The ruling is a direct blow to Britain's DNA databank, which holds samples and data for 7% of its citizens (4.5 million people, including children and crime victims). In England, Wales and Northern Ireland, police are authorized to collect and hold samples from citizens arrested for any recordable offense, whether or not the offense leads to formal charges or conviction, and hold them for the lifetime of the individual. (Scotland, like several other European nations, destroys samples when the case does not lead to a conviction). The court's decision also raises some timely questions about technology, privacy, and human rights (yesterday was the 60th anniversary of the UN Universal Declaration of Human Rights).
The case was brought to the European Court by two men who had been arrested but later cleared of crimes. One of them was arrested at age 12 and acquitted; the other was never charged. The plaintiffs' subsequent requests that their DNA samples and fingerprints be destroyed were denied by British law enforcement. Under the European Court ruling, the two men were awarded an amount less than the cost of their legal fees, but they will get their DNA samples destroyed - as will millions of their compatriots, apparently.
Under this new ruling, Britain will have to purge its databank of about 850,000 to 1 million DNA samples from people without criminal records. The government has until March to respond with plans to destroy those samples. In the meantime, they have announced their intent to continue operating under current DNA banking policies. According to Home Secretary Jacqui Smith,
DNA and fingerprinting is vital to the fight against crime, providing the police with more than 3,500 matches a month, and I am disappointed by the European Court of Human Rights' decision. The Government mounted a robust defense before the Court and I strongly believe DNA and fingerprints play an invaluable role in fighting crime and bringing people to justice. The existing law will remain in place while we carefully consider the judgment. 
On the other hand, Alec Jeffreys, one of the developers of DNA fingerprinting, told Nature that he was "delighted" by the European Court's ruling:
The point [the European Court of Human Rights] is making is that DNA carries information not just on yourself, but also on family relationships. So, it's an invasion of privacy and of family life. I totally agree. They also made the point that it stigmatizes branches of society. The innocent people are not a random cross-section of British society -- they are strongly biased towards juveniles, towards ethnic minorities and so on. . . the criminal database should be for criminals, and innocent people should be removed - it's as simple as that. 
Since Jeffreys and his colleagues developed DNA fingerprinting, molecular biology has undergone a technological revolution. Not only are DNA tests easier and cheaper, they are also more sensitive. And they carry great weight with juries and the public, who have come to expect DNA fingerprinting to be part of a criminal case. Jeffreys says, "I never expected to be in the situation now, where the most common forensic test to be carried out is the DNA test. It's not the technology of last resort, it's the technology now of first resort." 
As I blogged earlier , recent advances in DNA analysis have made it possible to identify whether individuals are represented in pools of DNA from large numbers of people, such as a mixed sample that might be found at a dirty crime scene. But in order to determine whether an individual's DNA is present in the pooled sample, a reference is needed - a DNA sample from the individual in question or a close relative. With 7% of citizens represented in the British database, a substantial proportion of the law-abiding British public could hypothetically have their banked DNA or sequence data compared to crime scene evidence in an ongoing fashion, without their knowledge. Even more alarming, close relatives of those 7% would also be implicated by a DNA match, even if their own DNA had never been collected.
If you add it up, a very large segment of the British population is potentially vulnerable to genetic surveillance, even if the police were not actually using the database in that way. The European Court objected to this potential violation of privacy:
The Court noted that cellular samples contained much sensitive information about an individual, including information about his or her health. In addition, samples contained a unique genetic code of great relevance to both the individual concerned and his or her relatives. Given the nature and the amount of personal information contained in cellular samples, their retention per se had to be regarded as interfering with the right to respect for the private lives of the individuals concerned. In the Court's view, the capacity of DNA profiles to provide a means of identifying genetic relationships between individuals was in itself sufficient to conclude that their retention interfered with the right to the private life of those individuals. The possibility created by DNA profiles for drawing inferences about ethnic origin made their retention all the more sensitive and susceptible of affecting the right to private life. 
An editorial in today's Nature applauds the Court's decision, and makes the Orwellian analogy explicit:
DNA databases are but one small tip of the emerging surveillance society. Even leaving aside law-enforcement and security initiatives, vast amounts of data are being collected by private firms through citizens' use of credit cards, mobile telephones and electronic travel tickets, not to mention the Internet and e-mail. These data are typically gathered not for any sinister purpose, but as legitimate efforts to offer customers better service. But the databases exist. And without strong safeguards, they could slowly and steadily be linked into an all-pervasive monitoring system that would make George Orwell's concept of 1984 look technologically tame -- all in the name of security, efficiency and convenience. . .
Such concerns are certainly not new; Orwell's book was published in 1949. But the dizzying pace of technological advance makes them ever more salient -- even as it makes the world's multitude of existing privacy acts seem light-years behind. Scientists, in particular, have an ongoing responsibility to reflect on the human-rights issues raised by the technologies they develop, and to lobby for appropriate oversight and controls.
This "ongoing responsibility" asserted by Nature's editors poses quite a challenge. Jeffreys admits that he never anticipated the fingerprinting technology he developed becoming the "technology of first resort." If he had anticipated how, when and why this would occur, he would have been an individual of rare foresight (and probably should have spent his time investing in technology stocks, not in the lab). Just a few months ago, the NIH and other organizations were surprised that the pools of genetic data used in genome-wide association studies could pose a risk to individuals' privacy.
Even if we do our best to anticipate the social issues raised by the invention of new technologies, we can never foresee all the potential applications and outcomes. In fact, the unpredictable nature of science is one of the strongest arguments for funding basic research!
This unpredictability doesn't clear scientists of responsibility for self-examination. But it does suggest that if we are to go beyond simply "reflecting" on our research, to identifying and flagging problematic developments for ethicists and policy-makers in advance - which seems to be what the Nature editors want - we could use a bit of help. A time machine would be nice. But failing that, I'm not sure what that help should look like.
 BBC News, DNA database 'breach of rights'
 MSNBC, European court makes ruling on DNA rights
 Nature, UK DNA database needs overhaul
 bioephemera, Good for Cops, Bad for Geneticists
 European Court on Human Rights Ruling, S and Marper vs. the United Kingdom
 Nature, Watching Big Brother
Receiving such an accusation is a bad sign for a country, especially a developed one, like Great Britain.