When the map of the human genome was unveiled in 2001 it was hailed as the harbinger of a new age in medicine. Increased understanding of how individuals’ genes contribute to disease would revolutionise treatment, allowing scientists to target drugs and other therapies more precisely than ever.

Where once medicines worked — or just as often didn’t — on a one-size-fits-all basis, they might now be tailored to those who are most likely to benefit. Effective drugs that were rejected because of adverse reactions in a genetically susceptible minority might also be “rescued”, as tests tell doctors who should avoid them.

These exciting predictions are starting to be realised. Bespoke medicine has even acquired a poster drug, in the shape of Herceptin, the breast cancer therapy. Though it was developed before the human genetic code was finished, it is exactly the sort of treatment that genomic insights will bring. It targets a breast cancer protein, HER-2, for which about one patient in five tests positive. For these women, it is a life-saver, halving the risk of tumours returning after chemotherapy.

We can expect many similar drugs to be developed over the coming years. They will, however, create as many challenges as opportunities. These were spelt out this week by Professor Fran Balkwill, of Queen Mary Medical School, and Melanie Lee, of UCB Pharma, in an essay for Newton’s Apple, a new science think-tank.

While it is clear that personalised medicine has great potential, it is far less certain that society can afford it. Herceptin makes a fine example. For all its effectiveness, the drug costs nearly £20,000 per patient a year, and many NHS trusts refused to fund it. It was eventually made available on the NHS, but only after court cases and a media campaign.

This is the first skirmish of what could be a drawn-out battle. As Balkwill and Lee say: “Individualised medicine dramatically changes the economics of drug research and development because such drugs will be suitable only for a relatively small group of patients, but each will still cost around £500 million to take from discovery to launch.”

Many of the costs of developing a drug, such as animal testing and regulatory controls, are fixed, no matter how many people end up taking it. The greater benefits of genetically targeted drugs will thus come at a price because the fact that they are targeted substantially reduces the size of the potential market. Such medicines are going to be more expensive than existing ones.

In the long term, some of these extra costs will be balanced by the savings made as broad-spectrum medicines are no longer prescribed to patients in whom they are useless. But before that, the NHS has a problem. It might be able to find the cash to fund one or two expensive novelties such as Herceptin, but what happens when dozens of effective but expensive drugs are queuing for approval, each backed by a patient lobby? The dilemma will be painful. Paying for everything could break the NHS financially, but refusing is equally unnattractive. That would deny thousands of people the best possible treatment, and perhaps even persuade pharmaceutical companies that it is not worth developing targeted drugs: a handful of well-heeled private patients will not repay their investment in research.

The only way forward is to start the creative thinking now, before much bespoke medicine is on the market. Making decisions on an ad hoc basis as the drugs arrive will cause chaos and injustice.

For all their opinions on funding and structure, politicians have not yet started to consider the deeper issue of what the NHS can and should deliver in the genomic age. Perhaps scientists such as Balkwill and Lee, and groups such as Newton’s Apple, will spur them into action.

Mark Henderson is Science Editor of The Times