Polymorphism Identification: Methods and Applications

A genetic polymorphism is the presence of two or more different forms of a DNA sequence within a population. These variations are a natural part of a species’ genetic landscape and a source of its biological diversity. For a variation to be considered a polymorphism, it must be present in at least 1% of the population. These differences in our genetic code contribute to what makes each individual unique.

Understanding Genetic Variation

Genetic polymorphisms are differences in the sequence of nucleotides, the building blocks of DNA. These variations can range from a single change to the alteration of large segments of a chromosome. Common types of polymorphisms include:

• Single Nucleotide Polymorphisms (SNPs), which are changes in a single nucleotide base. For example, where most people have an “A” nucleotide, a minority might have a “G” instead.
• Insertions and Deletions (indels), which involve the addition or removal of one or more nucleotides from the DNA sequence.
• Copy Number Variations (CNVs), where entire sections of the genome are repeated, and the number of repeats varies between people.
• Short Tandem Repeats (STRs), which are short DNA sequences repeated multiple times in a row. The number of repeated units differs among individuals.

Polymorphisms arise from spontaneous mutations or the shuffling of genetic material during recombination. These events introduce and spread new genetic variants throughout a population over generations.

Techniques for Polymorphism Discovery

Identifying unknown genetic polymorphisms has been advanced by high-throughput sequencing technologies. Whole Genome Sequencing (WGS) is a comprehensive method that determines nearly the complete DNA sequence of a genome. By comparing an individual’s genome to a reference, scientists can pinpoint novel SNPs, indels, and structural variants, providing a full picture of genetic variation.

A more targeted technique is Whole Exome Sequencing (WES), which focuses on the protein-coding regions of genes. The exome constitutes about 1-2% of the genome but contains most known disease-causing mutations. WES is an efficient strategy to find variations with likely functional consequences, especially rare variants associated with specific diseases.

These sequencing methods generate large amounts of data requiring bioinformatic analysis. Computational tools align the sequenced DNA fragments to a reference genome, revealing differences that may be new polymorphisms. Further analysis confirms if these are genuine variations, which are then cataloged in public databases.

Genotyping Known Polymorphisms

After a polymorphism is discovered, researchers use genotyping methods to screen for its presence in individuals. Unlike discovery methods, genotyping techniques detect specific, pre-identified variations. The Polymerase Chain Reaction (PCR) is a common approach that can be adapted for this purpose.

One PCR-based method is PCR-RFLP (Restriction Fragment Length Polymorphism), which uses enzymes to cut DNA at specific sequences. A polymorphism can alter a cutting site, resulting in DNA fragments of different lengths that can be distinguished. Another method, allele-specific PCR, uses primers that bind only to a specific variant, allowing direct identification.

For large-scale studies, DNA microarrays, or “SNP chips,” are used. These chips contain probes for specific SNPs, and a fluorescent signal indicates which alleles are present when an individual’s DNA binds to them. For smaller projects or for validation, Sanger sequencing is an option for determining the exact DNA sequence of a targeted region.

Applications in Health and Research

In personalized medicine, genetic variations can help predict disease risk. For instance, variants in the BRCA1 and BRCA2 genes are associated with increased risk for breast and ovarian cancers. Certain forms of the APOE gene are linked to a higher risk for Alzheimer’s disease, allowing for tailored screening and preventative strategies.

This information is also used in pharmacogenomics to predict responses to medications. Variations in genes for metabolic enzymes affect how quickly a drug is processed. For example, variants in the CYP2C9 and VKORC1 genes influence sensitivity to the blood thinner warfarin, helping doctors determine the appropriate starting dose.

Polymorphism analysis is also important in population genetics to study evolutionary history and migration patterns. In forensic science, the high variability of STRs provides the basis for DNA fingerprinting to identify individuals from biological samples. In agriculture, identifying polymorphisms for desirable traits like drought resistance enables selective breeding of crops and livestock.