Defining the Effect of the 16P11.2 Duplication on Cognition, Behavior, and Medical Comorbidities

Supplementary Online Content D’Angelo D, Lebon S, Chen Q, et al; Cardiff University Experiences of Children With Copy Number Variants (ECHO) study; 16p11.2 European Consortium; Simons Variation in Individuals Project (VIP) Consortium. Defining the effect of the 16p11.2 duplication on cognition, behavior, and medical comorbidities. JAMA Psychiatry. Published online December 2, 2015. doi:10.1001/jamapsychiatry.2015.2123. eMethods. Data Sources and Additional CNVs eResults. Malformations, Medical Problems, and Sex Differences eTable 1. Ascertainment of 16p11.2 Duplication and Deletion Carriers eTable 2. Effect of the Deletion on Global Intelligence and Anthropometric Measures eTable 3. Effect of the Duplication on Full-Scale IQ (FSIQ), Controlling for ASD and Seizures eTable 4. Effect of the Deletion on Full-Scale IQ (FSIQ), Controlling for ASD and Seizures eTable 5. Effect of the Duplication on Nonverbal IQ (NVIQ), Controlling for ASD and Seizures eTable 6. Effect of the Deletion on Nonverbal IQ (NVIQ), Controlling for ASD and Seizures eTable 7. Effect of the Duplication on Verbal IQ (VIQ), Controlling for ASD and Seizures eTable 8. Effect of the Deletion on Verbal IQ (VIQ), Controlling for ASD and Seizures eTable 9. Additional Deleterious CNVs in 16p11.2 Probands Carriers Excluded From the Main Analysis eTable 10. Duplication Inheritance Subanalysis eTable 11. Deletion Inheritance Subanalysis eTable 12. Neurologic Features in 16p11.2 Duplication Carriers According to Ascertainment eTable 13. Neurologic Features in 16p11.2 Deletion Carriers According to Ascertainment eTable 14. Behavioral and Psychiatric Features of 16p11.2 Duplication Carriers eTable 15. Behavioral and Psychiatric Features of 16p11.2 Deletion Carriers eTable 16. Effect of the Duplication on Body Mass Index (BMI) z Score, Controlling for ASD, Seizures, and NVIQ eTable 17. Effect of the Deletion on Body Mass Index (BMI) z Score, Controlling for ASD, Seizures, and NVIQ eTable 18. Effect of the Duplication on Head Circumference (HC) z Score, Controlling for ASD, Seizures, and NVIQ eTable 19. Effect of the Deletion on Head Circumference (HC) z Score, Controlling for ASD, Seizures, and NVIQ eTable 20. Major Malformations and Medical Problems in 16p11.2 Duplication Carriers According to Ascertainment eTable 21. Major Malformations and Medical Problems in 16p11.2 Deletion Carriers According to Ascertainment eTable 22. Duplication Carriers With Multiple Medical Conditions According to Ascertainment eTable 23. Deletion Carriers With Multiple Medical Conditions According to Ascertainment eFigure 1. Distribution of IQ Scores by Region eFigure 2. Full-Scale IQ (FSIQ) in Probands Stratified by Site, Sex, Seizure Status, and HC z Score Above vs Below 0 eFigure 3. Distribution of Additional Deleterious CNVs by Size and Their Numbers of Protein-Coding Genes Included in Duplication and Deletion Carriers eFigure 4. FSIQ of Inherited and De Novo Duplication and Deletion Probands vs Parent FSIQ eFigure 5. Age of Walking in Duplication Proband Carriers vs Deletion Proband Carriers This supplementary material has been provided by the authors to give readers additional information about their work.

Downloaded From: https://jamanetwork.com/ on 09/23/2021 eMethods. Data Sources and Additional CNVs Data sources: Clinical information was collected for a total of 270 duplication carriers ascertained through different cohorts, and 102 of their familial non-carrier controls. Ascertainment of duplication carriers is summarized in Table S1. Most probands were ascertained on the basis of a neurodevelopmental disorder (ND) including developmental delay/intellectual disability (DD/ID) or autism spectrum disorder (ASD) and were identified through genetic testing performed for clinical diagnostic purposes. In a few cases, ascertainment was based on a specific psychiatric diagnosis (schizophrenia or bipolar affective disorder) as well as genotyping of a general population cohort (Estonian Genome Center, University of Tartu: EGCUT).1,2 Individuals were recruited from the 16p11.2 European consortium, the Cardiff University ECHO study in the UK and Simons VIP in the United States, as well as other genetic centers or previously published studies.3-10 All data (including literature) were grouped into EU and USA cohorts for statistical analysis. Deletion carrier comparison group: A sample of 390 16p11.2 deletion carriers (Table S1), some of which were previously published,11 was available for comparison. Data for full-scale intelligence quotient (FSIQ), nonverbal IQ (NVIQ) or verbal IQ (VIQ) were available for n=200, n=205 and n=184 deletion carriers, respectively. These data were compared to n=242, n=242 and n=230 of their intrafamilial controls, respectively. Additional CNVs: Data on additional deleterious CNVs were available for probands ascertained for NDs. Information on these additional variants was provided by different diagnostic platforms with varying resolution (eg. Agilent 44K, 105K, 180K, 244K, 250K; Affymetrix 250K, Illumina Human370CNV and Human OMNIExpress). The group of 142 duplication probands ascertained for NDs (Table S1) was obtained after exclusion of 16 duplication probands carrying an additional deleterious CNV (10.1% second hit rate). The group of 283 deletion probands ascertained for NDs (Table S1) was obtained after exclusion of 15 deletion probands carrying an additional deleterious CNV (5.0% second hit rate) (Supplementary Table S9). We used an independent replication dataset from Signature Genomics showing with 7/65 (10.7%) and 3/107 (2.8%) of additional deleterious CNV in duplication and deletion carriers ascertained for NDs, respectively.

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Malformations and medical problems Major malformations are present in 16.7% (30/180) of duplication probands. Among these 30 probands, 17 had one and 13 had two or more malformations. In relatives, 9/90 (10.0%) have major malformations which are isolated in all cases except one. In probands and relatives ascertained for NDs major malformations are present in 21.6% (24/111) and 10.6% (9/85) of EU and the VIP duplication carriers respectively. Scoliosis, genital and cardiac malformations and are the most frequent medical conditions in duplications (Supplementary Tables S20 and S21). Magnetic resonance imaging (MRI) of the brain in a subset of 86 duplication carriers showed cerebellar hypoplasia and enlarged ventricles as the most frequent findings (15.1% and 11.6%, respectively, Supplementary Table S12). Characteristic facial dysmorphism is absent in duplication carriers. In comparison, major malformations are present in 67/317 (21.1%) deletion proband carriers. Among these 67 probands, 42 had one and 25 had two or more malformations. In relatives, 8/73 (11.0%) have major malformations, four had one and four had two malformations. Like, duplication carriers, scoliosis (secondary to vertebral anomalies in 42.1%), genital and cardiac malformations are the most frequent medical conditions in deletion carriers (Supplementary Table S22). Brain malformations/anomalies are observed in 49.0% (53/108) of a subset of 108 deletion carriers and mainly involve posterior fossa (36/108, 33.3%); among them 11 carriers had Chiari I malformation (11/36, 30.6%, Supplementary Table S13).

Downloaded From: https://jamanetwork.com/ on 09/23/2021 Sex differences We used the Binomial test to assess the equality of gender proportions in each ascertainment group in supplementary Table S1. There are significantly more males among duplication probands (p=0.04), and this is driven by carriers ascertained for NDs (p=0.001). A similar pattern is observed for deletion proband carriers ascertained for NDs (p<0.001). There is no gender difference in other carrier groups. Among duplication families, gender had a significant effect on nonverbal IQ (p=0.04), with males having an average 4-point increase over females. There was no significant effect of gender on verbal IQ (p=0.78), full-scale IQ (p=0.42), BMI z score (p=0.69) or head circumference (HC) z score (p=0.25) (Table 3). In deletion families, there was a similar effect of gender on nonverbal IQ with males higher than females by an average of 3 points (p=0.02). Gender additionally had a significant effect on HC z score, with males having larger average z scores (p<0.001) (Table S2). There was a marginally significant effect of gender on full-scale IQ, again with males higher (p=0.06), but no significant effect on verbal IQ (p=0.71) or BMI z score (p=0.13).

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1. Firmann M, Mayor V, Vidal PM, et al. The CoLaus study: a population-based study to investigate the epidemiology and genetic determinants of cardiovascular risk factors and metabolic syndrome. BMC cardiovascular disorders 2008; 8: 6. 2. Leitsalu L, Haller T, Esko T, et al. Cohort Profile: Estonian Biobank of the Estonian Genome Center, University of Tartu. International journal of epidemiology 2014. 3. Weiss LA, Shen Y, Korn JM, et al. Association between microdeletion and microduplication at 16p11.2 and autism. The New England journal of medicine 2008; 358(7): 667-75. 4. McCarthy SE, Makarov V, Kirov G, et al. Microduplications of 16p11.2 are associated with schizophrenia. Nature genetics 2009; 41(11): 1223-7. 5. Shinawi M, Liu P, Kang SH, et al. Recurrent reciprocal 16p11.2 rearrangements associated with global developmental delay, behavioural problems, dysmorphism, epilepsy, and abnormal head size. Journal of medical genetics 2010; 47(5): 332-41. 6. Fernandez BA, Roberts W, Chung B, et al. Phenotypic spectrum associated with de novo and inherited deletions and duplications at 16p11.2 in individuals ascertained for diagnosis of autism spectrum disorder. Journal of medical genetics 2010; 47(3): 195-203. 7. Bedoyan JK, Kumar RA, Sudi J, et al. Duplication 16p11.2 in a child with infantile seizure disorder. American journal of medical genetics Part A 2010; 152A(6): 1567-74. 8. Pietilainen OP, Rehnstrom K, Jakkula E, et al. Phenotype mining in CNV carriers from a population cohort. Human molecular genetics 2011; 20(13): 2686-95. 9. Laxy M, Holle R, Doring A, Peters A, Hunger M. The longitudinal association between weight change and health-related quality of life: the KORA S4/F4 cohort study. International journal of public health 2014; 59(2): 279-88. 10. Schmidt CO, Watzke AB, Schulz A, Baumeister SE, Freyberger HJ, Grabe HJ. [The lifetime prevalence of mental disorders in north-eastern Germany. What is the influence of earlier mental morbidity on survey participation and prevalence estimates? Results from the SHIP-study]. Psychiatrische Praxis 2013; 40(4): 192-9. 11. Zufferey F, Sherr EH, Beckmann ND, et al. A 600 kb deletion syndrome at 16p11.2 leads to energy imbalance and neuropsychiatric disorders. Journal of medical genetics 2012; 49(10): 660-8.

Downloaded From: https://jamanetwork.com/ on 09/23/2021 eTable 1. Ascertainment of 16p11.2 Duplication and Deletion Carriers

Origin Ascertainment Relationship Duplication Deletion in Family N M/F p- N M/F p- value value European NDs Probands 61 42/19 0.003 123 81/42 <.001 Consortium/ Relatives 29 15/14 0.85 52 24/28 0.58 ECHO study General Probands 12 5/7 0.56 5 2/3 -- Population Relatives 1 1/0 -- 0 -- -- Psychiatry Probands 3 1/2 -- 0 -- -- Relatives 0 -- -- 0 -- -- Literature NDs Probands 2 0/2 -- 14 9/5 0.29

EUROPE EUROPE Relatives 0 -- -- 0 -- -- General Probands 19 6/13 0.11 13 5/8 0.41 Population Relatives 0 -- -- 0 -- -- Obesity Probands 0 -- -- 15 4/11 0.07 Relatives 0 -- -- 0 -- -- Simons VIP NDs Probands 50 28/22 0.40 108 59/49 0.34 Relatives 56 28/28 1.00 18 9/9 1.00 Other NDs Probands 16 11/5 0.13 0 -- -- Genetic Relatives 1 1/0 -- 0 -- -- Centers

USA USA Literature NDs Probands 13 9/4 0.17 38 26/12 0.02 Relatives 3 0/3 - 3 2/1 -- Psychiatry Probands 4 2/2 1.00 1 1/0 -- Relatives 0 -- -- 0 -- -- Probands 180 104/76 0.04 317 187/130 0.001 TOTALS Ascertained 142 90/52 0.001 283 175/108 <.001 for NDs Relatives 90 45/45 1.00 73 35/38 0.73 All Carriers 270 149/121 0.09 390 222/168 0.01 Legend: All carriers of an additional deleterious CNV are excluded from this table and subsequent analyses. Denominators vary depending on missing data for each measure. M/F: Male/female NDs: Neurodevelopmental Disorders. Literature refers to data collected from previously published studies 1,4,15-17,32-34 All data, including literature, were grouped into EU and USA cohorts for statistical analysis.

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FSIQ NVIQ VIQ BMI Z Score HC Z Score (n=442) (n=447) (n=414) (n=596) (n=556)

Estimat p- Estimat p- Estimat p- Estimat p- Estimat p- e valu e valu e valu e valu e value e e e e

Fixed Effects Parameters Interce 106.0 <.00 106.4 <.00 104.4 <.00 0.1 0.77 0.6 0.00 pt 1 1 1 1 Proban -24.1 <.00 -19.2 <.00 -26.2 <.00 0.8 <.001 0.5 0.00 d 1 1 1 1 Carrier vs. Non- Carrier Pediatri -21.6 <.00 -16.9 <.00 -22.4 <.00 0.6 0.09 0.4 0.24 c 1 1 1 Carrier Relativ e vs. Non- Carrier Adult -20.8 <.00 -20.9 <.00 -16.6 <.00 0.8 0.02 0.7 <.00 Carrier 1 1 1 1 Relativ e vs. Non- Carrier EU vs. -13.9 <.00 -12.4 <.00 -10.1 <.00 0.4 0.03 -0.4 0.02 USA 1 1 1 Age 0.1 0.01 0.2 0.00 0.1 0.43 0.03 <.001 -0.003 0.45 (Years) 1 Female -2.5 0.06 -3.1 0.02 -0.6 0.71 -0.2 0.13 -0.4 <.00 vs. 1 Male Additional Contrasts Carrier -22.1 <.001 -19.0 <.00 -21.8 <.00 0.7 0.001 0.5 <.00 † vs. 1 1 1 Non- Carrier Proban -2.4 0.46 -2.3 0.48 -3.8 0.30 0.2 0.54 0.2 0.52 d Carrier vs. Pediatri c Carrier Relativ e Proban -3.3 0.33 1.6 0.63 -9.6 0.03 0.1 0.78 -0.2 0.52 © 2015 American Medical Association. All rights reserved. 7

Downloaded From: https://jamanetwork.com/ on 09/23/2021 d Carrier vs. Adult Carrier Relativ e Pediatri -0.9 0.84 4.0 0.36 -5.8 0.27 -0.1 0.76 -0.4 0.32 c vs. Adult Carrier Relativ e FSIQ = Full-Scale IQ; NVIQ = Non-Verbal IQ; VIQ = Verbal IQ; BMI = Body Mass Index; HC = Head Circumference. † Carriers include proband carriers (individuals ascertained for a neurodevelopmental disorder), pediatric carrier relatives (mostly siblings of the probands), and adult carrier relatives (this group mostly represents transmitting parents)

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Controlling for Controlling for Controlling for ASD Seizures ASD & Seizures (n=247) (n=252) (n=246)

Estimate p- Estimate p- Estimate p-value value value

Fixed Effects Parameters Intercept 99.4 <.001 97.7 <.001 99.2 <.001 Proband Carrier vs. Non-Carrier -21.7 <.001 -22.9 <.001 -19.2 <.001 Pediatric Carrier Relative vs. Non-Carrier -15.3 <.001 -16.1 <.001 -15.1 <.001 Adult Carrier Relative vs. Non-Carrier -11.7 <.001 -11.5 <.001 -11.8 <.001 EU vs. USA -13.3 0.001 -13.5 0.001 -13.5 <.001 Age (Years) 0.2 0.001 0.3 <.001 0.3 <.001 Female vs. Male -2.3 0.21 -1.9 0.31 -2.6 0.15 ASD Yes vs. No -19.6 <.001 -- -- -17.7 <.001 Seizures Yes vs. No -- -- -16.3 0.001 -12.6 <.001

Additional Contrasts Carrier† vs. Non-Carrier -16.2 <.001 -16.8 <.001 -15.4 <.001 Proband Carrier vs. Pediatric Carrier -6.4 0.11 -6.8 0.10 -4.1 0.30 Relative Proband Carrier vs. Adult Carrier -10.0 0.01 -11.5 0.002 -7.4 0.04 Relative Pediatric vs. Adult Carrier Relative -3.6 0.43 -4.6 0.34 -3.3 0.48 † Carriers include proband carriers (individuals ascertained for a neurodevelopmental disorder), pediatric carrier relatives (mostly siblings of the probands), and adult carrier relatives (this group mostly represents transmitting parents) -- Denotes covariate not entered in the model

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Controlling for Controlling for Controlling for ASD Seizures ASD & Seizures (n=430) (n=442) (n=430)

Estimate p- Estimate p- Estimate p- value value value

Fixed Effects Parameters Intercept 106.1 <.001 106.0 <.001 106.1 <.001 Proband Carrier vs. Non-Carrier -23.3 <.001 -24.1 <.001 -23.3 <.001 Pediatric Carrier Relative vs. Non-Carrier -21.0 <.001 -21.6 <.001 -20.9 <.001 Adult Carrier Relative vs. Non-Carrier -20.0 <.001 -20.7 <.001 -20.0 <.001 EU vs. USA -14.5 <.001 -14.1 <.001 -14.6 <.001 Age (Years) 0.1 0.01 0.1 0.01 0.1 0.01 Female vs. Male -2.5 0.06 -2.5 0.06 -2.5 0.06 ASD Yes vs. No -4.6 0.13 -- -- -4.6 0.13 Seizures Yes vs. No -- -- 1.7 0.75 0.7 0.91

Additional Contrasts Carrier† vs. Non-Carrier -21.4 <.001 -22.1 <.001 -21.4 <.001 Proband Carrier vs. Pediatric Carrier -2.3 0.51 -2.5 0.46 -2.3 0.51 Relative Proband Carrier vs. Adult Carrier Relative -3.2 0.34 -3.4 0.31 -3.3 0.34 Pediatric vs. Adult Carrier Relative -0.9 0.83 -1.0 0.83 -1.0 0.83 † Carriers include proband carriers (individuals ascertained for a neurodevelopmental disorder), pediatric carrier relatives (mostly siblings of the probands), and adult carrier relatives (this group mostly represents transmitting parents) -- Denotes covariate not entered in the model

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Controlling for Controlling for Controlling for ASD Seizures ASD & Seizures (n=245) (n=251) (n=245)

Estimate p- Estimate p- Estimate p- value value value

Fixed Effects Parameters Intercept 101.8 <.001 100.1 <.001 101.6 <.001 Proband Carrier vs. Non-Carrier -23.0 <.001 -23.7 <.001 -20.8 <.001 Pediatric Carrier Relative vs. Non-Carrier -16.2 <.001 -16.6 <.001 -16.2 <.001 Adult Carrier Relative vs. Non-Carrier -15.0 <.001 -14.9 <.001 -15.1 <.001 EU vs. USA -13.6 <.001 -14.2 <.001 -13.7 <.001 Age (Years) 0.3 0.001 0.3 <.001 0.3 <.001 Female vs. Male -4.9 0.01 -4.3 0.03 -5.0 0.01 ASD Yes vs. No -18.3 <.001 -- -- -16.5 <.001 Seizures Yes vs. No -- -- -15.3 0.001 -12.4 0.01

Additional Contrasts Carrier† vs. Non-Carrier -18.1 <.001 -18.4 <.001 -17.3 <.001 Proband Carrier vs. Pediatric Carrier -6.8 0.08 -7.1 0.08 -4.6 0.24 Relative Proband Carrier vs. Adult Carrier Relative -8.0 0.03 -8.8 0.02 -5.7 0.12 Pediatric vs. Adult Carrier Relative -1.2 0.79 -1.7 0.72 -1.1 0.81 † Carriers include proband carriers (individuals ascertained for a neurodevelopmental disorder), pediatric carrier relatives (mostly siblings of the probands), and adult carrier relatives (this group mostly represents transmitting parents) -- Denotes covariate not entered in the model

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Controlling for Controlling for Controlling for ASD Seizures ASD & Seizures (n=435) (n=447) (n=435)

Estimate p-value Estimate p-value Estimate p-value

Fixed Effects Parameters

Intercept 106.4 <.001 106.4 <.001 106.4 <.001 Proband Carrier vs. Non-Carrier -18.6 <.001 -19.2 <.001 -18.6 <.001 Pediatric Carrier Relative vs. Non-Carrier -16.5 <.001 -16.9 <.001 -16.6 <.001 Adult Carrier Relative vs. Non-Carrier -20.3 <.001 -20.9 <.001 -20.4 <.001 EU vs. USA -13.2 <.001 -12.4 <.001 -13.1 <.001

Downloaded From: https://jamanetwork.com/ on 09/23/2021 Age (Years) 0.2 0.001 0.2 0.001 0.2 0.001 Female vs. Male -3.1 0.02 -3.1 0.02 -3.1 0.02 ASD Yes vs. No -3.4 0.24 -- -- -3.4 0.25 Seizures Yes vs. No -- -- -1.0 0.88 -2.4 0.75

Additional Contrasts Carrier† vs. Non-Carrier -18.5 <.001 -19.0 <.001 -18.5 <.001 Proband Carrier vs. Pediatric Carrier Relative -2.1 0.54 -2.3 0.48 -2.1 0.56 Proband Carrier vs. Adult Carrier Relative 1.7 0.63 1.7 0.62 1.8 0.61 Pediatric vs. Adult Carrier Relative 3.8 0.40 4.0 0.36 3.9 0.39 † Carriers include proband carriers (individuals ascertained for a neurodevelopmental disorder), pediatric carrier relatives (mostly siblings of the probands), and adult carrier relatives (this group mostly represents transmitting parents) -- Denotes covariate not entered in the model

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Controlling for Controlling for Controlling for ASD Seizures ASD & Seizures (n=217) (n=223) (n=217)

Estimate p-value Estimate p-value Estimate p-value

Fixed Effects Parameters

Intercept 100.3 <.001 98.4 <.001 100.0 <.001 Proband Carrier vs. Non-Carrier -19.8 <.001 -19.7 <.001 -16.5 <.001 Pediatric Carrier Relative vs. Non-Carrier -14.8 <.001 -15.2 0.01 -14.5 0.004 Adult Carrier Relative vs. Non-Carrier -5.9 0.11 -6.6 0.09 -6.5 0.08 EU vs. USA -7.8 0.12 -8.8 0.07 -8.0 0.09 Age (Years) 0.1 0.17 0.2 0.03 0.1 0.10 Female vs. Male -0.02 0.99 0.5 0.82 -0.04 0.99 ASD Yes vs. No -21.6 <.001 -- -- -18.8 <.001 Seizures Yes vs. No -- -- -22.5 <.001 -17.6 0.002

Additional Contrasts

Carrier† vs. Non-Carrier -13.5 <.001 -13.8 <.001 -12.5 <.001 Proband Carrier vs. Pediatric Carrier Relative -5.0 0.29 -4.5 0.37 -2.0 0.67 Proband Carrier vs. Adult Carrier Relative -13.9 0.002 -13.1 0.01 -10.1 0.03 Pediatric vs. Adult Carrier Relative -8.9 0.11 -8.6 0.14 -8.1 0.15 † Carriers include proband carriers (individuals ascertained for a neurodevelopmental disorder), pediatric carrier relatives (mostly siblings of the probands), and adult carrier relatives (this group mostly represents transmitting parents) -- Denotes covariate not entered in the model

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Controlling for Controlling for Controlling for ASD Seizures ASD & Seizures (n=404) (n=414) (n=404)

Estimate p- Estimate p- Estimate p- value value value

Fixed Effects Parameters Intercept 104.5 <.001 104.4 <.001 104.5 <.001 Proband Carrier vs. Non-Carrier -25.8 <.001 -26.2 <.001 -25.7 <.001 Pediatric Carrier Relative vs. Non-Carrier -20.9 <.001 -22.4 <.001 -21.0 <.001 Adult Carrier Relative vs. Non-Carrier -16.3 <.001 -16.6 <.001 -16.3 <.001 EU vs. USA -10.7 <.001 -9.9 <.001 -10.4 <.001 Age (Years) 0.1 0.43 0.1 0.44 0.1 0.44 Female vs. Male -0.6 0.69 -0.6 0.70 -0.6 0.69 ASD Yes vs. No -3.3 0.32 -- -- -3.2 0.35 Seizures Yes vs. No -- -- -3.8 0.65 -5.5 0.56

Additional Contrasts Carrier† vs. Non-Carrier -21.0 <.001 -21.8 <.001 -21.0 <.001 Proband Carrier vs. Pediatric Carrier -4.9 0.21 -3.8 0.30 -4.7 0.22 Relative Proband Carrier vs. Adult Carrier Relative -9.5 0.03 -9.6 0.03 -9.4 0.04 Pediatric vs. Adult Carrier Relative -4.6 0.40 -5.8 0.28 -4.7 0.39 † Carriers include proband carriers (individuals ascertained for a neurodevelopmental disorder), pediatric carrier relatives (mostly siblings of the probands), and adult carrier relatives (this group mostly represents transmitting parents) -- Denotes covariate not entered in the model

Downloaded From: https://jamanetwork.com/ on 09/23/2021 eTable 9. Additional Deleterious CNVs in 16p11.2 Probands Carriers Excluded From the Main Analysis

16p11.2 probands ID Chr CNV Size (Kb) Genes* Gene symbols Boundaries (Hg19)

Cohort Dup/Del Proximal Distal

EU and USA Dup 169 22 18894634 21505557 3 2,610 68 SEPT5, AIFM3, ARVCF, BCRP2, C22ORF29, probands C22ORF39, CDC45, CLDN5, CLTCL1, ascertained for COMT, CRKL, DGCR10, DGCR11, DGCR14, NDs DGCR2, DGCR6, DGCR6L, DGCR8, DGCR9, GGT2, GNB1L, GSC2, HIRA, KLHL22, LINC00896, LOC100652736, LOC100996415, LOC101927859, LOC101928891, LOC284865, LOC388849, LOC400891, LOC729444, LZTR1, MED15, MIR1286, MIR1306, MIR185, MIR3618, MIR4761, MIR649, MRPL40, P2RX6, P2RX6P, PI4KA, PI4KAP1, PRODH, RANBP1, RIMBP3, RTN4R, SCARF2, SERPIND1, SLC25A1, SLC7A4, SNAP29, TANGO2, TBX1, THAP7, THAP7-AS1, TMEM191A, TRMT2A, TSSK2, TUBA3FP, TXNRD2, UFD1L, USP41, ZDHHC8, ZNF74 174 3 67617261 69018938 1 1,401 4 FAM19A1, FAM19A4, LOC101927090, SUCLG2 176 15 66907197 69434853 1 2,527 21 AAGAB, ANP32A, C15ORF61, CALML4, CLN6, CORO2B, FEM1B, IQCH, IQCH-AS1, ITGA11, LINC00277, MAP2K5, MIR4312, NOX5, PIAS1, RNU6-1, RP11-34F13.2, SKOR1, SMAD3, SMAD6, SPESP1 209 2 205354258 208993534 1 3,639 30 AC007383.4, SNORD51, SNORA41, MIR3130-1, MIR2355, AC007879.2, ENSG00000223725, MIR1302-4, MIR4775, AC083900.1, PARD3B, NRP2, INO80D, NDUFS1, EEF1B2, GPR1, ZDBF2, ADAM23, DYTN, MDH1B, FASTKD2, CPO, KLF7, CREB1, METTL21A, CCNYL1, FZD5, PLEKHM3, CRYGD, CRYGC

Downloaded From: https://jamanetwork.com/ on 09/23/2021 253 15 30938215 32438943 1 1,500 10 ARHGAP11B, FAN1, MTMR10, TRPM1, KLF13, OTUD7A, CHRNA7, HERC2P10, MIR211, RP11-16E12.1 315 9 140447749 140954147 1 506 8 MIR602, RP11-188C12.3, DPH7, ZMYND19, ARRDC1, C9ORF37, EHMT1, CACNA1B 324 10 46390000 51490000 1 5,100 57 GDF2, GDF10, PTPN20B, FAM25C, FRMPD2, MAPK8, BMS1P1, RP11- 342C24.8, FAM35BP, ARHGAP22, RP11- 38L15.3, LINC00842, BMS1P2, CTSLP7, RHEBP2, RP11-292F22.5, ANTXRLP1, WDFY4, FRMPD2P1, BMS1P5, CTGLF12P, MIR4294, FAM170B-AS1, LRRC18, VSTM4, FAM170B, C10ORF128, C10ORF71, DRGX, ERCC6, PGBD3, ERCC6-PGBD3, CHAT, SLC18A3, C10ORF53, OGDHL, PARG, AGAP8, TIMM23B, AGAP7, PTPN20A, SYT15, GPRIN2, NPY4R, ANXA8L1, FAM25B, AGAP10, ANTXRL, ANXA8L2, AL603965.1, FAM21B, AGAP9, FAM25G, ANXA8, AL591684.1, ZNF488, RBP3 349 19 3894861 4948627 1 1,053 38 MIR637, SNORD37, MIR4746, MIR7-3HG, MIR7-3, MIR4747, ATCAY, NMRK2, DAPK3, EEF2, PIAS4, ZBTB7A, MAP2K2, CREB3L3, SIRT6, ANKRD24, EBI3, CCDC94, SHD, TMIGD2, FSD1, STAP2, MPND, SH3GL1, CHAF1A, UBXN6, HDGFRP2, PLIN4, PLIN5, LRG1, SEMA6B, TNFAIP8L1, C19ORF10, DPP9, FEM1A, TICAM1, PLIN3, ARRDC5 385 X 1 155000000 3 1,550e05 1024 459 1 146507711 148321790 1 1,701 23 LOC728989, LOC100505794, PDIA3P1, LINC00624, PDZK1P1, RNVU1-9, LOC100505824, LOC101929325, RNVU1-10, RNVU1-12, RNVU1-14, PRKAB2, FMO5, CHD1L, BCL9, ACP6, GJA5, GJA8, GPR89B, PPIAL4A, NBPF14, PPIAL4D, NBPF20 536 12 31287233 31393164 3 105 1 RP11-551L14.1 616 22 18844632 21822774 3 2,978 72 DGCR9, DGCR10, DGCR11,

Downloaded From: https://jamanetwork.com/ on 09/23/2021 LOC100652736, MIR4761, MIR185, MIR3618, MIR1306, LOC284865, LINC00896, MIR1286, LOC100996415, PI4KAP1, TMEM191A, LOC101928891, THAP7-AS1, TUBA3FP, MIR649, P2RX6P, BCRP2, FAM230C, DGCR6, PRODH, DGCR2, DGCR14, TSSK2, GSC2, SLC25A1, CLTCL1, HIRA, C22ORF39, MRPL40, UFD1L, CDC45, CLDN5, SEP5, GP1BB, TBX1, GNB1L, C22ORF29, TXNRD2, COMT, ARVCF, TANGO2, DGCR8, TRMT2A, RANBP1, ZDHHC8, LOC388849, RTN4R, DGCR6L, GGT2, RIMBP3, LOC101927859, USP41, ZNF74, SCARF2, KLHL22, MED15, PI4KA, SERPIND1, SNAP29, CRKL, AIFM3, LZTR1, THAP7, P2RX6, SLC7A4, LOC400891, GGT2, RIMBP3B, HIC2 626 16 32442304 33795687 1 1,353 76 TP53TG3, TP53TG3C, RP11-812E19.9, TP53TG3B, N/A 709 X 31574736 31843530 1 268 1 DMD NA 12 86462752 86635187 1 172 1 MGAT4C 9 71549398 71737562 3 188 NA 17 14129050 15422557 3 1,294 4 PIP5K1B, PRKACG, FXN, TJP2 Del 93 15 28725507 30701432 3 1,975 12 MGC12916, LOC101928475, CDRT7, CDRT8, MIR4731, CDRT15, HS3ST3B1, PMP22, TEKT3, CDRT4, TVP23C-CDRT4, TVP23C 198 10 527212 2417608 1 1,890 19 GOLGA8G, GOLGA8M, APBA2, FAM189A1, NDNL2, TJP1, GOLGA8J, GOLGA8T, CHRFAM7A, GOLGA8R, MIR4509-2, HERC2P9, WHAMMP2, LOC100289656, LOC101929232, GOLGA6L7P, LOC100130111, ULK4P3, DKFZP434L187 257 NA NA NA NA NA NA NA 363 9 39140222 47041104 3 7,900 14 RP11-809C18.3, MIR5699, IDI2-AS1, LINC00200, ADARB2-AS1, LINC00700, LINC00701, DIP2C, LARP4B, GTPBP4, IDI2,

Downloaded From: https://jamanetwork.com/ on 09/23/2021 IDI1, WDR37, ADARB2 550 7 72740000 74140000 3 1,400 29 ZNF658B, FAM74A3, LOC101927448, LOC101927475, KGFLP2, FAM95B1, LOC101930147, LOC100133920, RP11- 327I22.6, RP11-475I24.8, FAM27E, KGFLP1, RP11-475I24.8, MGC21881, LOC100126582, CNTNAP3, SPATA31A1, SPATA31A2, SPATA31A3, ZNF658, SPATA31A4, SPATA31A5, ANKRD20A2, CBWD7, FOXD4L2, ANKRD20A3, SPATA31A6, CNTNAP3, LOC101928102 666 NA NA NA NA NA NA NA 912 4 175419993 179029682 1 3,609 28 MIR4284, LINC00035, MIR590, AC083884.8, TRIM50, FKBP6, FZD9, BAZ1B, BCL7B, TBL2, MLXIPL, VPS37D, DNAJC30, WBSCR22, STX1A, ABHD11, CLDN3, CLDN4, WBSCR27, WBSCR28, ELN, LIMK1, EIF4H, LAT2, RFC2, CLIP2, GTF2IRD1, GTF2I 929 14 86755058 88749387 1 1,994 5 RP11-300J18.1, LINC01146, GALC, GPR65, KCNK10 1053 9 131441494 132655410 3 1,214 33 RP11-545E17.3, RP11-247A12.2, RP11- 344B5.2, LINC00963, RP11-483H20.6, SET, PKN3, ZDHHC12, ZER1, TBC1D13, ENDOG, C9ORF114, CCBL1, LRRC8A, PHYHD1, DOLK, NUP188, SH3GLB2, FAM73B, DOLPP1, CRAT, PPP2R4, IER5L, NTMT1, C9ORF50, ASB6, PRRX2, PTGES, TOR1B, TOR1A, C9ORF78, USP20, FNBP1 NA X 8532234 19480559 3 10,948 14 TSEN2, RP11-806K15.1, LINC01099, HPGD, GLRA3, ADAM29, GPM6A, WDR17, SPATA4, ASB5, SPCS3, VEGFC, NEIL3, AGA NA X 32890339 32954188 1 64 71 KAL1, FAM9A, FAM9B, TBL1X, GPR143, AC002365.1, WWC3, CLCN4, MID1, HCCS, ARHGAP6, AMELX, MSL3, FRMPD4, PRPS2, TLR7, TLR8, TMSB4X, FAM9C, ATXN3L, EGFL6, TCEANC, RAB9A, TRAPPC2, OFD1, GPM6B, GEMIN8,

Downloaded From: https://jamanetwork.com/ on 09/23/2021 GLRA2, FANCB, MOSPD2, ASB9, ASB11, PIGA, FIGF, PIR, BMX, ACE2, TMEM27, CA5B, ZRSR2, AP1S2, GRPR, MAGEB17, CTPS2, S100G, SYAP1, TXLNG, RBBP7, REPS2, NHS, SCML1, RAI2, BEND2, SCML2, CDKL5, RS1, PPEF1, PHKA2, GPR64, PDHA1, MAP3K15, RP11-120D5.1, MIR548AX, TLR8-AS1, GS1-600G8.3, RP11- 142G7.2, CA5BP1, MIR548AM, MIR4768, RP1-60N8.1, NHS-AS1 NA 1 159343438 161918472 1 2,575 1 DMD NA 15 31140415 32439113 3 1,299 75 LINC01133, RP11-536C5.7, RP11-544M22.1, MIR5187, HSPA7, RPL31P11, OR10J1, OR10J5, APCS, CRP, DUSP23, FCRL6, SLAMF8, C1ORF204, VSIG8, CCDC19, TAGLN2, IGSF9, SLAMF9, PIGM, KCNJ10, KCNJ9, IGSF8, ATP1A2, ATP1A4, CASQ1, PEA15, DCAF8, PEX19, COPA, NCSTN, NHLH1, VANGL2, SLAMF6, CD84, SLAMF1, CD48, SLAMF7, LY9, CD244, ITLN1, ITLN2, F11R, TSTD1, USF1, ARHGAP30, PVRL4, KLHDC9, PFDN2, NIT1, DEDD, UFC1, USP21, PPOX, B4GALT3, ADAMTS4, NDUFS2, FCER1G, APOA2, TOMM40L, NR1I3, PCP4L1, MPZ, SDHC, C1ORF192, FCGR2A, HSPA6, FCGR3A, FCGR2B, FCGR2C, FCGR3B, FCRLA, FCRLB, DUSP12, ATF6 NA X 121002378 129881323 1 8,879 8 FAN1, MTMR10, TRPM1, KLF13, OTUD7A, CHRNA7, MIR211, LOC101929961 NA 17 80550532 81043894 1 493 28 LOC101928402, RP11-13E5.2, GRIA3, THOC2, XIAP, STAG2, SH2D1A, TENM1, DCAF12L2, DCAF12L1, CXORF64, ACTRT1, SMARCA1, OCRL, APLN, XPNPEP2, SASH3, ZDHHC9, UTP14A, BCORL1, ELF4, AIFM1, RAB33A, ZNF280C, SLC25A14, GPR119, RBMX2, ENOX2 Signature Dup 639 10 81684596 88847381 1 7,162 11 FOXK2, MIR4525, LOC101929552,

Downloaded From: https://jamanetwork.com/ on 09/23/2021 Genomics WDR45B, RAB40B, FN3KRP, FN3K, TBCD, ZNF750, B3GNTL1, METRNL 640 1 195200555 197061228 1 1,860 39 GRID1, WAPAL, OPN4, LDB3, BMPR1A, MBL1P, TMEM254-AS1, LINC00857, MMRN2, LOC101929574, SNCG, ADIRF, FAM25A, GLUD1, LINC00858, RP11- 181F12.1, LOC101929646, RP11-475D12.2, RP11-113E21.1, MIR346, RPAP2, SFTPD, TMEM254, PLAC9, ANXA11, MAT1A, DYDC1, DYDC2, FAM213A, TSPAN14, SH2D4B, NRG3, GHITM, C10ORF99, CDHR1, LRIT2, LRIT1, RGR, CCSER2 641 22 18919941 21939974 3 3,020 10 MIR4735, KCNT2, CFH, CFHR3, CFHR1, CFHR2, CFHR4, CFHR5, F13B, ASPM 648 22 21078946 22467677 1 1,388 73 DGCR9, DGCR10, DGCR11, LOC100652736, MIR4761, MIR185, MIR3618, MIR1306, LOC284865, LINC00896, MIR1286, LOC100996415, PI4KAP1, TMEM191A, LOC101928891, THAP7-AS1, TUBA3FP, MIR649, P2RX6P, BCRP2, FAM230C, PRODH, DGCR2, DGCR14, TSSK2, GSC2, SLC25A1, CLTCL1, HIRA, C22ORF39, MRPL40, UFD1L, CDC45, CLDN5, SEPT5, GP1BB, TBX1, GNB1L, C22ORF29, TXNRD2, COMT, ARVCF, TANGO2, DGCR8, TRMT2A, RANBP1, ZDHHC8, LOC388849, RTN4R, DGCR6L, GGT2, RIMBP3, LOC101927859, USP41, ZNF74, SCARF2, KLHL22, MED15, PI4KA, SERPIND1, SNAP29, CRKL, AIFM3, LZTR1, THAP7, P2RX6, SLC7A4, LOC400891, GGT2, RIMBP3B, HIC2, RIMBP3C, UBE2L3 1135 21 15484229 28820560 1 13,336 33 LOC101928891, THAP7-AS1, TUBA3FP, MIR649, P2RX6P, BCRP2, FAM230C, MIR301B, MIR130B, PRAMENP, PI4KA, SERPIND1, SNAP29, CRKL, AIFM3, LZTR1, THAP7, P2RX6, SLC7A4, LOC400891, GGT2, RIMBP3B, HIC2, RIMBP3C, UBE2L3,

Downloaded From: https://jamanetwork.com/ on 09/23/2021 YDJC, CCDC116, SDF2L1, PPIL2, YPEL1, MAPK1, PPM1F, TOP3B 1142 1 59608994 65195483 1 5,586 44 MIR548X, LINC00320, LINC00317, AP000475.2, AP000472.2, LINC00308, D21S2088E, AP000469.2, LIPI, RBM11, LOC339622, HSPA13, SAMSN1, LOC388813, NRIP1, LINC00158, MIR155HG, LINC00515, USP25, LOC100996571, MIR4759, CXADR, BTG3, C21ORF91, CHODL, TMPRSS15, NCAM2, MRPL39, JAM2, ATP5J, GABPA, APP, CYYR1, ADAMTS1, ADAMTS5, ABCC13, SAMSN1-AS1, LINC00478, MIR99A, MIRLET7C, MIR125B2, C21ORF91-OT1, CHODL-AS1, AL109763.2 1144 15 22821537 28513316 3 5,691 32 HSD52, MIR4711, RP4-782L23.1, RP11- 436K8.1, RP5-833A20.1, MGC34796, MIR3116-2, RP11-230B22.1, LINC00466, RP11-24J23.2, MIR4794, FGGY, HOOK1, CYP2J2, C1ORF87, NFIA, TM2D1, INADL, L1TD1, KANK4, USP1, DOCK7, ANGPTL3, ATG4C, FOXD3, ALG6, ITGB3BP, EFCAB7, PGM1, ROR1, UBE2U, CACHD1 Del 1104 3 191970863 196336071 1 4,365 103 TUBGCP5, CYFIP1, NIPA2, NIPA1, GOLGA8I, GOLGA8S, GOLGA6L2, MKRN3, MAGEL2, NDN, NPAP1, SNRPN, SNURF, UBE3A, ATP10A, GABRB3, GABRA5, GABRG3, OCA2, HERC2, LOC283683, WHAMMP3, LOC101930157, GOLGA8EP, MIR4508, PWRN2, PWRN1, SNHG14, PWAR5, SNORD108, SNORD109A, SNORD116-1, SNORD116-2, SNORD116-3, SNORD116-5, SNORD116-6, SNORD116-7, SNORD116-8, SNORD116-9, SNORD116-10, SNORD116-11, SNORD116-12, SNORD116- 13, SNORD116-14, SNORD116-15, SNORD116-16, SNORD116-18, SNORD116- 20, SNORD116-23, SNORD116-24, SNORD116-25, SNORD116-26, SNORD116- 27, SNORD116-29, SNORD115-1,

Downloaded From: https://jamanetwork.com/ on 09/23/2021 SNORD115-2, SNORD115-3, SNORD115-4, SNORD115-5, SNORD115-6, SNORD115-8, SNORD115-9, SNORD115-10, SNORD115- 11, SNORD115-12, SNORD115-14, SNORD115-15, SNORD115-16, SNORD115- 17, SNORD115-18, SNORD115-19, SNORD115-20, SNORD115-21, SNORD115- 22, SNORD115-23, SNORD115-24, SNORD115-25, SNORD115-27, SNORD115- 28, SNORD115-29, SNORD115-30, SNORD115-31, SNORD115-32, SNORD115- 33, SNORD115-34, SNORD115-35, SNORD115-36, SNORD115-37, SNORD115- 38, SNORD115-39, SNORD115-40, SNORD115-41, SNORD115-42, SNORD115- 43, SNORD115-44, SNORD115-45, SNORD115-47, SNORD115-48, SNORD109B, MIR4715, RP11-1084I9.1, LINC00929, AC136896.1 1106 17 43713566 44275529 3 561 50 OPA1-AS1, RP11-699L21.1, LOC285389, LOC100505920, RP11-513G11.3, LINC00884, LOC100507033, TMEM44-AS1, AC090505.6, XXYLT1-AS1, MIR3137, XXYLT1-AS2, LOC101930485, MIR570, LOC101929697, SDHAP1, LINC00885, UBXN7-AS1, FGF12, MB21D2, HRASLS, ATP13A5, ATP13A4, OPA1, HES1, CPN2, LRRC15, GP5, ATP13A3, TMEM44, LSG1, FAM43A, XXYLT1, ACAP2, PPP1R2, APOD, MUC20, MUC4, TNK2, TFRC, ZDHHC19, SLC51A, PCYT1A, TCTEX1D2, TM4SF19, UBXN7, RNF168, C3ORF43, WDR53, FBXO45 1108 3 101058963 113873929 1 12,814 7 CRHR1, SPPL2C, MAPT, STH, KANSL1, CRHR1-IT1, KANSL1-AS1 Chr: chromosome Dup: Duplication; Del: Deletion *Numbers of genes were calculated using Ensembl BioMart (Ensembl GRCh37, Feb 2014) for counting genes with EntrezGene ID. NA refers to carriers without an ID. They were excluded from the Simons VIP cohort because they had a deleterious additional variant.

Downloaded From: https://jamanetwork.com/ on 09/23/2021 eTable 10. Duplication Inheritance Subanalysis

FSIQ NVIQ VIQ BMI Z Score HC Z Score (n=158) (n=159) (n=144) (n=191) (n=189)

†DN: 19/23/12/0 DN: 16/23/12/0 DN: 14/19/10/0 DN: 31/23/12/0 DN: 29/23/11/0

INH: 45/31/15/13 INH: 47/31/17/13 INH: 44/29/15/13 INH: 67/30/15/13 INH: 69/30/14/13

Estimate p-value Estimate p-value Estimate p-value Estimate p-value Estimate p-value

Fixed Effects Parameters Intercept 98.4 <.001 98.4 <.001 96.9 <.001 0.9 0.07 -0.04 0.95 De Novo Proband vs. Non-Carrier Parent -28.4 <.001 -28.5 <.001 -19.6 0.02 -0.2 0.64 -0.7 0.21 Inherited Proband vs. Non-Carrier Parent -25.9 <.001 -27.4 <.001 -17.6 0.002 -1.5 <.001 -1.5 0.002 EU vs. USA -14.5 0.004 -15.2 0.001 -9.6 0.10 -0.5 0.02 -0.5 0.12 Age (Years) 0.3 0.04 0.3 0.02 0.3 0.04 0.01 0.19 0.003 0.83 Female vs. Male -0.3 0.91 -4.4 0.08 1.8 0.43 -0.2 0.24 -0.2 0.35

Additional Contrasts De Novo Proband vs. Sibling Control -30.6 <.001 -31.4 <.001 -26.7 <.001 0.2 0.65 -1.3 0.01 De Novo Proband vs Other†† Control ------Inherited Proband vs. Sibling Control -29.1 <.001 -27.8 <.001 -27.6 <.001 -0.9 0.02 -1.3 0.003 Inherited Proband vs. Inherited Other†† -27.1 0.001 -24.4 0.001 -23.2 0.01 -1.2 0.01 -0.9 0.16 Control De Novo Proband Carrier vs. Inherited 4.4 0.38 1.7 0.75 7.1 0.25 0.3 0.31 0.5 0.12 Proband Carrier De-Novo Parent Control vs. Inherited 7.0 0.22 2.8 0.60 9.1 0.20 -1.0 0.004 -0.3 0.54 Parent Control FSIQ = Full-Scale IQ; NVIQ = Non Verbal IQ; VIQ = Verbal IQ; BMI = Body Mass Index; HC = Head Circumference † Denotes number of proband carriers / non-carrier parents / non-carrier siblings / other non-carriers in the de novo (DN) and inherited (INH) groups †† Others controls may include: half siblings, cousins, aunts, uncles, grandparents, great aunts, great uncles --Denotes lack of results due to 0 observations in Other De Novo Control group

Downloaded From: https://jamanetwork.com/ on 09/23/2021 eTable 11. Deletion Inheritance Subanalysis

FSIQ NVIQ VIQ BMI Z Score HC Z Score (n=342) (n=345) (n=326) (n=407) (n=409) †DN: 86/138/63/2 DN: 88/138/63/2 DN: 82/128/62/2 DN: DN: 127/136/58/2 134/136/62/2 INH: 35/11/6/1 INH: 36/11/6/1 INH: 34/11/6/1 INH: 66/11/6/1 INH: 57/11/6/1

Estimate p- Estimate p- Estimate p- Estimate p- Estimate p- value value value value value

Fixed Effects Parameters Intercept 67.2 <.001 65.2 <.001 66.0 <.001 -1.1 0.52 -1.9 0.18 De Novo -10.2 0.02 -10.7 0.02 -5.3 0.30 1.6 0.001 1.9 <.001 Proband vs. Non-Carrier Parent Inherited -8.8 0.13 -11.0 0.06 -0.2 0.98 2.1 0.001 1.5 0.004 Proband vs. Non-Carrier Parent EU vs. USA -13.8 <.001 -10.1 <.001 -9.3 0.001 0.2 0.53 -0.6 0.001 Age (Years) 0.5 <.001 0.4 0.001 0.7 <.001 0.1 <.001 0.03 0.01 Female vs. -0.7 0.63 -2.1 0.15 1.2 0.44 -0.1 0.41 -0.3 0.03 Male Additional Contrasts De Novo -22.7 <.001 -17.7 <.001 -24.8 <.001 0.9 <.001 0.7 <.001 Proband vs. Sibling Control De Novo -19.8 0.03 -17.7 0.06 -18.4 0.07 2.2 0.02 1.1 0.17 Proband vs Other†† Control Inherited -17.2 0.004 -11.9 0.05 -21.2 0.001 1.2 0.04 1.1 0.04 Proband vs. Sibling Control Inherited 4.7 0.75 12.2 0.42 0.7 0.97 2.1 0.18 2.9 0.04 Proband vs. Inherited Other†† Control De Novo 9.4 0.001 10.1 0.001 9.3 0.004 -0.2 0.48 0.1 0.64 Proband Carrier vs. Inherited Proband Carrier De-Novo 10.7 0.01 9.9 0.02 14.4 0.003 0.3 0.54 -0.3 0.48 Parent Control vs. Inherited Parent Control © 2015 American Medical Association. All rights reserved. 25

Downloaded From: https://jamanetwork.com/ on 09/23/2021 FSIQ = Full-Scale IQ; NVIQ = Non Verbal IQ; VIQ = Verbal IQ; BMI = Body Mass Index; HC = Head Circumference † Denotes number of proband carriers / non-carrier parents / non-carrier siblings / other non-carriers in the de novo (DN) and inherited (INH) groups †† Others controls may include: half siblings, cousins, aunts, uncles, grandparents, great aunts, great uncles

Downloaded From: https://jamanetwork.com/ on 09/23/2021 eTable 12. Neurologic Features in 16p11.2 Duplication Carriers According to Ascertainment Neurological Findings Probands Carrier All ND Non-ND Relatives Carriers (n=142) (n=38) (n=90) (n=270) Epilepsy All Seizure Types 34 (23.9%) 1 (2.6%) 2 (2.2%) 37 (13.7%) Unclassified 10 1 1 12 (4.4%) Generalized 6 0 0 6 (2.2%) Focal 15 0 1 16 (5.9%) Infantile Spasms 3 0 0 3 (1.1%) MRI (n=65) (n=0) (n=21) (n=86) CNS abnormalities Cortical malformation/ 3 -- 0 3 (3.5%) gyral simplification Myelination delay 2 -- 0 2 (2.3%) Enlarged ventricle/pericerebral 9 -- 1 10 (11.6%) spaces Posterior fossa abnormality 11 -- 2 13 (15.1%) (cerebellar hypoplasia/cisterna magna) Corpus callosum abnormality 6 -- 1 7 (2.6%) (hypoplasia/agenesis) ND: Ascertained for neurodevelopmental disorders Non ND: carriers not ascertained for NDs include cases from general population (Estonian cohort) and European psychiatric cohorts. CNS: Central Nervous System

Downloaded From: https://jamanetwork.com/ on 09/23/2021 eTable 13. Neurologic Features in 16p11.2 Deletion Carriers According to Ascertainment

Neurological Findings Probands Carrier All ND Non-ND Relatives Carriers (n=283) (n=34) (n=73) (n=390) Epilepsy All Seizure Types 68 (24.0%) 1 (2.9%) 4 (5.5%) 73 (18.7%) Unclassified 15 1 2 18 (4.6%) Generalized 33 0 1 34 (8.7%) Focal 18 0 1 19 (4.9%) Infantile Spasms 2 0 0 2 (0.5%) MRI (n=89) (n=4) (n=15) (n=108) CNS Abnormalities Cortical malformation/ 4 0 0 4 (3.7%) gyral simplification Enlarged ventricle/pericerebral 3 0 0 3 (2.8%) spaces Posterior fossa abnormality 29 0 7 36 (33.3%) (cerebellar/ vermian hypoplasia/ cisterna magna, Chiari I malformation1, cerebellar ectopia) Corpus callosum abnormality 3 0 0 3 (2.8%) (hypoplasia/agenesis) Spinal dysraphism, Syringomyelia 6 0 0 6 (5.6%) Dural arterio-venous fistula 1 0 0 1 (0.9%) ND: Ascertained for neurodevelopmental disorders Non ND: carriers not ascertained for NDs include cases from general population (Estonian cohort) and European psychiatric cohorts. CNS: Central Nervous System 1 Chiari I malformation = 10 ND probands, 1 Non-ND relative

Downloaded From: https://jamanetwork.com/ on 09/23/2021 eTable 14. Behavioral and Psychiatric Features of 16p11.2 Duplication Carriers

DSM-IV-TR Diagnosis Probands Carrier All ND Non-ND Relatives Carriers (n=142) (n=38) (n=90) (n=270) ASD + Other DSM-IV-TR Diagnoses 23 (16.3%) 0 (0%) 2 (2.3%) 25 (9.4%) ASD Only 13 (9.2%) 0 (0%) 0 (0%) 13 (4.9%) Other DSM-IV-TR Diagnoses Only§ 63 (44.7%) 8 (21.1%) 38 (43.2%) 109 (40.8%) No Diagnosis† 42 (29.8%) 30 (78.9%) 48 (54.5%) 120 (44.9%) ND: Ascertained for neurodevelopmental disorders Non ND: carriers not ascertained for ND include cases from general population Estonian cohort and European psychiatric cohorts † 1 proband and 2 relatives not included due to missing data for Other DSM-IV-TR diagnosis other than ASD § Only cases without ASD are included, however, 2 cases have communication disorders and 2 others have ASD features without strict criteria for ASD diagnosis. DSM-IV diagnoses includes: attention deficit and hyperactivity, anxiety disorder, obsessive compulsive disorder, oppositional defiant disorder, learning disorder, sleep disorder, developmental coordination/motor disorder, feeding disorder, post-traumatic stress disorder, depression.

Downloaded From: https://jamanetwork.com/ on 09/23/2021 eTable 15. Behavioral and Psychiatric Features of 16p11.2 Deletion Carriers DSM-IV-TR Diagnosis Probands Carrier All ND Non-ND Relatives Carriers (n=283) (n=34) (n=73) (n=390) ASD + Other DSM-IV-TR Diagnoses 42 (14.8%) 0 (0%) 3 (4.1%) 45 (11.5%) ASD Only 9 (3.2%) 0 (0%) 1 (1.4%) 10 (2.6%) Other DSM-IV-TR Diagnoses Only§ 154 (54.4%) 3 (8.8%) 31 (42.5%) 188 (48.2%) No Diagnosis 78 (27.6%) 31 (91.2%) 38 (52.1%) 147 (37.7%) ND: Ascertained for neurodevelopmental disorders Non ND: carriers not ascertained for ND include cases from general population Estonian cohort and European psychiatric cohorts ASD includes 15 carriers with a clinical diagnosis was made but ADOS/ADI-R but for whom we had no access to ADOS/ADI-R data. § Only cases without ASD are included, however, 36 cases have communication disorders or PDD-NOS without strict criteria for ASD diagnosis. DSM-IV diagnoses includes: attention deficit and hyperactivity, anxiety disorder, obsessive compulsive disorder, oppositional defiant disorder, learning disorder, sleep disorder, developmental coordination/motor disorder, feeding disorder, post-traumatic stress disorder, depression.

Downloaded From: https://jamanetwork.com/ on 09/23/2021 eTable 16. Effect of the Duplication on Body Mass Index (BMI) z Score, Controlling for ASD, Seizures, and NVIQ

Controlling for Controlling for Controlling for Controlling for ASD Seizures ASD & NVIQ (n=315) (n=347) Seizures (n=236) (n=311)

Estimate p- Estimate p- Estimate p- Estimate p- value value value value

Fixed Effects Parameters Intercept 0.5 0.06 0.4 0.07 0.5 0.07 0.3 0.52 Proband Carrier vs. Non- -0.6 0.01 -0.5 0.01 -0.5 0.02 -0.5 0.04 Carrier Pediatric Carrier Relative vs. -0.7 0.06 -0.5 0.11 -0.6 0.08 -0.4 0.26 Non-Carrier Adult Carrier Relative vs. -0.6 0.01 -0.5 0.01 -0.6 0.01 -0.5 0.02 Non-Carrier EU vs. USA -0.7 0.001 -0.8 <.001 -0.8 <.001 -0.6 0.01 Age (Years) 0.01 0.01 0.02 <.001 0.02 0.004 0.02 0.001 Female vs. Male -0.1 0.62 -0.1 0.66 -0.1 0.62 -0.2 0.11 ASD Yes vs. No -0.2 0.49 -- -- -0.2 0.38 -- -- Seizures Yes vs. No -- -- -0.1 0.80 0.03 0.93 -- -- Nonverbal IQ (NVIQ) ------0.001 0.87

Additional Contrasts Carrier† vs. Non-Carrier -0.6 0.002 -0.5 0.01 -0.6 0.004 -0.5 0.02 Proband Carrier vs. Pediatric 0.03 0.92 0.03 0.91 0.1 0.84 -0.2 0.61 Carrier Relative Proband Carrier vs. Adult -0.1 0.83 0.04 0.84 0.04 0.87 -0.01 0.96 Carrier Relative Pediatric vs. Adult Carrier -0.1 0.81 0.01 0.98 -0.02 0.95 0.1 0.69 Relative † Carriers include proband carriers (individuals ascertained for a neurodevelopmental disorder), pediatric carrier relatives (mostly siblings of the probands), and adult carrier relatives (this group mostly represents transmitting parents) -- Denotes covariate not enteredin the model

Downloaded From: https://jamanetwork.com/ on 09/23/2021 eTable 17. Effect of the Deletion on Body Mass Index (BMI) z Score, Controlling for ASD, Seizures, and NVIQ

Controlling for Controlling for Controlling for Controlling for ASD Seizures ASD & Seizures NVIQ (n=521) (n=580) (n=520) (n=422)

Estimate p- Estimate p- Estimate p- Estimate p- value value value value

Fixed Effects Parameters Intercept 0.1 0.54 0.2 0.32 0.1 0.54 0.5 0.40 Proband Carrier vs. Non-Carrier 0.8 <.001 0.7 <.001 0.8 <.001 0.8 <.001 Pediatric Carrier Relative vs. Non- 0.6 0.07 0.5 0.10 0.6 0.08 0.7 0.05 Carrier Adult Carrier Relative vs. Non- 0.8 0.003 0.8 0.002 0.8 0.003 0.6 0.04 Carrier EU vs. USA 0.4 0.07 0.3 0.10 0.4 0.07 0.3 0.26 Age (Years) 0.03 <.001 0.02 <.001 0.03 <.001 0.02 <.001 Female vs. Male -0.2 0.12 -0.1 0.24 -0.2 0.13 -0.1 0.45 ASD Yes vs. No -0.2 0.43 -- -- -0.2 0.46 -- -- Seizures Yes vs. No -- -- -0.1 0.88 -0.01 0.99 -- -- Nonverbal IQ (NVIQ) ------0.003 0.59

Additional Contrasts Carrier† vs. Non-Carrier 0.8 <.001 0.7 <.001 0.7 <.001 0.7 0.001 Proband Carrier vs. Pediatric 0.2 0.42 0.2 0.49 0.2 0.43 0.1 0.79 Carrier Relative Proband Carrier vs. Adult Carrier 0.02 0.95 -0.1 0.74 0.01 0.98 0.2 0.56 Relative Pediatric vs. Adult Carrier -0.2 0.56 -0.3 0.42 -0.2 0.54 0.1 0.81 Relative † Carriers include proband carriers (individuals ascertained for a neurodevelopmental disorder), pediatric carrier relatives (mostly siblings of the probands), and adult carrier relatives (this group mostly represents transmitting parents) -- Denotes covariate not entered in the model

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eTable 18. Effect of the Duplication on Head Circumference (HC) z Score, Controlling for ASD, Seizures, and NVIQ

Controlling for Controlling for Controlling for Controlling for ASD Seizures ASD & Seizures NVIQ (n=304) (n=312) (n=302) (n=239)

Estimate p- Estimate p- Estimate p- Estimate p- value value value value

Fixed Effects Parameters Intercept 0.6 0.05 0.5 0.06 0.6 0.05 -0.5 0.39 Proband Carrier vs. Non-Carrier -1.1 <.001 -1.1 <.001 -1.0 <.001 -0.9 0.001 Pediatric Carrier Relative vs. Non- -1.1 0.003 -1.1 0.003 -1.1 0.004 -0.9 0.02 Carrier Adult Carrier Relative vs. Non- -1.1 <.001 -1.2 <.001 -1.1 <.001 -0.9 <.001 Carrier EU vs. USA -0.4 0.06 -0.4 0.07 -0.4 0.07 -0.2 0.48 Age (Years) -0.001 0.88 -0.001 0.93 -0.0005 0.94 -0.005 0.49 Female vs. Male -0.2 0.13 -0.2 0.21 -0.2 0.12 -0.3 0.07 ASD Yes vs. No -0.4 0.16 -- -- -0.3 0.20 -- -- Seizures Yes vs. No -- -- -0.4 0.16 -0.4 0.23 -- -- Nonverbal IQ (NVIQ) ------0.01 0.03

Additional Contrasts Carrier† vs. Non-Carrier -1.1 <.001 -1.1 <.001 -1.1 <.001 -0.9 <.001 Proband Carrier vs. Pediatric -0.03 0.93 -0.03 0.91 0.04 0.91 -0.03 0.92 Carrier Relative Proband Carrier vs. Adult Carrier 0.05 0.87 -0.01 0.98 0.1 0.70 0.04 0.89 Relative Pediatric vs. Adult Carrier 0.1 0.85 0.02 0.95 0.1 0.84 0.1 0.85 Relative † Carriers include proband carriers (individuals ascertained for a neurodevelopmental disorder), pediatric carrier relatives (mostly siblings of the probands), and adult carrier relatives (this group mostly represents transmitting parents) -- Denotes covariate not entered in the model

Downloaded From: https://jamanetwork.com/ on 09/23/2021 eTable 19. Effect of the Deletion on Head Circumference (HC) z Score, Controlling for ASD, Seizures, and NVIQ

Controlling for Controlling for Controlling for Controlling for ASD Seizures ASD & Seizures NVIQ (n=508) (n=556) (n=508) (n=423)

Estimate p- Estimate p- Estimate p- Estimate p- value value value value

Fixed Effects Parameters Intercept 0.7 0.001 0.6 0.001 0.7 0.001 0.2 0.67 Proband Carrier vs. Non-Carrier 0.4 0.01 0.5 0.001 0.4 0.01 0.6 0.001 Pediatric Carrier Relative vs. Non- 0.2 0.65 0.4 0.24 0.2 0.65 0.7 0.06 Carrier Adult Carrier Relative vs. Non- 0.7 0.01 0.7 0.004 0.7 0.01 0.5 0.05 Carrier EU vs. USA -0.3 0.05 -0.4 0.02 -0.4 0.05 -0.4 0.07 Age (Years) -0.004 0.44 -0.004 0.45 -0.004 0.45 -0.01 0.29 Female vs. Male -0.4 <.001 -0.4 <.001 -0.4 <.001 -0.5 <.001 ASD Yes vs. No 0.4 0.07 -- -- 0.4 0.07 -- -- Seizures Yes vs. No -- -- -0.01 0.96 0.04 0.90 -- -- Nonverbal IQ (NVIQ) ------0.01 0.28

Additional Contrasts Carrier† vs. Non-Carrier 0.4 0.02 0.5 0.002 0.4 0.02 0.6 0.002 Proband Carrier vs. Pediatric 0.3 0.32 0.2 0.52 0.3 0.32 -0.1 0.81 Carrier Relative Proband Carrier vs. Adult Carrier -0.2 0.42 -0.2 0.52 -0.2 0.42 0.1 0.84 Relative Pediatric vs. Adult Carrier -0.5 0.17 -0.4 0.32 -0.5 0.16 0.1 0.73 Relative † Carriers include proband carriers (individuals ascertained for a neurodevelopmental disorder), pediatric carrier relatives (mostly siblings of the probands), and adult carrier relatives (this group mostly represents transmitting parents) -- Denotes covariate not entered in the model

Downloaded From: https://jamanetwork.com/ on 09/23/2021 eTable 20. Major Malformations and Medical Problems in 16p11.2 Duplication Carriers According to Ascertainment

Probands Carrier All ND Non-ND Relatives Carriers (n=142) (n=38) (n=90) (n=270) MAJOR CONGENITAL MALFORMATIONS Craniosynostosis 2 0 0 2 (0.7%) Osteo- Vertebral anomalies, 0 0 2 2 (0.7%) articular rib anomaly† Ophthalmic Microphthalmia, 0 0 3 3 (1.1%) coloboma, cataract, keratoconus Genitalia Hypospadias, 15 0 1 16 (5.9%) cryptorchidism, micropenis, ambiguous genitalia Urinary Vesico-ureteric reflux, 3 0 1 4 (1.5%) tract Hydronephrosis Digestive Diaphragmatic hernia, gall 4 0 0 4 (1.5%) bladder agenesis, Poly-splenia Cardio- Structural heart defect‡ 9 1 2 12 (4.4%) vascular Orofacial Cleft palate, 6 0 0 6 (2.2%) choanal atresia TOTAL 39 1 9 49 (18.1%)

MAJOR MEDICAL PROBLEMS Scoliosis 9 0 12 21 (7.8%) Decreased hearing 7 0 3 10 (3.7%) Interstitial nephritis 0 2 0 2 (0.7%) Recurrent infections 1 0 1 2 (0.7% ) TOTAL 17 2 16 35 (13.0%) ND: Ascertained for neurodevelopmental disorders Non ND: carriers not ascertained for ND include cases from general population Estonian cohort and European psychiatric cohorts. †Hemivertebrae, costal malformation ‡Atrial/ventricular septal defect (n=5), Shone malformation (n=1), unspecified structural heart defect (n=5), tetralogy of Fallot (n=1)Conditions present in a single carrier (proband or relative) are not present in the table and include: Major medical problem: blindness of unknown origin, intestinal lymphangitis, eosinophilic esophagitis, celiac disease, endometriosis, infertility of unknown origin, bilateral ptosis, meconium ileus, ovarian cyst, diabetes, rheumatic heart disease. We did not include minor or frequently observed medical conditions such as: gastroesophageal reflux disease (n=28), visual disorders such as strabismus (n=18) and refractive errors (hypermetropia, myopia, astigmatism, and presbyopia) (n=24), hypertension (n=2), minor genital anomalies (phimosis/hydrocele) (n=2), inguinal hernia (n=3), umbilical hernia (n=1), auricular appendix (n=1), hypothyroidism/thyroiditis (n=2), delayed puberty (n=1), minor osteo-articular anomalies (pectus carinatum/pectus excavatum/clinodactyly/syndactyly/congenital hip luxation) (n=10), asthma (n=12), facial hemangioma (n=1), dermoid cysts (n=1), giant congenital nevi (n=1), micrognathia (n=1), psoriasis (n=1), radiculo-discopathy (n=1). © 2015 American Medical Association. All rights reserved. 35

Downloaded From: https://jamanetwork.com/ on 09/23/2021 eTable 21. Major Malformations and Medical Problems in 16p11.2 Deletion Carriers According to Ascertainment

Probands Carrier All ND Non ND Relatives Carriers (n=283) (n=34) (n=73) (n=390) MAJOR CONGENITAL MALFORMATIONS Craniosynostosis 3 0 2 5 (1.3%) Osteo- Vertebral anomalies, 14 0 1 15 (3.8%) articular rib anomalies† Ophthalmic Microphthalmia, 8 0 1 9 (2.3%) coloboma, cataract, optic hypoplasia Genitalia Hypospadias, 12 0 0 12 (3.1%) cryptorchidism, micropenis, ambiguous genitalia, Mullerian agenesis Urinary Vesico-ureteric reflux, 10 0 1 11 (2.8%) tract Hydronephrosis, renal dysplasia Digestive Diaphragmatic hernia, 13 0 2 15 (3.8%) Hirschprung disease, hypertrophic pyloric stenosis, gastric malrotation Cardio- Structural heart defect‡ 14 1 1 18 (4.6%) vascular Myocardiopathy 1 1 0 Orofacial Cleft palate 8 0 1 9 (2.3%) TOTAL 83 2 9 94 (24.1%)

MAJOR MEDICAL PROBLEMS Scoliosis 21 0 3 24 (6.1%) Decreased hearing 36 0 1 37 (9.5%) Tumor† 3 1 1 5 (1.3%) TOTAL 60 1 5 66 (17.0%) ND: Ascertained for neurodevelopmental disorders Non ND: carriers not ascertained for ND include cases from general population Estonian cohort and European psychiatric cohorts. ‡ Structural heart defect includes: atrial/ventricular septal defect (n=3), congenital valvulopathy (n=7), supravavular aortic stenosis (n=1), double outlet right ventricle (n=2),patent ductus arteriosus (n=3), coarctation of aorta (n=1), tetralogy of Fallot (n=2), patent foramen ovale (n=2), unspecified structural heart defect (n=1) †Tumor includes seminoma, Wilms tumor, myoma uteri, leiomyoma and cholesteatoma Conditions present in a single carrier (proband or relative) are not present in the table and include: Major medical problem: Behcet disease (n=1), ovarian dysfunction (n=1), Diabetes mellitus (n=2), Hepatitis (n=1), intestinal lymphangectasia (n=1), blindness of unknown origin (n=1), longitudinal vaginal septum (n=1) We did not include minor or frequently observed medical conditions such as: gastroesophageal reflux disease (n=5),visual disorders such as strabismus (n=19), refractive errors (n=24) and nystagmus (n=1),

Downloaded From: https://jamanetwork.com/ on 09/23/2021 arterial hypertension (n=2), sleep apnea syndrome (n=6), asthma (n=8); allergy/atopy (n=7), hypo- /hyperthyroidism/thyroiditis (n=3), minor osteo-articular anomalies (pectus excavatum/pes cavus/pes varus/pes planus/joint hypermobility/poly-, brachy-, clino-, syndactyly/hip dysplasia/hip anteversion) (n=22), hydrocele (n=2), preauricular tag (n=2), inguinal hernia (n=3), hypercholesterolemia (n=1), constitutional leukopenia (n=1)

Downloaded From: https://jamanetwork.com/ on 09/23/2021 eTable 22. Duplication Carriers With Multiple Medical Conditions According to Ascertainment ND (n=231) Osteo- Congenita Oro- Sensori Brain Ophthal Genita Urinar Digestive Articular l heart facial - malformatio -mic l y tract § * defect † neural‡ n Osteo- 0 0 1 0 0 0 0 0 articular* Congenital 0 0 3 0 0 0 0 3 heart defect Ophthalmic 0 0 1 0 0 0 0 0 Genital 0 0 0 0 0 2 0 0 Urinary tract 0 0 0 0 0 0 0 1 Digestive 0 0 0 0 0 0 0 0 Oro-facial† 0 0 0 0 0 0 0 1

Non ND (n=39) Sensori- 0 0 0 0 0 0 0 0 neural‡ Brain 0 0 0 0 0 0 0 0 malformatio n ND: Ascertained for neurodevelopmental disorders Non ND: carriers not ascertained for ND include cases from general population Estonian cohort and European psychiatric cohorts.

Downloaded From: https://jamanetwork.com/ on 09/23/2021 eTable 23. Deletion Carriers With Multiple Medical Conditions According to Ascertainment ND (n=356) Osteo- Congenita Oro- Sensori Brain Ophthal Genita Urinar Digestive Articular l heart facial - malformatio -mic l y tract § * defect † neural‡ n Osteo- 2 0 3 0 0 0 0 0 articular* Congenital 0 1 3 0 0 1 0 0 heart defect Ophthalmic 0 0 1 1 0 0 0 0 Genital 0 1 0 0 0 0 0 0 Urinary tract 0 0 0 0 0 0 0 0 Digestive 0 0 0 0 0 1 0 0 Oro-facial† 0 0 0 0 0 0 0 0

Non ND (n=34) Sensori- 0 0 0 0 0 0 0 0 neural‡ Brain 0 0 0 0 0 0 0 0 malformatio n ND: Ascertained for neurodevelopmental disorders Non ND: carriers not ascertained for ND include cases from general population Estonian cohort and European psychiatric cohorts. 1 carrier ascertained for ND displayed 4 malformations (hemivertebrae, cryptorchidia, hydronephrosis and congenital malformative cardiopathy)

Downloaded From: https://jamanetwork.com/ on 09/23/2021 eFigure 1. Distribution of IQ Scores by Region

EU and USA duplication cohorts contribute to the lower (16.7% of EU carriers with FSIQ ≤ 40 and 6.6% in the US carriers) and higher functioning participants (6.3% in the EU carriers and 25.5% of US carriers with FSIQ > 100).

Downloaded From: https://jamanetwork.com/ on 09/23/2021 eFigure 2. Full-Scale IQ (FSIQ) in Probands Stratified by Site, Sex, Seizure Status, and HC z Score Above vs Below 0

Downloaded From: https://jamanetwork.com/ on 09/23/2021 eFigure 3. Distribution of Additional Deleterious CNV by Size and Their Numbers of Protein-Coding Genes Included in Duplication and Deletion Carriers*

The median size of the additional CNVs as well as the mean number of genes included in were not different between deletion and duplication groups (1401Kb vs. 1932.5Kb, Wilcoxon Rank Sum test, p=0.42 and 28.3 vs. 23.6, Student’s t-test, p=0.62, respectively) IQ data were available on only three carriers with a second deleterious CNV (FSIQ: 30, 61 and 70), which did not allow us to estimate the average impact of an additional deleterious CNV on IQ. * carriers of X chromosomal aneuploidies were excluded from this analysis.

Downloaded From: https://jamanetwork.com/ on 09/23/2021 eFigure 4. FSIQ of Inherited and De Novo Duplication and Deletion Probands vs Parent FSIQ

Downloaded From: https://jamanetwork.com/ on 09/23/2021 eFigure 5. Age of Walking in Duplication Proband Carriers vs Deletion Proband Carriers

The median age of walking was 18 months in 82 duplication proband carriers ascertained for NDs. Motor delay is more pronounced in duplication compared to deletion probands ascertained for NDs (n=164 median=16; Wilcoxon Rank Sum test, p=0.02). This is mainly driven by the proportion of very late onset walkers (>24 months), which is increased 2.6-fold in the duplication probands compared to the deletion probands (13/82 vs. 10/164 respectively; Fisher exact test, p=0.01)

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