The present invention provides methods for the rapid and cost effective identification of the presence of a disease-associated mutation and a particular SNP in the same allele of a gene without the need to clone and sequence the entire gene. The compositions and methods of the invention are useful for identification of patient to subpopulations amenable to treatment as part of a therapeutic strategy for treating genetic disorders, for example, dominant, gain-of-function gene mutations, for example, Huntington's Disease (HD).