Ahead of a new report into what happened at scandal-hit Stafford Hospital, repeated denials by NHS bosses that they knew what was going on are cast into doubt by evidence shown to Channel 4 News.

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The Francis inquiry into what happened at the hospital between 2005 and 2008 is due to report shortly and is expected to be critical of failures by the statutory and regulatory bodies meant to be overseeing the NHS.

Those in charge at the time at West Midlands strategic health authority and at the hospital itself told the inquiry and the previous independent inquiry which reported in 2010 that they had not known about what was later described as the “appalling lack of care”.

While that may be true in some cases, Channel 4 News has seen data which shows the level of access to a real-time mortality alert system - a computer programme designed to warn a hospital if its death rates were too high in certain illnesses or procedures.

Mortality alerts

This system was used by staff at Mid Staffordshire trust and across the West Midlands strategic health authority region, including other hospitals and the primary care trust. From the data provided to us, we are able to see that it was accessed thousands of times between 2005 and 2009.

In 2006, for instance, staff at Mid Staffs logged in 212 times. (If a member of staff logs in more than once during the day, this is counted as one log-in). The following year, they logged in 127 times.

Across the health authority region, between 2005 and 2009, NHS staff logged in more than 8,000 times.

Yet the health authority claimed in its closing statement to the Francis inquiry that it had not been aware of the mortality alerts until the Healthcare Commission launched its investigation into the trust in March 2008.

'Unimaginable suffering'

The alerts system was devised by Professor Sir Brian Jarman, an international authority on hospital performance. He told Channel 4 News that there was no possible way those in charge at the time did not know. "I actually sent letters to the chief executive of the trust from July 2007 onwards pointing out that they had high death rates in certain procedures and diagnoses."

Prof Jarman was only able to submit the figures to the Francis inquiry after it had officially closed, so we understand they may not feature in the final report.

The first independent inquiry found patients were caused "unimaginable suffering" by the care at the hospital. A shortage of staff, an obsession with meeting targets, and a determination to achieve foundation trust status were all blamed. But relatives also spoke of the lack of compassion from staff, the failure to ensure patients were fed and hydrated properly, of those left in soiled sheets, and of medication not being given.

This inquiry by Robert Francis QC has concentrated on the failures by the system which allowed this to happen, including why the regulatory authorities were unaware of the problems, why the complaints system did not work, and why the trust board did not intervene.

Excess death rate

More than a decade ago Professor Jarman developed his early warning to detect unexpectedly high death rates. This followed his work on the inquiry into the Bristol heart babies. He said he had never got over the fact that if parents had only known, they could have taken their babies to another hospital where the cardiac surgery rates were better.

He developed hospital standardised mortality ratios - HSMRs - and they have been published by the company Dr Foster in the media for every trust in England since 2001. They enable the public and health staff to see each trust's excess death rates.

Right from the beginning, the figures showed that Mid Staffs had an excess death rate above the national average. By 2006 in fact it was 27 per cent above that average.

Not everybody agreed with the methodology behind the HSMRs, but it is not disputed that they at least gave an indication of problems. But now Channel 4 News has learned that the health authority's reaction to the poor Mid Staffs figures in 2007 was not to start asking probing questions about the state of the hospital but to hire some academics from Birmingham University to review the HSMRs.

Discrediting HSMRs

But at the subsequent independent inquiry, another team of experts from Harvard were asked to look at the report commissioned by the health authority to look at the methodology behind HSMRs.

The conclusion from Harvard was that the exercise was to "discredit" the HSMRs and that it was completely irresponsible of the authorities not to have aggressively investigated why the figures were so high.

But this was not all those in charge did. The trust changed the way it recorded or coded patient deaths. This had the effect of making their terrible figures look better.

In 2007 the trust recorded fewer than 1 per cent of patients with the NHS palliative care code - that is, patients admitted to hospital who would be expected to die. The change in coding patients meant that by the following year nearly 35 per cent of patients were palliative.

At the time the national average in England's hospitals for palliative care deaths was 9 per cent. The trust has always denied the coding was inaccurate.

Prof Jarman said that when he pointed out that making a large increase in a trusts palliative care coding was effectively turning them into a hospice and that, as he said, he knew what they were doing, the coding started to change and began to reduce towards levels in other hospitals across the country.

The problem is, he said, while they were arguing about coding, people were still dying. Indeed, he estimates that while the academics at Birmingham were reviewing his figures on behalf of the health authority and before the Healthcare Commission launched its own investigation in 2008, 221 more patients than would have been expected died at Mid Staffs.