DNA collection while on supervised release is constitutional, even if the terms of supervised release in your original sentence did not provide for it and the DNA Analysis Backlog Elimination Act (“DNA Act”), which mandates it, became effective only after you were sentenced. In United States v. Lujan, case no. 02-30237 (9th Cir. Sept. 25, 2007), the court rejects arguments that collection under these circumstances violates the Fourth Amendment and Ex Post Facto Clause, constitutes an unlawful bill of attainder, and violates the separation of powers.
Lujan’s appeal was stayed pending the outcome in two other appeals, and the outcomes of those cases allow the Ninth to dispose easily of the first three challenges. Sentencing Law and Policy notes that with this decision the Ninth joins all other circuits that have “considered these and related issues,” and the first comment there calls the case “cleanup work” and notes that the Supreme Court denied certiorari just yesterday in United States v. Reynard (9th Cir. 2007) 473 F.3d 1008, which the Ninth relied upon in rejecting the Ex Post Facto Clause and bill of attainder challenges. (The other case relied upon was United States v. Kincade (9th Cir. 2004) 379 F.3d 813 (en banc).)
The separation of powers challenge requires a little more analysis from the court, as this question apparently has not been previously addressed. The court nonetheless dispatches it rather quickly. No separation of powers violation occurs by having the probation department, part of the judicial branch, collect the DNA. The probation office does not encroach on the executive branch because its role is limited to collection. It does not analyze the sample or use the results to investigate or prosecute other crimes. Moreover, the purpose of the DNA Act is consistent with the function of the judiciary because, by instilling a fear in defendants that their role in any future crimes will be quickly identified, it deters future crime and thus furthers two goals of supervised release: “rehabilitation and the prevention of harm to others.”
You can access the amicus brief filed in support of the government by the Criminal Justice Legal Foundation here.