October 14, 2012

Individual genomes show extensive variation

  • Polymorphism (more fully genetic polymorphism) refers to the simultaneous occurrence in the population of genomes showing variations at a given position. The original definition applied to alleles producing different phenotypes. Now it is also used to describe changes in DNA affecting the restriction pattern or even the sequence. For practical purposes, to be considered as an example of a polymorphism, an allele should be found at a frequency > 1% in the population.
  • Single nucleotide polymorphism (SNP) describes a polymorphism (variation in sequence between individuals) caused by a change in a single nucleotide. This is responsible for most of the genetic variation between individuals.
  • Restriction fragment length polymorphism (RFLP) refers to inherited differences in sites for restriction enzymes (for example, caused by base changes in the target site) that result in differences in the lengths of the fragments produced by cleavage with the relevant restriction enzyme. RFLPs are used for genetic mapping to link the genome directly to a conventional genetic marker.
  • Polymorphism may be detected at the phenotypic level when a sequence affects gene function, at the restriction fragment level when it affects a restriction enzyme target site, and at the sequence level by direct analysis of DNA.
  • The alleles of a gene show extensive polymorphism at the sequence level, but many sequence changes do not affect function.  

The original Mendelian view of the genome classified alleles as either wild-type or mutant. Subsequently we recognized the existence of multiple alleles, each with a different effect on the phenotype. In some cases it may not even be appropriate to define any one allele as "wild-type".
The coexistence of multiple alleles at a locus is called genetic polymorphism. Any site at which multiple alleles exist as stable components of the population is by definition polymorphic. An allele is usually defined as polymorphic if it is present at a frequency of >1% in the population.
What is the basis for the polymorphism among the mutant alleles? They possess different mutations that alter the protein function, thus producing changes in phenotype. If we compare the restriction maps or the DNA sequences of these alleles, they too will be polymorphic in the sense that each map or sequence will be different from the others.
Although not evident from the phenotype, the wild type may itself be polymorphic. Multiple versions of the wild-type allele may be distinguished by differences in sequence that do not affect their function, and which therefore do not produce phenotypic variants. A population may have extensive polymorphism at the level of genotype. Many different sequence variants may exist at a given locus; some of them are evident because they affect the phenotype, but others are hidden because they have no visible effect.
So there may be a continuum of changes at a locus, including those that change DNA sequence but do not change protein sequence, those that change protein sequence without changing function, those that create proteins with different activities, and those that create mutant proteins that are nonfunctional.
A change in a single nucleotide when alleles are compared is called a single nucleotide polymorphism (SNP). One occurs every ~1330 bases in the human genome. Defined by their SNPs, every human being is unique. SNPs can be detected by various means, ranging from direct comparisons of sequence to mass spectroscopy or biochemical methods that produce differences based on sequence variations in a defined region (for examples of SNP maps see Altshuler et al., 2000; Mullikin et al., 2000).
One aim of genetic mapping is to obtain a catalog of common variants. The observed frequency of SNPs per genome predicts that, over the human population as a whole (taking the sum of all human genomes of all living individuals), there should be >10 million SNPs that occur at a frequency of >1%. Already >1 million have been identified.

Some polymorphisms in the genome can be detected by comparing the restriction maps of different individuals. The criterion is a change in the pattern of fragments produced by cleavage with a restriction enzyme. Figure 3.1 shows that when a target site is present in the genome of one individual and absent from another, the extra cleavage in the first genome will generate two fragments corresponding to the single fragment in the second genome.
Because the restriction map is independent of gene function, a polymorphism at this level can be detected irrespective of whether the sequence change affects the phenotype. Probably very few of the restriction site polymorphisms in a genome actually affect the phenotype. Most involve sequence changes that have no effect on the production of proteins (for example, because they lie between genes).

A difference in restriction maps between two individuals is called a restriction fragment length polymorphism (RFLP). Basically a RFLP is a SNP that is located in the target site for a restriction enzyme. It can be used as a genetic marker in exactly the same way as any other marker. Instead of examining some feature of the phenotype, we directly assess the genotype, as revealed by the restriction map. Figure 3.2 shows a pedigree of a restriction polymorphism followed through three generations. It displays Mendelian segregation at the level of DNA marker fragments.

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