Table 4 Extended HLA haplotype (5 loci) frequencies above 0.01 determined by direct counting and computational methods (n = 61 individuals)
From: Evaluation of two methods for computational HLA haplotypes inference using a real dataset
Correct Haplotypes | Haplotype Frequency | |||
|---|---|---|---|---|
Real | Arlequin V3.0 | PHASE V2.1.1 | ||
1 | A*24-B*27-Cw*02-DQB1*03-DRB1*04 | 0.033 | 0.041 | 0.036 |
2 | A*02-B*27-Cw*01-DQB1*05-DRB1*01 | 0.033 | 0.049 | 0.040 |
3 | A*24-B*27-Cw*01-DQB1*05-DRB1*15 | 0.025 | 0.025 | 0.020 |
4 | A*24-B*27-Cw*02-DQB1*02-DRB1*03 | 0.025 | 0.033 | 0.013 |
5 | A*03-B*27-Cw*02-DQB1*03-DRB1*04 | 0.025 | 0.025 | 0.018 |
6 | A*26-B*27-Cw*02-DQB1*03-DRB1*11 | 0.025 | 0.025 | 0.021 |
7 | A*26-B*52-Cw*12-DQB1*06-DRB1*15 | 0.016 | 0.016 | 0.015 |
8 | A*29-B*44-Cw*16-DQB1*02-DRB1*07 | 0.016 | 0.008 | 0.006 |
9 | A*30-B*35-Cw*06-DQB1*04-DRB1*08 | 0.016 | 0.016 | - |
10 | A*24-B*07-Cw*07-DQB1*06-DRB1*15 | 0.016 | - | - |
11 | A*23-B*44-Cw*04-DQB1*02-DRB1*07 | 0.016 | 0.016 | 0.016 |
12 | A*11-B*27-Cw*01-DQB1*05-DRB1*01 | 0.016 | - | 0.005 |
13 | A*02-B*27-Cw*02-DQB1*03-DRB1*04 | 0.016 | - | 0.014 |
14 | A*02-B*15-Cw*02-DQB1*05-DRB1*10 | 0.016 | 0.016 | 0.016 |
I F | 0.955 | 0.952 | ||
I H | 0.880 | 0.923 | ||
MSE | 1.3E-05 | 1.1E-05 | ||
Incorrect Haplotypes | ||||
1 | A*01-B*08-Cw*07-DQB1*02-DRB1*03 | - | 0.015 | |
2 | A*02-B*07-Cw*02-DQB1*03-DRB1*04 | 0.016 | - | |
3 | A*02-B*15-Cw*03-DQB1*03-DRB1*01 | 0.016 | - | |
4 | A*02-B*27-Cw*01-DQB1*02-DRB1*07 | - | 0.011 | |
5 | A*02-B*27-Cw*07-DQB1*02-DRB1*03 | 0.016 | - | |
6 | A*03-B*27-Cw*01-DQB1*05-DRB1*01 | - | 0.015 | |
7 | A*03-B*27-Cw*02-DQB1*02-DRB1*07 | 0.016 | 0.013 | |
8 | A*11-B*14-Cw*08-DQB1*02-DRB1*07 | 0.016 | - | |
9 | A*24-B*35-Cw*04-DQB1*05-DRB1*01 | - | 0.020 | |
10 | A*29-B*27-Cw*02-DQB1*05-DRB1*01 | 0.016 | - | |
11 | A*29-B*27-Cw*16-DQB1*02-DRB1*07 | 0.016 | 0.009 |