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Understanding Gene Mutations

 

Genes and DNA Each chromosome contains thousands of genes. The genes are blueprints for creating proteins in cells. Each type of protein has a different function in the cell. Genes are made up of a string of components called nucleotides. In human beings there are four nucleotides and each is designated by a letter. The four nucleotides are:

  • Adenine A
  • Guanine G
  • Cytosine C
  • Thymine T

The information in genes is encoded in the order of the nucleotides. For example, the sequence AGCTAGC would give different information than the sequence CATAGTA. When building a protein, the machinery inside the cell needs to know certain information such as:

  • Where on the chromosome does the gene start?
  • Which amino acids make up the protein and in what order do they go?
  • Where does the gene end?

There are several abnormalities that can occur in genes:

Point mutation
This is when a single nucleotide has been switched. For example, in the spot where an “A” was supposed to go, there is instead a “T”. This is the type of abnormality that causes diseases like sickle cell anemia and cystic fibrosis. There two types of point mutations:

Missense mutation
This type of mutation is a change in one nucleotide that results in the substitution of one amino acid for another in the protein made by a gene.

Nonsense mutation
A nonsense mutation is also a change in one DNA nucleotide. Instead of substituting one amino acid for another, however, the altered DNA sequence prematurely signals the cell to stop building a protein. This type of mutation results in a shortened protein that may function improperly or not at all.

Deletion
This is when part or all of a gene has been deleted from the chromosome. The deleted DNA may alter the function of the resulting protein or eliminate it entirely. Common examples of diseases caused by gene deletions include Duchenne Muscular Dystrophy and retinitis pigmentosa.

Insertion
An insertion changes the number of DNA bases in a gene by adding a piece of DNA. As a result, the protein made by the gene may not function properly.

Duplication
A duplication consists of a piece of DNA that is abnormally copied one or more times. This type of mutation may alter the function of the resulting protein.

Frame shift mutation
This type of mutation occurs when the addition or loss of DNA bases changes a gene’s reading frame. A reading frame consists of groups of 3 bases that each code for one amino acid. A frame shift mutation shifts the grouping of these bases and changes the code for amino acids. The resulting protein is usually nonfunctional. Insertions, deletions, and duplications can all be frame shift mutations.

Repeat expansion
Nucleotide repeats are short DNA sequences that are repeated a number of times in a row. For example, a trinucleotide repeat is made up of 3-base-pair sequences, and a tetranucleotide repeat is made up of 4-base-pair sequences. A repeat expansion is a mutation that increases the number of times that the short DNA sequence is repeated. This type of mutation can cause the resulting protein to function improperly.

Genetic mutations may be consider to be “dominant” or “recessive” depending on the type of mutation and the disease. Mutations may be located on the “sex” chromosomes, X or Y, or they may be on the non-sex chromosomes which are called autosomes.
PGD is indicated for couples at risk for transmitting a specific genetic disease or abnormality to their offspring. For carriers of autosomal dominant disorders, the risk that any given embryo may be affected is 50%, and for carriers of autosomal recessive disorders, the risk is 25%. For female carriers of mutations on the X chromosome, the risk of having an affected embryo is 25% (half of male embryos).
PGD also can be performed and may be elected by patients who carry mutations such as BRCA-1 that do not cause a specific disease but are thought to confer significantly increased risk for a disease – in this case breast cancer.

PGD for gene abnormalities

In order to use PGD to analyze an embryo for a gene mutation, it is first necessary to understand what type of mutation is present and where it is located. In some cases, knowing the location of the gene mutation may be sufficient.

Since the amount of material we are studying is very small, it is first necessary to expand it so it can be tested more easily. This is done with a technology known as PCR (polymerase chain reaction). The DNA produced can then be analyzed by a variety of techniques such as restriction endonuclease digestion or “cutting” of the DNA into smaller segments followed by gel electrophoresis.
The major challenges of PGD relate primarily to the relatively short interval of time available for analysis and the fact that only one or two cells can be analyzed (compared with the hundreds of cells obtained via amniocentesis).
With PCR misdiagnoses may result from
  • use of cell from the embryo which did not contain a nucleus
  • failure of a segment a DNA to be identified
  • external contamination.
The risk for misdiagnosis relates directly to the type of genetic disorder for which testing is performed. The estimated risk of transferring an affected embryo mistakenly identified as normal by PGD is approximately 2% for recessive disorders and 11% for dominant disorders. The error rate can be significantly reduced if the PGD laboratory also analyzes areas of DNA that are close to the area where the mutation is located. This is called linkage analysis. Our laboratory performs linkage analysis routinely for PGD cases.
For couples known to be at risk for having children with inherited genetic disease, IVF with PGD represents a major scientific advance. Two professional fertility societies recommend counseling patients that patients that pregnancy rates may be lower than those achieved with IVF when PGD is not performed. Pregnancy rates after PGD may be reduced because genetic testing will decrease the number of embryos suitable for transfer. Embryos in IVF are typically chosen based on their appearacne under the microscope. However, if the best appearing embryos have genetic mutations then they cannot be used. The use of other embryos may lower the pregnancy rate.

PCR: Polymerase Chain Reaction
Technique for increasing the amount of DNA

Restriction endonuclease
Technique for findings gene mutations

Gel electrophoresis
Technique for separating fragments of DNA

 

List of genetic diseases that have had PGD testing at our lab