Table 3 HLA Class I haplotype (3 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 | 0.074 | 0.096 | 0.053 |
2 | A*02-B*27-Cw*01 | 0.049 | 0.074 | 0.039 |
3 | A*02-B*27-Cw*02 | 0.033 | 0.034 | 0.031 |
4 | A*03-B*27-Cw*02 | 0.033 | 0.041 | 0.040 |
5 | A*03-B*35-Cw*04 | 0.033 | 0.041 | 0.033 |
6 | A*02-B*15-Cw*02 | 0.025 | 0.010 | 0.024 |
7 | A*11-B*35-Cw*04 | 0.025 | 0.033 | - |
8 | A*24-B*27-Cw*01 | 0.025 | 0.018 | 0.018 |
9 | A*26-B*27-Cw*02 | 0.025 | 0.016 | 0.024 |
10 | A*29-B*44-Cw*16 | 0.025 | 0.025 | 0.024 |
11 | A*01-B*37-Cw*06 | 0.016 | 0.016 | 0.016 |
12 | A*02-B*07-Cw*07 | 0.016 | 0.032 | 0.025 |
13 | A*02-B*27-Cw*06 | 0.016 | 0.016 | 0.016 |
14 | A*02-B*44-Cw*05 | 0.016 | 0.008 | 0.010 |
15 | A*03-B*07-Cw*07 | 0.016 | - | 0.016 |
16 | A*11-B*27-Cw*01 | 0.016 | - | 0.007 |
17 | A*23-B*44-Cw*04 | 0.016 | 0.016 | 0.016 |
18 | A*24-B*07-Cw*07 | 0.016 | 0.009 | - |
19 | A*26-B*52-Cw*12 | 0.016 | 0.016 | 0.016 |
20 | A*30-B*35-Cw*06 | 0.016 | 0.016 | 0.016 |
21 | A*32-B*27-Cw*01 | 0.016 | - | 0.016 |
I F | 0.906 | 0.944 | ||
I H | 0.923 | 0.950 | ||
MSE | 3.7E-05 | 2.2E-05 | ||
Incorrect Haplotypes | ||||
1 | A*11-B*14-Cw*08 | 0.008 | 0.015 | |
2 | A*32-B*27-Cw*07 | 0.016 | - | |
3 | A*02-B*18-Cw*01 | - | 0.011 | |
4 | A*29-B*27-Cw*02 | - | 0.017 |