Table 1.
Data-Elements in 17th IHIW Typing Reports
| Data-Elements | Data Type | Description | Typing Report Formata |
|---|---|---|---|
| 17th IHIW Lab-code | Identifier | A 6-character code provided by the 17th IHIW to identify each participating laboratory. | ABCDE |
| Report ID | Identifier | A code provided by the originating lab to identify each report. | ABCDE |
| Specimen ID | Identifier | A 17th IHIW code that uniquely identifies the specimen that was genotyped. | ABCDE |
| Instrument | Meta-data | Parameters that document the name, manufacturer, model, and on-board software of each instrument used to generate the typing. | AB |
| Reagent Protocol | Meta-data | Parameters that document the name, manufacturer, and reference source for any reagents or kits used to generate the typing, along with protocol deviations. | AB |
| Software | Meta-data | Parameters that document the name, manufacturer and version of each program used to generate the typing, along with the use to which that program was applied, and any non-default parameters applied. | ABC |
| Reference Database Version | Meta-data | Documentation of the IPD-IMGT/HLA Database release version(s) used for the sequence alignment and base-calling that generated the consensus sequence and genotype. | ABCDE |
| Reference Sequence | Meta-data | The identifiers for the reference sequences used for the sequence alignment and base calling that generated the consensus sequence and genotype | CDE1 |
| Locus | Genotyping data | The locus associated with each genotype and consensus sequence. | ABCDE |
| Genotype | Genotyping data | A genotype written in GL-String format[40] for each locus typed. | ABDE2 |
| Consensus Sequence | Genotyping data | A nucleotide sequence representing a contiguous phased region of DNA. | ABCDE |
| Sequence Coordinate | Meta-data | The start and end positions of the consensus sequence(s) with respect to the reference sequence. | ABCDE |
| Phasing | Meta-data | Parameters that describe the phase relationships between the consensus sequences at each locus. | ABCDE |
| Sequence Feature | Meta-data | The gene feature or features (exons, introns or untranslated regions) represented by the consensus sequence | AB3 |
| Sequence Quality | Meta-data | The mean depth of reads used to generate a given consensus sequence | AC |
| Typing Annotation | Meta-data | A structured notation for identifying instances when allele names included in the genotype are the closest matches to the consensus sequence, but do not correspond exactly to the reported consensus sequence. | A4 |
| Novel Polymorphism | Genotyping data | A description of any novel polymorphism detected. | ABCDE |
| FASTQ Location | Meta-data | The name and location (in the WS Database, or online) of the primary (“raw”) FASTQ data for each genotype | ACDE |
IHIW: International HLA and Immunogenetics Workshop
GL: Genotype List
IPD-IMGT: ImmunoPolymorphism Database-ImMunoGeneTics
a
For each data-element, the typing report format in which it is found it is listed. As referenced in Figure 1, A: Manual IHIW XML; B: Illumina and laboratory-generated IHIW XML; C: GenDx XML; D: HLA Twin, HistoGenetics, MIA FORA and TypeStream Visual HML; E: HLA Twin and MIA FORA HML.
1
The A and B formats use the reference sequences in Table 3.
2
The WS Database conversion daemon generates GL Strings for format C.
3
The C, D, and E formats use the “Genomic - Unknown Location” sequence feature.
4
The hlaPoly tool identifies this information for all typing report formats.