DNA was first used as evidence in a criminal case in 1986. Leicester University’s Alec J. Jeffreys—who coined the term "DNA fingerprints"—used DNA to show that a 17-year-old suspect had not committed two rape-murders in the English Midlands, though he had confessed to one of them. DNA evidence also allowed prosecutors to eventually identify the attacker.

But it wasn’t until three years and many landmark cases later that use of DNA evidence in criminal trials faced its first real legal challenge. In a 12-week pretrial hearing for murder case People v. Castro, the Supreme Court of Bronx County, New York ruled that DNA evidence could be admitted in court as long as it was determined in pretrial hearings that the providing lab’s methodology met scientific standards and produced reliable results. The judge argued that DNA forensic identification techniques were widely accepted by the scientific community, but the individual lab’s techniques in the case were called into question.

In general, the admissibility of new scientific evidence in federal courts and some state courts is subject to the Daubert standard. Set in the 1993 case Daubert v. Merrell Dow Pharmaceuticals, it states that to determine the validity of the relevant technique, it must be testable and subject to peer review, its operation must be governed by control standards, its error rate must be known or knowable and it must be widely accepted by the relevant scientific community. Some states still rely on the older and much less stringent Frye standard instead, which posits only that the scientific evidence must “have gained general acceptance” in the relevant field.

Given that next generation sequencing has been used in clinical diagnostic labs and hospitals and research labs for at least a decade, courts may have some confidence that it is generally accepted in the field. The 19-month effort under way to evaluate the applicability of NGS to forensics by organizations as diverse as the Bureau of Alcohol, Tobacco Firearms and Explosives, the California Department of Justice, and the Office of Chief Medical Examiner of the City of New York should help, too.

But there may be an additional hurdle for NGS, according to Ted Hunt, chief trial attorney and DNA cold case project director in the Jackson County Prosecutor’s Office in Kansas City, Mo., and a member of the U.S. Department of Justice’s National Commission on Forensic Science. That’s because where current STR analysis techniques focus exclusively on non-coding regions of the DNA, “some of the newer NGS applications look at coding regions of the DNA that are related to bodily functions, phenotype and ancestry, which could trigger legal privacy issues,” says Hunt.

“I think what we are going to see with next generation sequencing are challenges based on the Fourth Amendment,” he says.

There are even a few states—Indiana, New Mexico, Rhode Island and Wyoming—that currently specifically prohibit what's called phenotyping of DNA held in CODIS, for example. Texas, by contrast, specifically allows it, says Hunt.

Hunt is hopeful that these hurdles will be overcome. “I think it's in everybody's best interest to make sure that next generation sequencing, in a reasonable and timely manner, makes its way into the forensic and legal main stream. Reasonable regulation can ensure that it is not abused,” says Hunt. “Bottom line, I think the enormous benefits far outweigh the risks.”