NomenCleaner is a module to help researchers to solve challenges related to HLA nomenclature. Two major challenges would be (1) Conversion between nomenclatures, and (2) Field checking.
- Conversion
NomenCleaner converts a given set of HLA alleles which is in arbitrary nomenclature to the ones in the updated nomenclature. The conversion from the updated to old nomenclature is NOT available.
- Field checking
Often, the field separator is removed though given HLA allele conforms to the updated nomenclature. This barely causes a problem in most cases, however, there is definitely some case that may confuse researchers. For example, if the HLA allele DPB1*101101 is given, then some researchers may be perplexed as to which one is right among DBP1*10:11:01, DPB1*101:101 and DPB1*1011:01. NomenCleaner searches the HAT(HLA Allele Table) file, which contains whole HLA allele name information of the IMGT database of a specific version, and determines that DPB1*1011:01 is the only valid solution. (cf. DBP1*1011:01 is in the IMGT database of the version 3.37.0.)
NomenCleaner basically takes PED file(e.g. '*.ped') and HAT(HLA Allele Table) file (e.g. '*.hat') as input, then performs its jobs as required by the user. Finally the NomenCleaner generates Cleaned HPED(CHPED) file, e.g. '*.chped', which contains the converted HLA alleles and its log file, e.g. '*.chped.log'.
You can find more information about the official HLA allele nomenclature defined by "IMGT-HLA" organization(go to IMGT-HLA Nomenclature), which indicates that "Maximum 4-field Nomenclature" is currently used as the standard for HLA allele names.
When converting a lower resolution allele to a higher resolution (two-field to four-field, say), this module neither conduct a prediction nor make a guess. It just chooses a first option among possible candidates. For example,if a HLA allele "A\*01:01" is given, then the possible candidates are
| Allele | G_group | P_group |
|---|---|---|
| A*01:01:01:01 | 01:01:01G | 01:01P |
| A*01:01:01:02N | 01:01:01G | 0 |
| A*01:01:01:03 | 01:01:01G | 01:01P |
| A*01:01:01:04 | 01:01:01G | 01:01P |
| A*01:01:01:05 | 01:01:01G | 01:01P |
| A*01:01:01:06 | 01:01:01G | 01:01P |
| ... | ... | ... |
The total number of possible candidates for "A*01:01" is 96. But this module will just transform "A*01:01" to "A*01:01:01:01".
It is important to format the PED file correctly. HLA PED file contains the HLA alleles of eight classical genes (FID,IID,pID,mID,SEX,PHENO,A,B,C,DPA1,DPB1,DQA1,DQB1,DRB1). HLA alleles must be in the following (alphabetical) order: HLA-A, B, C, DPA1, DPB1, DQA1, DQB1, DRB1
Note that each HLA allele spans two columns per individual (i.e. two chromosomes).
Put "0" for unknown HLA alleles.
As a result, an example row of HLA PED file will be
HG00319 HG00319 0 0 0 0 A*02:01:01G A*03:01:01G B*07:02:01G B*56:01:01G C*01:02:01G C*03:04:01G DPA1*01:03:01G DPA1*01:03:01G DPB1*04:01:01G DPB1*04:01:01G DQA1*01:01:01G DQA1*01:02:01G DQB1*05:01:01G DQB1*06:02:01G DRB1*01:01:01G DRB1*15:01:01G
Look at our example file example/g1k_subset.ped for an example formatting.
NomenCleaner in HLA-TAPAS has to be implemented in the directory of main project folder. (i.e. 'HLA-TAPAS/' where 'HLA-TAPAS.py' script is.)
$ cd ../
# Change your current directory to the HLA-TAPAS main project folder.
$ python -m NomenCleaner \
--hped NomenCleaner/example/g1k_subset.ped \
--out NomenCleaner/example/g1k_subset \
--4field