HML Examples - nmdp-bioinformatics/dash GitHub Wiki
| Locus | Method | Interpretation Format |
HML | Other info |
|---|---|---|---|---|
| A B |
NGS Sanger |
GL String | 0.9.5 | NGS used for HLA-A Sanger used for HLA-B |
| A B |
NGS Sanger |
GL Resource | 0.9.5 | Same as above, except format for interpretation is GL Resource instead of GL String. This is an example of why GL Resource shouldn't be used. |
| DRB1 | NGS | GL String | 0.9.5 |
| Locus | Method | Interpretation Format |
HML | Other info |
|---|---|---|---|---|
| A B C |
Haploid | 0.9.5 | three samples; no primary data or interpretation Note: while the schema shows that at least one typing-method is required, typing-method is an abstract type that requires a choice. In this case the choice is none. Yes, it can be confusing. |
|
| DRB1 DQB1 DPB1 |
SBT | Haploid (allele code and allele) |
0.9.5 | |
| A B C |
SBT | Haploid (allele code and allele) |
0.9.5 | |
| DPA1 DPB1 |
SSO | Haploid (allele) |
0.9.5 |
| Locus | Method | Interpretation
Format | HML | Other info |
| ----- | ------ | --------------------- | ------- | ------- ||
| A | DNA | allele code | 0.3.0 | Lab 999 typed a sample for center 123 for the ABDR project for NMDP ID: 444-333-2. The typing was performed on Jan 23, 2004. The results are:
A0102, A0103
A0103, A0106 |
| A | DNA | genotype list | 0.3.0
0.9.3 | (same as above, but reported as genotype list instead of allele code)<br >Lab 999 typed a sample for center 123 for the ABDR project for NMDP ID: 444-333-2. The typing was performed on Jan 23, 2004. The results are:
A0102, A0103
A0103, A0106 |
| B | SBT | genotype list | 0.3.3
0.9.3| In this case there is an intronic or exon1 gSSP reagent that is uninformative for our local interpretation. The gssp tag with no contents is an indicator of a hemizygous product |
| B | SBT | genotype list | 0.3.3
0.9.3| In this case there is an intronic or exon1 gSSP reagent that is uninformative for our local interpretation. The gssp tag with no contents is an indicator of a hemizygous product |
| B | SBT | genotype list | 0.3.3<br > 0.9.3| example showing GSSP as sequence instead of registered-name |
| DRB1 | SBT | genotype list | 0.3.3
0.9.3| There is no generic sequence in this example. It contains GSSPs that are specific for DRB113 and DRB115 |
| DRB1 | SBT | genotype list | 0.3.3
0.9.3| This is a homozygous sample with no generic sequence. This is up-front GSSP that is DR13 specific. |
| 2DL1
2DL2
2DL3
2DL4
2DL5
2DS1
2DS2
2DS3
2DS4
2DS5
3DL1
3DL2
3DL3
3DS1
| SSO | genotype list | 0.3.0
0.9.3| Lab 999 typed a sample for center 789 for a project entitled "KIR". The typing was performed on Sep 8, 2008. They tested fourteen KIR genes and reported presence/absence for each,along with the probe information. Each locus was reported in its own 'typing' HML element. |
| 2DL1
2DL2
2DL3
2DL4
2DL5
2DS1
2DS2
2DS3
2DS4
2DS5
3DL1
3DL2
3DL3
3DS1
| SSO | genotype list | 0.3.0
0.9.3| Same as above (6.1) except for each sample (one, in this case), all loci were reported in a single 'interpretation' element. |