subjects agreed to participate in the EDIC follow-up study [2].

Transcription

1 Supplementary Table 1. Subject recruitment and assessments in different studies Study Type Subject/Measurement Details DCCT/EDIC T1D Subjects 1,441 subjects aged between 13 and 39 with T1D were recruited between1983 and 1989 in DCCT. The primary cohort included subjects with 1-5 years of diabetes; no pre-existing retinopathy; normal albuminuria; fasting and stimulated C-peptide 0.2 and 0.5 pmol/ml respectively. The secondary cohort included subjects with 1-15 years of diabetes; pre-existing mild retinopathy; albumin excretion rate < 200 mg/24 h; fasting C-peptide 0.2; and for patients with diabetes duration 1-5 and 5-15 years stimulated C-peptide 0.5 and 0.2 pmol/ml, respectively. [1]. They were randomly assigned to intensive or conventional treatment groups and were monitored until 1994 on average for 6.5 years (ranged between 3-10 years). After completion of DCCT, 1,375 subjects agreed to participate in the EDIC follow-up study [2]. Genotyping In a single center using Illumina 1M BeadArray (Illumina, San Diego, CA, USA); randomization of the samples on plates was not based on SIF measurement or its value [3]. SF Duplicate measurements of SIF were obtained from the underside of the left forearm near the elbow using SCOUT DS SF spectrometer (Miraculins, MB, Canada) in 1,185 EDIC subjects during 2010 to 2011 (EDIC years 16-17). Skin was excited with light emitting diodes (LEDs) centered at 375, 405, 416, 435 and 456 nm; and detected over the emission ranged from 435 to 655 nm with the reflectance corrected for factors affecting light absorption (e.g melanin and hemoglobin) and scattering (subject-specific), and adjusted by the dimensionless excitation (kx) and emission (km) exponents. The intraday Hoorn coefficient of variation was 4.2%, and the between-measurement correlation was (R2 = 0.927), which explains 7.3% of the total variance in the SIF1 measurement. The first SIF measurement per subject was used for the analyses [4, 5]. Skin tone is measured using the white LED which emits light over the 435 to 655 nm portion of the spectrum. Skin tone is computed by summing the measured white LED reflectance of the subject's skin over the 435 to 655 nm region, nominally giving skin tone values that range from 35 (very dark skin) to 500 (very fair skin). In the intrinsic correction formula, the white LED reflectance is scaled by Km and used on a wavelength by wavelength basis to correct the measured skin fluorescence (i.e. white LED reflectance at 490 nm corrects skin fluorescence at 490 nm, white LED reflectance at 495 nm corrects skin fluorescence at 495 nm, etc). HbA1c HbA1c was measured at the eligibility visit, every three months during DCCT and annually during EDIC [1, 2]. Time-weighted HbA1c was calculated by summing (DCCT eligibility HbA1c x duration of diabetes at DCCT baseline), (DCCT mean HbA1c x years of follow-up in DCCT) and (EDIC mean HbA1c x years of follow-up in EDIC); and dividing by total duration of diabetes. GA GA was measured in a case-cohort subpopulation of the DCCT including 497 subjects as described before [6]. In brief, 250 subjects were randomly selected from the DCCT cohort providing more than 145 control subjects for each of the diabetic complications (i.e. retinopathy, nephropathy and

2 cardiovascular diseases (CVD)) as well as some cases for each complication. Additional cases were drawn at random from the reminder of the cohort to provide a total of 145 retinopathy and 145 nephropathy cases. All 127 known cases of CVD at the time were selected. GA was measured on stored, frozen sera collected at each DCCT annual visit between 1983 and % of the expected GA values were missing. To address the missing data, multiple imputation was employed to provide 10 estimates of each missing value [6]. BG 7- point capillary blood glucose profiles (before breakfast, lunch and dinner; 90 minutes after breakfast, lunch and dinner; and at bedtime) were obtained every 3 months in DCCT for all subjects [7]. 12.4% of the expected BG values were missing. To address the missing data, multiple imputation was employed to provide 5 estimates of each missing value [6]. egfr Creatinine was measured annually during DCCT and EDIC, and egfr was calculated using the Chronic Kidney Disease Epidemiology Collaboration equation [8]. Retinopathy Seven-field stereoscopic fundus photography was performed every 6 months during DCCT and 2-4 times over 10 years during EDIC. Severe non-proliferative diabetic retinopathy or worse was defined as Early Therapy Diabetic Retinopathy Study (ETDRS) level of 53/<53 or worse, or a history of panretinal photocoagulation (scatter laser) treatment. Retinopathy status for each patient was ascertained at the last follow-up visit. Participants without retinopathy or with milder forms of retinopathy not reaching this level were considered as controls. Skin biopsy measured AGEs In a subset of DCCT participants (n=216), skin biopsies were obtained from the medial region of the right buttock about 8cm below the iliac crest at or near close-out. Subsequently, collagen linked AGEs (furosine, pentosidine, Nε-carboxymethyl-lysine (CML), glucosepane, glyoxal and methylglyoxal hydroimidazolones (G-H1 and MG-H1) and fructose-lysine(fl)); protein-linked (long wavelength (LW)) fluorescence (excitation/emission: 370/440 nm), LW-1; and collagen cross-linking variables (acid and pepsin solubility) levels were measured [9-11]. WESDR T1D Subjects Diabetic patients who received primary care in an 11-county area in southern Wisconsin from 1979 to 1980 were observed for diabetic complications [12, 13]. The subjects were all younger-onset individuals diagnosed before 32 years of age and treated with insulin (T1D individuals). These subjects were followed for up to 30 years and examined at baseline (WESDR1) and follow-up years 4, 10, 14, 20, 25 and 32 (WESDR2-7). Genotyping In the Centre for Applied Genomics (TCAG), The Hospital for Sick Children, Toronto, ON, Canada ( using Illumina HumanOmni1 Quad BeadChip assay (Illumina, San Diego, CA, USA); randomization of the samples on plates was not based on SIF measurement or its value [14]. SF Measurements of SIF were obtained from the underside of both forearms using the SCOUT DS SF spectrometer (Miraculins, MB, Canada) during the year 30 follow-up in 301 subjects, similar to DCCT/EDIC [4, 5]. Mean of the 2 measurements was used for the current analyses.

3 HbA1c HbA1 was measured at eligibility; and 4, 10 and 14 year follow-ups which were then converted to HbA1c. HbA1c was measured at 20, 25 and 30 year follow-ups [13]. Time-weighted HbA1c was calculated by summing (eligibility HbA1c x duration of diabetes at baseline) and (mean HbA1c during the study x years of follow-up); and dividing by total duration of diabetes. egfr Creatinine was measured approximately every 5 years through the study and egfr was calculated using the Chronic Kidney Disease Epidemiology Collaboration equation [8]. Retinopathy Seven-field stereoscopic fundus film photography was performed at baseline and approximately at 4,10,14 25 and 32 years from baseline in WESDR. Severe non-proliferative diabetic retinopathy or worse was defined as DCCT/EDIC. LonGenity ND/T2D Subjects Ashkenazi Jewish adults age 65 and older were recruited to explore why some people enjoy extremely long life spans with physical health and brain function far better than expected in the 9th and 10th decades of life. They were defined as either OPEL (having at least one parent who lived to age 95 or older) or OPUS (neither parent survived to age 95) [15]. Genotyping In a single center using HumanOmniExpress (Illumina, San Diego, CA, USA); randomization of the samples on plates was not based on SIF measurement or its value [16]. SF SIF was measured using the SCOUT DS SF spectrometer (Miraculins, MB, Canada) at the baseline or wave 1 exam similar to DCCT/EDIC and WESDR [4, 5]. LifeLines ND/T2D Subjects Subjects were recruited from the inhabitants of the northern part of the Netherlands and their families between 2006 and 2013 in the LifeLines, a large population-based cohort study and biobank. Genotyping In a single center using Illumina CytoSNP-12v2 array (Illumina, San Diego, CA, USA); randomization of the samples on plates was not based on SIF measurement or its value [17]. SF SAF was measured with the AGE Reader (DiagnOptics Technologies BV, Groningen, the Netherlands) at three different sites of the same forearm at baseline for subjects above the age of 18 years. The excitation light source used a peak at 370 nm; and emitted and reflected light were measured by spectrometer measures over nm and nm, respectively. SAF was calculated from the ratio between the emitted and the reflected light taking skin color into account [16]. Mean of the 3 measurements was used in the current analyses.

4 Supplementary Table 2. Association of environmental and genetic factors with SIF1/SAF in DCCT/EDIC, WESDR, LonGenity and LifeLines DCCT/EDIC WESDR LonGenity LifeLines T1D T1D OPEL, ND OPUS, ND OPEL+OPUS, T2D ND T2D Covariate β (SE) R2 β (SE) R2 β (SE) R2 β (SE) R2 β (SE) R2 β (SE) R2 β (SE) R2 Age (0.001) (0.001) (0.003) (0.002) (0.003) (0.000) (0.003) Sex (Female) (0.012) (0.026) (0.028) (0.023) (0.048) (0.010) (0.065) Smoking status (0.003)* (0.047) (0.030) (0.025) (0.050) (0.011) (0.086) (0.004) (0.003) Skin tone (0.0001) (0.000) (0.000) (0.000) (0.001) Clinic latitude (South) (0.014) egfr (0.001) (0.001) (0.001) (0.001) (0.001) (0.000) (0.001) BMI (0.001) (0.006) All covariates Time-weighted HbA1c (0.006) (0.014) (0.015) (0.029) All covariates + HbA1c All covariates + HbA1c rs (NAT2) All covariates + HbA1c rs rs SIF: Skin intrinsic fluorescence, SAF: Skin auto fluorescence, T1D: Type 1 diabetes, T2D: Type 2 diabetes, ND: Non-diabetic, egfr: estimated glomerular filtration rate, BMI: Body mass index β and SEs are based on univariable analysis. * Smoking status during EDIC year 1-5 as a continuous variable (min = 0, max = 5) calculated by summing smoking status (smoker=1, non-smoker = 0) in EDIC year 1-5 Mean of smoking status (smoker=1, non-smoker = 0) asked every 5 years through the study Smoking status during EDIC year 6-10 as a continuous variable (min = 0, max = 5) calculated by summing smoking status (smoker=1, non-smoker = 0) in EDIC year 6-10 Smoking status during EDIC year as a continuous variable (min = 0, max = 6) calculated by summing smoking status (smoker=1, non-smoker = 0) in EDIC year 11-1 DCCT/EDIC: Mean egfr trough DCCT/EDIC calculated using annually measured serum creatinine and the Chronic Kidney Disease Epidemiology Collaboration equation [8]; WESDR: Mean egfr trough WESDR calculated using serum creatinine measured every 5 years and the Chronic Kidney Disease Epidemiology Collaboration equation [8]; LonGenity: egfr calculated using serum creatinine and the Chronic Kidney Disease Epidemiology Collaboration equation [8]; LifeLines: Cockcroft Gault egfr

5 Time-weighted in DCCT/EDIC (calculated by summing (DCCT eligibility HbA1c x duration of diabetes at DCCT baseline), (DCCT mean HbA1c x years of follow-up in DCCT) and (EDIC mean HbA1c x years of follow-up in EDIC); and dividing by total duration of diabetes) and WESDR ( ]calculated by summing (eligibility HbA1c x duration of diabetes at baseline) and (mean HbA1c during the study x years of followup); and dividing by total duration of diabetes) ; single measurement in LifeLines

6 Supplementary Table 3. Details of the statistical tests and models used for testing association of the identified SNP with other related phenotypes Phenotype Study Measurement Covariates Interaction Terms Statistical Test Covariates DCCT/EDIC Age, smoking status, skin tone, egfr - - Linear regression Sex, latitude - - Logistic regression WESDR Age, smoking status, skin tone, egfr - - Linear regression Sex - - Logistic regression HbA1c DCCT/EDIC Time-weighted HbA1c* - - Linear regression WESDR Time-weighted HbA1c* - - Linear regression DCCT/EDIC Time-weighted HbA1c* LnSIF1 - Linear regression WESDR Time-weighted HbA1c* LnSIF1 - Linear regression DCCT HbA1c at Eligibility and Mean HbA1c - - Linear regression EDIC Mean HbA1c - - Linear regression WESDR HbA1c at Eligibility and each follow-up - - Linear regression GA DCCT Mean GA Treatment group - Linear regression Mean GA Treatment group, 3 indicators - Linear regression regarding retinopathy, nephropathy and CVD status Mean GA Treatment group, LnSIF1 - Linear regression Mean GA Treatment group, retinopathy status SNP-retinopathy status Linear regression Mean GA Treatment group, nephropathy SNP-nephropathy status Linear regression status Mean GA Treatment group, CVD status SNP-CVD status Linear regression 7-point capillary BG DCCT Mean of all BG measurements taken within a day Treatment group - Linear regression across all time points Repeated measures of pre-prandial (mean of prebreakfast, Treatment group - Linear mixed models lunch and dinner) Repeated measures of post-prandial (mean of postbreakfast, Treatment group - Linear mixed models lunch and dinner) Nephropathy EDIC Sustained AER 30 mg/24 h at EDIC years 13/ Logistic regression and 15/16 [5] DCCT/EDIC Repeated egfr - SNP-time Linear mixed models DCCT/EDIC Slope of change in egfr over time [18, 19] * - - Linear regression WESDR Slope of change in egfr over time [18, 19] * - - Linear regression CACTI Slope of change in egfr over time [18, 19] * - - Linear regression RASS Slope of change in egfr over time [18, 19] * - - Linear regression Retinopathy DCCT/EDIC Sever NPDR or worse* - - Logistic regression WESDR Sever NPDR or worse* - - Logistic regression DCCT/EDIC Time since the start of study to the first development - - Complementary log-log model of sever NPDR or worse* WESDR Time since the start of study to the first development - - complementary log-log model of sever NPDR or worse* Neuropathy EDIC Cardiac autonomic neuropathy in EDIC years - - Logistic regression 16/17[5] EDIC Confirmed clinical neuropathy in EDIC year 13/14[5] - - Logistic regression CAC EDIC CAC in EDIC year 12 [5] - - Logistic regression Hypoglycemia DCCT Episode/s of hypoglycemia requiring assistance Treatment group - Logistic regression DCCT Episode/s of hypoglycemia resulting in coma Treatment group - Logistic regression Skin biopsy AGEs DCCT Pepsin soluble collagen, acid soluble collagen, fluorescence, furosine, pentosidine, Nεcarboxymethyl-lysine, carboxyethyl-lysine, methylglyoxal hydroimidazolones, glyoxal Age, duration of diabetes, treatment group - Linear regression

7 hydroimidazolones, fructose-lysine, glucosepane, total Glucose Bound, LW1 egfr: Estimated glomerular filtration rate, SIF: Skin intrinsic fluorescence, GA: Glycated albumin, CVD: Cardiovascular disease, BG: Blood glucose, AER: Albumin excretion rate, NPDR: Non-proliferative diabetic retinopathy, CAD: Coronary artery calcification, AGE: Advanced glycation end products, * The results regarding association of the SNP with each outcome in different studies were then combined through meta-analysis using METAL v1.5 with STDERR method. Natural log transformed. The test was performed in all imputed datasets. Subsequently, the results were averaged using Rubin and Schenker s method [20]. At two consecutive visits at EDIC years 13/14 and 15/16 [5] CACTI: Coronary Artery Calcification in Type 1 Diabetes (CACTI), an observational population-based study of type 1 diabetes subjects and non-diabetic subjects recruited between March 2000 and April 2002 [21]. RASS: Renin-Angiotensin System Study, a 5-year multicenter, randomized, double-blind, placebo-controlled investigator-initiated trial comparing effects of enalapril and losartan with those of placebo on early renal structural changes from diabetic nephropathy in type 1 diabetes [22].

8 Supplementary Table 4. Spearman Correlation coefficient of SIFs in DCCT/EDIC (above the diagonal line) and WESDR (below the diagonal line) SIF1 SIF2 SIF3 SIF4 SIF5 SIF6 SIF7 SIF8 SIF9 SIF10 SIF11 SIF12 SIF13 SIF14 SIF15 SIF SIF SIF SIF SIF SIF SIF SIF SIF SIF SIF SIF SIF SIF SIF SIF: Skin intrinsic fluorescence The p-value for all correlations is <

9 Supplementary Table 5. Association of rs with covariates and HbA1c in DCCT/EDIC and WESDR DCCT/EDIC WESDR Covariate β (SE)/OR(95% CI) p β (SE)/OR(95% CI) p Sex (Female) (0.466, 1.600) (0.911, ) Latitude (South) (0.550, 2.336) Age (1.099) (2.469) Smoking status (0.272)* (0.078) (0.249) (0.277) Skin tone (6.495) (13.073) Mean egfr (1.592) (5.655) Time-weighted HbA1c (0.147) (0.261) egfr: estimated glomerular filtration rate * Smoking status during EDIC year 1-5 as a continuous variable (min = 0, max = 5) calculated by summing smoking status (smoker=1, non-smoker = 0) in EDIC year 1-5 Mean of smoking status (smoker=1, non-smoker = 0) asked every 5 years through the study Smoking status during EDIC year 6-10 as a continuous variable (min = 0, max = 5) calculated by summing smoking status (smoker=1, non-smoker = 0) in EDIC year 6-10 Smoking status during EDIC year as a continuous variable (min = 0, max = 6) calculated by summing smoking status (smoker=1, non-smoker = 0) in EDIC year DCCT/EDIC: Mean egfr trough DCCT/EDIC calculated using annually measured serum creatinine and the Chronic Kidney Disease Epidemiology Collaboration equation [8]; WESDR: Mean egfr trough WESDR calculated using serum creatinine measured every 5 years and the Chronic Kidney Disease Epidemiology Collaboration equation [8] Time-weighted in DCCT/EDIC (calculated by summing (DCCT eligibility HbA1c x duration of diabetes at DCCT baseline), (DCCT mean HbA1c x years of follow-up in DCCT) and (EDIC mean HbA1c x years of follow-up in EDIC); and dividing by total duration of diabetes) and WESDR (calculated by summing (eligibility HbA1c x duration of diabetes at baseline) and (mean HbA1c during the study x years of follow-up); and dividing by total duration of diabetes)

10 Supplementary Table 6. Interaction of rs with covariates/phenotypes on SIF1 in DCCT/EDIC Phenotype β (SE)* p Cohort (0.053) Treatment Group (Intensive) (0.053) Further Adjusted for Time-weighted HbA1c (0.051) Caffeine Mean during DCCT (0.0001) 2.66E-4 Mean during EDIC (0.0001) Sex (Female) (0.053) Age (0.003) Skin Tone (0.001) Latitude (0.062) Smoking Status EDIC Year (0.015) EDIC Year (0.014) EDIC Year (0.014) Mean egfr (0.002) HbA1c DCCT Eligibility (0.015) Mean during DCCT (0.019) Mean during EDIC (0.023) Time-weighted (0.024) egfr: estimated glomerular filtration rate * The effect estimate and SE regarding the interaction term. Age; sex; smoking status during EDIC year 1-5, 6-10 and 11-16; clinic latitude; skin tone and mean egfr were included in the model as covariates.

11 Supplementary Table 7. Interaction of rs with covariates/phenotypes on SIF1 in WESDR Phenotype β (SE)* p Sex (Female) (0.113) Age (0.005) Skin Tone (0.053) Smoking Status (0.215) Mean egfr (0.003) HbA1c WESDR (0.026) WESDR (0.031) WESDR (0.058) WESDR (0.036) WESDR (0.057) WESDR (0.050) WESDR (0.048) Time-weighted (0.044) NS: Not significant (p > 0.05), egfr: estimated glomerular filtration rate * The effect estimate and SE regarding the interaction term. Age, sex, smoking status, skin tone and mean egfr were included in the model as covariates.

12 Supplementary Table 8. Association of time-weighted HbA1c with SIF1-15 in DCCT/EDIC and WESDR DCCT/EDIC WESDR SIF β (SE) p R Square β (SE) P R Square SIF (0.006) 6.75E (0.014) 4.53E SIF (0.008) 2.82E (0.018) 4.00E SIF (0.006) 2.49E (0.013) 4.25E SIF (0.007) 3.94E (0.015) 3.45E SIF (0.007) 1.52E (0.015) 4.54E SIF (0.007) 7.15E (0.016) 7.59E SIF (0.007) 1.37E (0.015) 2.66E SIF (0.008) 5.86E (0.016) 4.40E SIF (0.008) 3.90E (0.014) 4.06E SIF (0.008) 1.17E (0.016) 3.23E SIF (0.008) 4.14E (0.015) 1.70E SIF (0.008) 3.56E (0.015) 2.48E SIF (0.007) 1.48E (0.016) 1.55E SIF (0.007) 2.53E (0.015) 8.87E SIF (0.007) 1.69E (0.015) 1.17E Association of time-weighted HbA1c with natural log transformed skin intrinsic fluorescence (SIF) was tested using linear regression.

13 Supplementary Table 9. Association of rs with HbA1c at different time points in DCCT/EDIC and WESDR Study Time N Beta (SE) p DCCT/EDIC Eligibility (0.249) DCCT Mean (0.218) EDIC Mean (0.163) WESDR Baseline (0.511) Year (0.496) Year (0.428) Year (0.409) Year (0.438) Year (0.374) Year (0.346)

14 Supplementary Table 10. Association of mean glycated albumin during DCCT with SIF1 in all ten imputed datasets Imputed Dataset Beta SE P Average Association of glycated albumin with LnSIF1 was tested using linear regression adjusting for treatment group in all 10 imputed datasets. It was restricted to 364 subjects having both slycated albumin and SIF data. The results were averaged using Rubin and Schenker s method [20]. SIF: Skin intrinsic fluorescence

15 Supplementary Table 11. Association of rs with mean glycated albumin during DCCT (natural log transformed) in all ten imputed datasets in DCCT Adjusted for Treatment Group Adjusted for Treatment Group and 3 Indicators Regarding each Case-control Status Adjusted for Treatment Group, 3 Indicators Regarding each Case-control Status and LnSIF1 Imputed Dataset Beta SE P Beta SE P Beta SE P Average* * The results were averaged using Rubin and Schenker s method [20].

16 Supplementary Table 12. Association of rs with diabetic complications and hypoglycemia required assistant/resulting in coma in DCCT/EDIC Complication N (Cases/Controls) N (Total) OR (95% CI) p Power* Sustained AER > 30 mg/24 hr 285/ (0.449, 1.763) Presence of confirmed clinical neuropathy 303/ (0.361, 1.337) Presence of cardiac autonomic neuropathy 341/ (0.484, 1.722) CAC > 0 Agatston units 288/ (0.522, 2.164) CAC > 200 Agatston units 72/ (0.198, 1.378) Hypoglycemia requiring assistance 550/ (0.373, 1.369) Hypoglycemia resulting in coma 310/ (0.682, 3.140) AER: albumin excretion rate, CAC: Coronary artery calcium * The statistical power is calculated using QUANTO v1.2.4 ( for each complication, with α = 0.05, minor allele frequency of 0.02, population risk = N cases/ N (total), genetic effect of estimated OR, and N (total) individuals under an additive genetic model.

17 Supplementary Table 13. Association of rs (T>C) with estimated slope of change in egfr Study N Years of Follow-up Mean (SD) N of Observations/Person Median (Max) INFO MAF Beta (SE) P DCCTEDIC 1, (4) 22 (26) (0.140) WESDR (6) 4 (5) Genotyped (0.225) CACTI (2) 3 (3) (0.314) RASS (0.3) 3 (3) Genotyped (0.341) Meta-analysis 2, (0.106) egfr: Estimated glomerular filtration rate, MAF: Minor allele frequency

18 Supplementary Table 14. Association of rs (T>C) with non-proliferative diabetic nephropathy or worse Case/Control Analysis Time to Event Analysis Study Case/Control β (SE) P N β (SE) P WESDR 309/ (0.454) (0.272) DCCT, Primary Cohort 53/ (0.710) (0.548) DCCT, Secondary Cohort, Conventional Therapy 114/ (0.676) (0.466) DCCT, Secondary Cohort, Intensive Therapy 42/ (1.390) (1.050) Meta-analysis 518/1, (0.308) 0.658* 1, (0.213) * There is almost 100% statistical power to detect genetic effect of 0.14 with α = 0.05, minor allele frequency of 0.02, population risk = 0.27, and 1,907 individuals under an additive genetic model calculated using QUANTO v1.2.4 (

19 Supplementary Table 15. Association of skin biopsy measured AGEs with SIF1 Univariable Multivariable Skin AGE N Median (25th, 75th Percentile) β (SE) P R square β(se) P Pepsin soluble collagen (%) (4.43, 8.04) (0.0046) 9.00E (0.0048) 5.61E-02 Acid soluble collagen (%) (0.35, 0.63) (0.0484) 4.68E (0.0464) 8.21E-01 Fluorescence (AU) (154.02, ) (0.0003) 1.00E (0.0003) 1.97E-01 Furosine (pmol/mg collagen) (596.66, ) (0.0001) 5.20E (0.0001) 2.66E-05 Pentosidine (pmol/mg collagen) (19.28, 32.83) (0.0016) 1.96E (0.0024) 5.25E-01 Nε-carboxymethyl-lysine (pmol/mg collagen) (87.80, ) (0.0001) 3.71E (0.0001) 9.21E-01 Carboxyethyl-lysine (pmol/mg) (75.38, ) (0.0002) 4.61E (0.0001) 5.61E-01 Methylglyoxal hydroimidazolones (nmol/mg) (0.50, 0.94) (0.0348) 3.22E (0.0345) 5.69E-01 Glyoxal hydroimidazolones (pmol/mg) (42.20, 82.11) (0.0005) 2.90E (0.0005) 8.79E-02 Fructose-lysine (nmol/mg) (4.06, 6.50) (0.0073) 4.90E (0.0075) 1.75E-05 Glucosepane (nmol/mg) (1.96, 3.15) (0.0185) 1.62E (0.0232) 6.26E-04 Total Glucose Bound (fructose-lysine plus glucosepane) (6.29, 9.14) (0.0060) 4.20E (0.0062) 6.47E-06 LW (237.00, ) (0.0001) 3.00E (0.0001) 9.95E-02 Association of skin biopsy measured AGEs with LnSIF1 was tested using linear regression. Multivariable analysis was adjusted for age, duration of diabetes and treatment group. AGE: Advanced glycation end products, SIF: Skin intrinsic fluorescence

20 Supplementary Table 16. Association of rs with HbA1c, lipid levels, risk of type 2 diabetes and coronary artery disease based on publicly available meta- GWAS data Phenotype Effect Allele N (Cases) N (Controls) N (Total) β/or (SE/95% CI) P Source HbA1c T , (0.012) HDL C , (0.018) LDL T , (0.021) TC T , (0.020) TG T , (0.019) T2D C 8,782 30, ( ) CAD C 16,590 52, (0.067) The data is accessed in Jan HDL: High-density lipoprotein, LDL: Low-density lipoprotein, TC: Total cholesterol, TG: Triglycerides, T2D: Type 2 diabetes, CAD: Coronary artery disease

21 Supplementary Figure 1. The study design GWAS: Genome-wide association study, T1D: Type 1 diabetes, SIF: skin intrinsic fluorescence, SAF: Skin auto fluorescence, ND: Non-diabetic, T2D: Type 2 diabetes, GA: glycated albumin, BG: Blood glucose, AGE: Advanced glycation end products

22 Supplementary Figure 2. The QQ-plot DCCT/EDIC, WESDR and meta-analysis A. B. C. D. The quantiles of observed versus expected -log 10 (p-values) regarding SNP (Chr1-22 genotyped and imputed SNPs with a minor allele frequency of > 0.01 and an INFO > 0.80) associations with LnSIF1 were plotted. A: DCCT/EDIC adjusted for sex, age, smoking status, skin tone, clinic latitude, mean estimated glomerular filtration rate (egfr) and NAT2 genotype; B: WESDR adjusted for sex, age, smoking status, skin tone, mean egfr and NAT2 genotype; C: DCCT/EDIC and WESDR meta-analysis; D: DCCT/EDIC and WESDR meta-analysis further adjusted for rs genotype

23 Supplementary Figure 3. The Manhattan plot DCCT/EDIC and WESDR meta-gwas A. DCCT/EDIC and WESDR meta-gwas B. DCCT/EDIC and WESDR meta-gwas adjusted for rs The Manhattan plot for the LnSIF1 DCCT/EDIC and WESDR meta-gwas shows -log 10 (p-values) (y-axis) of SNPs plotted against their chromosomal positions (x-axis). The red horizontal line represents the genome-wide significant threshold (p = 5x10-8) and the blue line represents suggestive association threshold (p = 1x10-5 ). A: DCCT/EDIC and WESDR meta-analysis (N = 7,735,748); B: DCCT/EDIC and WESDR meta-analysis further adjusted for rs genotype (N = 7,735,746)

24 Supplementary Figure 4. Genotype Clusters for rs in WESDR The cluster plot for rs shows polar coordinates, where x=0 represent a pure T-allele signal and x=1 represents a pure C-allele signal and the y-axis represents the distance of the point to the origin (intensity for allele T = intensity for allele C). Red, purple and blue circles represent the TT, TC and CC genotype groups, respectively. A clear separation of rs genotypes can be seen for participants in WESDR.

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