Increasing Prevalence of Genetic Disorders and Launch of New Products to Boost Demand for SNP Genotyping and Analysis
Single Nucleotide Polymorphism (SNP) represents the most common type of mutation in genomes of all life forms. As an individual DNA test is run in a laboratory, specific genetic variants are identified by DNA sequence variation tests. Variation is shown as differences in sequence between different cells. The aim of genotyping is to identify genetic variations that could potentially affect a disease or trait. In most cases, one or two genes have multiple variations, leading to variable numbers of DNA variants (SNPs.) Hence, multiple tests can be run on the same samples to detect differences and hence gain information on the genotype of the person.
For
SNP genotyping and analysis, different sets of DNA are used for each
individual. Typically, the entire set of human DNA is used for analysis. In
some cases, shorter insertions and deletions are made, resulting in minor
changes in the sequence of the genetic material. For example, an individual
could have many differences in the four sets of DNA at the same time but only
one single-nucleation mutation, resulting in a mismatch at the genetic
location.
In
the laboratory setting, SNP genotyping and analysis requires DNA isolation from
a single parent of unknown origin using PCR amplification of a primer and
template derived from the individual's genome. Primer sequences can be
constructed from amplicons of known mutations in the genome. There are three
types of primer used for this procedure. These are genotype specific genomics
primers, intergenic primer and non-genetic template primer. Since the locations
of mutations are known in humans, these sequences are called synonymous.
The
next step in the process is to generate a collection of quality DNA samples
from the individuals for SNP genotyping and analysis. The best source of DNA
for the procedure is a cell-free DNA extract kit from companies such as LGC
Limited, Fluidigm Corporation, Thermo Fisher Scientific, and Sequenom, Inc.
In July 2019, U.S.-based Thermo Fisher
Scientific launched three new Applied Biosystems AgriSeq targeted genotyping by
sequencing solutions that will allow customers to genotype canines and felines.
The
third and final step in the procedure is to calculate the genotype frequency of
each sequence of the insertion and deletion mutations by using the SNP
genotyping profile and variants database. This database contains information on
all loci tested for SNPs and the frequency of their occurrence in patients with
known genotypes. Only rare mutations that are not detected using traditional
methods are present in the database. These rare mutations are referred to as
micro-evolutionary mutations. A micro-evolutionary mutation occurs in an
organism over a very short span of evolution, usually only a few hundred
nucleotides, but in some cases may occur over thousands of nucleotides. The
frequency of the mutation increases as the length of the insertion interval
increases, therefore these are called 'micro-evolutionary' mutations.
After
the SNPs have been typed and their corresponding variants genotyped, a
comparison of their sequences with the samples in the database is performed to
determine discrepancies between them. Any errors in this step of the process
are called out by a mismatch between the genotype and the reference DNA. If the
mismatches are found, then the samples are excluded and new DNA samples have to
be collected for further analysis. The whole procedure takes three to four weeks
depending on the number of Illumines performed on the samples and the
complexity of the task. This has made the process of SNP genotyping more
accurate than the traditional method of manual sequence analysis.
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