 0.0028000 | 0.011300 | 0.00010 | 0.00440 | 0.000070 |
| DRB1*11:03 | 12 | 0.0060 | 0.000700 | 0.000095 | 0.0061000 | 0.003400 | 0.00010 | 0.00330 | 0.000200 |
| DRB1*11:04 | 93 | 0.0465 | 0.005800 | 0.002500 | 0.0295000 | 0.028000 | 0.00120 | 0.01630 | 0.019700 |
| DRB1*11:14 | 1 | 0.0005 | 0.000074 | NA | 0.0000893 | 0.000100 | NA | 0.00007 | 0.000005 |
| DRB1*12:01 | 38 | 0.0190 | 0.038200 | 0.034200 | 0.0164000 | 0.010900 | 0.03750 | 0.01330 | 0.006000 |
| DRB1*12:02 | 18 | 0.0090 | 0.002900 | 0.115000 | 0.0002000 | 0.000800 | 0.01710 | 0.00030 | 0.029900 |
| DRB1*12:10 | 2 | 0.0010 | NA | NA | NA | NA | NA | NA | NA |
| DRB1*13:01 | 105 | 0.0525 | 0.054200 | 0.007800 | 0.0563000 | 0.047800 | 0.00760 | 0.04270 | 0.067300 |
| DRB1*13:02 | 89 | 0.0445 | 0.073000 | 0.024200 | 0.0488000 | 0.042100 | 0.05750 | 0.03790 | 0.033700 |
| DRB1*13:03 | 26 | 0.0130 | 0.032600 | 0.000200 | 0.0109000 | 0.013300 | 0.00050 | 0.00930 | 0.001300 |
| DRB1*13:05 | 4 | 0.0020 | 0.000300 | 0.000010 | 0.0025000 | 0.003600 | 0.00004 | 0.00090 | 0.000032 |
| DRB1*13:12 | 2 | 0.0010 | 0.000006 | 0.008100 | 0.0000008 | 0.000055 | NA | NA | 0.000097 |
| DRB1*13:27 | 1 | 0.0005 | 0.000020 | NA | 0.0000020 | NA | NA | NA | 0.000005 |
| DRB1*14:01 | 7 | 0.0035 | 0.018600 | 0.033300 | 0.0261000 | 0.019000 | 0.03010 | 0.02750 | 0.011300 |
| DRB1*14:02 | 3 | 0.0015 | 0.000800 | 0.000200 | 0.0003000 | 0.025600 | 0.00020 | 0.06350 | 0.000400 |
| DRB1*14:03 | 2 | 0.0010 | NA | 0.002500 | 0.0000221 | 0.000007 | NA | NA | 0.000089 |
| DRB1*14:04 | 3 | 0.0015 | 0.000500 | 0.005100 | 0.0007000 | 0.000800 | 0.00020 | 0.00120 | 0.071300 |
| DRB1*14:05 | 2 | 0.0010 | 0.000025 | 0.022800 | 0.0000294 | 0.000051 | 0.02420 | 0.00002 | 0.000900 |
| DRB1*14:06 | 6 | 0.0030 | 0.000100 | 0.000200 | 0.0002000 | 0.017300 | 0.01420 | 0.00290 | 0.000500 |
| DRB1*14:07 | 1 | 0.0005 | 0.000062 | 0.001000 | 0.0002000 | 0.000200 | 0.00090 | 0.00020 | 0.001500 |
| DRB1*14:18 | 1 | 0.0005 | 0.000001 | 0.001100 | 0.0000004 | NA | NA | NA | 0.000011 |
| DRB1*14:54 | 40 | 0.0200 | NA | NA | NA | NA | NA | NA | NA |
| DRB1*15:01 | 228 | 0.1140 | 0.028200 | 0.101200 | 0.1346000 | 0.059200 | 0.08670 | 0.10410 | 0.090200 |
| DRB1*15:02 | 37 | 0.0185 | 0.002300 | 0.026600 | 0.0072000 | 0.011100 | 0.09670 | 0.00450 | 0.107300 |
| DRB1*15:03 | 4 | 0.0020 | 0.116600 | 0.000025 | 0.0005000 | 0.013700 | 0.00006 | 0.00270 | 0.000200 |
| DRB1*16:01 | 39 | 0.0195 | 0.002000 | 0.000400 | 0.0143000 | 0.010500 | 0.00030 | 0.00840 | 0.000600 |
| DRB1*16:02 | 5 | 0.0025 | 0.013800 | 0.043500 | 0.0015000 | 0.022000 | 0.00670 | 0.02910 | 0.006700 |
| DRB1*16:15 | 10 | 0.0050 | NA | NA | NA | NA | NA | NA | NA |
| DRB1*16:32 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
| DRB1*16:42 | 1 | 0.0005 | NA | NA | NA | NA | NA | NA | NA |
midas <-
filterByFrequency(
object = midas,
experiment = "hla_alleles",
lower_frequency_cutoff = 0.01
)Before the actual analysis can be run, we still need to define a
statistical model we would like to use. We can use most of the
statistical models available in R, such as lm,
glm, coxme etc. (technically, they need to
have a tidy method available). MiDAS then provides a
wrapper function that will evaluate our model for each HLA allele in our
data.
Here we will use a very simple formula disease ~ term,
term being a placeholder for each tested HLA allele. This notation is
necessary to also allow interaction tests
(e.g. disease ~ lab_value:term) and also works with other
appropriate operations.
midas has to be passed as a data argument
to our statistical function, here glm.
To run our analysis, we will use the runMiDAS function.
This function offers multiple analysis scenarios which can be tuned
using conditional and omnibus arguments. It
can also pre-filter input data based on frequency (check
?runMiDAS to learn more).
results <-
runMiDAS(
object = object,
experiment = "hla_alleles",
inheritance_model = "dominant",
conditional = FALSE,
omnibus = FALSE,
lower_frequency_cutoff = 0.05
)
kableResults(results)| allele | p.value | p.adjusted | estimate | std.error | conf.low | conf.high | statistic | Ntotal | Ntotal [%] | N(disease=0) | N(disease=0) [%] | N(disease=1) | N(disease=1) [%] |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| DQB1*06:02 | 2.600e-06 | 1.184e-04 | 7.756e-01 | 0.1651 | 4.552e-01 | 1.103e+00 | 4.698e+00 | 198 | 9.90% | 69 | 6.90% | 129 | 12.90% |
| DRB1*15:01 | 7.300e-06 | 3.303e-04 | 7.251e-01 | 0.1617 | 4.109e-01 | 1.046e+00 | 4.484e+00 | 206 | 10.30% | 74 | 7.40% | 132 | 13.20% |
| C*07:02 | 1.859e-04 | 8.367e-03 | 6.003e-01 | 0.1606 | 2.877e-01 | 9.181e-01 | 3.737e+00 | 204 | 10.20% | 78 | 7.80% | 126 | 12.60% |
| B*18:01 | 6.012e-04 | 2.705e-02 | -6.903e-01 | 0.2012 | -1.092e+00 | -3.011e-01 | -3.431e+00 | 122 | 6.10% | 79 | 7.90% | 43 | 4.30% |
| DRA*01:02 | 2.701e-03 | 1.216e-01 | 3.855e-01 | 0.1285 | 1.341e-01 | 6.379e-01 | 3.000e+00 | 573 | 28.65% | 263 | 26.30% | 310 | 31.00% |
| DQB1*02:02 | 4.569e-03 | 2.056e-01 | -4.689e-01 | 0.1654 | -7.957e-01 | -1.467e-01 | -2.836e+00 | 185 | 9.25% | 110 | 11.00% | 75 | 7.50% |
| B*51:01 | 4.863e-03 | 2.188e-01 | 5.465e-01 | 0.1941 | 1.697e-01 | 9.320e-01 | 2.816e+00 | 128 | 6.40% | 49 | 4.90% | 79 | 7.90% |
| DRA*01:01 | 1.073e-02 | 4.826e-01 | -4.765e-01 | 0.1867 | -8.466e-01 | -1.132e-01 | -2.552e+00 | 862 | 43.10% | 445 | 44.50% | 417 | 41.70% |
| B*44:02 | 2.068e-02 | 9.306e-01 | 4.030e-01 | 0.1742 | 6.344e-02 | 7.472e-01 | 2.314e+00 | 161 | 8.05% | 67 | 6.70% | 94 | 9.40% |
| DRB1*11:01 | 3.188e-02 | 1.000e+00 | -4.078e-01 | 0.1900 | -7.841e-01 | -3.770e-02 | -2.146e+00 | 131 | 6.55% | 77 | 7.70% | 54 | 5.40% |
| DRB1*07:01 | 3.518e-02 | 1.000e+00 | -3.194e-01 | 0.1517 | -6.181e-01 | -2.303e-02 | -2.106e+00 | 228 | 11.40% | 128 | 12.80% | 100 | 10.00% |
| DPB1*04:01 | 6.596e-02 | 1.000e+00 | 2.337e-01 | 0.1271 | -1.519e-02 | 4.832e-01 | 1.839e+00 | 539 | 26.95% | 255 | 25.50% | 284 | 28.40% |
| B*08:01 | 8.299e-02 | 1.000e+00 | -3.383e-01 | 0.1951 | -7.243e-01 | 4.218e-02 | -1.734e+00 | 122 | 6.10% | 70 | 7.00% | 52 | 5.20% |
| DQA1*01:02 | 9.218e-02 | 1.000e+00 | 2.275e-01 | 0.1351 | -3.697e-02 | 4.929e-01 | 1.684e+00 | 327 | 16.35% | 151 | 15.10% | 176 | 17.60% |
| B*07:02 | 1.037e-01 | 1.000e+00 | 2.969e-01 | 0.1825 | -5.937e-02 | 6.571e-01 | 1.627e+00 | 142 | 7.10% | 62 | 6.20% | 80 | 8.00% |
| DRB1*03:01 | 1.102e-01 | 1.000e+00 | -2.566e-01 | 0.1606 | -5.729e-01 | 5.751e-02 | -1.597e+00 | 194 | 9.70% | 107 | 10.70% | 87 | 8.70% |
| DQA1*02:01 | 1.177e-01 | 1.000e+00 | -2.341e-01 | 0.1496 | -5.284e-01 | 5.863e-02 | -1.565e+00 | 235 | 11.75% | 128 | 12.80% | 107 | 10.70% |
| C*07:01 | 1.309e-01 | 1.000e+00 | -2.291e-01 | 0.1517 | -5.275e-01 | 6.762e-02 | -1.511e+00 | 226 | 11.30% | 123 | 12.30% | 103 | 10.30% |
| DQB1*02:01 | 1.314e-01 | 1.000e+00 | -2.408e-01 | 0.1596 | -5.551e-01 | 7.133e-02 | -1.509e+00 | 197 | 9.85% | 108 | 10.80% | 89 | 8.90% |
| DQA1*01:01 | 1.613e-01 | 1.000e+00 | 2.319e-01 | 0.1656 | -9.190e-02 | 5.581e-01 | 1.401e+00 | 179 | 8.95% | 81 | 8.10% | 98 | 9.80% |
| DQB1*03:01 | 1.699e-01 | 1.000e+00 | -1.797e-01 | 0.1309 | -4.368e-01 | 7.671e-02 | -1.373e+00 | 373 | 18.65% | 197 | 19.70% | 176 | 17.60% |
| A*02:01 | 1.796e-01 | 1.000e+00 | 1.718e-01 | 0.1280 | -7.893e-02 | 4.229e-01 | 1.342e+00 | 427 | 21.35% | 203 | 20.30% | 224 | 22.40% |
| DQA1*05:05 | 2.041e-01 | 1.000e+00 | -1.795e-01 | 0.1414 | -4.573e-01 | 9.730e-02 | -1.270e+00 | 278 | 13.90% | 148 | 14.80% | 130 | 13.00% |
| A*11:01 | 2.223e-01 | 1.000e+00 | -2.501e-01 | 0.2049 | -6.550e-01 | 1.501e-01 | -1.220e+00 | 108 | 5.40% | 60 | 6.00% | 48 | 4.80% |
| DPA1*01:03 | 2.340e-01 | 1.000e+00 | 2.863e-01 | 0.2406 | -1.828e-01 | 7.639e-01 | 1.190e+00 | 924 | 46.20% | 457 | 45.70% | 467 | 46.70% |
| DQA1*05:01 | 2.369e-01 | 1.000e+00 | -1.871e-01 | 0.1582 | -4.982e-01 | 1.225e-01 | -1.183e+00 | 201 | 10.05% | 108 | 10.80% | 93 | 9.30% |
| DPB1*04:02 | 2.921e-01 | 1.000e+00 | -1.712e-01 | 0.1625 | -4.910e-01 | 1.469e-01 | -1.054e+00 | 187 | 9.35% | 100 | 10.00% | 87 | 8.70% |
| A*03:01 | 2.960e-01 | 1.000e+00 | 1.685e-01 | 0.1612 | -1.471e-01 | 4.855e-01 | 1.045e+00 | 191 | 9.55% | 89 | 8.90% | 102 | 10.20% |
| DPA1*02:02 | 2.968e-01 | 1.000e+00 | 2.190e-01 | 0.2099 | -1.912e-01 | 6.337e-01 | 1.043e+00 | 102 | 5.10% | 46 | 4.60% | 56 | 5.60% |
| DQA1*03:01 | 2.986e-01 | 1.000e+00 | 1.807e-01 | 0.1738 | -1.594e-01 | 5.229e-01 | 1.040e+00 | 158 | 7.90% | 73 | 7.30% | 85 | 8.50% |
| DQA1*01:03 | 3.208e-01 | 1.000e+00 | 1.798e-01 | 0.1811 | -1.746e-01 | 5.366e-01 | 9.928e-01 | 143 | 7.15% | 66 | 6.60% | 77 | 7.70% |
| C*12:03 | 5.147e-01 | 1.000e+00 | -1.215e-01 | 0.1865 | -4.886e-01 | 2.438e-01 | -6.516e-01 | 133 | 6.65% | 70 | 7.00% | 63 | 6.30% |
| DRB1*01:01 | 5.622e-01 | 1.000e+00 | -1.121e-01 | 0.1934 | -4.930e-01 | 2.669e-01 | -5.795e-01 | 122 | 6.10% | 64 | 6.40% | 58 | 5.80% |
| DQB1*03:02 | 6.084e-01 | 1.000e+00 | 8.756e-02 | 0.1709 | -2.474e-01 | 4.235e-01 | 5.123e-01 | 164 | 8.20% | 79 | 7.90% | 85 | 8.50% |
| DPA1*02:01 | 6.217e-01 | 1.000e+00 | -6.961e-02 | 0.1410 | -3.464e-01 | 2.068e-01 | -4.935e-01 | 279 | 13.95% | 143 | 14.30% | 136 | 13.60% |
| DPB1*03:01 | 7.087e-01 | 1.000e+00 | -6.984e-02 | 0.1869 | -4.374e-01 | 2.967e-01 | -3.736e-01 | 132 | 6.60% | 68 | 6.80% | 64 | 6.40% |
| DPB1*02:01 | 7.233e-01 | 1.000e+00 | -5.016e-02 | 0.1417 | -3.281e-01 | 2.275e-01 | -3.541e-01 | 275 | 13.75% | 140 | 14.00% | 135 | 13.50% |
| A*24:02 | 7.586e-01 | 1.000e+00 | 4.725e-02 | 0.1537 | -2.541e-01 | 3.490e-01 | 3.074e-01 | 216 | 10.80% | 106 | 10.60% | 110 | 11.00% |
| C*05:01 | 7.899e-01 | 1.000e+00 | -4.732e-02 | 0.1776 | -3.963e-01 | 3.011e-01 | -2.664e-01 | 149 | 7.45% | 76 | 7.60% | 73 | 7.30% |
| DQB1*06:03 | 8.385e-01 | 1.000e+00 | 4.153e-02 | 0.2038 | -3.585e-01 | 4.423e-01 | 2.038e-01 | 108 | 5.40% | 53 | 5.30% | 55 | 5.50% |
| DQB1*05:01 | 8.724e-01 | 1.000e+00 | 2.578e-02 | 0.1606 | -2.892e-01 | 3.410e-01 | 1.606e-01 | 192 | 9.60% | 95 | 9.50% | 97 | 9.70% |
| DQA1*03:03 | 9.248e-01 | 1.000e+00 | -1.780e-02 | 0.1887 | -3.885e-01 | 3.526e-01 | -9.434e-02 | 129 | 6.45% | 65 | 6.50% | 64 | 6.40% |
| C*06:02 | 9.348e-01 | 1.000e+00 | -1.338e-02 | 0.1636 | -3.344e-01 | 3.075e-01 | -8.178e-02 | 183 | 9.15% | 92 | 9.20% | 91 | 9.10% |
| C*04:01 | 9.396e-01 | 1.000e+00 | 1.147e-02 | 0.1515 | -2.856e-01 | 3.086e-01 | 7.573e-02 | 225 | 11.25% | 112 | 11.20% | 113 | 11.30% |
| A*01:01 | 1.000e+00 | 1.000e+00 | 0.000e+00 | 0.1522 | -2.985e-01 | 2.985e-01 | 0.000e+00 | 222 | 11.10% | 111 | 11.10% | 111 | 11.10% |