What Diseases are Associated with HLA Alleles?

The set of HLA alleles are associated with a wide variety of disease states.  Some of the more common HLA - disease associations are listed here.   What diseases are associated with HLA-A? The diseases associated with HLA-A include:…

Discovery of a Recombination Event

In a recent HLA Next Gen sequencing run, one of our client's samples displayed some puzzling results.  A standard HLA typing report showed a near-perfect sequence alignment across the first two exons (and first intron) in allele HLA-DPA1 followed…

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

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…

Can you perform HLA typing from FFPE samples?

FFPE (Formalin-Fixed Paraffin-Embedded) is a tissue fixation method used for archival storage of tissue samples in biobanks and clinical repositories.  Both normal and diseased tissue types are stored in FFPE format, often for years or decades. Unfortunately,…

Can you perform single-cell HLA typing?

We occasionally get inquiries as to whether we can perform HLA sequencing and typing from single-cell samples or samples with very low cell counts (i.e. blastomeres, etc.).  Unfortunately, we cannot run HLA typing from samples with low, or…
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Why does DRB1/3/4/5 show ‘No typing result available’?

We use the GenDx NGSengine application for HLA typing and HLA report generation. The HLA loci DRB3, DRB4 and DRB5 are paralogs of locus DRB1.  Thus, they share a significant fraction of their genetic sequence with DRB1. The NGSengine HLA…
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What does an HLA report look like?

Our HLA reports are generated automatically by the GenDX NGSengine® software and includes information about HLA allele typing calls, allele ambiguities and relevant metadata. The exact set of loci displayed in an HLA report will depend on…
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HLA PIRCHE matching service

NGSengine can now export HLA typing results of an individual sample directly to the PIRCHE matching services website. This will facilitate laboratories to predict indirectly recognizable HLA epitopes for either hematopoietic stem cells or solid…

What is the IMGT/HLA database?

IMGT Database The IPD-IMGT/HLA database contains genetic sequence and allele data for the human major histocompatibility complex (MHC). This database is foundational for many HLA Typing algorithms and Next-Generation sequencing projects.  It…
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What does “exon mismatch” mean in HLA reports?

If you see the identifier "exon mismatch" in some alleles in our HLA reports, there may be a good explanation for it.  We'll explain briefly here.   IMGT Database The IMGT HLA database is a standard reference library for determining…
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What version of HLA NGSengine do you use?

GenDx Reports We use GenDx NGSengine for HLA typing and HLA report generation.  The current version of NGSengine v.2.27.1.  This version of NGSengine includes the IMGT/HLA database v.3.49.0.    
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Do you have a GenDx HLA publication list?

We vet our vendors carefully before using products in our sequencing workflows.  The Sequencing Center uses the GenDx libraries for NGS (Next Generation Sequencing)-based HLA typing.  The combination of substantial immunological research,…
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How do you read HLA reports?

We deliver detailed HLA reports to clients immediately after their HLA sequencing runs are complete. The reports include information about HLA allele typing calls, allele ambiguities, and relevant metadata. HLA Loci The full set of HLA loci…
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Can you explain HLA allele nomenclature?

The standardized HLA gene and allele nomenclature is managed by the WHO Nomenclature Committee for Factors of the HLA System.  A high-level summary of their nomenclature system is reproduced here for easy reference.  A thorough and detailed…