It was the number assigned to JFK's PT boat that was cut in half by a Japanese destroyer on August 2, 1943
[DOC] [TLE] John F. Kennedy and PT 109 - John F. Kennedy Presidential Library ... [PAR] JFK in History ... PT-109 stood at her station, one of fifteen PT boats ("Patrol 
Torpedo" boats) that had set out ... Painting of the August 2, 1943 sinking of 
PT109 by the Japanese destroyer Amagiri.