As shown in Figures 1-2 and 1-3A, variation at the cutting site of a restriction enzyme can result in two alternative forms (alleles): the enzyme cuts or it does not. That is called a diallelic system; three genotypes are possible. If a person received the same allele at a particular site (locus) from both parents, the genotype (or person) is said to be homozygous for that allele; if different alleles were inherited from the two parents, the person is heterozygous at that locus. (Some use the term locus, rather than site. Others reserve locus for use in relation to expressed genes.)
As also shown in Figure 1-3B, when the variation is in the number of tandem repeats, there can be many alleles, of which a given person can have only two. That is called a multiallelic, or hypervariable, system. The number of genotypes possible is the sum of the positive integers from 1 to the number of alleles; e.g., in a three-allele system, as shown in Fig. 1-3B, there are expected to be 6 genotypes (1 + 2 + 3). The number of genotypes is also given by the formula n(n + 1)/2, where n is the number of alleles.
Inheritance of variation in the noncoding segments of DNA follows the same rules that Mendel inferred for expressed genes. A given individual inherits one of the father's two alleles and one of the mother's two alleles. When two variable sites, each on a different chromosome, are examined, the inheritance at one site is independent of that at the other; i.e., which paternal allele is inherited at site 1 bears no relation to which paternal allele is inherited at site 2. When the two sites are on the same chromosome, they might also be transmitted independently, if they are sufficiently far apart. When they are very close on the same chromosome, the phenomenon of linkage disequilibrium can result—a deviation from independent inheritance in which particular alleles at the two sites tend to be transmitted together.
Forensic DNA typing usually consists of comparing "evidence DNA" i.e., DNA extracted from material—most often semen—left at a crime scene with "suspect DNA" (i.e., DNA extracted from the blood of a suspect). The tools of DNA typing include restriction enzymes, electrophoresis, probes, and the polymerase chain reaction.11,12,13
In the RFLP approach shown in Figure 1-4, DNA is subjected to controlled fragmentation with restriction enzymes that cut double-stranded DNA at sequence-specific positions. The long DNA molecules are thereby reduced to a reproducible set of short pieces called restriction fragments (RFs), which are usually several hundred to several thousand basepairs long. Many hundreds of thousands of fragments are produced by digestion of human