The key to unlocking the Madeleine McCann case may lie in a clue so small that it cannot be seen with the naked eye. It may even hinge on a single cell, weighing no more than six picograms, or six trillionths of a gram, but enough to yield a strand of DNA.

Madeleine’s DNA was allegedly recovered from the boot of the car her parents hired several weeks after she disappeared, but that discovery, while important, is open to widely differing scientific and legal interpretations.

“The television shows tend to make it seem very simple,” Paul Debenham, director of technology and innovation at LGC, Britain’s largest independent forensics laboratory, says. “DNA science is not that easy.”

LGC provides forensic science services predominantly for police work. At its laboratories scientists extract clues from physical evidence: blood, urine, hair, fibres, insects, guns, footprints, paint, telephones, computers, drugs, corpses, clothes and glass.

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LGC’s headquarters in Teddington, West London, is one of Europe’s main centres for the extraction, analysis and identification of DNA samples – the unique genetic signature that has revolutionised policing and detective work.

In the past two decades, hundreds of murderers, rapists, drug dealers and thieves have been tracked down by their DNA, often long after the cases had gone “cold”. But as Mr Debenham points out, the science is not the universal crime-cure that the public imagines, or shows such asCSI: Crime Scene Investigation make it appear.

“What DNA can do is say who is the originator of a sample,” he said. “What it can’t tell us is why that sample is where it is.”

There has been much confusion in the McCann case over the match between Madeleine’s DNA and that found in the car: this has been reported variously as between 60 and 100 per cent. While declining to comment directly on the case, Mr Debenham pointed out that DNA matches are seldom expressed as percentages but rather in terms of the probability of finding another person with the same DNA at random in the population.

If all 20 markers used to identify DNA are present and match, the average probability of finding a match at random in the population is roughly one in a billion. If only 16 markers are present, and the other four cannot be identified, there is just a small mathematical possibility that the DNA could have come from someone else.

“If you got down to only three or four matches, then you would be worried,” said Mr Debenham. “You have to ask why there is only a partial match: it could be because only a very small amount of DNA was recovered, or because the sample had degraded, or because it has been transferred from something else.”

In essence, the task of the DNA scientists is to prove (or disprove) beyond reasonable doubt that a sample comes (or does not come) from a specific individual, but with DNA being deposited and gathered in such a multitude of different circumstances the extraction of a reliable sample is paramount. “You’ve got to be sure that whatever you’re producing is so robust and accurate that it’s acceptable in court,” Ros Hammond, a scientific adviser at LGC, said.

The analysis in the McCann case has been done at the Government’s Forensic Science Service laboratory in Birmingham, but the process is identical to that carried out on hundreds of DNA samples at LGC every day.

The evidence arrives in carefully labelled blue crates, usually with specific instructions from police. Technicians first extract the genetic material from the evidence, then use heating blocks and enzymes to separate the DNA strands and replicate it. Once the specific DNA sequence is identified, it is matched, if possible, with samples in the national DNA database.

Extraordinary precautions are taken to ensure that the sample is not contaminated with other DNA. The air is purified and sterilised “scene suits” are worn by the technicians over specially laundered scrubs, which are replaced daily. Visitors must provide a DNA sample via an oral swab before entering the lab to ensure that if any contamination occurs the intrusive DNA can be identified and ruled out.

Samples may be degraded, or present in very small quantities, for a variety of reasons: perhaps an item of clothing has been worn briefly or only once, or it has been washed. In that case, extra precautions are taken with a process called “high sensitivity profiling”, with rigorously regulated sterile lab conditions for extracting, diluting and then replicating the DNA samples.

This is the procedure that will have been followed with the samples in the McCann case. Among the other techniques used to gather the samples, forensic scientists in Portugal will have used a method called “touch DNA”, gathering the smallest flecks of human material from the seat, boot and other parts of car using a swab to try to pick up microscopic particles of Madeleine’s DNA.

In another part of the LCG laboratory, Gavin Trotter, lead scientist in toxicology, tests blood, urine and body tissue for evidence of drugs, alcohol, poisons and sedatives. He speaks over the din from what looks like a large sewing machine with robotic arms, processing samples from workers such as bus drivers, airline pilots and soldiers. The machine can test for drugs, alcohol and other substances at the rate of 2,000 samples a day.

Hair – particularly dark hair, which retains chemical signatures longer than blond or grey hair – can be a particularly useful source of evidence. “Since hair grows at roughly one centimetre a month, you can use it to find out what a person has ingested over a fairly lengthy period of time,” Mr Trotter said.

If sufficient amounts of Madeleine’s hair are recovered, these could provide important evidence as to whether she was alive when the sample was deposited and what was in her body. If the hairs have roots attached, a full DNA profile can usually be obtained.

“If hair has fallen out because of decomposition, you may be able to tell,” Mr Debenham said.

DNA science is advancing at breath-taking speed. Two decades ago a DNA sample the size of a 2p piece was needed to make a meaningful test. Today, thanks to advanced replication technology, the tiniest fragment of DNA may be sufficient to make an identification if it is preserved adequately. But with advanced DNA testing techniques has come a faith in the science that is sometimes unrealistic.

“There is a tendency to be DNA-focused,” Ms Hammond said. “Sometimes we need to remind police that there are other ways of investigating besides forensics.”

In the McCann case, a DNA sample has been found, but that has raised a host of questions that would certainly be asked in court if the case were to get that far. How good is the sample? What else can it tell us and, above all, how did it get where it was found?

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