A next generation sequencing based test that helps find the best match for donor selection in allogenic organ and tissue transplant. Major Histocompatibility complex is Group of genes coding for a set of host surface molecules that bind to peptide fragments derived from pathogens and foreign antigens and display them on host cell surface for recognition by the appropriate T cells. It is also called as Human Leukocyte Antigens (HLA). It Serves as a unique identification marker for every individual. In organ and tissue transplantation, HLA antigens of the donor identified as invaders by the recipient,causing rejection. Careful selection of the matched donor and recipient critically affect the outcome of transplantation.
During bone marrow transplant, the donor's bone marrow might be considered as foreign body and rejected by recipient's immune system. More the mis-match, higher the chances of rejection. HLA (Human Leukocyte Antigen) gene sequences the proteins that can lead to this rejection and hence it is important to match the immune signature of potential donor(s) with that of recipient.
HLA typing test has to be performed on the samples from recipient and donor(s). 50% or higher match in the HLA gene allelic sequence indicates that such a transplant will have least possibility of graft versus host disease or in other words lowest risk of a transplant rejection.
Advantages over conventional typing methods
HLA testing is challenging due to its high polymorphic nature and high levels of sequence homology between the loci. Using conventional typing methods, Serology, SSP, SSO and SBT, is laborious and time consuming and may not resolve ambiguities between homologous regions at allelic resolutions. Besides, different HLA loci (genes and pseudogenes) share nucleotide sequences which is difficult to map with conventional techniques. NGS allows a single nucleotide based sequencing to derive an accurate map of each HLA gene loci.
|Serotyping||Non-sequencing based typing method where antibodies specific to HLA proteins are used to identify the proteins on the cell surface.|| - Low Cost|
| - Crude Method|
- Protein based detection
- Inaccurate typing
- Protein binding to more than
|Sequence Specific Oligonucleotide Hybridization (SSO)||Typing .method where specific oligos are first designed for genes of interest and then hybridized to patient or donor DNA to check for hybridization.|| - Checking of specific |
| - Cannot account for
unrecorded alleles |
- Hybridization errors
- Need to know target sequence
- Cannot phase
|Sanger Sequencing||Sanger sequencing or Sequencing by Termination (SBT) is a classical method used for sequencing specific regions of the MHC.|| - Used to sequence
regions of interest|
- Base pair resolution
- Coverage only 2X
| - Different HLA alleles |
share similar sequences,
- Cannot phase
|Next-gen Sequencing||Performing long range PCR to amplify HLA genes in MHC region, fragmenting the amplified genes.|| - Deep coverage (1000x) |
- Total MHC coverage
- Rapid high throughput
- Accurate and efficient
|- Data Analysis|
The customised high coverage of MedGenome’s high resolution allelic HLA testing Panel provides the highest level of resolution, eliminating the need for follow-up testing to obtain a confident typing result.
The HLA locus is sequenced with high-quality, paired-end 2 × 150 bp reads, enabling use of dense polymorphisms to assign phase accurately. This allows unambiguous HLA typing results to be derived directly from the sequencing data.
The Venn diagram illustrates increasing levels of HLA typing resolution. The figure below shows the antigen binding site of a HLA class I molecule. Through NGS, the specific DNA sequence of the region of genome that codes for the 'antigen binding site' is deciphered.
The highest degree of resolution to which a HLA coding gene can be deciphered is known as 'Allelic resolution'. Allelic resolution coding enables to indentify whenever there are 'synonymous DNA substitutions within the coding region as well as major introns' leading to change in expression of HLA antigen.
There have been various studies showing the enhanced effect of ultra high-allelic resolution HLA typing on overall survival post transplant.
Such resolution of gene sequence is depicted as four digits separated by colons eg A*01:01:01:01.