Array-based methods for analysing mixed samples using differently labelled allele-specific probes

A method for detecting a copy number in a fetus, comprising:

• obtaining a biological sample from a subject who is a pregnant female, the biological sample including nucleic acid of both maternal and fetal origin containing a target nucleic acid sequence located on a first chromosome, the target nucleic acid sequence containing a polymorphic site for a single nucleotide polymorphism (SNP);
• generating a population of nucleic acid fragments containing or derived from the target nucleic acid sequence;
• conducting a first assay comprising (a) contacting the population of nucleic acid fragments with an oligonucleotide array containing a first oligonucleotide probe configured to hybridize to the target nucleic acid sequence containing the polymorphic site of the SNP;
• and (b) detecting, using a detector, first signals indicating hybridization of the oligonucleotide probe to one or more nucleic acid fragments of the population containing a first allelic variant (“A allele”) of the SNP and second signals indicating hybridization of the oligonucleotide probe to one or more nucleic acid fragments of the population containing a second allelic variant (“B allele”) of the SNP;
• and
• determining, using the first signals and the second signals, any one or more of the following:
• (i) the copy number of the first chromosome in the fetus;
• (ii) a fetal genotype for the SNP;
• (iii) a maternal genotype for the SNP;
• and
• (iv) a fetal fraction of the sample.