Hotspots and minisatellites

On Monday morning at 9.05am on 10 September 1984, Alec Jeffreys, now Professor Sir Alec Jeffreys, FRS, and the Royal Society Wolfson Research Professor in the University of Leicester Department of Genetics, discovered the world's first genetic fingerprint.

As the technique began to solve paternity and immigration cases and to revolutionise criminal investigations, he refined and simplified the process, turning it into what became known as "genetic profiling", producing a pattern of DNA unique to a particular person.

Minisatellites: their use and importance

Instrumental to these techniques were 'minisatellites', short sequences of chemical building blocks used to chart human DNA instability. Minisatellites show greater variation from one person to the next than most of other DNA material, exhibiting this variation in the numbers of repeat units or stutters.

Now, twenty years on, Sir Alec has moved away from minisatellites, using them as a platform to think about alternative ways of detecting inherited rearrangements in our DNA. He is looking at two genetic processes, mutation (change) and recombination (reshuffling) and their impact on human DNA diversity.

"We appreciated early on that minisatellites were variable because they were unstable," he said, adding: "We faced two problems. The first is that DNA changes at extremely low rates. Minisatellites have allowed us to get round that. The second is the smallness of family sizes.

"Even if you have ten children, you will only get at most only one or two minisatellite mutants. We needed families of millions of children, particularly to study other modes of DNA instability, so we started to use minisatellites to find an alternative way of research. For us, a child is simply a complex and expensive way of amplifying DNA from a single sperm and egg. However, using the most sophisticated methods, we found we could type the DNA of a single molecule or cell as an alternative approach to studying inherited DNA rearrangements."

Once able to dispense with children in favour of cells, Sir Alec turned to the study of sperm. "A single ejaculation will produce one hundred million sperm, equivalent to one hundred million offspring. This gives us numbers of progeny that go way beyond mouse or fruit fly production and well into the realm enjoyed by microbial geneticists."

Hotspots of activity

What came as a surprise was that the mutation in minisatellites comes about by abnormal recombination and that mutation and recombination are not different processes in these stuttered regions of DNA. Minisatellites, it seems evolve as parasites in hotspots of crossover activity, propagating themselves through recombination.

Sir Alec said: "That then led us to ask a very simple set of questions:

• How recombination events are distributed along human chromosomes;
• What sort of processes are going on during human recombination;
• How these patterns and processes impact on human diversity.

"Over the past few years we have developed a whole range of technologies to look at the DNA in sperm, searching for ones that show crossover in a given region. Our findings have transformed how people view human recombination. Crossovers are far from randomly formed, but are concentrated in hotspots, in between which are areas dead of activity. It is as if you shuffle a pack of cards with some blocks of cards stuck together so that they don't get reshuffled."

The HapMap Project

This turned out to be crucial in sparking off a major international project, known as the HapMap Project, to investigate how human DNA diversity is organised in human chromosomes. The project is specifically aimed at identifying the 'blocks of cards' that are stuck together and not reshuffled by recombination from generation to generation. These so-called haplotype blocks and their associated recombination hotspots are not just of academic interest - they also hold considerable promise for disease analysis.

"Our recombination work is important for understanding how human DNA diversity is organised, and underpins international efforts into trying to analyse common human diseases," Sir Alec said. "To find a disease gene then you have to find the mutation that predisposes people to that condition. However, if the mutation resides in one of these haplotype blocks then it will tend to follow markers in the block in patients, and thus the problem can be reduced first to finding the relevant block, then to searching within the block for the real mutation. This has changed the way people think about genetic association studies and reduced the cost of scanning the whole human genome. It is a very exciting time."

Future research

In trying to understand hotspots, Sir Alec is investigating why they occur where they occur, and to grasp the rules that appear to prevent crossover hotspots from triggering dangerous rearrangements in the genome. "There is something going on in humans that prevents this," he said. "We are also trying to extend the whole concept of using single sperm analysis to look at other processes of DNA instability, for example jumping DNA and single base changes in our chromosomes. We understand very little about these processes and how and where they occur."

In developing new systems to chart the alteration of the DNA sequence, Sir Alec is quietly optimistic that they will work. So far, he says, things are looking good, and there are few else in the world following the same challenging avenues of enquiry.

While the research done by his laboratory team feeds into medical genetics, as well as studies of genome diversity, the genetic analysis of human origins and the work done by Professor Yuri Dubrova on radiation and DNA, it is, in itself, pure research. "We are not specifically looking at applications, though almost inevitably applications will arise" Professor Sir Alec Jeffreys said. "I feel I've done my bit on research application." Police officers and those fighting immigration and paternity cases must surely agree.