Besides the DNA article, there was Fawn Brodie's book about Jefferson, and much earlier, an 1873 newspaper article in Ohio based on information from Madison Hemings, one of Sally's children, in which Madison alleged that Jefferson was his father. Also, the 1870 census (of course not made public until much later) shows that the census taker wrote next to Madison Hemings' name "This man is the son of Thomas Jefferson" (obviously having been told that by Madison).
There are records of the rumor going back to 1802. In 1811, a school headmaster who visited Jefferson wrote in his diary that day, "The story of black Sal is no farceThat he cohabits with her and has a number of children by her is a sacred truthand the worst of it is he keeps the same children slavesan unnatural crime which is very common in these parts."