The only molecular studies prior to this one used mtDNA. mtDNA has a few limitations from the way it goes down from mother to child with no sexual recombination. You can't use mtDNA to show that you're related to your daddy, for instance.
Neanderthal was a beast related to no other creature on earth.
No molecular study shows anything of the sort. The mtDNA studies do tend to show that neanderthals were not our direct ancestors but more of an "uncle" group. However, even that is not clear due to the matrilineal limitation.
Some say we have 98% of the genes of a chimpanzee bur they have not sequenced a chimp so that is a guess. I like the one that we have 70% of the DNA of a carrot!
We are more related to chimps than chimps are to orangutans or gorillas. That's not a guess.