Identification and Investigation of Novel Alleles

Identification and Investigation of Novel Alleles


Hello Everyone, welcome to the latest video in Omixon’s “Learn Me” Video Series. My name is Adel Juhos and I’m going to take
you through this training video today. In this short video, I am going to guide you
through the identification and investigation of novel alleles.
Alleles that are not present in the IMGT database. Identifying novel alleles is straightforward
in HLA Twin as they are always distinguished by an icon next to each novel allele and a
special naming convention containing the closest related IMGT allele, a hash mark (#) and an
additional number to identify the actual sequence. We can start the investigation by opening
the ‘HLA Typing sample result screen selecting the genotype containing the novelty and checking out the contents of the ‘Show novelties’ window. Here you can get detailed information
including the gene region where it was found, the exact location within that region and
the type of the novelty. Types of novelty can be “SNP” as in: Single
Nucleotide Polymorphism when one base has been substituted for another, “INSERT”:
when an insertion of DNA has been observed relative to the closest reference sequence
or “DELETE”: when a deletion of DNA has been observed relative to the closest reference sequence. For further in-depth analysis we will take
a peek into the genome browser by clicking on the ‘Jump to novelty’ button.
The novelty is highlighted by the locked cursor and there is also an additional ‘Novel allele
reference’ track and a ‘Related original reference track’ displaying the novel allele
sequence and the closest IMGT allele sequence. We attempt to pick closest match from the
IMGT database in terms of biochemical functionality and we also use it to name the novel allele.
In case of class 1 loci we pick the allele that is the most similar in key exons 2 and
3 and for the class 2 loci the priority is to find the closest allele on exon 2. It is important to remember that the name of a novel allele is not verified, and just an indication
of similar based on the sequence matching in the sample. In this example if we have
two Class 1 alleles in the database where one has 2 mismatches on exon 1 and the other
has only 1 mismatch on exon 3 then the former will be selected. This is important from the
aspect of the expressed protein and it also helps with the verification of the novelty.
To check the validity of a novel allele it is advised to add the base allele as a custom
allele candidate and compare the alignments next to each other. If the Illumina reads
map well to the novel allele reference and a coverage drop or gap can be seen on the
alignment of the base allele, then the novelty passes this visual inspection quality check.
If there are no Illumina reads supporting the novel variant and the base allele has
an even coverage then selecting the base allele as final genotype is suggested instead of
accepting the novelty. Once you are certain about the presence of
a novelty please take steps towards submitting it to the IMGT database to help improve genotyping
for the whole community. Omixon HLA Twin software helps you with the first step towards the
independent validation of your new allele by exporting the consensus sequences straight
from the genome browser. I hope you’ve found this short video useful.
If you have any questions contact us at [email protected] or place an inquiry with our Sales Team at
[email protected] For more videos, please see the Omixon YouTube Channel. See you next time!

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