The parents and children were found dead in their home Friday morning, state Trooper M.L. Anders said. He did not identify the victims or say how old the children were.
The suspect, whom Anders identified only as a family member, was apprehended later Friday morning during a traffic stop in West Virginia, about 400 miles from the home in Mifflintown. Anders said the stop was unrelated to the shooting.
"As for motive, I have no idea," Anders said.
Police were called to the home at about 7 a.m., but Anders said he didn't know who notified authorities about the shooting.
East Juniata Junior-Senior High School, where the suspect is enrolled, was locked down and police officers were posted outside the building early Friday before the teen was found, Anders said.
School superintendent Thomas Muir declined to comment.
West Virginia authorities said the teen-ager was pulled over for speeding on the West Virginia Turnpike near Beckley, W.Va. He was alone in the vehicle, said Randy Coleman, spokesman for the West Virginia Department of Military and Public Safety.
"The trooper down there was suspicious of a couple of things and then a thing came over the teletype from Pennsylvania saying this person was a suspect," West Virginia Senior Trooper J.C. Powers said.
Pennsylvania authorities were on their way to West Virginia with a warrant late Friday morning, Coleman said. The teen was being held on suspicion of murder.
West Virginia State Police were trying to determine if the juvenile could be turned over to Pennsylvania authorities immediately, or if he had to go through an extradition process, Coleman said.
Mifflintown is in central Pennsylvania, 35 miles northwest of Harrisburg.
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