Systems and Methods For Probe Design to Detect the Presence of Simple and Complex Indels

A nucleic acid array comprising:

• a substrate;
• a plurality of probes attached to the substrate, wherein a first end of the plurality of probes is attached to the substrate;
• wherein one set of said plurality of probes are SNP probes configured to genotype SNPs in a sample;
• wherein a second set of said plurality of probes are indel probes configured to genotype indels in a sample;
• and
• wherein the indel probes are configured to genotype the indels by addition of one or more labeled bases to a second end of the indel probes after hybridization with a target.

A method for determining one or more indel (insertion/deletion) probes able to identify one or more indels wherein said indel probes can identify a variety of insertions and deletions, the method comprising the steps of:

• accessing a data set of one or more genomes, said data set comprising information regarding genomic locations of a plurality of indels and sequences flanking at least one direction of the plurality of indels;
• designing an indel probe by:
• (a) generate a probe sequence that is complementary to a sequence flanking the indel, and compare interrogation bases for a deletion allele probe and for an insertion allele probe;
• (b) if the compared interrogation bases are different and are in different detection channels, create and output a single indel probe using the interrogation bases to differentiate the indel alleles and END;
• (c) if the compared interrogation bases are different and in the same detection channel, EXIT (a)-(c) and apply additional available indel probe design methods;
• (d) if the compared interrogation bases are the same, repeat beginning at step (a), but setting the interrogation base one base downstream of the previously compared interrogation base as a current compared interrogation base and increasing an interrogation distance counter by one;
• (e) repeat steps a-c until (b OR c) is TRUE or until the an interrogation distance counter exceeds an allowed maximum.

A computer program stored on a non-transitory computer readable medium, the computer program comprising code to perform:

• accessing a data set of one or more genomes, said data set comprising information regarding genomic locations of a plurality of indels and sequences flanking at least one direction of the plurality of indels;
• designing an indel probe by:
• access or generate a probe sequence that is complementary to a sequence flanking the indel;
• compare a deletion allele interrogation base to an interrogation allele interrogation base and if the compared interrogation bases are different and are in different detection channels, create and output a single indel probe using the interrogation bases to differentiate the deletion allele and the insertion allele;
• if the compared interrogation bases are the same, incorporate the interrogation base into the probe and set the interrogation base one base downstream as a current compared interrogation base and repeat until a successful indel probe is designed and output or a stop condition is reached.