What is the meaning of "The Molecular Basis of Disease"
There is an ELSEVIER research journal by the name of BBA Molecular Basis of Disease (link to journal). I think their synopsis of what the journal is about will illuminate what is meant by The Molecular Basis of Disease.


  BBA Molecular Basis of Disease addresses the biochemistry and
  molecular genetics of disease processes and models of human disease.
  This journal covers aspects of aging, cancer, metabolic-,
  neurological-, and immunological-based disease. Manuscripts focused on
  using animal models to elucidate biochemical and mechanistic insight
  in each of these conditions, are particularly encouraged.


The keywords here are biochemistry and molecular genetics, so I would think of what kind of mutations, at what chromosomal locations can cause genetic disorders for example. Or in terms of biochemistry, what kind of biochemical environment can lead to alcoholic liver disease etc.