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…
, ,

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…

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…
, , , ,

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…
, ,

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,…
, ,

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…
,

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…

How can you access your sequencing data?

When sequencing runs are finished, we automatically upload FastQ files to a client's Box.com account. These files are typically found in the directory: ClientName-> Reports-> ReportID-> FastQ The FastQ files in this directory…