Dozens of serious criminal cases, including prosecutions for murder, rape and terrorist offences, could be in jeopardy because of growing uncertainty over a controversial DNA technique. The Times has discovered that prosecuting authorities in different parts of Britain have adopted contradictory positions on the use of the Low Copy Number (LCN) method of DNA testing, which was heavily criticised by a judge in the Omagh bombing case last month.

In England and Wales prosecutors say that they have full confidence in LCN DNA testing and will submit it as evidence in court. But their counterparts in Northern Ireland want to adjourn all cases involving it until a Home Office study is completed.

In Scotland the technique is under review. The confusion will be seized on by defence lawyers in about 60 current cases where low copy DNA evidence is in use, and could prompt a wave of appeals in earlier cases.

LCN, or low template, DNA, was pioneered by the government-owned Forensic Science Service and has been used in cases around the world, including the Peter Falconio murder trial in Australia, the conviction of the serial rapist Antoni Imiela and in the search for Madeleine McCann.

But the LCN method, which works by amplifying microscopic particles of DNA to produce a larger sample, is not accepted everywhere and is regarded with scepticism by the US courts. Doubts over the technique have led the Home Office to commission a review of LCN DNA testing, to be led by Professor Brian Caddy, of the University of Strathclyde.

In the Omagh bomb case, defence lawyers revealed that the amplification process had produced a DNA match not only with the defendant, Sean Hoey, but also with a 15-year-old boy from Sussex who had never visited Northern Ireland. Mr Justice Weir, acquitting Hoey of mass murder in the 1998 Real IRA bombing, questioned the validity of LCN DNA and emphasised concerns that the science was not accepted internationally.

In the case of a man facing trial at Belfast Crown Court, for planting an incendiary device, Judge Burgess, the Recorder of Belfast, echoed his fellow judge’s “fundamental concerns about the present state of the validation of the science and the methodology associated with it”.

The Crown Prosecution Service suspended the use of LCN DNA after the Omagh judgment. It has since reinstated the technique. A spokesman said: “The CPS has not seen anything to suggest that any current problems exist with LCN. Accordingly, we conclude that LCN DNA analysis should remain available as potentially admissible evidence.”

But Ken Preston, from the Public Prosecution Service in Belfast, said that prosecutors had to take note of the judiciary’s concerns. “In our view the prudent thing to do is to seek adjournments of these cases until the Caddy review is completed.

Peter Corrigan, the defence solicitor in the Omagh case, criticised the CPS. “Low copy DNA is inherently unreliable – it’s junk science,” he told The Times. “This technique falsely implicated a teenager from Sussex in the Omagh bombing. If that boy had been from South Armagh he would have been imprisoned because of that false DNA result.”

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