This application relates to multiplexed methods for the identification and quantification of minor alleles and polymorphisms. Products and methods are provided for detecting the presence of minor
nucleic acid substances in a sample containing a mixture of minor
nucleic acid substances and one or more major
nucleic acid substances, wherein the amount (frequency or copy number) of the minor nucleic
acid substances is less than the amount of the major nucleic
acid substances. Some methods involve amplifying the mixture and extending the resulting amplicons with a chain terminator and an extension primer that hybridizes specifically to the amplicons, wherein the chain terminator specific to the major nucleic
acid substances has a lower concentration than the chain terminator specific to the minor nucleic acid substances. A higher concentration of the chain terminator specific to the minor nucleic acid substances, relative to the chain terminator specific to the major nucleic acid substances, improves the
detection limit (sensitivity) for detecting minor nucleic acid substances present in the mixture at
low frequency or copy number. Additionally, the
signal generated from the extension product of the major
nucleic acid substance amplicons can be used as a
positive control and allows for the quantification of the minor nucleic acid substances relative to the major nucleic acid substances in the mixture.