Table 6D:
Manually edited HLA-DQB1~HLA-DPA1~HLA-DPB1 haplotypes
| Sample | Relation | Likely incorrect | Corrected |
|---|---|---|---|
| 10C3 | child | DQB1*02:01:01~DPA1*01:03:01:03~DPB1*06:01:01+ DQB1*03:02:01~DPA1*01:03:01:05~DPB1*04:02:01:02 |
DQB1*02:01:01~DPA1*01:03:01:05~DPB1*04:02:01:02+ DQB1*03:02:01~DPA1*01:03:01:03~DPB1*06:01:01 |
| 10C7 | child | DQB1*02:01:01~DPA1*01:03:01:05~DPB1*04:02:01:02+ DQB1*04:02:01~DPA1*01:03:01:05~DPB1*04:02:01:02 |
DQB1*02:01:01~DPA1*01:03:01:05~DPB1*04:02:01:02+ DQB1*04:02:01~DPA1*01:03:01:05~DPB1*04:02:01:02 |
| 10C4 | father | DQB1*02:01:01~DPA1*01:03:01:05~DPB1*04:02:01:02+ DQB1*03:02:01~DPA1*01:03:01:03~DPB1*06:01:01 |
DQB1*02:01:01~DPA1*01:03:01:05~DPB1*04:02:01:02+ DQB1*03:02:01~DPA1*01:03:01:03~DPB1*06:01:01 |
| 10C5 | mother | DQB1*04:02:01~DPA1*01:03:01:05~DPB1*04:02:01:02+ DQB1*03:02:01~DPA1*01:03:01:03~DPB1*06:01:01 |
DQB1*04:02:01~DPA1*01:03:01:05~DPB1*04:02:01:02+ DQB1*03:02:01~DPA1*01:03:01:03~DPB1*06:01:01 |
Table 6A shows a family that had two children, a father and a mother, all of whom had identical HLA-DQB1 genotypes. This is an uninformative genotype example, in which haplotypes cannot be built using segregation. In this case, we applied HLAHapV to review known haplotypes in order to identify the most likely HLA-DRB1~HLA-DQB1 haplotypes [8]. The “HLAHapV” column shows the high priority haplotypes. The “Final” column shows the manually edited haplotypes based on the HLAHapV results. We confirmed the haplotypes by executing HLAHapV using the haplotype frequency tables from the IHIW17 Family Haplotype Project (data not shown). Table 6B shows another uninformative family of three children and both parents, all of whom had identical HLA-B genotypes. Similar to Table 6A, we initially applied HLAHapV using g group haplotype table to identify known haplotypes for these uninformative segregation cases [column “HapV (g group)”]. Later we performed HLAHapV analyses using the accumulated haplotypes of the IHIW17 Family Haplotype Project to identify most likely haplotypes for these uninformative segregation cases [column “HapV (IHIW)”]. Tables 6C and 6D show families for which haplotypes were manually corrected after visual inspection. The HLA-DQB1~HLA-DPA1~HLA-DPB1 haplotype frequency is not available from NMDP.