Supplementary Tables:
Supplementary Table 1: Demographic data of the study population
Variable / Men / Women / Totaln
(%) / 521 (34.8%) / 975 (65.2%) / 1496 (100%)
Age
(mean ± SD; years) / 53.3 ± 13.1 / 53.8 ± 12.8 / 53.6 ± 12.9
n with diabetes
(%) / 406 (77.9%) / 802 (82.3%) / 1,208 (80.8%)
Onset age of diabetes diagnosis (mean ± SD; years) / 45.2 ± 11.7 / 44.8 ± 12.5 / 44.9 ± 12.3
Body Mass Index (BMI)
(mean ± SD; kg/m2) / 30.1 ± 6.2 / 34.4 ± 8.6 / 32.9 ± 8.1
Waist to Hip Ratio (WHR)
(mean ± SD) / 0.96 ± 0.10 / 0.93 ± 0.13 / 0.94 ± 0.12
Fasting Glucose
(mean ± SD; mmol/l) / 8.77 ± 4.53 / 8.59 ± 4.05 / 8.65 ± 4.23
Fasting Insulin
(mean ± SD; pmol/l) / 136 ± 235 / 148 ± 224 / 144 ± 228
Body mass index (BMI) is calculated by weight (kg)/[height(m)]2.
The waist-hip ratio (WHR) equals the waist circumference divided by the hip circumference. Strictly, the waist circumference is measured at a level midway between the lowest rib and the iliac crest, and the hip circumference at the level of the great trochanters with the legs close together.
SD, standard deviation
Supplementary Table 2: Details of Genotyping assays for selected GWAS SNPs
FTO / rs8050136 / SNPstream / 1-5 / Forward Primer: TGCCAGCTTCATAGCCTAGT
Reverse Primer: AATTTTCCAAGCATTCCATG
Single Base Extension (SBE) Primer: CGACTGTAGGTGCGTAACTCGGCAAAAACCACAGGCTCAGATATT
IGF2BP2 / rs4402960 / SNPstream / 2-4,6 / Forward Primer: GTTTGGAACCCTGGAATTC
Reverse Primer: TTTGACCATTCCTTATCTGGG
SBE Primer: GACCTGGGTGTCGATACCTAAGTAAGGTAGGATGGACAGTAGATT
IGF2BP2 / rs1470579 / SNPstream / 5,6 / Forward Primer: GTAAAATAATAACTGATGAAAAATGGC
Reverse Primer: ATAGGCTTGTCTATGAGTGAGAGG
SBE Primer: AGCGATCTGCGAGACCGTATTCATTAGATAAGATCCATACGAGTT
SLC30A8 / rs13266634 / SNPstream / 2-8 / Forward Primer: TGTGCAATCAGTGCTAATCTC
Reverse Primer: TGCATCGTAAAGCTTTTGC
SBE Primer: AGAGCGAGTGACGCATACTATGCTTCTTTATCAACAGCAGCCAGC
ADAM30/NOTCH2 / rs2641348 / SNPstream / 2,9 / Forward Primer: ATGCTGTAGGAATGTCACATGA
Reverse Primer: ATATTATTTAGACATGTTGCTCCCG
SBE Primer: AGATAGAGTCGATGCCAGCTCAATACTGCCAATGTAGGGGTAGGC
HHEX / rs1111875 / SNPstream / 2-8 / Forward Primer: AACTTCTCACTCCCTTCCAC
Reverse Primer: GATTAGACCAGACTAATTCAATAAATGTT
SBE Primer: GTGATTCTGTACGTGTCGCCTCCGTACCATCAAGTCATTTCCTCT
HHEX / rs5015480 / SNPstream / 4 / Forward Primer: GTCCATATATTTTCAAACAAATAATAGG
Reverse Primer: TACTGAGCCTTATGCAAATTTATATC
SBE Primer: AGCGATCTGCGAGACCGTATGAAGTAAACTCGAATGTTGATTATA
EXT2 / rs11037909 / SNPstream / 8 / Forward Primer: AAAGCTTGTCCCCATGCC
Reverse Primer: GTGAGACAGAAAGAAGAAATATTCAAA
SBE Primer: GGCTATGATTCGCAATGCTTATATTCAAAAATAGCAGTTCCCTTT
JAZF1 / rs864745 / SNPstream / 2,5,9 / Forward Primer: TGTAAAGTTCTTTCTGCGTTAAAAC
Reverse Primer: AAGCACAATTTCTTAAAATCACTGA
SBE Primer: AGGGTCTCTACGCTGACGATATTTCCTACAACCATTCAAAACATT
FLJ39370 / rs17044137 / SNPstream / 6 / Forward Primer: TTCACTGTAGCTTGAATTATTAGAAGTT
Reverse Primer: ATTTATAATTTCAGGAGATTGCTGTAG
SBE Primer: GCGGTAGGTTCCCGACATATGTAATAGTAAAAATTACCTCCACGA
NOTCH2 / rs10923931 / SNPstream / 5,9 / Forward Primer: TCACCTCCATGCTGATCTTT
Reverse Primer: AATTATAGGCGTGAGCCACC
SBE Primer: GACCTGGGTGTCGATACCTACTTGTTGCTCCATCCTCTGGCTTCA
CDKN2B / rs564398 / SNPstream / 2,4,5,7 / Forward Primer: AAAGATGATGGTTTCCCAAAC
Reverse Primer: TCCTCTCATCTGATCTCCGT
SBE Primer: GTGATTCTGTACGTGTCGCCTGGCACATACCACACCCTAACTACC
TCF7L2 / rs7903146 / SNPstream / 2,3,5-8,10 / Forward Primer: AGAAGATTCCTTTTTAAATGGTGAC
Reverse Primer: GTCTGAAAACTAAGGGTGCCT
SBE Primer: AGGGTCTCTACGCTGACGATTAGAGAGCTAAGCACTTTTTAGATA
LOC387761 / rs7480010 / SNPstream / 7,8 / Forward Primer: AATTAGTTTTGAAAGAGAACAGATGAC
Reverse Primer: TTTTAAGGAGATTTACCTGCATAACT
SBE Primer: GGCTATGATTCGCAATGCTTATCAGTTTGGTGGATAACTCAGATG
CDKAL1 / rs10946398 / SNPstream / 2,4,5 / Forward Primer: TTGAACTGGTTTTTCCTCT
Reverse Primer: TAAGACAAGTGTTCTGATATTAATGCA
SBE Primer: GGATGGCGTTCCGTCCTATTTTTGGGAAAAGGGTTTAGTATCGTT
KCNJ11 / rs5219 / SNPstream / 2,3,5,6 / Forward Primer: GTTGCAGTTGCCTTTCTTG
Reverse Primer: ATCATCCCCGAGGAATACG
SBE Primer: ACGCACGTCCACGGTGATTTCGCTGGCGGGCACGGTACCTGGGCT
TCF7L2 / rs12255372 / Taqman / 3,4,6,10 / Assay ID: C_291484_20
ADAMTS9 / rs4607103 / Taqman / 2,5,9 / Assay ID: C_26129590_10
BCL11A / rs10490072 / Taqman / 9 / Assay ID: C_3216076_10
CDC123 / rs11257622 / Taqman / 5,11 / Assay ID: C_31078212_10
CDKN2AB / rs10811661 / Taqman / 2-4,6,7 / Assay ID: C_31288917_10
DCD / rs1153188 / Taqman / 9 / Assay ID: C_2694176_10
GCK / rs730497 / Taqman / 12 / Assay ID: C_14224_10
HK1 / rs906216 / Taqman / 12 / Assay ID: C_8863422_10
KCNQ1 / rs2237892 / Taqman / 13,14 / Assay ID: C_16171025_10
MTNR1B / rs1387153 / Taqman / 15 / Assay ID: C_1932612_10
MTNR1B / rs10830963 / Taqman / 16,17 / Assay ID: C_3256858_10
PKN2 / rs6698181 / Taqman / 6 / Assay ID: C_30192216_10
THADA / rs7578597 / Taqman / 2,5,9 / Assay ID: C_32653841_10
TSPAN8/LGR5 / rs7961581 / Taqman / 2,5,9 / Assay ID: C_121473_10
VEGFA / rs9472138 / Taqman / 9 / Assay ID: C_11400700_20
WFS1 / rs10010131 / Taqman / 2,5,18 / Assay ID: C_30473796_10
* Studies from which this SNP was selected
Supplementary Table 3: Primer and probe sequences for JAZF1 and BCL11A haplotype block tag SNPs genotyped on the Sequenome platform
rs13034231 / ACGTTGGATGTGCACACATCTGTTGGTAGG / ACGTTGGATGGACACACACATGTGGCTTAC / AAGGCATGCAGAGTT
rs6718203 / ACGTTGGATGTAACATGTATTGGGGTTAGC / ACGTTGGATGTGCCTCGTAAATACTCCCAG / CCCAAACAGCCCCTGAA
rs12468946 / ACGTTGGATGTGGGCCTCAAGGTCTTTATC / ACGTTGGATGCCATCAAAGACTGTAGAAGC / TCCTTATGGGTTGATCC
rs849140 / ACGTTGGATGTGCAATGGAGAGAATGTGGC / ACGTTGGATGGGGAAAGAACTAGGAACAGG / AACAGGTTCTGCATTTG
rs9789627 / ACGTTGGATGGAGCATGGGTACCCAGTAAA / ACGTTGGATGCAGGATTTTTCTGCTTTGGG / AGTTTAATGGCAGGAAGA
rs530649 / ACGTTGGATGCACTTGCATATTTTGCCTG / ACGTTGGATGCGTCTGATGAAAGGTAAAGC / ccACATTCCTATGGCTTCA
rs11520706 / ACGTTGGATGATAAGGCTGATGTGTGAGGG / ACGTTGGATGAATGCTGCCTGTTGTGCTTG / AAGCATTATCAGCTCATGG
rs17331129 / ACGTTGGATGTAAACCAACCACAGGTCGAG / ACGTTGGATGAGAGGTCAGAGATACTTGGG / GGAGGCTGAGTTTGAAATC
rs11894442 / ACGTTGGATGAAACGTTCCCACTAGTCACC / ACGTTGGATGTGTGTGGCTTCTTAGCCATC / GCTTCTTAGCCATCACATTT
rs17156497 / ACGTTGGATGGGCTCTCAGAAAATGTTTGC / ACGTTGGATGGTGGAAGTGTGATGCTTTTT / TTTTATCATTCGCAAAGAGC
rs10276381 / ACGTTGGATGCACCTTCGAATAAAGGCCAC / ACGTTGGATGTAGACACGCTGTCATGACTG / TTTCTTCAAGTTAGATACGGC
rs17402905 / ACGTTGGATGCCAGAGACTCCATTCATCAG / ACGTTGGATGGTCAGGCTAGTGAGGCATAG / GCTAGTGAGGCATAGTTCTAC
rs506154 / ACGTTGGATGCAGAGAATCCAGCTTCTACC / ACGTTGGATGCTGTTGTAACAAATAGGCCC / ttcaAAATAGGCCCAACCTTAC
rs12154248 / ACGTTGGATGCCTTCTTCCTTTTCCTGTCC / ACGTTGGATGGTAGTGATTGAAGAATGAG / ctAAGAATGAGTTATGCAGAGG
rs13034649 / ACGTTGGATGTCCATTTCTGATGCTGGGAG / ACGTTGGATGGCAGATGGAGAATACTGGAG / GGAGAATACTGGAGAGTGAATT
rs8179712 / ACGTTGGATGCCCAGGTGTATAGCCAAAAG / ACGTTGGATGCTACTTTGCGTTTATTGTGAC / ATTGTGACTAATACTGCTATGAA
rs849141 / ACGTTGGATGCCTACAAGAAACTATGGTGC / ACGTTGGATGGCTGACTCTGCAGCTTAATC / gACTTAATCTTACCCCTAAGTAAC
rs864745 / ACGTTGGATGCATTGAACATTTCCTACAACC / ACGTTGGATGCCGTAAGAGCCATATAAGTG / GCTCAAATATAATTTGAACTGTTA
rs17156479 / ACGTTGGATGCACTAAACGACTAGGCCTTG / ACGTTGGATGTCCTACCCTGCTCTAAGTTC / ggtcAGGGCAGGATATAGATGTCT
rs10490072 / ACGTTGGATGCCATTTGGCCACAACATTAG / ACGTTGGATGTGCAGAGAATGCTTCTTTGG / acTCTTTGGTTATGTATATACATGC
rs1011407 / ACGTTGGATGTGGGTGAGCCTGCGGTTATT / ACGTTGGATGTTAAGGAAATCCAGACCTTG / ccagtAAATCCAGACCTTGGCAGTTT
Supplementary Table 4: Effect of SNPs identified in Caucasian GWAS studies with Type 2 diabetes in GENNID AA families. Values indicate genotype relative risks at age 50 for T2D and the decrease (in years) for age of T2D diagnosis (AOD) in heterozygotes for the risk allele.
Nearest gene / SNP rsID / T2D / T2Dadj BMI / T2D
adj WHR / AOD
ADAM30-NOTCH2 / rs2641348 / 1.04 / 1.04 / 1.01 / 0.20
ADAMTS9 / rs4607103 / 1.04 / 1.03 / 1.01 / 0.39
BCL11A / rs10490072 / 1.18 / 1.23 / 1.12 / 2.38
CDC123 / rs11257622 / 1.09 / 1.09 / 1.09 / 0.23
CDKAL1 / rs10946398 / 1.02 / 1.05 / 1.03 / 0.13
CDKN2A/2B / rs10811661 / 1.04 / 1.10 / 1.03 / 1.22
CDKN2B / rs564398 / 1.12 / 1.14 / 1.01 / 0.03
DCD / rs1153188 / 1.02 / 1.00 / 1.00 / 0.15
EXT2 / rs11037909 / 1.01 / 1.05 / 1.05 / 0.26
FLJ39370 / rs17044137 / 1.05 / 1.04 / 1.03 / 0.79
FTO / rs8050136 / 1.07 / 1.04 / 1.00 / 0.64
GCK / rs730497 / 1.01 / 1.00 / 1.01 / 0.50
HHEX / rs1111875 / 1.03 / 1.01 / 1.03 / 0.55
HHEX / rs5015480 / 1.06 / 1.07 / 1.07 / 0.36
HK1 / rs906216 / 1.03 / 1.05 / 1.03 / 0.41
IGF2BP2 / rs4402960 / 1.01 / 1.02 / 1.02 / 0.36
IGF2BP2 / rs1470579 / 1.05 / 1.07 / 1.04 / 0.82
JAZF1 / rs864745 / 1.16 / 1.20 / 1.14 / 0.67
KCNJ11 / rs5219 / 1.05 / 1.03 / 1.05 / 0.63
KCNQ1 / rs2237892 / 1.11 / 1.08 / 1.09 / 0.79
LOC387761 / rs7480010 / 1.01 / 1.00 / 1.00 / 0.55
MTNR1B / rs1387153 / 1.02 / 1.05 / 1.02 / 0.33
MTNR1B / rs10830963 / 1.10 / 1.13 / 1.05 / 0.04
NOTCH2 / rs10923931 / 1.11 / 1.19 / 1.05 / 0.11
PKN2 / rs6698181 / 1.13 / 1.12 / 1.15 / 0.90
SLC30A8 / rs13266634 / 1.06 / 1.18 / 1.16 / 0.57
TCF7L2 / rs7903146 / 1.05 / 1.02 / 1.00 / 0.39
TCF7L2 / rs12255372 / 1.04 / 1.01 / 1.02 / 1.08
THADA / rs7578597 / 1.04 / 1.04 / 1.10 / 0.88
TSPAN8-LGR5 / rs7961581 / 1.14 / 1.14 / 1.07 / 1.60
VEGFA / rs9472138 / 1.11 / 1.10 / 1.09 / 1.55
WFS1 / rs10010131 / 1.12 / 1.15 / 1.13 / 1.11
WHR: waist /hip ratio; AOD: age at onset of diabetes; BMI: body mass index; adj, adjusted for
Supplementary Figures:
Supplementary Figure 1: Linkage Disequilibrium between tag SNPs genotyped within haplotype block that includes T2DM associated index SNPs of JAZF1 and BCL11A region in GENNID pedigrees. Ten SNPs were genotyped for JAZF1 and 11 SNPs were genotyped around BCAL11A haplotype block. Index SNPs are marked by *. Both D’ and r2 values are shown. LD (r2) relationships among all SNPs within haplotype block that includes T2DM associated index SNPs in Hapmap Caucasian (CEU phase II+III) subjects are shown for comparison
Supplementary references:
1. Frayling,T.M. et al. A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Science. 316, 889-894 (2007).
2. Lango,H. et al. Assessing the combined impact of 18 common genetic variants of modest effect sizes on type 2 diabetes risk. Diabetes. 57, 3129-3135 (2008).
3. Scott,L.J. et al. A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science. 316, 1341-1345 (2007).
4. Zeggini,E. et al. Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes. Science. 316, 1336-1341 (2007).
5. Waters,K.M. et al. Consistent association of type 2 diabetes risk variants found in europeans in diverse racial and ethnic groups. PLoS. Genet. 6, e1001078 (2010).
6. Saxena,R. et al. Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science. 316, 1331-1336 (2007).
7. Lewis,J.P. et al. Association analysis in african americans of European-derived type 2 diabetes single nucleotide polymorphisms from whole-genome association studies. Diabetes. 57, 2220-2225 (2008).
8. Sladek,R. et al. A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature. 445, 881-885 (2007).
9. Zeggini,E. et al. Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat. Genet. 40, 638-645 (2008).
10. Grant,S.F. et al. Variant of transcription factor 7-like 2 (TCF7L2) gene confers risk of type 2 diabetes. Nat. Genet. 38, 320-323 (2006).
11. van Hoek,M. et al. Predicting type 2 diabetes based on polymorphisms from genome-wide association studies: a population-based study. Diabetes. 57, 3122-3128 (2008).
12. Pare,G. et al. Novel association of HK1 with glycated hemoglobin in a non-diabetic population: a genome-wide evaluation of 14,618 participants in the Women's Genome Health Study. PLoS. Genet. 4, e1000312 (2008).
13. Yasuda,K. et al. Variants in KCNQ1 are associated with susceptibility to type 2 diabetes mellitus. Nat. Genet. 40, 1092-1097 (2008).
14. Unoki,H. et al. SNPs in KCNQ1 are associated with susceptibility to type 2 diabetes in East Asian and European populations. Nat. Genet. 40, 1098-1102 (2008).
15. Bouatia-Naji,N. et al. A variant near MTNR1B is associated with increased fasting plasma glucose levels and type 2 diabetes risk. Nat. Genet. 41, 89-94 (2009).
16. Lyssenko,V. et al. Common variant in MTNR1B associated with increased risk of type 2 diabetes and impaired early insulin secretion. Nat. Genet. 41, 82-88 (2009).
17. Prokopenko,I. et al. Variants in MTNR1B influence fasting glucose levels. Nat. Genet. 41, 77-81 (2009).
18. Sandhu,M.S. et al. Common variants in WFS1 confer risk of type 2 diabetes. Nat. Genet. 39, 951-953 (2007).