A method for assessing loss of heterozygosity in a tumor, wherein one or more sequence variants are detected in a nucleic acid population derived from tumor samples and non-cancerous tissue samples obtained from a plurality of subjects, wherein the subjects have the same type of tumor, the method comprising the steps of: (a) amplifying a polynucleotide segment common to said nucleic acid population with a pair of PCR nucleic acid primers that define a plurality of loci to produce a first population of amplicons, each amplicon comprising said polynucleotide segment; (b) delivering the first population of amplicons into aqueous microreactors in a water-in-oil emulsion such that a plurality of aqueous microreactors comprise a single amplicon of the first population of amplicons, a single bead, and amplification reaction solution containing reagents necessary to perform nucleic acid amplification, wherein the bead comprises a plurality of oligonucleotides which hybridise and immobilise said first amplicon; (c) clonally amplifying a plurality of the members of said first population of amplicons by polymerase chain reaction to produce a plurality of populations of second amplicons wherein each population of second amplicons derives from one member of said first population of amplicons; (d) hybridizing and immobilizing said second amplicons to the plurality of oligonucleotides attached to the beads such that each bead comprises one population of said second amplicons; (e) breaking the emulsion to recover the beads from the microreactors; (f) determining in parallel a nucleic acid sequence for the second amplicons on each bead to produce a population of nucleic acid sequences; and (g) comparing said nucleic acid sequences of said polynucleotide segment to detect the one or more sequence variants in said nucleic acid population; wherein the method does not require prior knowledge of the nucleic acid sequence composition of the sequence variants; and wherein the absence of an SNP allele from the tumor sample compared to the SNP alleles generated from non-cancerous tissue indicates loss of heterozygosity in the tumor. (a) amplifying a polynucleotide segment common to said nucleic acid population with a pair of PCR nucleic acid primers that define a plurality of loci to produce a first population of amplicons, each amplicon comprising said polynucleotide segment; (b) delivering the first population of amplicons into aqueous microreactors in a water-in-oil emulsion such that a plurality of aqueous microreactors comprise a single amplicon of the first population of amplicons, a single bead, and amplification reaction solution containing reagents necessary to perform nucleic acid amplification, wherein the bead comprises a plurality of oligonucleotides which hybridise and immobilise said first amplicon; (c) clonally amplifying a plurality of the members of said first population of amplicons by polymerase chain reaction to produce a plurality of populations of second amplicons wherein each population of second amplicons derives from one member of said first population of amplicons; (d) hybridizing and immobilizing said second amplicons to the plurality of oligonucleotides attached to the beads such that each bead comprises one population of said second amplicons; (e) breaking the emulsion to recover the beads from the microreactors; (f) determining in parallel a nucleic acid sequence for the second amplicons on each bead to produce a population of nucleic acid sequences; and (g) comparing said nucleic acid sequences of said polynucleotide segment to detect the one or more sequence variants in said nucleic acid population; wherein the method does not require prior knowledge of the nucleic acid sequence composition of the sequence variants; and wherein the absence of an SNP allele from the tumor sample compared to the SNP alleles generated from non-cancerous tissue indicates loss of heterozygosity in the tumor.