Systems and methods for probe design to detect the presence of simple and complex indels

Abstract

Methods and systems for the determination of a collection of relevant single nucleotide polymorphisms (SNP) probe compatible insertion/deletion probes across a genome to determine probes that can detect a variety of insertions and deletions.

1 - 31 . (canceled) 
     
     
         32 . A computer program product comprising executable instructions stored in a non-transitory computer-readable medium that, when executed by one or more processors cause the one or more processors to perform processing to design a plurality of indel probes for a plurality of complex or multi-base indels, the processing comprising, for each complex or multi-base indel of the plurality of complex or multi-base indels:
 (a) accessing or generating a probe sequence that is complementary to a target sequence flanking the complex or multi-base indel;   (b) determining if an indel interrogation base in an indel identification sequence is a same base as a downstream base in the target sequence,   (c) in response to the indel interrogation base and the downstream base in the target sequence being the same, then incorporating the indel interrogation base into the probe sequence, and setting a new indel interrogation base to be based on a next base in the indel identification sequence and a new downstream base in the target sequence to be based on a next downstream base in the target sequence and repeat (b)-(c), and   (d) in response to the indel interrogation base and the downstream base in the target sequence not being the same, creating and outputting an indel probe adapted for using the probe sequence to differentiate a deletion allele and an insertion allele of the complex or multi-base indel.   
     
     
         33 . The computer program product of  claim 32 , wherein in (d) the indel probe is created and outputted in response to the indel interrogation base and the downstream base in the target sequence not being in the same detection channel. 
     
     
         34 . The computer program product of  claim 32  wherein the processing further comprises:
 (e) in response to the indel interrogation base and the downstream base in the target sequence not being the same and being in the same detection channel, creating and outputting two different indel probes corresponding to two allele-specific oligonucleotides (ASO) adapted for using the probe sequence to differentiate a deletion allele and an insertion allele of the complex or multi-base indel. 
 
     
     
         35 . The computer program product of  claim 32  wherein the processing further comprises:
 (e) in response to the indel interrogation base and the downstream base in the target sequence not being the same and being in the same detection channel, determining allele-specific oligonucleotides (ASO) for creating two different indel probes, one for an insertion allele and one for a deletion allele by moving one base downstream in an insertion allele sequence and one base downstream in a deletion allele sequence to incorporate the intel interrogation base and the downstream base, respectively, into each indel probe; 
 (f) identifying a new interrogation base for a first probe that measures a first of the alleles; 
 (g) move downstream one base in a sequence of a second of the alleles to incorporate a base one downstream of the compared interrogation bases into a second probe that measures a second of the alleles; 
 (h) identify a new interrogation base for the second probe and compare to the new interrogation base for the first probe; 
 (i) repeat (g) and (h) until the new interrogation bases are the same or an interrogation distance threshold is exceeded; 
 (j) when an interrogation distance threshold is first exceeded, switch the second probe to the first probe and repeat (f), (g) and (h) until the new interrogation bases are the same or an interrogation distance threshold is exceeded; and 
 (k) output the first and second probes as allele-specific oligonucleotides indel probes. 
 
     
     
         36 . The computer program product of  claim 32  wherein the processing further comprises:
 in response to the compared bases being different and being in the same detection channel, determine allele-specific oligonucleotides (ASO), creating two ASO probes comprising an insertion probe and a deletion probe for two different alleles by:
 sliding one base downstream and incorporate the previous compared base into each ASO probe; and 
 for both the insertion and deletion probes, using a next base as a new interrogation base; 
 wherein determining final allele-specific probes requires the addition of only a single additional base into the deletion probe and the insertion probe. 
 
 
     
     
         37 . A method for genotyping a plurality of complex or multi-base indels within one or more sample genomes comprising:
 for each synthesized indel probe of a plurality of synthesized indel probes on a genotyping array, adding one or more nucleotides or oligonucleotides including a label to the synthesized indel probe after hybridization with a sample, the one or more nucleotides or oligonucleotides being added corresponding to an indel interrogation base; and   genotyping a complex or multi-base indel of the plurality of complex or multi-base indels by detecting a respective label corresponding to a respective one or more nucleotides or oligonucleotides added to a respective synthesized indel probe of the plurality of synthesized indel probes;   wherein each of the plurality of synthesized indel probes are designed by:
 (a) generating a probe sequence that is complementary to a target sequence flanking the complex or multi-base indel; 
 (b) determining if an indel interrogation base in an indel identification sequence is the same as a downstream base in the target sequence, 
 (c) in response to the indel interrogation base and the downstream base in the target sequence being the same, then incorporate the indel interrogation base into the probe sequence, set a new indel interrogation base to be based on a next base in the indel identification sequence and a new downstream base in the in the target sequence to be based on a next downstream base in the target sequence and repeat (b)-(c), and 
 (d) in response to the indel interrogation base and the downstream base in the target sequence not being the same, create and output a single indel probe adapted for using the probe sequence to differentiate a deletion allele and an insertion allele of the complex or multi-base indel. 
   
     
     
         38 . The method of  claim 37 , wherein in (d) the single indel probe is created and outputted in response to the indel interrogation base and the downstream base in the target sequence not being in the same detection channel. 
     
     
         39 . The method of  claim 37  further comprising:
 (e) in response to the indel interrogation base and the downstream base in the target sequence not being the same and being in the same detection channel, create and output two different indel probes corresponding to two allele-specific oligonucleotides (ASO) adapted for using the probe sequence to differentiate a deletion allele and an insertion allele of the complex or multi-base indel. 
 
     
     
         40 . The method of  claim 37  wherein indel probes are compatible with a system and analysis software using SNP probes to identify single nucleotide polymorphisms (SNPs) by detecting the identity of an interrogation base added to the SNP probes. 
     
     
         41 . The method of  claim 40  wherein creating and outputting indel probes further comprises:
 storing data representing the indel probe on a tangible computer readable media as a SNP probe either immediately or after design of a plurality of SNP probes. 
 
     
     
         42 . The method of  claim 41  wherein creating and outputting a SNP probe further comprises:
 creating an oligonucleotide probe and configuring the oligonucleotide probe with other probes for use in an oligonucleotide array. 
 
     
     
         43 . The method of  claim 37  further comprising:
 if the compared bases are different and in the same detection channel, determine allele-specific oligonucleotides (ASO), creating two different indel probes for the insertion allele and the deletion allele by:
 sliding one base downstream and incorporating the previous base into each ASO probe; 
 identifying a new interrogation base for the probe that measures the deletion; 
 sliding downstream one base the probe that measures the insertion until an identical interrogation base is found; and 
 determining final allele-specific indel probes. 
 
 
     
     
         44 . The method of  claim 43  further comprising:
 if no nearby identical interrogation base can be found, sliding the deletion or insertion probe one base downstream and retrying until an interrogation distance threshold is exceeded. 
 
     
     
         45 . The method of  claim 44  wherein the interrogation distance threshold is 5. 
     
     
         46 . The method of  claim 37  further comprising:
 if the compared bases are different and in the same detection channel, determine allele-specific oligonucleotides (ASO), creating two different indel probes for the insertion allele and the deletion allele by:
 sliding one base downstream and incorporating the previous compared base into each ASO probe; 
 identifying a new interrogation base for the probe that measures the insertion; 
 sliding downstream one base the probe that measures the deletion until an identical interrogation base is found; and 
 determining final allele-specific indel probes. 
 
 
     
     
         47 . The method of  claim 46  further comprising:
 if no nearby identical interrogation base in the same channel can be found, sliding deletion (or insertion) probe one downstream and retrying until an interrogation distance threshold is exceeded. 
 
     
     
         48 . The method of  claim 47  wherein the interrogation distance threshold is 5. 
     
     
         49 . The method of  claim 37  further comprising:
 if the indel interrogation base and the downstream base are different and in the same detection channel, determine allele-specific oligonucleotides (ASO), creating insertion and deletion probes for two different alleles by:
 sliding one base downstream and incorporating the previous compared base into each ASO probe; 
 for both the insertion and deletion probes, using the next base as the new indel interrogation base; and 
 determining final allele-specific probes comprising only the addition of a single additional base into the ASO probe for both the deletion and the insertion probe. 
 
 
     
     
         50 . The method of  claim 37  further comprising:
 creating indel probes from both left and right sides. 
 
     
     
         51 . The method of  claim 37  wherein the genotyping array is designed so that each indel is represented by a collection of indel probes.