Can you explain typing 3′-UTR polymorphisms in the HLA-G allele?

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The non-classical HLA-G allele is associated with numerous disease states, including pre-eclampsia, asthma, several types of cancer and autoimmune diseases.  We sequence HLA-G using a whole-gene amplification strategy from GenDx.  In HLA-G there are several well-known polymorphisms in the 3′-UTR region that may contribute to various diease conditions, hence, we are seeing increased interest in sequencing HLA-G specifically to examine 3′-UTR mutations.

The GenDx technote “HLA-G typing including 3′ UTR polymorphisms”  describes a 14-bp indel (dbSNP ID rs66554220) and nine SNP’s in HLA-G 3′-UTR that we can view with NextGen Sequencing protocols.  As part of this process we use the bioinformatics tool NGSengine from GenDx for analysis of this region.

Figures 1 – 4 show four possible 14-bp indels at locus 2961 (rs66554220) – deletion/deletion, insertion/insertion, deletion/insertion and insertion/deletion, respectively.

Fig. 1.  14-bp deletion/deletion at locus 2961.


Fig. 2. 14-bp insertion/insertion at locus 2961.


Fig. 3. 14-bp deletion/insertion at locus 2961.


Fig. 4. 14-bp insertion/deletion at locus 2961.

These well-known indels are easily identified in NGSengine and captured in our client reports.

Table 1.  Sample HLA-G report.

We deliver a standardized report for the HLA-G allele based upon the nomenclature defined in the GenDx technote “HLA-G typing including 3′ UTR polymorphisms”.

The report includes:

  • Sample ID.  This is a unique internal identifier that we use for sample tracking.
  • Client Vial Label. The sample name or ID as specified on sample vials.
  • Genotype. The HLA-G genotype in 4-field resolution for allele 1 and allele 2.
  • 2961. The insertion/deletion indels at locus 2961 (dbSNP ID rs66554220).
  • SNP’s. Polymorphisms at loci 3001, 3003, 3010, 3027, 3035, 3142, 3187, 3196, 3509.

If you’re interested in HLA-G typing and in particular the 3′-UTR region, please contact us for more information and quotes for service.