A method for detecting the presence, absence or amount of a plurality of genetic variants in a composition, comprising: (a) preparing a plurality of amplicons derived from a plurality of target nucleic acid species, or of portions of the target nucleic acid species, wherein each target nucleic acid species comprises a first variant and a second variant, wherein the first variant is a lower abundance variation and the second variant is a higher abundance variation and the lower abundance variation is less than 10% of the target nucleic acid species; (b) hybridizing the amplicons to oligonucleotide species, wherein each oligonucleotide species hybridizes to an amplicon derived from a target nucleic acid species, thereby generating hybridized oligonucleotide species; and (c) contacting the hybridized oligonucleotide species under extension conditions with an extension composition comprising one or more terminating nucleotides that correspond to one or more of the first variants of the target nucleic acid species and that excludes terminating nucleotides that correspond to the second variants of the target nucleic acid species; wherein: (i) at least one of the one or more terminating nucleotide comprises a capture agent, and (ii) the hybridized oligonucleotide species that hybridize to the first variant are extended by a terminating nucleotide, thereby generating extended oligonucleotide species and the hybridized oligonucleotide species that hybridize to the second variant are not extended by a terminating nucleotide; (d) capturing the extended oligonucleotide species to a solid phase that captures the capture agent; (e) releasing the extended oligonucleotide species bound to the solid phase in (d) from the solid phase by contacting the solid phase with a releasing agent that is the free form of the capture agent at elevated temperature conditions; and (f) detecting the mass of each extended oligonucleotide species released from the solid phase in (e) by mass spectrometry; whereby the presence, absence or amount of the genetic variants is detected. (a) preparing a plurality of amplicons derived from a plurality of target nucleic acid species, or of portions of the target nucleic acid species, wherein each target nucleic acid species comprises a first variant and a second variant, wherein the first variant is a lower abundance variation and the second variant is a higher abundance variation and the lower abundance variation is less than 10% of the target nucleic acid species; (b) hybridizing the amplicons to oligonucleotide species, wherein each oligonucleotide species hybridizes to an amplicon derived from a target nucleic acid species, thereby generating hybridized oligonucleotide species; and (c) contacting the hybridized oligonucleotide species under extension conditions with an extension composition comprising one or more terminating nucleotides that correspond to one or more of the first variants of the target nucleic acid species and that excludes terminating nucleotides that correspond to the second variants of the target nucleic acid species; wherein: (i) at least one of the one or more terminating nucleotide comprises a capture agent, and (ii) the hybridized oligonucleotide species that hybridize to the first variant are extended by a terminating nucleotide, thereby generating extended oligonucleotide species and the hybridized oligonucleotide species that hybridize to the second variant are not extended by a terminating nucleotide; (i) at least one of the one or more terminating nucleotide comprises a capture agent, and (ii) the hybridized oligonucleotide species that hybridize to the first variant are extended by a terminating nucleotide, thereby generating extended oligonucleotide species and the hybridized oligonucleotide species that hybridize to the second variant are not extended by a terminating nucleotide; (d) capturing the extended oligonucleotide species to a solid phase that captures the capture agent; (e) releasing the extended oligonucleotide species bound to the solid phase in (d) from the solid phase by contacting the solid phase with a releasing agent that is the free form of the capture agent at elevated temperature conditions; and (f) detecting the mass of each extended oligonucleotide species released from the solid phase in (e) by mass spectrometry; whereby the presence, absence or amount of the genetic variants is detected.