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:
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.
The Sequencing Center is one of the leading service providers for HLA Typing and Whole Genome Sequencing (WGS) in the USA. Offering affordable, high-coverage HLA typing results with 4-field resolution and microbial scale WGS, we provide clients with exceptional services, including DNA extraction, library prep, sequencing and bioinformatics. We work with leading research organizations world-wide in various fields including immunology, oncology, transplantation, inherited diseases, neurodegenerative diseases, and drug discovery and development.
1020 Luke Street
Fort Collins, CO 80524
(970) 682-1288 (Direct to lab)
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