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When DNA evidence began appearing in U.S. courtrooms in the late 1980s, it was heralded as the greatest leap forward in criminal investigation since fingerprinting. In the following decades, its analysis has helped identify and incarcerate the guilty as well as exonerate and free the innocent.

Now, the next generation of DNA analysis, which researchers say can reveal a level of detail far beyond what currently is used in criminal investigation, is awaiting its first courtroom test in Massachusetts.

Prosecutors there plan to prove in court that a pair of abductions and rapes were committed by the defendant and not by his identical twin brother. The DNA shared by identical twins was one of the problems of earlier testing, which was not nuanced enough to point out differences between twins that scientists say exist.

“The forensic application of this testing is new, and to the best of our knowledge, our case will be the first prosecution to use it,” Suffolk County District Attorney Daniel F. Connelly said in September, when he announced charges against the man. “The scientific...