Actually, the "proof" that Jefferson had children by one of his slaves is oral tradition among some of the descendants of Sally Hemings. (Her son Madison Hemings was claiming to be a son of TJ in 1870--on the US census that year the census taker wrote "This man is the son of Thomas Jefferson" on the line with his name.)
There was a lot of hype in 1998 about a DNA study that showed that descendants of one of Sally's sons had a distinctive Jefferson Y-chromosome marker, but that could have been inherited from Jefferson's brother or a number of other relatives who lived reasonably close to Monticello. The reason for saying that Thomas Jefferson rather than another Jefferson was the father is the oral tradition.
As evidenced by the variations in color of african-americans, then and now, there was some mixing between owners and slaves.
Are we individually judged by the actions of our fore-bearers?