Reminder on RFLP and SSR analysis (SRR analysis)

SSR analysis exploits the presence of the highly variable tandem repeat in human DNA. This highly variable region contains short repeating sequences of nucleotides, the repeats usually only 2-5 bp in length. The typical SSR has a repeat length of 2-9 nucleotides. A polymorphism in the number of repeats when the repeating unit is longer (in the range of 10-60 nucleotides) is called a variable number of tandem repeats (VNTR). A genetic polymorphism resulting from differences in copy number of a particular SSR is called a simple sequence repeat polymorphism (SSRP, pronounced “surp”), although the term simple tandem repeat polymorphism (STRP, pronounced “strip”) is also in widespread use (Hartl & Jones, 2004).

In most cases, these sequences exist in non-coding regions, while in several cases, their presence in coding regions has been implicated in the manifestation of a genetic diseases, most notably, Huntington’s disease. However, for purposes of genetic fingerprinting, these sequences are highly valuable. Since these sequences tend to shrink and expand between generations, comparison of only a few of these regions between any group of individuals will usually allow researchers to distinguish the individuals using their DNA. Since, on average, the human genome has one SSR every 2kb of human DNA, or about 1.5 million SSRs altogether, it is easy to find sequences to compare. This is done by applying RNA templates of sequences flanking the SSR, and then amplifying the SSR via PCR to create enough DNA for visualization. Since with every repeat, the length of the resulting fragments increases, even highly similar species of fragments (with differences of only 1-2 repeats) can be easily separated using electrophoresis.

Of course, these techniques are mostly good for placing someone at the scene of an event. However, the Genomic Revolution – beginning with the sequencing of the Human Genome, and J. Craig Venter’s application of shotgun cloning technique to whole-genome sequencing – has much more to offer.