The DNA just happened to be the icing on the cake after much study, and over a period of many years, that determined Thomas Jefferson was in all probability the father of Sally Hemings' children.
Taken together the 1873 memoir of son Madison Hemings pointing to the relationship, the birth patterns of Sally Hemings (the fact that Jefferson was there nine months prior to each and every time Sally conceived), the statistical analysis which resulted in a less than 1 percent chance T. Jefferson was NOT the father based on these patterns, as well as Jefferson's perplexing decision to free ALL of Sally's children; he freed only 11 slaves during his entire lifetime and had debts totaling over 100,000 at his death and would have profited from selling Sally's children; and the fact that it cannot be proven ANY other Jefferson relative/candidate was present when Sally conceived (including Randolph Jefferson, who lived 20 miles away from Monticello, had his own slaves to bother, and was absent when one of Sally's children was conceived); and considering Jefferson's own grandson T.J. Randolph admitted Sally's children resembled Thomas Jefferson closely, and there was no indication, ever, that Sally Hemings was promiscuous, all led a vast number of scholars, historians, and other interested parties, to determine way before DNA, that yes, Thomas Jefferson was most likely the father of Beverley, Harriet, Madison, and Eston Hemings.
On a side note, Thomas Jefferson had an affair with -- or at least propostioned -- 2 married women (one of them the wife of a best friend), and he owned over 200 slaves when the Declaration was signed. Jefferson also built a nailery where 10 year old slave boys were forced to churn out nails all day long, in all seasons. The nailery was the most profitable business on the plantation because of the quotas set by Jefferson, imposed on these hapless boys. The Sage of Monticello made many positive contributions to our world, but he was also an active participant in the slavery system.
Check the TJMF report at www.monticello.org and read Annette Gordon-Reed's thorough and dispassionate analysis of the affair if you're interested.