MTV Games has confirmed to Joystiq that 39 positions at developer Harmonix were eliminated today. The move was part of a restructuring to "better align [the] staffing to best suit [Harmonix's] product development plans and schedules moving forward." The publisher claims that "those affected were primarily in QA. The others affected ranged from administrative to other various roles within the company." At least one staff designer seems to have fallen under the "other" category.
Although Electronic Arts has a partnership with Harmonix, these layoffs are "totally and completely unrelated" to EA's issues.
Update: MTV Games/Harmonix answer some follow-up questions.