Spatially encoded biological assays

A method of detecting a SNP allele at a genetic locus at a location in a biological sample comprising:

• (a) contacting a biological sample comprising a target nucleic acid comprising the SNP allele at the genetic locus with a first probe and a second probe, wherein:
• the first probe comprises a first sequence that hybridizes to a first portion of the target nucleic acid and a first universal priming site;
• the second probe comprises a second sequence that hybridizes to a second portion of the target nucleic acid and a second universal priming site;
• the first portion of the target nucleic acid or the second portion of the target nucleic acid comprises the SNP allele at the genetic locus;
• the first probe and the second probe hybridized to the target nucleic acid are capable of being ligated together;
• and
• one or both of:
• (i) the first probe further comprises a nucleic acid sequence identifying the location to where the first probe was delivered and (ii) the second probe further comprises a nucleic acid sequence identifying the location to where the second probe was delivered;
• (b) ligating the first and second probes together to generate a ligation product;
• (c) amplifying the ligation product using a first amplification primer that is capable of hybridizing to the first universal priming site, and a second amplification primer that is capable of hybridizing to the second universal primer site, to produce an amplification product;
• and
• (d) determining all or a portion of the sequence of the amplification product or a complement thereof, and using the determined sequence to detect the SNP allele at the genetic locus at a location in the biological sample.