A method, comprising amplifying a nucleic acid sequence of interest in a sample comprising genomic DNA of a subject; amplifying a reference nucleic acid sequence in the sample; quantifying the amplified sequence of interest relative to the amplified reference sequence; and determining a copy number of the sequence of interest from the relative quantified amplified sequence of interest. The reference sequence may have at least 80% sequence identity to at least one of SEQ ID NO:1-38, such as SEQ ID NO:1-13. Also disclosed are kits and compositions, each comprising a first probe which specifically hybridizes to at least a portion of at least one reference sequence. Also disclosed is a system configured to perform the above method.