single nucleotide polymorphism (SNP)

[Myanmar Journal of Surgery]

single nucleotide polymorphism

The most common type of change in DNA (molecules inside cells that
carry genetic information). Single nucleotide polymorphisms occur when
a single nucleotide (building block of DNA) is replaced with another.
These changes may cause disease, and may affect how a person reacts to
bacteria, viruses, drugs, and other substances. Also called SNP.


What are single nucleotide polymorphisms (SNPs)?

Single nucleotide polymorphisms, frequently called SNPs (pronounced
“snips”), are the most common type of genetic variation among people.
Each SNP represents a difference in a single DNA building block,
called a nucleotide. For example, a SNP may replace the nucleotide
cytosine (C) with the nucleotide thymine (T) in a certain stretch of
DNA.

SNPs occur normally throughout a person’s DNA. They occur once in
every 300 nucleotides on average, which means there are roughly 10
million SNPs in the human genome. Most commonly, these variations are
found in the DNA between genes. They can act as biological markers,
helping scientists locate genes that are associated with disease. When
SNPs occur within a gene or in a regulatory region near a gene, they
may play a more direct role in disease by affecting the gene’s
function.

Most SNPs have no effect on health or development. Some of these
genetic differences, however, have proven to be very important in the
study of human health. Researchers have found SNPs that may help
predict an individual’s response to certain drugs, susceptibility to
environmental factors such as toxins, and risk of developing
particular diseases. SNPs can also be used to track the inheritance of
disease genes within families. Future studies will work to identify
SNPs associated with complex diseases such as heart disease, diabetes,
and cancer.


Types of SNPs

Single nucleotides may be changed (substitution), removed (deletions)
or added (insertion) to a polynucleotide sequence. Ins/del SNP may
shift translational frame.

Single nucleotide polymorphisms may fall within coding sequences of
genes, non-coding regions of genes, or in the intergenic regions
between genes. SNPs within a coding sequence will not necessarily
change the amino acid sequence of the protein that is produced, due to
degeneracy of the genetic code. A SNP in which both forms lead to the
same polypeptide sequence is termed synonymous (sometimes called a
silent mutation) — if a different polypeptide sequence is produced
they are nonsynonymous. A nonsynonymous change may either be missense
or nonsense, where a missense change results in a different amino
acid, while a nonsense change results in a premature stop codon. SNPs
that are not in protein-coding regions may still have consequences for
gene splicing, transcription factor binding, or the sequence of non-
coding RNA.

Use and importance of SNPs

Variations in the DNA sequences of humans can affect how humans
develop diseases and respond to pathogens, chemicals, drugs, vaccines,
and other agents. SNPs are also thought to be key enablers in
realizing the concept of personalized medicine. However, their
greatest importance in biomedical research is for comparing regions of
the genome between cohorts (such as with matched cohorts with and
without a disease).

The study of single-nucleotide polymorphisms is also important in crop
and livestock breeding programs (see genotyping). See SNP genotyping
for details on the various methods used to identify SNPs.

They are usually biallelic and thus easily assayed.