Most books are set up in Adobe InDesign. Very few independent authors subscribe to Indesign, and therefore have no capacity to directly edit or correct their own book. Typically they will supply a list of corrections to the designer. However, Adobe have recently added an interesting feature to InDesign that will at give authors the chance to at least annotate the PDF proof, and have the designer import the PDF (and annotations) directly into Indesign (provided the comments are properly made). This should increase the speed and accuracy of book proofing and streamline the workflow. An article on the process from Adobe.