Question

2.Some tumor suppressor genes inactivated during multi-step tumorigenesis may be readily identified because of LOH in the chromosomal region carrying them, while others may be difficult to identify in this way. Describe the factors that allow or complicate this identification.

Answer 1

LOH stands for Loss of Heterozygosity. It is defined as the loss of one parent's contribution to the cell whic can be caused by deletion, gene conversion, mitotic recombination or loss of chromosome. LOH analysis is a technique used to identify the loss of genetic material. In cancer it used to identify the loss of TSG (tumor suppressor gene). LOH in cancer leads to the inactivation of the second copy of a gene, typically the TSG. One fundamental requirement of the anaysis is that one should be able to disccriminate between the two copies of a particular gene. Because the coding regions of the gene contains few itragenenic sequence polymorphisms and the maternal and the allele have identical sequences. Hence, LOH analysis uses polymorphisms that occur near TSG as surrogate markers for the gene itself.

When a whole genome or a large segment of the genome is lost, the remaining segment or part is often duplicated. With complete duplication of the genetic material the karyotype might appear normal though no nomal genes are present.

The changes in the karotype makes it easy to identiify the LOH.

An earlier LOH would be more easily identifiable.

The factors that complicate LOH analysis are :

Contaminated tumor samples. tumor samples contain inflammatory cells and other cellular contaminants. This can cause problems in the process. LOH can be masked by heavy contamination of normal DNA.

Poor markers. It is important to realize that polymorphic repeat units near TSGs are only surrogate markers of the gene itself. of the polymorphism is dar from the tsg of interest it will not represent an accurate measurement of the tsg.

Lack of normal comparison sample.

Low DNA concentration. Major problems can arise when there is an inadequate amount of DNA. When DNA conc. is very low maaybe preferentally amplified over the other. When one allele has insufficient amplification, this is termed as allelic dropout.