Table 3

Large-scale GWAS that reveal common and rare variants associated with ASD

Reference

Stage

Families

Type

Most significant findings

Wang et al. 2009 [46]

1

780 families, 3,101 participants (AGRE)

Multiplex

Top SNP rs4307059 (p = 1.1 × 10^-5)* between CDH9 and CDH10; may disrupt a regulatory non-coding RNA [158].

2

1,204 cases, 6,491 controls (ACC)

Case/control

Top SNP rs4307059 (p = 2.2 × 10^-4)*

3

Combined

GWS at rs4307059 (p = 3.4 × 10^-8 combined with discovery cohorts; p = 2.1 × 10^-10 combined with replication cohorts)

Weiss et al. 2009 [47]

1

1,031 families, 4,233 participants (AGRE, NIMH)

Multiplex and simplex

Top SNP rs10513025 (p = 1.7 × 10^-6)* between SEMA5A and TAS2R1

2

318 trios (Boston Autism Consortium/Montreal), 1,755 trios (AGP, Finnish families, Iranian trios)

Multiplex and simplex

Top SNP rs10513025; p = 2.1 × 10^-7*, combining replication and scan data

Anney et al. 2010 [48]

1

1,369 families (AGP), 1,385 cases(typically only one proband genotyped per family)

Multiplex and simplex

GWS at rs4141463 (p = 2.1 × 10^-8) in MACROD2 (intronic)

2

2,179 families (AGP group above/AGRE)

Multiplex and simplex

GWS at rs4141463 (p = 4.7 × 10^-8) in MACROD2 (intronic)

*Not genome-wide significant; GWS, genome-wide significant defined as p < 5 × 10^-8.

Berg and Geschwind Genome Biology 2012 13:247   doi:10.1186/gb-2012-13-7-247