Methods, tools and systems for the assessment, prevention, management and treatment selection for type 2 diabetes

Abstract

The present invention provides a method of assessing type 2 diabetes susceptibility and/or predicting treatment responsiveness in a human subject, the method comprising determining the identity of at least one allele at each of three or more positions of single nucleotide polymorphism (SNP) selected from the group consisting of: SLC16A11—rs75493593; HNF1A—rs483353044; TCF7L2—rs7903146; CDKN2A/B—rs10811661; CDKAL1—rs7756992; SLC30A8—rs3802177; IGF2BP2—rs4402960; FTO—rs9936385; PPARG—rs1801282; HHEX/IDE—rs1111875; ADCY5—rs11717195; JAZF1—rs849135; WSF1—rs4458523; INS—IGF2—rs149483638; KCNQ1—rs2237897; and KCNJ11—rs5219, and/or an SNP in linkage disequilibrium with any one of said SNPs at r 2 >0.8. Also provided are a genotyping tool and a type 2 diabetes risk assessment system for use in the method of the invention.

1 . A method of assessing type 2 diabetes susceptibility and/or predicting treatment responsiveness in a human subject, the method comprising determining the identity of at least one allele at each of three or more positions of single nucleotide polymorphism (SNP) selected from the group consisting of:
 SLC16A11—rs75493593;   HNF1A—rs483353044;   TCF7L2—rs7903146;   CDKN2A/B—rs10811661;   CDKAL1—rs7756992;   SLC30A8—rs3802177;   IGF2BP2—rs4402960;   FTO—rs9936385;   PPARG—rs1801282;   HHEX/IDE—rs1111875;   ADCY5—rs11717195;   JAZF1—rs849135;   WSF1—rs4458523;   INS—IGF2—rs149483638;   KCNQ1—rs2237897; and   KCNJ11—rs5219,   and/or an SNP in linkage disequilibrium with any one of said SNPs at r 2 >0.8.   
     
     
         2 . The method according to  claim 1 , wherein the method comprises determining the identity of at least one allele at each of the following SNPs:
 SLC16A11—rs75493593;   HNF1A—rs483353044;   KCNQ1—rs2237897; and   TCF7L2—rs7903146.   
     
     
         3 . The method according to  claim 2 , wherein the method comprises determining the identity of at least one allele at each of the following SNPs:
 SLC16A11—rs75493593;   HNF1A—rs483353044;   KCNQ1—rs2237897;   TCF7L2—rs7903146;   FTO—rs9936385; and   PPARG—rs1801282.   
     
     
         4 . The method according to  claim 3 , wherein the method comprises determining the identity of at least one allele at each of the following SNPs:
 SLC16A11—rs75493593;   HNF1A—rs483353044;   TCF7L2—rs7903146;   CDKN2A/B—rs10811661;   CDKAL1—rs7756992;   SLC30A8—rs3802177;   IGF2BP2—rs4402960;   FTO—rs9936385;   PPARG—rs1801282;   HHEX/IDE—rs1111875;   ADCY5—rs11717195;   JAZF1—rs849135;   WSF1—rs4458523;   INS—IGF2—rs149483638;   KCNQ1—rs2237897; and   KCNJ11—rs5219.   
     
     
         5 . The method according to any one of the preceding claims, wherein allele determination is carried out at not more than 20 SNP positions. 
     
     
         6 . The method according to any one of the preceding claims, wherein presence of one or more of the following risk alleles indicates that the subject greater susceptibility to type 2 diabetes:
 T at rs75493593 in SLC16A11;   A at rs483353044 in HNF1A;   T at rs7903146 in TCF7L2;   T at rs10811661 in CDKN2A/B;   G at rs7756992 in CDKAL1;   G at rs3802177 in SLC30A8;   T at rs4402960 IGF2BP2;   C at rs9936385 in FTO;   C at rs1801282 in PPARG;   C at rs1111875 in HHEX/IDE;   T at rs11717195 in ADCY5;   G at rs849135 in JAZF1;   G at rs4458523 in WSF1;   C at rs149483638 in INS—IGF2;   C at rs2237897 in KCNQ1; and   T at rs5219 in KCNJ11.   
     
     
         7 . The method according to any one of the preceding claims wherein the method comprises determining the identity of both alleles at each SNP thereby obtaining the genotype of the subject at each SNP. 
     
     
         8 . The method according to  claim 6  or  claim 7 , wherein the subject is determined to be heterozygous or to be homozygous for the risk allele at at least one of said SNPs. 
     
     
         9 . The method according to  claim 8 , wherein the method comprises assaying a DNA-containing sample that has previously been obtained from said subject. 
     
     
         10 . The method according to  claim 9 , wherein said sample is selected from the group consisting of: blood, hair, skin, amniotic fluid, buccal swab, saliva, and faeces. 
     
     
         11 . The method according to  claim 9  or  claim 10 , wherein the method comprises isolating and/or amplifying genomic DNA from said subject. 
     
     
         12 . The method according to any one of the preceding claims, wherein determining the identity of said at least one allele at each SNP comprises: probe hybridization, real time PCR, array analysis, bead analysis, primer extension, restriction analysis and/or DNA sequencing. 
     
     
         13 . The method according to any one of the preceding claims, wherein the method employs a plurality of oligonucleotide probes, which plurality includes a pair of allele-specific oligonucleotide probes for each SNP, said allele-specific oligonucleotide probes each spanning the polymorphic position as set forth in the context sequence column of Table 2. 
     
     
         14 . The method according to  claim 12  or  claim 13 , wherein determining the identity of said at least one allele at each SNP comprises TaqMan® SNP genotyping and/or comprises Dynamic Arrays IFCs using TaqMan® chemistry and Integrated Fluidics Circuits (IFCs). 
     
     
         15 . The method according to  claim 14 , wherein the method employs TaqMan® OpenArray® SNP genotyping. 
     
     
         16 . The method according to any one of the preceding claims, wherein the method comprises determining the number of and identity of SNP risk alleles, and wherein the method further comprises computing a type 2 diabetes risk score for said subject. 
     
     
         17 . The method according to  claim 16 , wherein the method comprises inputting the SNP risk allele determinations into a probability function to compute said risk score. 
     
     
         18 . The method according to any one of the preceding claims, wherein said SNPs include: the E508K polymorphism in HNF1A, and wherein the presence of at least one A allele indicates that the subject will have a greater hypoglycaemic response to antidiabetic therapy with a sulfonylurea as compared with a biguanide. 
     
     
         19 . The method according to  claim 18 , wherein said sulfonylurea comprises glipizide. 
     
     
         20 . The method according to  claim 18  or  claim 19 , wherein the method further comprises administering, or recommending administration of, sulfonylurea therapy to a type 2 diabetic subject who carries at least one A allele of the E508K polymorphism in HNF1A. 
     
     
         21 . The method according to any one of the preceding claims, wherein the subject is of Mexican, Latino American, European, East Asian, African and/or Indigenous Mexican origin or ancestry. 
     
     
         22 . The method according to any one of the preceding claims, wherein the subject has at least one first degree relative who has, or has previously been diagnosed with, type 2 diabetes. 
     
     
         23 . The method according to any one of the preceding claims, wherein the subject has one or more clinical risk factors for type 2 diabetes selected from: body mass index>30, waist circumference>80 cm for female or >94 cm for male, age>40, impaired glucose regulation, raised fasting blood glucose, and insulin resistance. 
     
     
         24 . The method according to any one of the preceding claims, wherein the subject is determined to carry one or more of said risk alleles at one or more of said SNPs and therefore to be at greater risk of type 2 diabetes, the method further comprising an intervention selected from the group consisting of:
 making a video game electronically accessible to the subject, said video game having predefined game objectives selected to reinforce healthy eating habits that avoid or minimize consumption of diabetogenic food and drink and/or to reinforce exercise habits;   making a movement activity monitor available to the subject, said movement activity monitor being capable of recording and/or reporting movement activity data on the subject to a display interface that presents the movement activity data or a summary or score derived from said data;   making a calorific counter device available to the subject, said device being capable of recording and/or reporting dietary nutritional data on the food and/or drink consumed by the subject; and   making a social network available to the subject, said network having type 2 diabetes self-management advice, a plurality of diabetic network participants and a reward system that encourages healthy eating and/or exercise.   
     
     
         25 . The method according to  claim 24 , wherein the video game comprises a player character presented with food and/or drink choices, wherein the game rewards selection of healthy food and/or drink by the player character. 
     
     
         26 . The method according to  claim 24 , wherein the movement activity monitor comprises a pedometer that communicates or can be configured to communicate to a computer or mobile electronic device. 
     
     
         27 . The method according to  claim 24 , wherein the calorific counter device comprises a mobile electronic device programmed to receive information on dietary intake of the subject and to display calorific values corresponding the dietary intake. 
     
     
         28 . The method according to any one of the preceding claims, wherein the subject is classified into one of the following three risk categories according to the fold-change (FC) value:
 low risk: FC between 0 and 1.00   moderate risk: FC between 1.01 and 1.5;   intermediate risk: FC between 1.51 and 2.0; and   high risk: FC greater than 2.0.   
     
     
         29 . The method according to  claim 28 , wherein the fold-change value for the subject is calculated by assigning a risk score for each SNP, wherein the fold-change value is given by multiplying the risk scores of each of the SNPs together, and wherein for each SNP the risk score is assigned as follows:
 the absence of risk marker, i.e. homozygous non-risk allele genotype, at the SNP is assigned a value of 1,   the presence of a single risk marker, i.e. heterozygous genotype, at the SNP is assigned a value equal to the odds ratio (OR) for the risk allele at that SNP,   the presence of two risk markers, i.e. homozygous risk allele genotype is assigned a value equal to the square of the odds ratio (OR) 2 .   
     
     
         30 . The method according to  claim 29 , wherein the OR for the risk allele at each SNP is as follows:
 T at rs75493593 in SLC16A11=1.29±0.05;   A at rs483353044 in HNF1A=5.48±0.05;   T at rs7903146 in TCF7L2=1.37±0.05;   T at rs10811661 in CDKN2A/B=1.08±0.05;   G at rs7756992 in CDKAL1=1.05±0.05;   G at rs3802177 in SLC30A8=1.12±0.05;   T at rs4402960 IGF2BP2=1.12±0.05;   C at rs9936385 in FTO=1.17±0.05;   C at rs1801282 in PPARG=1.1±0.05;   C at rs1111875 in HHEX/IDE=1.06±0.05;   T at rs11717195 in ADCY5=1.14±0.05;   G at rs849135 in JAZF1=1.16±0.05;   G at rs4458523 in WSF1=1.13±0.05;   C at rs149483638 in INS—IGF2=1.28±0.05;   C at rs2237897 in KCNQ1=1.31±0.05; and   T at rs5219 in KCNJ11=1.08±0.05.   
     
     
         31 . A genotyping tool for use in a method of any one of  claims 1  to  30 , said tool comprising an array having a plurality of oligonucleotide probe pairs, each of said probe pairs comprising a first probe specific for a first allele of a single nucleotide polymorphism (SNP) and a second probe specific for a second allele of the SNP, wherein said plurality of oligonucleotide probe pairs comprises probe pairs that interrogate at least three SNPs selected from the group consisting of:
 SLC16A11—rs75493593; 
 HNF1A—rs483353044; 
 TCF7L2—rs7903146; 
 CDKN2A/B—rs10811661; 
 CDKAL1—rs7756992; 
 SLC30A8—rs3802177; 
 IGF2BP2—rs4402960; 
 FTO—rs9936385; 
 PPARG—rs1801282; 
 HHEX/IDE—rs1111875; 
 ADCY5—rs11717195; 
 JAZF1—rs849135; 
 WSF1—rs4458523; 
 INS—IGF2—rs149483638; 
 KCNQ1—rs2237897; and 
 KCNJ11—rs5219, 
 and/or an SNP in linkage disequilibrium with any one of said SNPs at r 2 >0.8. 
 
     
     
         32 . The genotyping tool according to  claim 31 , wherein the oligonucleotide probes of the array that interrogate SNPs selected from: rs75493593; rs483353044; rs7903146; rs10811661; rs7756992; rs3802177; rs4402960; rs9936385; rs1801282; rs1111875; rs11717195; rs849135; rs4458523; rs149483638; rs2237897; and rs5219, make up at least 50% of the probes present in the array. 
     
     
         33 . The genotyping tool according to  claim 31  or  claim 32 , wherein said plurality of oligonucleotide probe pairs comprises probe pairs that interrogate at least:
 SLC16A11—rs75493593; 
 HNF1A—rs483353044; 
 KCNQ1—rs2237897; and 
 TCF7L2—rs7903146. 
 
     
     
         34 . The genotyping tool according to  claim 33 , wherein said plurality of oligonucleotide probe pairs comprises probe pairs that interrogate at least:
 SLC16A11—rs75493593;   HNF1A—rs483353044;   KCNQ1—rs2237897;   TCF7L2—rs7903146;   FTO—rs9936385; and   PPARG—rs1801282.   
     
     
         35 . The genotyping tool according to  claim 34 , wherein said plurality of oligonucleotide probe pairs comprises probe pairs that interrogate at least:
 SLC16A11—rs75493593;   HNF1A—rs483353044;   TCF7L2—rs7903146;   CDKN2A/B—rs10811661;   CDKAL1—rs7756992;   SLC30A8—rs3802177;   IGF2BP2—rs4402960;   FTO—rs9936385;   PPARG—rs1801282;   HHEX/IDE—rs1111875;   ADCY5—rs11717195;   JAZF1—rs849135;   WSF1—rs4458523;   INS—IGF2—rs149483638;   KCNQ1—rs2237897; and   KCNJ11—rs5219.   
     
     
         36 . The genotyping tool according to any one of  claims 31  to  35 , wherein total number of different SNPs for which allele-specific probes are provided does not exceed twenty. 
     
     
         37 . The genotyping tool according to any one of  claims 31  to  36 , wherein the allele-specific oligonucleotide probes are each covalently attached to a fluorophore. 
     
     
         38 . The genotyping tool according to any one of  claims 31  to  37 , wherein the nucleotide sequence of each of the allele-specific probes is of 13 to 18 nucleotides in length and is, or is complementary to, a contiguous SNP context sequence as set forth in Table 2 and which spans the polymorphic site. 
     
     
         39 . The genotyping tool according to any one of  claims 31  to  38 , wherein the array further comprises a primer pair for each said SNPs, said primer pair for each SNP comprising an oligonucleotide primer that hybridizes to a target sequence upstream of the SNP and an oligonucleotide primer that hybridizes to a target sequence downstream of the SNP. 
     
     
         40 . The genotyping tool according to any one of  claims 31  to  39 , wherein the tool further comprises one or more reagents for amplification of DNA comprising said SNPs and/or for detection of said allele-specific probes. 
     
     
         41 . The genotyping tool according to any one of  claims 31  to  40 , wherein the array comprises an OpenArray® of between 1000 and 10000 array positions. 
     
     
         42 . The genotyping tool according to  claim 41 , wherein the tool is in the form of a TaqMan® OpenArray® SNP genotyping platform. 
     
     
         43 . The genotyping tool according to any one of  claims 31  to  40 , wherein the tool is in the form of a Dynamic Array IFCs Genotyping platform. 
     
     
         44 . A type 2 diabetes risk assessment system for use in a method as defined in any one of  claims 1  to  30 , the system comprising a genotyping tool as defined in any one of  claims 31  to  43  and a computer programmed to compute a type 2 diabetes risk score from the genotype data of the subject at each of at least three SNPs selected from the SNPs set forth in  claim 1 . 
     
     
         45 . The type 2 diabetes risk assessment system of  claim 44 , wherein computing the risk score from the genotype data comprises weighting the contribution of each SNP risk allele found to be present such that the contribution of to the risk score is commensurate with an odds ratio for the association of the SNP to type 2 diabetes, as set forth in Table 1 or Table 3. 
     
     
         46 . A method according to any one of  claims 1  to  30 , wherein the method employs a genotyping tool as defined in any one of  claims 31  to  43  or a type 2 risk assessment system as defined in  claim 44  or  claim 45 .