MPs were criticised yesterday for failing to ask crucial questions about the death of an overweight three-year-old girl before they used her to illustrate the obesity pandemic sweeping Britain in the report that shocked the country two weeks ago. The girl's condition is now known to have been genetic.

The Guardian has established that the doctor who told the Commons health select committee of the child's death was horrified by the prominent use of the case in the second paragraph of the report, which said that it "offered a powerful insight into the crisis posed to the nation's health".

Sheila McKenzie is a specialist in children's breathing problems, not an expert in obesity, and had written to the committee more than a year earlier because she was worried about the number of children coming to her with sleep apnoea, a condition once only seen in adults, in which the patient stops breathing because of pressure on the windpipe.

Immediately after the report was published, the Guardian understands, she told other paediatricians that she had been misreported and was shocked by the subsequent press coverage.

Earlier yesterday Sadaf Farooqi of the department of clinical biochemistry at Cambridge University said her departments tests had established that the girl had a defective gene.

"I was appalled and I must say I felt immediately for the parents and family of this child," she told BBC Radio 4's Today programme. "The clear implication was that the child had been overfed, with bad parents, resulting in severe obesity and her death. That is simply not true."

The responses dismayed those in the anti-obesity lobby who had been delighted by the report, which became front-page news in every paper and challenged the government to do much more to curb the marketing of junk food and protect children.

One member of the health select committee, the independent MP Richard Taylor, said: "If we had known that this poor child had a genetic abnormality I think that should have been added. But we didn't know. In retrospect, perhaps we should have interviewed Dr McKenzie."

The second paragraph of the report said: "Dr Sheila McKenzie, a consultant at the Royal London hospital which recently opened an obesity service for children, offered a powerful insight into the crisis posed to the nation's health.

"Despite only being in existence for three years, her service had an eleven-month waiting list. Over the last two years, she had witnessed a child of three dying from heart failure where extreme obesity was a contributory factor. Four of the children in the care of her unit were being managed at home with non-invasive ventilatory assistance for sleep apnoea: as she put it, "in other words, they are choking on their own fat".

Dr Taylor said MPs saw the significance of the claim. "We had had a lot of evidence throughout the inquiry that obesity in children is a huge, huge increasing problem. As it is children, we have to get at more than anybody else. it was felt that this was a way of emphasising the danger for children."

David Hinchliffe, the Labour chairman of the committee, continued to defend the use of Dr McKenzie's letter, blaming tabloids for exaggerating the report. "What's really annoyed me about this is that the two people who were quoted on the Today programme appear to have drawn conclusions about our report from the tabloid treatment of part of our report. They don't appear to have read the report."

He added later: "When you've got a consultant paediatrician in a unit dealing with serious obesity saying that she's got children choking on their own fat, quite frankly it is pretty serious stuff. Had we not referred to her letter, which we do respecting in its entirety the way she put this, I think we would have been accused of suppressing some very important evidence."

Dr McKenzie wrote to the committee that her role was "to identify medical problems associated with obesity". She went on: "In the last two years one child at the age of three has died of heart failure due to extreme obesity."

It is not known whether Dr McKenzie was aware of the genetic problem before she wrote to the committee on April 28 last year. The Royal London hospital said yesterday she would not take any questions. "The trust considers it important that clinicians are able to add to public debates about health.

"Dr McKenzie and colleagues submitted their evidence on obesity to the select committee in good faith. We do not have the family's permission to discuss their situation in the media."

The Sun headlined its story: "Fat & dead ... at 3"; the Express: "Child 3 dies from being fat: The terrifying truth behind Britain's obesity epidemic"; and the Telegraph: "Now obesity kills child aged three".

The Cambridge scientists expressed doubts about about the thrust of the report and the absence of discussion of genetic factors in obesity from the moment of publication. Dr Farooqi's head of department, Steve O'Rahilly, did not join the general enthusiasm.

"We need to inject a degree of honesty into this debate and be a little more humble in the face of the real uncertainties about the causes of obesity," he said in a statement at the time.

"Ignoring the role of inherited factors in determining people's susceptibility to becoming fat is not only bad science, it also helps to perpetuate the blame culture which tends to permeate this field.

"If we applied more science and less political positioning we might get some clearer ideas for solutions."

Professor O'Rahilly and Dr Farooqi's work is to locate possible defective genes which might cause children to become obese.

They have published papers on mutations in the gene which governs the production of leptin, a protein which affects appetite and energy expenditure.

Margaret Lawson, senior research fellow at the Institute of Child Health, said that although 6% of two year olds were obese, genetic defects were rare and would not necessarily be suspected by paediatricians.

"The vast majority of children who are obese have been overfed really," she said.