Supplementary Information We also studied a subsample of the total Swedish population, the Stockholm Youth Cohort (SYC), for which ascertainment of ASD is based on national register data in addition to regional register data from outpatient, specialist, and treatment centers in Stockholm County. Consequently, while the total Swedish population sample is substantially larger, the SYC subsample has better ASD ascertainment and subtype information regarding comorbid ID. ASD case status as of December 31, 2011 was ascertained according to a validated casefinding approach covering all pathways to ASD diagnosis and care in Stockholm County, described in detail elsewhere.1 In brief, ASD case status was described following ICD-9: 299, ICD-10: F84, and DSM-IV: 299 classifications using: 1) the NPR; and regional registers including; 2) the Habilitation Register; 3) the Clinical Database for Child and Adolescent Psychiatry; 4) the VAL database recording all inpatient and outpatient health services usage in Stockholm County since 1997. The presence of comorbid intellectual disability was based on ICD-9: 317–319, ICD-10: F70–F79, and DSM-IV: 317–319 classifications and supplemented with the Habilitation Register, which categorizes service recipients as having autism with or without ID. Expert review of medical records for 177 ASD cases indicated that 96% were consistent with a diagnosis of ASD.1 The final SYC subsample consisted of 9 545 cases (2 361 with ID) matched to 80 986 controls (20 461 matched to an ID case), with case:control ratio varying from 1:2 to 1:10 (Supplementary Figure 1, Supplementary Table 1). Statistical analysis For the SYC sub-cohort, the outcome variable was stratified as ASD with and without ID and the analyses (Models 1-3, as described in the main text) were repeated. Results In the SYC subsample, maternal diagnosis of PCOS was associated with higher odds of ASD in the unadjusted model, though ORs were attenuated and confidence intervals included one in the adjusted analyses (Supplementary Table 2). After stratifying the outcome on the presence or absence of comorbid intellectual disability, we did not observe a striking difference between the two diagnostic groups, though ORs were higher for ASD with ID (Supplementary Table 2). 1 Idring S, Rai D, Dal H, Dalman C, Sturm H, Zander E et al. Autism Spectrum Disorders in the Stockholm Youth Cohort: Design, Prevalence and Validity. Plos One 2012; 7(7). Figures and tables for supplementary information Supplementary Figure 1: Derivation of the analytical Stockholm Youth Cohort sample. The Stockholm Youth Cohort Residents in Stockholm, 0-17 years old, born 1984-2011 N = 735 096 ASD cases N = 11 330 Case-Control sampling 10 sampled controls for every case N = 11 330 ASD cases N = 113 300 controls Excluded Not born in Sweden, born after 2007, adopted children, multiple births, or matched to such cases N = 1 659 ASD cases N = 30 386 controls Excluded Missing covariate data, or matched to such cases N = 126 ASD cases N = 1 928 controls Analytical sample Case:control ratio – 1:2 to 1:10 N = 9 545 ASD cases N = 80 986 controls Supplementary Table 1. Selected characteristics of birth cohorts 1984–2007 of the Stockholm Youth Cohort. Characteristic ASD cases (N = 9 545) n (%) Controls (N = 80 986) n (%) Mother’s country of birth Analysis p 0.081 Sweden 7 345 (77.0) 61 668 (76.1) Other 2 200 (23.0) 19 318 (23.9) Mother 5 702 (59.7) 34 932 (43.1) < 0.001 Father 3 670 (38.4) 22 894 (28.3) < 0.001 Lowest quintile for family income 1 470 (15.4) 11 733 (14.5) < 0.001 Parents with ≤ 9 years of schooling 1 712 (17.9) 12 865 (15.9) < 0.001 Gestational Diabetes 127 (1.3) 755 (0.9) < 0.001 Pre-eclampsia 374 (3.9) 2 406 (3.0) < 0.001 Apgar score <7 at 5 minutes 138 (1.4) 779 (1.0) < 0.001 94 (1.0) 649 (0.8) Parental history of psychiatric care Missing data Gestational age < 0.001 Preterm birth (<37 weeks) 651 (6.8) 3 715 (4.6) Postterm birth (≥42 weeks) 800 (8.4) 6 550 (8.1) Size for gestational age < 0.001 Small for gestational age 388 (4.1) 1 976 (2.4) Large for gestational age 391 (4.1) 2 518 (3.1) Missing data 52 (0.5) 337 (0.4) PCOS 67 (0.7) 389 (0.5) 0.004 Parental age at delivery (years) Mean (SD) Mean (SD) p Maternal 29.74 (5.5) 29.82 (5.2) 0.190 Paternal 32.76 (6.7) 32.75 (6.3) 0.874 Supplementary Table 2. Odds ratios (OR) and 95% confidence interval (CI) of maternal PCOS and autism spectrum disorders in birth cohorts 1984–2007 in the Stockholm Youth Cohort. ASD ASD without ID ASD with ID No PCOS Maternal PCOS No PCOS Maternal PCOS No PCOS Maternal PCOS N Cases (%) 9 478 (99.3) 67 (0.7) 7 135 (99.3) 49 (0.7) 2 343 (99.2) 18 (0.8) N Controls (%) 80 597 (99.5) 389 (0.5) 60 214 (99.5) 311 (0.5) 20 383 (99.6) 78 (0.4) OR Model 1 (CI) Ref. 1.46 (1.12 - 1.89) Ref. 1.33 (0.98 - 1.80) Ref. 1.95 (1.17 – 3.27) OR Model 2 (CI) Ref. 1.29 (0.99 – 1.68) Ref. 1.18 (0.86 – 1.60) Ref. 1.74 (1.04 – 2.93) OR Model 3 (CI) Ref. 1.26 (0.97 – 1.65) Ref. 1.17 (0.86 – 1.59) Ref. 1.62 (0.96– 2.75) Model 1: Unadjusted. Model 2: Adjusted for maternal age, paternal age, parental psychiatric history, household income, parental education, and mother’s country of birth. Model 3: Adjusted as above, with further adjustment for gestational diabetes, Apgar score at 5 minutes, gestational age, size for gestational age, and pre-eclampsia.