What is HLA?
HLA molecules provides immunological unique identification to humans that modulates immune response with external and internal variables. Learn more about HLA here: http://en.wikipedia.org/wiki/Human_leukocyte_antigen
External variables are infectious agents (viruses, bacteria, fungi, parasites), food, foreign tissue, drugs and etc. Internal factors are tissue modification due to infections, cancer and physical trauma (heat, cold etc). Learn more here: http://en.wikipedia.org/wiki/Antigen_presentation
Why do we need to test for HLA?
In the 1950s it was shown that organ and tissue transplantation could offer a cure for numerous illnesses. But the success of these procedures depends to the matching degree between the patient and their donor for HLA.
What regions do we test and match for in HLA?
The regions of HLA proteins that interact with T-cell receptors polypeptides (proteins) are extremely variable from individual to individual (polymorphic), and they are called Antigen Recognition Sites (ARS). The polymorphism is conferred by DNA sequences that encode those polypeptides (proteins). In Class I molecules (HLA-A, -B, -C) exon 2 and 3 of Class I genes encodes for those polypeptides and they are called ARS exons. In Class II molecules (HLA-DRB1, -DQB1 and DPB1) exon 2 of class II genes encodes the ARS regions.
ARS T Cell receptor interaction is shown below:
Therefore in HLA testing we primarily sequence those exons and predict the protein sequences (1x High Resolution). DNA sequences that result in identical protein sequences for ARS regions are considered a match.
What other regions could routinely be tested for in HLA?
Some clinicians would like to test to see if it is possible to match for alpha-3 domain of HLA proteins. Exon 4 and Exon 3 of Class I and Class II genes encode alpha-3 polypeptides, respectively (2x high resolution). If alpha-3 regions are not matching but ARS regions match, if that donor is the best available donor otherwise, he/she could be selected for blood stem cell donation.
What are Null Alleles and Common and Well Defined (CWD) Null Alleles?
Some irregularities in DNA sequences may result in no expression or expression of totally non-functional protein. Those irregularities could be missing base(s) (deletions), have extra base(s) (insertions), or have base substitutions that result in premature termination of HLA protein synthesis (early stop codons). In certain cases those irregularities could happen in regions of the genes that are outside of the ARS regions. Therefore by just testing for ARS DNA sequences, one may miss those null alleles. This could result in calling a mismatch typing as a match and could affect the success of the transplant outcome.
Those null alleles that have seen at least five times in different ethnic populations are tested in donors and patients. We call this extra test as testing for CWD null alleles. (3x High resolution).
Can we test for other regions of the HLA genes?
Now with advances of Next Generation Sequencing (NGS) technologies, especially of Illumina and Pacific Biosciences we can sequence all exons of class I (7 Exons HLA-B, 8 exons HLA- and –C) and Class II (4x High Resolution). When requested we can also provide the sequences of non-coding region between the exons, introns, along with the exon sequences (8x High Resolution).