The Halloween of 2001 brought a very personal horror to Rachel and Stephen Reid. They were told that their second son Christopher, who was just nine months old, would not live past his first birthday without treatment. The options were stark: a bone-marrow transplant involving medication with ghastly side effects and a one in three chance that he would die within three years, or pioneering gene therapy which had at that point been tried on only a handful of children worldwide.

Rachel says: "It was in some ways an easy decision. They told us the risk of anything going wrong with gene therapy couldn't be quantified, but was perhaps one in a million."

Christopher is now two, a blond, blue-eyed toddler, and one of 16 people treated with the technique for a rare immune deficiency called X-SCID. It is commonly known as "bubble baby syndrome" because of the isolation in which affected children live; lacking immune systems of their own, they are fatally vulnerable to infection.

The reason that Stephen and Rachel have gone public with Christopher's story is that he has been given the all-clear, while two of four children treated similarly in Paris have developed leukaemia. The Reids want to speak out against critics who say this makes the method too risky.

Cancer was indeed the "unquantifiable risk" that the doctors explained to them before Christopher was treated. "What's happened in Paris is awful, but as far as we're concerned, the treatment was still absolutely right for Christopher," says Rachel. "Every day with him is a bonus; he is being fantastically well monitored and we have 100% faith in his doctors."

But didn't she feel let down, even deceived, when she first heard about the French children? "It was awful, yes," she says. "Christopher was in Great Ormond Street Hospital for several months after treatment and his doctors said they wanted us to know, before it hit the press, that a child like Christopher had leukaemia. We were in shock."

Six months later, the Reids were called back by the doctors and told about leukaemia in a second child on the French trial. But their optimism remained unshaken. "We reminded ourselves that no new technique is without its hiccups - that the first heart-transplant patients died," says Rachel. "I remember saying to Steve that we had to put it to the back of our minds, that we couldn't go through every day waiting for Christopher to get leukaemia."

So, can the Reids find comfort in the possibility that the children with leukaemia in France developed it for reasons unconnected with the treatment?

Professor Christine Kinnon, head of the molecular immunology unit at the Institute of Child Health in London, suggets they can. The unit developed the technique, and remains the only UK centre to use it, so far treating four children and one adult. "We cannot be certain, but the leukaemia probably did result from gene therapy," she says. "When the 'good' gene is inserted into bone-marrow cells it hitches a ride on a virus which inserts it randomly. There's always a chance that it could be put in near to, and trigger the activity of, a cancer-causing gene."

The French children apparently became ill 30 months after their treatment. Kinnon's team treated their first child only two years ago. Yet she is "cautiously optimistic" that subtle differences between the virus used in Paris and that in the UK will reduce the risk of cancer-causing effects in her patients, and she stresses that all of them are thriving.

Having seen the risks so starkly illustrated in the Paris trial, would Kinnon treat more children now, with the cause of the leukaemia unresolved and unidentified? "It has always been and remains offered as a last viable option," she says. "To treat a child now, we have to seek permission, and we would if parents wanted us to follow that route." She also points out that, while the Paris leukaemia cases are worrying, both children are in remission. Had bone-marrow transplants been chosen for all of those who had gene therapy, four or five deaths would have been likely.

It would be too cruel to ask the Reids what choice they would make now, if faced with the options of 2001. Rachel is due to give birth to a daughter, and the genetics of X-SCID mean that while there is a 50% chance that, like her mother, she will be a carrier able to pass it on to any sons, she will not herself be affected. Rachel says that if she is a carrier, "Perhaps in 20 or 25 years' time, when it's relevant, they'll have found out more and will be able to stop her from passing it on, or to cure it."

Kinnon agrees, but is pessimistic about more immediate prospects for progress. Last month, the government unveiled its white paper on genetics, Our Inheritance, Our Future. The health secretary, John Reid, said of the £50m strategy: "Our vision is for the NHS to lead the world in taking maximum advantage of the safe, effective and ethical application of the new genetic knowledge and technologies for all patients as soon as they become available."

Do his words belie a passivity about research and development, suggesting that we will follow while others lead? Kinnon says that the £3m allocated to research on gene therapy for single gene disorders "is totally insignificant" at a national level and could be used up in her centre alone.

"Our progress is now limited by money more than any other factor," she says. "We've only done what we have here thanks to our own Jeans for Genes charity which has raised over £15m since 1996."

Rachel also credits Jeans for Genes with being instrumental in saving Christopher's life, and Kinnon is not alone in her scepticism over the true value of government money. A survey of the research community found that while many welcome the white paper because it puts genetics in the spotlight, they also say it needs more money to make a real difference.

There has long been controversy about funding priorities in genetics. Some say it is fairer to target resources at genetic counselling and care for those affected by genetic disease than make heavy investment in gene therapy which has limited success, remains relevant to small numbers of patients and is undeniably expensive. It costs £100,000 to treat a child like Christopher (bone-marrow transplants cost many times more) without accounting for the research and development which make it possible.

The white paper has also been criticised for making its largest investment (£18m) in upgrading laboratories, while also making provision for training 90 new scientists to staff them. But it remains unclear who will train these scientists, and whether the salaries on offer will attract and retain them.

Such wrangles will be played out between the corridors of power and halls of academe. But they matter, ultimately to people like the Reids. And it is hard to believe they matter as much as the stunning smile on the face of the little boy from Derby who has emerged from his bubble and is catching up on his life.

As Rachel says: "He'd got used to living with doctors and nurses for company and no other children because of the infection risk. He didn't walk until he was 20 months old and only in the past six months has he really started to progress with talking and making friends."

· Sophie Petit-Zeman is writing a book, Snakes & Ladders, with Great Ormond Street Hospital, about professional, patient and family experiences of healthcare. Jeansforgenes, 0800 980 4800

The therapy

· Bone marrow cells were removed from Christopher's hips

· They were enriched in the laboratory, to isolate "stem cells" - the parent cells of the immune system

· The stem cells were infected with a virus carrying a good copy of the missing gene

· After two weeks, Christopher's immune system began to function