BMI = Body Mass Index SD = Standard Deviation

Supplementary Table 1a: Comparison of characteristics between the 4750 included in the analysis and 8929 liveborn singletons not included in the analysis – continuous variables

Included in analysis Not included in analysis N Mean SD N Mean SD Maternal height (cm) 4560 164.4 6.7 7399 163.7 6.8 Maternal pre-pregnancy BMI (kg/m2) 4337 22.8 3.7 6942 23.0 3.9 Paternal height (cm) 3472 176.5 6.8 4546 175.6 7.2 Paternal BMI at time of pregnancy (kg/m2) 3448 25.1 3.2 4476 22.3 3.4 Maternal age in pregnancy (y) 4750 29.2 4.5 8928 27.3 5.1 Gestation (weeks) 4750 39.5 1.8 8928 39.4 2.0 Birthweight (kg) 4689 3.4 0.5 8816 3.4 0.6 Energy intake at 38 months (kJ/day) 4281 5206.9 1240.1 5299 5283.2 1397.1 BMI = body mass index SD = standard deviation

Supplementary Table 1b: Comparison of characteristics between the 4750 included in the analysis and 8929 liveborn singletons not included in the analysis – categorical variables Categories Included in Not included analysis in analysis N % N % Parity 0 2277 49.2 3411 42.5 1 1599 34.6 2811 35.0 ≥ 2 750 16.2 1807 22.5 Social class in pregnancy V 121 2.7 379 5.6 IV 565 12.7 1185 17.5 III manual 1123 25.2 2127 31.3 III non-manual 1235 27.7 1578 23.2 II 1218 27.4 1338 19.7 I 190 4.3 183 2.7 Maternal education None/CSE 511 11.1 1936 25.8 Vocational 361 7.8 837 11.1 O levels 1604 34.7 2601 34.6 A levels 1313 28.4 1419 18.9 Degree 837 18.1 721 9.6 Gender Male 2267 47.7 4795 53.7 Female 2483 52.3 4131 46.3

1 Supplementary Table 2: Associations between maternal/paternal smoking at the time of pregnancy and body composition at age 15 – additional analyses

Minimally adjusted1 – Fully adjusted2 – Complete confounder Additionally adjusted for data only pubertal status  (95% CI) P value  (95% CI) P value Outcome = fat mass at 15 years (SD score) Separately Maternal smoking 0.17 0.08, 0.25 <0.001 0.16 0.08, 0.25 <0.001 Paternal smoking 0.12 0.05, 0.19 <0.001 0.08 0.01, 0.15 0.02 Simultaneously Maternal smoking 0.12 0.03, 0.22 0.01 0.14 0.04, 0.23 0.004 Paternal smoking 0.10 0.03, 0.17 0.01 0.07 -0.01, 0.14 0.07 Outcome = lean mass at 15 years (SD score) Separately Maternal smoking 0.06 0.01, 0.11 0.02 0.07 0.02, 0.12 0.01 Paternal smoking 0.03 -0.01, 0.07 0.1 0.02 -0.02, 0.05 0.4 Simultaneously Maternal smoking 0.05 0.002, 0.10 0.04 0.07 0.01, 0.12 0.01 Paternal smoking 0.02 -0.02, 0.06 0.4 0.001 -0.04, 0.04 0.9 CI = confidence interval 1 Adjusted for gender, age at time of 15y clinic, height 2Additionally adjusted for parental factors, social factors, birthweight and gestation

Supplementary Table 3: Fully adjusted1 regression coefficients for the association between maternal/paternal smoking (considered simultaneously) and body composition at age 15, assuming various proportions of non-paternity, with p values for differences in parental effects

Rate of non-paternity Paternal Maternal P-value for smoking smoking difference Outcome = fat mass at 15 years (SD score) 0.00 0.06 0.13 0.3 0.05 0.07 0.13 0.3 0.10 0.08 0.13 0.5 0.15 0.09 0.12 0.6 0.20 0.10 0.12 0.8 Outcome = lean mass at 15 years (SD score) 0.00 0.01 0.07 0.1 0.05 0.01 0.07 0.1 0.10 0.01 0.07 0.1 0.15 0.003 0.07 0.08 0.20 0.001 0.07 0.07 1 Adjusted for gender, age at time of 15y clinic, height, parental factors, social factors, birthweight and gestation

2 3 Supplementary Table 4: Associations between early feeding, diet and physical inactivity in infancy, and body composition at age 15 – additional analyses

Separate models Minimally adjusted1 – Fully adjusted2 – Complete confounder Additionally adjusted for data only pubertal status  (95% CI) P value  (95% CI) P value Outcome = fat mass at 15 years (SD score) Breastfeeding Partial 0.09 0.02, 0.15 0.01 -0.06, 0.07 (vs exclusive) None 0.18 0.08, 0.28 <0.001 0.03 -0.08, 0.13 0.6 Age at introduction to 3m -0.09 -0.18, 0.004 0.01 -0.08, 0.11 solids(vs ≤ 2 months) ≥ 4m -0.16 -0.26, -0.06 0.001 0.01 -0.10, 0.11 0.995 Dietary pattern at 38 months 0.11 0.07, 0.15 <0.001 0.06 0.02, 0.10 0.01 (factor loading):junk Dietary pattern at 38 months -0.04 -0.07, -0.001 0.3 0.004 -0.03, 0.04 0.8 (factor loading):healthy Dietary pattern at 38 months 0.03 -0.002, 0.6 0.06 -0.003 0.03, 0.03 0.8 (factor loading):traditional Dietary pattern at 38 months -0.03 -0.07, 0.01 0.2 -0.02 -0.06, 0.03 0.5 (factor loading):fussy/snack Time spent in car at 38 4-5 h/w 0.05 -0.03, 0.12 0.02 -0.05, 0.10 months (vs <4 h/w) >5 h/w 0.15 0.05, 0.25 0.002 0.09 -0.01, 0.18 0.1 Time spent watching 4.1-8 h/w 0.13 -0.05, 0.20 0.07 -0.001, 0.15 television at 38 months > 8 h/w 0.26 0.17, 0.34 <0.001 0.16 0.07, 0.24 <0.001 (vs ≤ 4 h/w) Frequency playing computer 1/m -0.02 -0.10, 0.07 -0.03 -0.11, 0.06 games at 57 months 1/w 0.08 -0.005, 0.15 0.04 -0.04, 0.12 (vs rarely/not at all) 2-7/w 0.02 -0.07, 0.11 0.2 0.01 -0.08, 0.10 0.5 Outcome = lean mass at 15 years (SD score) Breastfeeding Partial 0.02 -0.01, 0.06 0.01 -0.03, 0.04 (vs exclusive) None 0.01 -0.05, 0.06 0.5 -0.06 -0.12, -0.005 0.1 Age at introduction to 3m -0.02 -0.08, 0.03 -0.01 -0.06, 0.04 solids(vs ≤ 2 months) ≥ 4m -0.01 -0.07, 0.05 0.97 0.04 -0.02, 0.10 0.03 Dietary pattern at 38 months -0.01 -0.03, 0.01 0.2 -0.03 -0.05, -0.01 0.01 (factor loading):junk Dietary pattern at 38 months 0.02 0.002, 0.04 0.03 0.03 0.01, 0.05 0.002 (factor loading):healthy Dietary pattern at 38 months 0.01 -0.04, 0.03 0.1 0.005 -0.01, 0.02 0.6 (factor loading):traditional Dietary pattern at 38 months 0.004 -0.02, 0.03 0.7 0.001 -0.02, 0.02 0.96 (factor loading):fussy/snack Time spent in car at 38 4-5 h/w -0.005 -0.05, 0.04 -0.01 -0.05, 0.03 months (vs <4 h/w) >5 h/w 0.04 -0.02, 0.09 0.3 0.04 -0.02, 0.09 0.4 Time spent watching 4.1-8 h/w 0.003 -0.04, 0.05 -0.02 -0.07, 0.02 television at 38 months > 8 h/w -0.01 -0.05, 0.04 0.8 -0.05 -0.10, -0.01 0.03 (vs ≤ 4 h/w) Frequency playing computer 1/m 0.01 -0.03, 0.06 -0.02 -0.07, 0.03 games at 57 months 1/w 0.04 -0.01, 0.08 0.02 -0.02, 0.07 (vs rarely/not at all) 2-7/w 0.04 -0.005, 0.09 0.04 0.04 -0.01, 0.09 0.09 CI = confidence interval 1 Adjusted for gender, age at time of 15y clinic, height (plus energy intake at 38 months for dietary patterns) 2Additionally adjusted for parental factors, social factors, birthweight and gestation

4 Supplementary Table 5: Associations between trimester-specific maternal smoking variables and body composition at age 15, with simultaneous adjustment for all exposures1

Separate fully adjusted models2 Outcome = fat mass Outcome = lean at 15 years (SD score) mass at 15 years (SD score)  (95% CI) P value  (95% CI) P value Maternal smoking in 1st trimester 0.14 0.04, 0.24 0.01 0.07 0.01, 0.12 0.02 Maternal smoking in 2nd trimester 0.13 0.02, 0.24 0.03 0.07 0.04, 0.13 0.04 Maternal smoking in 3rd trimester 0.18 0.07, 0.30 0.002 0.10 0.04, 0.17 0.002 CI = confidence interval 1Separate models for each trimester-specific maternal smoking variable included instead of the combined maternal smoking variable 2 Adjusted for gender, age at time of 15y clinic, height, parental factors, social factors, birthweight and gestation (plus energy intake at 38 months for dietary patterns)

5 Supplementary Table 6: Associations between all exposures simultaneously, and BMI at age 15

Simultaneous fully adjusted models1 Outcome = BMI at 15 years (SD score)  (95% CI) P value Maternal smoking 0.19 0.08, 0.30 0.001 Paternal smoking 0.09 0.01, 0.18 0.03 Breastfeeding Partial 0.03 -0.05, 0.10 (vs exclusive) None 0.02 -0.10, 0.15 0.4 Age at introduction to solids(vs ≤ 2 3m -0.02 -0.13, 0.10 months) ≥ 4m 0.03 -0.10, 0.16 0.4 Dietary pattern at 38 months (factor 0.04 -0.02, 0.09 0.2 loading):junk Dietary pattern at 38 months (factor 0.04 -0.004, 0.09 0.07 loading):healthy Dietary pattern at 38 months (factor 0.03 -0.01, 0.07 0.09 loading):traditional Dietary pattern at 38 months (factor 0.05 -0.0002, 0.11 0.05 loading):fussy/snack Time spent in car at 38 months 4-5 h/w -0.04 -0.13, 0.05 (vs <4 h/w) >5 h/w 0.09 -0.03, 0.20 0.3 Time spent watching television at 38 4.1-8 h/w 0.01 -0.08, 0.10 months (vs ≤ 4 h/w) > 8 h/w 0.08 -0.03, 0.18 0.1 Frequency playing computer games at 57 1/m -0.005 -0.10, 0.09 months 1/w 0.10 0.003, 0.19 (vs rarely/not at all) 2-7/w 0.07 -0.03, 0.17 0.06 CI = confidence interval 1 Adjusted for gender, age at time of 15y clinic, height, parental factors, social factors, birthweight and gestation (plus energy intake at 38 months for dietary patterns)