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The inquiry is investigating the circumstances surrounding the apparent suicide of Dr Kelly.
The weapons expert died at the peak of a row between the government and the BBC over a report alleging that the government had "sexed up" a dossier on Iraq's weapons of mass destruction.
Speaking over an audio link from a room nearby, Janice Kelly told Lord Hutton that Dr Kelly had "received assurances" from the MoD, and felt "totally let down" by the way his name had become public.
Dr Kelly came forward at the end of June to tell the MoD he had met the BBC reporter whose broadcast sparked the row, Andrew Gilligan.
MoD press officers eventually confirmed Dr Kelly's name to journalists who suggested it.
Forced from home
Mrs Kelly described how on the evening of 8 July she and her husband had been at home watching a television news bulletin.
"The main story was that a source had identified itself and then immediately David said to me, 'It's me.'"
On 9 July, Mrs Kelly said, the MoD press office phoned and told them to leave their home immediately because reporters were on their way.
Mrs Kelly said her husband had told her several times how betrayed he felt.
The counsel to the inquiry, James Dingemans QC, asked her to whom she thought he was referring.
Mrs Kelly replied, "I believed he meant the MoD because they were the ones who had effectively let his name be known in the public domain.
"He had received assurances, and that was why he was so very upset about it."
Dr Kelly was then told by the MoD he would have to appear in public to give evidence to two committees - the Foreign Affairs Select Committee and the Intelligence and Security Committee.
The day after the committee hearings, on 17 July, he and his wife were at home having lunch. Mrs Kelly told the inquiry he looked "distracted and dejected".
"I just thought he had a broken heart," she said. "He had shrunk into himself."
He went for a walk at 1500, she said. His body was found in woodland near his home later that night.
Lord Hutton published his report in on 28 January 2004. It was highly critical of the BBC, and said the key allegations reported by Andrew Gilligan were "unfounded".
Soon after the report was published, BBC chairman Gavyn Davies, the Director General Greg Dyke, and reporter Andrew Gilligan resigned.
Lord Hutton absolved the government of any kind of "dishonourable, underhand or duplicitous strategy" in the leaking of Dr Kelly's name to the press.
But he said the MoD was "at fault" for failing to tell Dr Kelly that his identity as the suspected source would be confirmed to journalists who suggested it.
The Kelly family later released a statement, saying that if their personal tragedy was not to be compounded, "the government (must) take action to ensure the ordeal suffered by Dr Kelly is never repeated."
In July 2004, the Butler Report was published, criticising the "thinness" of the intelligence used to justify the war in Iraq, and saying it was presented in such a way as to seem "firmer and fuller" than it was.
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