• Home
  • Sitemap

Chapter 4 Genome type


1.SNP (Single Nucleotide Polymorphism)

We inherit a pair of genomes from our parents - one from our father, the other from our mother. At the same time, we also inherit the characteristic genomic sequences from our parents. Perhaps, you are familiar with "blood type", and in fact, the genomic type is very similar concept as the blood type.

For example, the blood type of a child born between a father of type AB and a mother of type O, will be either type A or type B.

Now, what about the case of genomic types? As described earlier, genomic sequence consists of the four different bases - A, T, G, C. Here, we focus on a specific sequence among the long chain where a particular position of the nucleotide base is different. The difference of nucleotide base in such particular position of the genomic sequence is called "SNP" (Single Nucleotide Polymorphism)

The following shows a typical SNP where a particular position is altered by either A or G. In the wild type, the particular position is A, and it is altered to G in the mutant type. If we compare the wild type and the mutant type, the only difference in the genomic sequence is this particular position. However, this difference sometimes makes distinct changes in certain characteristics of the nature of our body.


2.One SNP makes three different genome types

Three different genomic types can exist derived from one SNP. Since we inherit each one genome from our parents, the combination of each pair of genome makes three different genome types. In the case of previous example of A-G mutation,three different genome types can exist - namely, AA, AG, and GG.


3.Different genome types from one SNP

The following figure illustrates the possible genome types of children from the parents having both AG genome type. Each child inherits one genome from each parent, so that three different combinations exist due to A and G mutation.


4.Disease related SNP

The above example shows the possible combination derived from one SNP. Since there are many SNP sites in our genomes, possible combinations of these SNPs seem to be infinite. However, these combinations of SNP are limited only among the SNPs which exist in our parents.

Because of these limitations, we inherit "the original constitution" (the original nature of our body) from our parents, and it remains unchanged throughout the whole life. In a sense, we inherit SNPs from our parents to create the original nature of our body. Among these SNPs, there are certain SNPs which are closely related to the specific diseases. These SNPs are called "disease related SNPs".

A typical example of the disease related SNP is the one in the case of "metabolic syndrome". The metabolic syndromes mean syndromes related to obesity, which cause symptoms like high blood pressure, hyper cholesterol, high blood sugar, etc. These metabolic syndromes may have risks causing severe diseases like heart attack, brain hemorrhage, and diabetes.

The SNPs which are related to obesity have been investigated by many researchers worldwide. As the results of the investigations, the specific combinations of SNPs have been found as "obesity related SNPs". By analyzing the specific SNPs, it can be possible to suggest whether a person has a tendency to become obesity.

Another typical example of disease related SNP is the one in the case of alcohol digesting enzyme. When we drink wine, alcohol containing in the wine is digested in our liver. The mechanism of alcohol digestion in the liver is explained as follows. First, alcohol is decomposed into acetaldehyde by an enzyme called "alcohol dehydrogenase (ADH)". Next, acetaldehyde is decomposed by an enzyme called "acetaldehyde dehydrogenase (ALDH)" into acetic acid, then into carbon dioxide and water which are excreted from our body.

Throughout the whole process, the most important key is ALDH. If the ALDH enzyme is inactive, toxic acetaldehyde would accumulate in the body which causes various severe side effects. As the results of intensive studies on the activity of ALDH, it becomes clear that a particular genomic type of ALDH gene can cause a difference in resistance against alcohol.

ALDH is a protein which consists of 517 amino acids. Among these amino acids, it was found that the mutation at the number 487 amino acid could determine the activity of ALDH. Since the mutation is A - G, there are three genome types exist - namely, AA, AG, and GG, as we learned in the previous example.

Among these three genome types, the strongest activity against alcohol is the GG type, and the AA type is the weakest activity which can hardly digest alcohol.

The GG type (GG homo) is very popular among Caucasians and Africans, and approximately 50% of Japanese have GG homo. The activity of ALDH of the AG type (AG hetero) is approximately 1/16 of GG homo, and the AA type (AA homo) is totally inactive against alcohol.

It seems that the above story indicates GG homo are lucky because they can drink alcohol as much as they like. However, it has been reported that GG homo has a tendency to become alcoholic. In fact, 90% of Japanese alcoholic patients are identified as GG homo. GG homo may not be regarded as lucky simply because of having strong activity of ALDH.

  • BACK
  • NEXT
  • Chapter 1 Genome and our body
  • Chapter 2 Gene expression and protein synthesis
  • Chapter 3 Mechanism of gene expression
  • Chapter 4 Genome type
  • Chapter 5 Genomic diagnostics
  • Chapter 6 Personalized medicine