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Loss of heterozygosity (LOH). Most diploid cells, for example human somatic cells, contain two copies of the genome, one from each parent (chromosome pair); each copy contains approximately 3 billion bases (Adenine (A), Guanine (G), Cytosine (C) or Thymine (T)). For the majority of positions in the genome the base present is consistent between individuals, however a small percentage may contain different bases (usually one of two for instance ‘A’ or ‘G’) and these positions are called ‘single nucleotide polymorphisms’ or ‘SNPs’. When the genomic copies derived from each parent have different bases for these polymorphic regions (SNPs) the region is said to be heterozygous. Most of the chromosomes within somatic cells of individuals are paired, allowing for SNP locations to be potentially heterozygous. However, one parental copy of a region can sometimes be lost, which results in the region having just one copy. The single copy cannot be heterozygous at SNP locations and therefore the region shows loss of heterozygosity (LOH). Loss of heterozygosity due to loss of one parental copy in a region is also called hemizygosity in that region.
It is a common occurrence in cancer, where it indicates the absence of a functional tumor suppressor gene in the lost region. However, many people remain healthy with such a loss, because there still is one functional gene left on the other chromosome of the chromosome pair. However, the remaining copy of the tumor suppressor gene can be inactivated by a point mutation, leaving no tumor suppressor gene to protect the body. Loss of heterozygosity does not imply a reversal to the homozygous state.
Copy-neutral LOH is thus called because no net change in the copy number occurs in the affected individual. Other names for copy-neutral LOH are acquired uniparental disomy (UPD) or gene conversion. In UPD, a person receives two copies of a chromosome, or part of a chromosome, from one parent and no copies from the other parent due to errors in meiosis I or meiosis II. This acquired homozygosity could lead to development of cancer if the individual inherited a non-functional allele of a tumor suppressor gene.
In tumor cells copy-neutral LOH can be biologically equivalent to the second hit in the Knudson hypothesis. Acquired UPD is quite common in both hematologic and solid tumors, and is reported to constitute 20 to 80% of the LOH seen in human tumors. Determination of virtual karyotypes using SNP-based arrays can provide genome-wide copy number and LOH status, including detection of copy-neutral LOH. Copy-neutral LOH cannot be detected by arrayCGH, FISH, or conventional cytogenetics. SNP-based arrays are preferred for virtual karyotyping of tumors and can be performed on fresh or paraffin-embedded tissues.
The classical example of such a loss of protecting genes is hereditary retinoblastoma, in which one parent's contribution of the tumor suppressor Rb1 is flawed. Although most cells will have a functional second copy, chance loss of heterozygosity events in individual cells almost invariably lead to the development of this retinal cancer in the young child.
The genes BRCA1 and BRCA2 show loss of heterozygosity in samplings of tumors from patients who have germline mutations. BRCA1/2 are genes that produce proteins which regulate the DNA repair pathway by binding to Rad51.
Loss of heterozygosity can be identified in cancers by noting the presence of heterozygosity at a genetic locus in an organism's germline DNA, and the absence of heterozygosity at that locus in the cancer cells. This is often done using polymorphic markers, such as microsatellites or single-nucleotide polymorphisms, for which the two parents contributed different alleles. Genome-wide LOH status of fresh or paraffin embedded tissue samples can be assessed by virtual karyotyping using SNP arrays.
It has been proposed that LOH may limit the longevity of asexual organisms. The minor allele in heterozygous areas of the genome is likely to have mild fitness consequences compared to de-novo mutations because selection has had time to remove deleterious alleles. When allelic gene conversion removes the major allele at these sites organisms are likely to experience a mild decline in fintess. Because LOH is much more common than de-novo mutation, and because the fitness consequences are closer to neutrality, this process should drive Muller's ratchet more quickly than de-novo mutations. While this process has recived little experimental investigation, it is known that major signature of asexuality in metazoan genomes appears to be genome wide LOH, a sort of anti-meselson effect.