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Table 2 Strongest association signals for social-communication problems across developmental stages

From: Variability in the common genetic architecture of social-communication spectrum phenotypes during childhood and adolescence

 

8 years (N = 5,628)

11 years (N = 5,533)

14 years (N = 5,129)

17 years (N = 4,229)

Empirical GWAS P-value (SE)

Empirical GWAS P-value (SE) for co-location with autism loci

SNP

Chr

Gene

E,A

EAF

β (SE)a

P a

β (SE)

P

β (SE)

P

β (SE)a

P a

  

rs4453791

3

SCN11A

c,t

0.13

0.03 (0.04)

0.48

0.05 (0.04)

0.27

0.13 (0.04)

0.0014

0.23 (0.04)

9.3 × 10 −9

0.011 (0.0033)

0.002 (0.0014)

rs3761168

20

PLCB1

a,c

0.05

0.12 (0.05)

0.025

0.17 (0.06)

0.0041

0.09 (0.06)

0.16

0.32 (0.06)

7.9 × 10−8

0.085 (0.0088)

0.007 (0.0026)

  1. GWAS results for SCDC scores at 8 and 17 years of age are presented for the most significant independent signals (Genomic-control corrected single time-point P < 1 × 10−7). Regression estimates were obtained using quasi-Poisson regression analysis. SNPs were imputed with sufficient quality (rs4453791: MaCH R2 = 0.98, rs3761168: MaCH R2 = 0.96). Genome-wide significant results are indicated in bold. In addition, association results at the selected signals are also presented for SCDC scores at 11 and 14 years of age (not subjected to GWAS). A, Alternative allele; Chr, Chromosome; E, Effect allele; EAF, Effect allele frequency; Empirical GWAS-P (SE), Empirical genome-wide P-value based on 1,000 permutations accounting for multiple testing at ages 8 and 17 years; Empirical GWAS-P (SE) for co-location with autism loci, Empirical genome-wide P-value based on 1,000 permutations accounting for multiple testing at ages 8 and 17 years and conditional on the entire set of currently known putative autism loci (LD-based gene region: r2 > 0.3, ±500 kb, 375 autosomal genes; https://gene.sfari.org/autdb/Welcome.do). Gene, Nearest gene within ±500 kb of the SNP; GWAS, Genome-wide Association Study; SNP, Single-nucleotide polymorphism. aGenomic-control corrected during GWAS.