How to read a TruSight HLA Assign report

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We use the CareDx TruSight HLA v2 Sequencing Panel for HLA typing runs. And we use the CareDx TruSight HLA Assign v.2.1 software application to analyze HLA typing results.

An example Assign report is shown below:

Assign compares sample sequences against a standard library of sequences in the IMGT (International Immunogenetics Information System) HLA database.

Pxx_Syy:  This field refers to our internal sample tracking numbers (e.g. P12_S34, etc.).  In communications with us you may want to refer to this tracking number.

Created:  This field is the report creation date, which may differ somewhat from the date the HLA sequencing run was actually finished.

References: This field refers to the version number of the IMGT reference sequences used for sequence alignments of HLA samples against the IMGT database.  We update Assign to the newest reference sequence versions as soon as they are released by IMGT.

CWD Set:  This field refers to the version number for Common and Well-Documented alleles as released by IMGT.  We update Assign to the newest CWD versions as soon as they are released by IMGT.

Sample Name: This column refers to client sample names as defined by the client.  Typically, these names correspond to vial names as submitted by the client.

HLA Loci:  HLA gene names and gene loci are shown in the first row.  The CareDx TruSight HLA assay generates allele assignments for 11 HLA loci, as follows:

  • HLA-A
  • HLA-B
  • HLA-C
  • HLA-DPA1
  • HLA-DPB1
  • HLA-DQA1
  • HLA-DQB1
  • HLA-DRB1
  • HLA-DRB3
  • HLA-DRB4
  • HLA-DRB5

Sample fields:  Two rows are shown for each sample and gene locus – one row for each allele.  By default, Assign displays three-field resolution, i.e “00:00:00”, which is sufficient for most clients. However, we can generate four-field resolution “00:00:00:00” if clients request it. Definitions of HLA allele nomenclature are available online.

Double-dash(- -):  A double dash (- -) indicates an ambiguous field in the typing result. For example, “- -:01:01” indicates an ambiguity in the first field, “01:- -:01” indicates an ambiguity in the second field, and “01:01:- -” indicates an ambiguity in the third field.

Pound sign (#):  A # indicates an ambiguous expression in allele typing.

Capital ‘X’: An ‘X’ shown for the second allele indicates that no heterozygous positions were detected in the analyzed sequence. The presence of an X does not confirm homozygosity at this locus.

The DRB genes and alleles form a complicated set of paralogues and pseudogenes. The blank fields under DRB genes reflect this complexity; a full discussion of these blank fields is beyond the scope of this note.

We include this type of HLA report with all HLA runs.  And we include Assign software documentation in case you need to drill down for more detailed analysis of the results.

 

Wondering why you have ambiguous alleles? Please see our HLA Ambiguous Alleles article for more info.