Thursday, June 7, 2012
Human leukocyte antigen genotyping.
A Stanford University
team has developed a new human leukocyte antigen (HLA) sequencing method that could be more
cost effective and accurate than existing technologies to extend the
applications of HLA genotyping, which has previously focused on matching bone
marrow donors and recipients.
polymorphisms are clinically relevant because specific alleles have been
associated with various autoimmune diseases including multiple sclerosis (MS),
celiac disease, rheumatoid arthritis (RA) and type 1 diabetes.4-7
Additionally, matching HLA genotypes is essential for host acceptance of bone
Despite the clear importance of knowing a patient's HLA genotypes, the
actual sequencing is expensive and time consuming. Most methods exclusively
sequence the antigen-binding cleft because it is the most variable, but this
can lead to undetected sequence variation in other regions of the HLA genes.
In a paper
published in the Proceedings of the National Academy of Sciences, Stanford's Michael Mindrinos and
colleagues developed a high throughput HLA sequencing method that maps most of
genome to reduce or eliminate ambiguity.
also identified previously undetected HLA alleles that could be implicated in
disease susceptibility or could further improve matching of patient and donor
is associate director of the Stanford Genome Technology Center. The
paper also included researchers from the university and the Howard Hughes
developed primers to sequence the major histocompatibility complex class I A
(HLA-A), HLA-B, HLA-C and major histocompatibility complex class II DR b1 (HLA-DRB1) genes.
Sequencing the amplified DNA matched 99% of reference DNA samples from
40 cell lines with known HLA genotypes. In 59 clinical samples, sequencing
determined HLA genotype and identified 3 new HLA alleles-2 previously
undetected short insertions and 1 single base pair deletion. Genotyping of a
few samples can be done within five days.
said the benefits of his sequencing technology are "higher resolution,
lower cost and higher throughput. This technology has reduced the cost of HLA
typing and improved its accuracy such that it can soon be part of a standard
patient profile, equivalent to a blood type." He told SciBX that the method is less expensive
because it can analyze more than 2,000 samples per instrument run, which is
over 1,000 samples more than competing high throughput sequencing technology.
to Mindrinos, applications of the technology include matching transplantations,
evaluating responses in clinical trials of therapeutics and vaccines, and
conducting disease association studies. His group is now working to extend the
HLA genotyping method to cover the four other HLA genes.
He said Stanford
University is filing a patent application. The technology is unavailable for