Abstract

Genomics data pose significant challenges
at two levels; a) understanding its disease relevance, b) figuring out its
anticipated potential clinical applications. 
To date, there has been an increasing number of sequence information
from Genomics projects that may suggest some diseases-relevance. GWAS studies
have identified over 116,109 SNP-trait associations have been identified in
human chromosomes¹.
Clinical studies have identified over 793,574 variants of clinical relevance
that are found in 30,273 genes².
Although these information may be useful, however, only through experimental
testing we can validate their potential clinical applications.

Sequence-phenotype relevance

Investigating the associated phenotype related to variants
and mutations is an important step towards identifying new therapeutic targets.
Gene silencing such as RNAi is the most common starting point in investigating
gene functions and identify disease phenotype relevance. However, selectively
targeting sequence-specific variants is challenging.

Allele-specific Gene Silencing

We pioneered the application of RNAi in selectively
targeting mutant alleles.

Designing siRNAs that can distinguish between two alleles
based on only difference in a single nucleotide change is a challenging. siRNA
that perfectly match the mutant allele mRNA sequence will trigger its
silencing. However, this siRNA will create a single mismatch with the normal mRNA
counterpart.

Would this single nucleotide mismatch be sufficient to stop
silencing the normal mRNA? Hence, designing allele-specific siRNAs require
significant optimisations.

We were the first to demonstrate RNAi allele-specific
silencing. The technology was initially used in targeting mutant alleles in the
AChR in a neuromuscular disease model and later adopted in other models.

Isoform-specific Gene Silencing

We pioneered the application of RNAi in selectively
targeting length-dependent isoform spliced variants.

Designing siRNAs that can distinguish between two mRNA
spliced variants that have 100% sequence similarity but only differ in their
length is a challenging. siRNA that perfectly match to one of the spliced
variant will also perfectly match the other one and accordingly trigger
silencing both of them with no selectivity.

Would designing siRNAs independently targeting the isoforms
at their end junctions be sufficient to selectively target them?

We are the first (and uniquely) to demonstrated RNAi application
in targeting length-dependant isoforms. We demonstrated isoform-specific
silencing of the Open4 gene to investigated isoform variant-phenotype.

Today, in the relevance
of Genomics data interpretation for the purpose of both Target Identification
and Validation, we think that variant-specific gene silencing may be a starting
point in linking sequence information to its potential phenotype relevance.

OMMTech is specialised in
Target Validation as a CRO and offers variant-specific RNAi services at two
formats:

a)      
Custom-siRNA
Design – custom-made allele—specific or isoform specific siRNAs tailored to
clients requested genes. It comes with a 6-month free consultation to assist clients’
experimental work.

b)     
Variant-specific
RNAi Projects – performing experimental projects on sequence specific
silencing and investigate the consequence phenotype change.

1. GWAS Catalogue 2019 release. https://www.ebi.ac.uk/gwas/.

2. ClinVar database. https://www.ncbi.nlm.nih.gov/clinvar/.