There is a sort of deep learning that got to be associated with the world of Litvak Talmud learning. It is easy to see. Just compare the achronim after the Rav Yoseph Karo until the world of Litvak yeshiva centered on the sort of learning done by Rav Haim of Brisk.

It is hard to know of see from where all that began. Even though the Litvak world is based on the Gra, you do not actually see this kind of learning in the Gra himself. It is implicit in his commentaries but nothing that is open and plain to see. This kind of learning it seems developed in the Litvak world slowly. You can see it in Rav Haim of Voloshin and the son of Rav Haim, the Netziv in his rarely printed writings of his  ideas in Gemara. It was like it was just under the surface like a seed developing and germinating until one day it spouts. Then around the time of Rav Haim and Rav Israel Salanter this kind of deep learning came to the surface.

The best example is Rav Haim's Hidushim and also the Steipler  and Rav Shach.