Exploring the Different Types of Human Genotyping

 

Modern genetics techniques have dramatically accelerated the speed of discovering and understanding disease genes. Many discoveries are associated with classic single-gene disorders such as cystic fibrosis and muscular dystrophy.

In other cases, a gene or set of genes appears to play a role in more common diseases such as heart disease and cancer. The search for these disease genes begins with mapping and cloning the associated gene or genes.

SNPs

The DNA sequence of an individual's genes is remarkably similar from person to person, but slight variations do occur. These are known as single-nucleotide polymorphisms or SNPs. SNPs are the minor differences in an individual's genetic code and are often found in non-coding genome regions. However, SNPs can also occur within coding regions and change the amino acid (protein) a gene makes, or they may affect the regulatory mechanisms of a gene.

SNPs are usually widespread, occurring in allele frequencies greater than 1% of the population. SNPs that alter the protein code are known as "coding SNPs," while those that do not affect the coding sequence are called "non-coding SNPs."

Although most SNPs do not affect a disease, they can serve as biological markers to identify the location of the gene responsible for the condition. This type of identification is known as a genome-wide association study (GWAS).

Once the gene that causes disease has been found, researchers can use SNP analysis to compare the DNA sequences of people with and without the condition and look for SNP patterns that distinguish the two groups. This information can then be used to develop an SNP-based "genetic fingerprint" that can be used to determine a person's risk for a particular disease, as well as their likely response to certain drugs.

Copy Number Variations

A human genome comprises 6 billion chemical bases (or nucleotides) packaged into two sets of 23 chromosomes, one inherited from each parent. It was once thought that all genes occurred in two copies in each genome, but recent discoveries have shown that large segments of DNA, encompassing genes, can vary in copy number. These alterations, called copy number variations or CNVs, cause dosage imbalances and disease. In experimental plans for chemical discovery and development, human genotyping is crucial. Studies of metabolic rates, drug-drug interactions, illness models, variety in preclinical investigations, and 3D model and co-culture systems can all benefit from its application.

A CNV is a deletion or duplication of a genomic segment that may range from a few kilobases to many megabases. They are intermediate-scale structural variants that differ from small insertions and deletions (indels), a single base difference, and significant structural variants that change whole chromosomes or chromosomal regions.

CNVs can be detected using next-generation sequencing (NGS), methylation-based approaches, and microarrays. However, they are most commonly identified using computational strategies that leverage signals from the genotyping and sequencing technologies.

These methods identify segments of DNA that are lost or gained and report the resulting copy number to the user. For example, a part of DNA that contains a gene called AMY1 is lost in some individuals, and gains are observed in others. This results in a difference in the total amount of AMY1 in each genome, which correlates with salivary amylase activity, indicating the amount of starch in diets.

Polymorphisms

Although the genetic sequences of most people are remarkably similar, tiny differences in their DNA make each person unique. These differences are called polymorphisms. The most common polymorphisms are single nucleotide polymorphisms or SNPs. Each SNP represents a difference in one of the DNA building blocks, a cytosine (C) or thymine (T), within a given stretch of DNA. These differences are found throughout the genome and can be detected by DNA sequencing, RFLP analysis, or allele-specific PCR. On average, humans have 11 SNPs that distinguish them from other individuals. SNPs are valuable because they can be used to map disease genes.

Many polymorphisms do not cause a change in the protein that is encoded by the gene they reside in. However, a growing number of genes contain polymorphisms that are associated with a clinical trait. These polymorphisms are called susceptibility genes. Examples include CYP1A2 and PEMT, which affect caffeine and choline metabolism, respectively.

Polymorphisms are a source of variation that is actively and steadily maintained in natural populations by types of balancing selection. They allow for a wide range of investigations, including identifying genotypes in paternity and forensic studies, mapping quantitative loci affecting economic traits in plants and animals, and evolutionary comparisons of the DNA sequences and chromosome organization between related species. Increasing the density of SNPs in a genome scan can significantly improve the power of these investigations.

Alleles

An allele is one form of a gene occupying a specific locus (a particular location on a chromosome) and controlling a particular trait in an organism. A living organism can have two different alleles of a gene at the same locus - each conferring a slightly different phenotype. Genes contain DNA - a complex molecule that codes for transmitting inherited characteristics.

Single-nucleotide polymorphisms (SNPs) are variations in the sequence of a gene at a specific bp position. According to the definition, SNPs are characterized by allele frequencies of more than 1% in a sample of unrelated individuals. However, a single bp variation in a gene can have many alleles depending on the mutation rate at that bp position.

In some cases, alleles interact in a dominant/recessive fashion to produce a certain phenotype. For example, eye color and blood group are both examples of dominant/recessive traits. If an individual has two alleles for a dominant trait (such as brown eyes), it will overrule the characteristics of a recessive allele (such as blue eyes).

It is important to note that variants that do not affect protein sequence or function do not necessarily represent alleles. For instance, many gene mutations cause loss of function and are referred to as mutant alleles even though they do not produce a different phenotype.