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There are also problems in convincing doctors that the system will help them to do their jobs better, the audit office says in a long-awaited report.
However, it is generally supportive of the way that the system has been procured and says that errors made in the past in nationwide IT systems have been avoided.
The report reaches no conclusions as to whether the system will be value for money, arguing that it is too soon to do so three years into a ten-year programme.
Its figure for the total cost of the programme, £12.4 billion, is double what the NHS said it would cost. But the earlier estimate of £6.2 billion was for the cost of central contracts alone and took no account of local costs, of training, or of the cost of switching to the new system from a plethora of older ones.
The audit office makes no criticism of the costs, which will be spread over ten years. The base contract costs have risen to £6.8 billion, but that is because the system is being asked to do more than originally planned, and changes in the specification have been properly agreed and costed.
The £12.4 billion still comes in well under the figure of £20 billion given in recent interviews by Lord Warner, the Health Minister. But that, he said yesterday, was intended to cover Connecting for Health and the run-of-the-mill IT requirements — for payroll and so on — of the 1.3 million NHS workforce.
Chris Shapcott, from the audit office, said that figure was a “reasonable estimate” for Lord Warner to have used.
Connecting for Health is made up of a dozen elements that are being introduced at different times in different places, so the audit office is unable to say if it will actually work.
The greatest delays are on the “central spine”, which will hold everybody’s health records, so that they can be accessed by doctors anywhere, eliminating complex and costly paper transfers.
The report says that the patient records system is running two years late. “Deployment of the national clinical record is now planned in pilot form from late 2006, compared to the original plan of December 2004, and in its full form from late 2007.”
The audit office adds that the take-up of Choose and Book, for direct booking of hospital appointments, has “been slower than initially planned”.
Mr Shapcott said that “time will tell” whether the project will have been good value for money and whether it can deliver “the best results”.
The challenges noted by the audit office include ensuring that IT suppliers “continue to deliver systems that meet the needs of the NHS and to agreed timescales without further slippage”.
This point is important because Richard Granger, the head of Connecting for Health, has pinned down suppliers to tough contracts on which many are making a loss.
He said yesterday that he could penalise them for late delivery but was not doing so in the interest of keeping “a balance between penalising suppliers and letting them cope with work in progress, which they haven’t been paid for”.
He added: “Contractors do have difficulties — if it had been easy it would have been done years ago. The fact is we are doing a lot more than we set out to do and it is extremely complicated. Has any other ten-year IT project achieved so much this early?” Edward Leigh, MP, chairman of the Commons Public Accounts Committee, said that the project “must not be allowed to go the way of so many other ill-fated government IT projects. We are only a third of the way through the life of the contracts, to 2013-14, but already the signs are ominous.”
Tony Collins, executive editor of Computer Weekly and a leading critic of the programme, said that while there had been substantial progress, that progress was in the least complex areas. “I think one of the concerns has to be that we still don’t know how much the programme is really going to cost,” he said.
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