Indian-American Patel, 25, shot seven-under 65 in the first round and then had an eagle and a birdie in his 69 in the second round. He was 10-under 134 and three clear of Brandon Hagy (68-68).
Patel's 69 included a birdie at the par-3 seventh hole, but the big moment came at the par-5 15th after his lead had just been cut to one.
Patel smashed the driver on 545-yard par-5 hitting over the bunker and down the hill before hitting 8 iron to 20 feet. He holed the eagle putt and parred out to set the 36-hole tournament scoring record.
Patel, who broke the 36-hole tournament record, is currently No. 11 on the money list. The USD 108,000 first-place prize would lock up his PGA TOUR card for the 2016-17 season.
This week's purse is USD 600,000, with USD 108,000 going to the champion and the cut fell at 2-over 146, with 71 players advancing to the weekend.