Methods and kits for linking polymorphic sequences to expanded repeat mutations

Abstract

Methods and kits are provided for determining which single nucleotide polymorphism (“SNP”) variant of an allele of a heterozygous patient is on the same allele as a disease-causing mutation. Also, provided are kits for multi-SNP diagnosis and treatment, targeting combinations of SNPs having greater joint prevalence of heterozygosity in Huntington's population than individual SNPs considered individually.

1 - 41 . (canceled) 
     
     
         42 . A kit for allele-specific diagnostics and/or allele-specific inhibition of mutated IT15 gene expression in a cell, the kit comprising:
 a) a first set of allele-specific RT-PCR primers, the first set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a first SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the first SNP; and   b) a second set of allele-specific RT-PCR primers, the second set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a second SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the second SNP; wherein   the first SNP and the second SNP are different,   the first SNP and the second SNP are selected from the group consisting of rs362331, rs362307, rs35892913, rs362267, rs2276881, rs17781557, and rs363125.   
     
     
         43 . The kit of  claim 42 , wherein, the members of the first set and the members of the second set are selected from the group consisting of SEQ ID NOs: 39, 47, 56, 63, 72, 79, 114, 121, 83, 90, 107, 100, 15, and 27. 
     
     
         44 . The kit of  claim 42 , wherein the first SNP and the second SNP are rs362331, and rs362307. 
     
     
         45 . The kit of  claim 42 , further comprising a first PCR primer hybridizing to a portion of IT15 cDNA located upstream of CAG region and a second PCR primer, hybridizing to a portion of IT15 cDNA located downstream of CAG region. 
     
     
         46 . The kit of  claim 45 , wherein the first PCR primer and the second PCR primer are SEQ ID NO: 122 and SEQ ID NO: 123. 
     
     
         47 . The kit of  claim 42 , further comprising:
 a) a first set of therapeutic agents, the first set comprising a first therapeutic agent capable of preferential suppression of a first variant of the first SNP, and a second therapeutic agent capable of preferential suppression of at least a second variant of the first SNP; and   b) a second set of therapeutic agents, the second set comprising a first therapeutic agent capable of preferential suppression of a first variant of the second SNP, and a second therapeutic agent capable of preferential suppression of at least a second variant of the second SNP,   wherein each of said therapeutic agents comprises a nucleic acid sequence.   
     
     
         48 . The kit of  claim 47 , wherein each of said therapeutic agents comprises a double-stranded portion having one strand selected from the group consisting of SEQ ID NOs 124-235 and 250-257, and
 if the first SNP and the second SNP are rs362331, and rs362307, then each of said therapeutic agents comprises a double-stranded portion having one strand selected from the group consisting of SEQ ID NOs 124-155.   
     
     
         49 . A kit for allele-specific diagnostics and/or allele-specific inhibition of mutated IT15 gene expression in a cell, the kit comprising:
 a) a first set of allele-specific RT-PCR primers, the first set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a first SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the first SNP;   b) a second set of allele-specific RT-PCR primers, the second set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a second SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the second SNP; and   c) a third set of allele-specific RT-PCR primers, the third set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a third SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the third SNP; wherein   the first SNP, the second SNP and the third SNP are different,   the first SNP, the second SNP, and the third SNP are selected from the group consisting of rs362331, rs362307, rs35892913, rs362267, rs2276881, rs17781557, and rs363125.   
     
     
         50 . The kit of  claim 49 , wherein the members of the first set, the members of the second set, and the members of the third set are selected from the group consisting of SEQ ID NOs: 39, 47, 56, 63, 72, 79, 114, 121, 83, 90, 107, 100, 15, and 27. 
     
     
         51 . The kit of  claim 49 , wherein the first SNP, the second SNP, and the third SNP are rs362331, rs362307, and rs35892913. 
     
     
         52 . The kit of  claim 49 , further comprising a first PCR primer hybridizing to a portion of IT15 cDNA located upstream of CAG region and a second PCR primer, hybridizing to a portion of IT15 cDNA located downstream of CAG region. 
     
     
         53 . The kit of  claim 52 , wherein the first PCR primer and the second PCR primer are SEQ ID NO: 122 and SEQ ID NO: 123. 
     
     
         54 . The kit of  claim 49 , further comprising:
 a) a first set of therapeutic agents, the first set comprising a first therapeutic agent capable of preferential suppression of a first variant of the first SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the first SNP;   b) a second set of therapeutic agents, the second set comprising a first therapeutic agent capable of preferential suppression of a first variant of the second SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the second SNP;   c) a third set of therapeutic agents, the third set comprising a first therapeutic agent capable of preferential suppression of a first variant of the third SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the third SNP,   wherein each of said therapeutic agents comprises a nucleic acid sequence.   
     
     
         55 . The kit of  claim 54 , wherein each of said therapeutic agents comprises a double-stranded portion having one strand selected from the group consisting of SEQ ID NOs 124-235 and 250-257, and
 if the first SNP, the second SNP, and the third SNP are rs362331, rs362307, and rs35892913, then each of said therapeutic agents comprises a double-stranded portion having one strand selected from the group consisting of SEQ ID NOs 124-171.   
     
     
         56 . A kit for allele-specific diagnostics and/or allele-specific inhibition of mutated IT15 gene expression in a cell, the kit comprising:
 a) a first set of allele-specific RT-PCR primers, the first set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a first SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the first SNP;   b) a second set of allele-specific RT-PCR primers, the second set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a second SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the second SNP;   c) a third set of allele-specific RT-PCR primers, the third set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a third SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the third SNP;   d) a fourth set of allele-specific RT-PCR primers, the fourth set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a fourth SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the fourth SNP; wherein   the first SNP, the second SNP, the third SNP, and the fourth SNP are different,   the first SNP, the second SNP, the third SNP, and the fourth SNP are selected from the group consisting of rs362331, rs362307, rs35892913, rs362267, rs2276881, rs17781557, and rs363125.   
     
     
         57 . The kit of  claim 56 , wherein the members of the first set, the members of the second set, the members of the third set, and the members of the fourth are selected from the group consisting of SEQ ID NOs: 39, 47, 56, 63, 72, 79, 114, 121, 83, 90, 107, 100, 15, and 27. 
     
     
         58 . The kit of  claim 56 , wherein the first SNP, the second SNP, the third SNP, and the fourth SNP are rs362331, rs362307, rs35892913, and rs362267. 
     
     
         59 . The kit of  claim 56 , further comprising a first PCR primer hybridizing to a portion of IT15 cDNA located upstream of CAG region and a second PCR primer, hybridizing to a portion of IT15 cDNA located downstream of CAG region. 
     
     
         60 . The kit of  claim 59 , wherein the first PCR primer and the second PCR primer are SEQ ID NO: 122 and SEQ ID NO: 123. 
     
     
         61 . The kit of  claim 56 , further comprising:
 a) a first set of therapeutic agents, the first set comprising a first therapeutic agent capable of preferential suppression of a first variant of the first SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the first SNP;   b) a second set of therapeutic agents, the second set comprising a first therapeutic agent capable of preferential suppression of a first variant of the second SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the second SNP;   c) a third set of therapeutic agents, the third set comprising a first therapeutic agent capable of preferential suppression of a first variant of the third SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the third SNP;   d) a fourth set of therapeutic agents, the fourth set comprising a first therapeutic agent capable of preferential suppression of a first variant of the fourth SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the fourth SNP,   wherein each of said therapeutic agents comprises a nucleic acid sequence.   
     
     
         62 . The kit of  claim 61 , wherein each of said therapeutic agents comprises a double-stranded portion having one strand selected from the group consisting of SEQ ID NOs 124-235 and 250-257, and
 if the first SNP, the second SNP, the third SNP, and the fourth SNP are rs362331, rs362307, rs35892913, and rs362267, then each of said therapeutic agents comprises a double-stranded portion having one strand selected from the group consisting of SEQ ID NOs 124-187.   
     
     
         63 . A kit for allele-specific diagnostics and/or allele-specific inhibition of mutated IT15 gene expression in a cell, the kit comprising:
 a) a first set of allele-specific RT-PCR primers, the first set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a first SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the first SNP;   b) a second set of allele-specific RT-PCR primers, the second set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a second SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the second SNP;   c) a third set of allele-specific RT-PCR primers, the third set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a third SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the third SNP;   d) a fourth set of allele-specific RT-PCR primers, the fourth set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a fourth SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the fourth SNP;   e) a fifth set of allele-specific RT-PCR primers, the fourth set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a fifth SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the fifth SNP; wherein   the first SNP, the second SNP, the third SNP, the fourth SNP, and the fifth SNP are different,   the first SNP, the second SNP, the third SNP, the fourth SNP, and the fifth SNP are selected from the group consisting of rs362331, rs362307, rs35892913, rs362267, rs2276881, rs17781557, and rs363125.   
     
     
         64 . The kit of  claim 63 , wherein the members of the first set, the members of the second set, the members of the third set, the members of the fourth set, and the members of the fifth set are selected from the group consisting of SEQ ID NOs: 39, 47, 56, 63, 72, 79, 114, 121, 83, 90, 107, 100, 15, and 27. 
     
     
         65 . The kit of  claim 63 , wherein the first SNP, the second SNP, the third SNP, the fourth SNP, and the fifth SNP are rs362331, rs362307, rs35892913, rs362267, and rs2276881. 
     
     
         66 . The kit of  claim 63 , further comprising a first PCR primer hybridizing to a portion of IT15 cDNA located upstream of CAG region and a second PCR primer, hybridizing to a portion of IT15 cDNA located downstream of CAG region. 
     
     
         67 . The kit of  claim 66 , wherein the first PCR primer and the second PCR primer are SEQ ID NO: 122 and SEQ ID NO: 123. 
     
     
         68 . The kit of  claim 63 , further comprising:
 a) a first set of therapeutic agents, the first set comprising a first therapeutic agent capable of preferential suppression of a first variant of the first SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the first SNP;   b) a second set of therapeutic agents, the second set comprising a first therapeutic agent capable of preferential suppression of a first variant of the second SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the second SNP;   c) a third set of therapeutic agents, the third set comprising a first therapeutic agent capable of preferential suppression of a first variant of the third SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the third SNP;   d) a fourth set of therapeutic agents, the fourth set comprising a first therapeutic agent capable of preferential suppression of a first variant of the fourth SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the fourth SNP;   e) a fifth set of therapeutic agents, the fifth set comprising a first therapeutic agent capable of preferential suppression of a first variant of the fifth SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the fifth SNP,   wherein each of said therapeutic agents comprises a nucleic acid sequence.   
     
     
         69 . The kit of  claim 68 , wherein each of said therapeutic agents comprises a double-stranded portion having one strand selected from the group consisting of SEQ ID NOs 124-235 and 250-257, and
 if the first SNP, the second SNP, the third SNP, the fourth SNP, and the fifth SNP are rs362331, rs362307, rs35892913, rs362267, and rs2276881 then each of said therapeutic agents comprises a double-stranded portion having one strand selected from the group consisting of SEQ ID NOs 124-203.   
     
     
         70 . A kit for allele-specific diagnostics and/or allele-specific inhibition of mutated IT15 gene expression in a cell, the kit comprising:
 a) a first set of allele-specific RT-PCR primers, the first set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a first SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the first SNP;   b) a second set of allele-specific RT-PCR primers, the second set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a second SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the second SNP;   c) a third set of allele-specific RT-PCR primers, the third set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a third SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the third SNP;   d) a fourth set of allele-specific RT-PCR primers, the fourth set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a fourth SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the fourth SNP;   e) a fifth set of allele-specific RT-PCR primers, the fifth set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a fifth SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the fifth SNP;   f) a sixth set of allele-specific RT-PCR primers, the sixth set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a sixth SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the sixth SNP; wherein   the first SNP, the second SNP, the third SNP, the fourth SNP, the fifth SNP, and the six SNP are different,   the first SNP, the second SNP, the third SNP, the fourth SNP, the fifth SNP, and the sixth SNP are selected from the group consisting of rs362331, rs362307, rs35892913, rs362267, rs2276881, rs17781557, and rs363125.   
     
     
         71 . The kit of  claim 70 , wherein the members of the first set, the members of the second set, the members of the third set, the members of the fourth set, the members of the fifth set, and the members of the sixth set are selected from the group consisting of SEQ ID NOs: 39, 47, 56, 63, 72, 79, 114, 121, 83, 90, 107, 100, 15, and 27. 
     
     
         72 . The kit of  claim 70 , wherein the first SNP, the second SNP, the third SNP, the fourth SNP, the fifth SNP, and the sixth SNP are rs362331, rs362307, rs35892913, rs362267, rs2276881, rs17781557. 
     
     
         73 . The kit of  claim 70 , further comprising a first PCR primer hybridizing to a portion of IT15 cDNA located upstream of CAG region and a second PCR primer, hybridizing to a portion of IT15 cDNA located downstream of CAG region. 
     
     
         74 . The kit of  claim 73 , wherein the first PCR primer and the second PCR primer are SEQ ID NO: 122 and SEQ ID NO: 123. 
     
     
         75 . The kit of  claim 70 , further comprising:
 a) a first set of therapeutic agents, the first set comprising a first therapeutic agent capable of preferential suppression of a first variant of the first SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the first SNP;   b) a second set of therapeutic agents, the second set comprising a first therapeutic agent capable of preferential suppression of a first variant of the second SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the second SNP;   c) a third set of therapeutic agents, the third set comprising a first therapeutic agent capable of preferential suppression of a first variant of the third SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the third SNP;   d) a fourth set of therapeutic agents, the fourth set comprising a first therapeutic agent capable of preferential suppression of a first variant of the fourth SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the fourth SNP;   e) a fifth set of therapeutic agents, the fifth set comprising a first therapeutic agent capable of preferential suppression of a first variant of the fifth SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the fifth SNP;   f) a sixth set of therapeutic agents, the sixth set comprising a first therapeutic agent capable of preferential suppression of a first variant of the sixth SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the sixth SNP   wherein each of said therapeutic agents comprises a nucleic acid sequence.   
     
     
         76 . The kit of  claim 75 , wherein each of said therapeutic agents comprises a double-stranded portion having one strand selected from the group consisting of SEQ ID NOs 124-235 and 250-257, and
 if the first SNP, the second SNP, the third SNP, the fourth SNP, the fifth SNP, and the sixth SNP are rs362331, rs362307, rs35892913, rs362267, rs2276881, and rs17781557, then each of said therapeutic agents comprises a double-stranded portion having one strand selected from the group consisting of SEQ ID NOs 124-219.   
     
     
         77 . A kit for allele-specific diagnostics and/or allele-specific inhibition of mutated IT15 gene expression in a cell, the kit comprising:
 a) a first set of allele-specific RT-PCR primers, the first set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a first SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the first SNP;   b) a second set of allele-specific RT-PCR primers, the second set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a second SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the second SNP;   c) a third set of allele-specific RT-PCR primers, the third set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a third SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the third SNP;   d) a fourth set of allele-specific RT-PCR primers, the fourth set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a fourth SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the fourth SNP;   e) a fifth set of allele-specific RT-PCR primers, the fifth set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a fifth SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the fifth SNP;   f) a sixth set of allele-specific RT-PCR primers, the sixth set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a sixth SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the sixth SNP;   g) a seventh set of allele-specific RT-PCR primers, the seventh set comprising a first allele-specific RT-PCR primer, capable of selectively hybridizing to a first variant of a seventh SNP and at least a second allele-specific RT-PCR primer capable of selectively hybridizing to at least a second variant of the seventh SNP; wherein   the first SNP, the second SNP, the third SNP, the fourth SNP, the fifth SNP, the six SNP, and the seventh SNP are different,   the first SNP, the second SNP, the third SNP, the fourth SNP, the fifth SNP, the sixth SNP, and the seventh SNP are selected from the group consisting of rs362331, rs362307, rs35892913, rs362267, rs2276881, rs17781557, and rs363125.   
     
     
         78 . The kit of  claim 77 , wherein the members of the first set, the members of the second set, the members of the third set, the members of the fourth set, the members of the fifth set, the members of the sixth set, and the members of the seventh set are selected from the group consisting of SEQ ID NOs: 39, 47, 56, 63, 72, 79, 114, 121, 83, 90, 107, 100, 15, and 27. 
     
     
         79 . The kit of  claim 77 , further comprising a first PCR primer hybridizing to a portion of IT15 cDNA located upstream of CAG region and a second PCR primer, hybridizing to a portion of IT15 cDNA located downstream of CAG region. 
     
     
         80 . The kit of  claim 79 , wherein the first PCR primer and the second PCR primer are SEQ ID NO: 122 and SEQ ID NO: 123. 
     
     
         81 . The kit of  claim 77 , further comprising:
 a) a first set of therapeutic agents, the first set comprising a first therapeutic agent capable of preferential suppression of a first variant of the first SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the first SNP;   b) a second set of therapeutic agents, the second set comprising a first therapeutic agent capable of preferential suppression of a first variant of the second SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the second SNP;   c) a third set of therapeutic agents, the third set comprising a first therapeutic agent capable of preferential suppression of a first variant of the third SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the third SNP;   d) a fourth set of therapeutic agents, the fourth set comprising a first therapeutic agent capable of preferential suppression of a first variant of the fourth SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the fourth SNP;   e) a fifth set of therapeutic agents, the fifth set comprising a first therapeutic agent capable of preferential suppression of a first variant of the fifth SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the fifth SNP;   f) a sixth set of therapeutic agents, the sixth set comprising a first therapeutic agent capable of preferential suppression of a first variant of the sixth SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the sixth SNP;   g) a seventh set of therapeutic agents, the seventh set comprising a first therapeutic agent capable of preferential suppression of a first variant of the seventh SNP, and at least a second therapeutic agent capable of preferential suppression of at least a second variant of the seventh SNP,   wherein each of said therapeutic agents comprises a nucleic acid sequence.   
     
     
         82 . The kit of  claim 81 , wherein each of said therapeutic agents comprises a double-stranded portion having one strand selected from the group consisting of SEQ ID NOs 124-235 and 250-257.