Association Study of a Linkage Region on Chromosome 3P25 in 816 Families Shows Strong Evidence for association of ATP2B2 with Autism and Language Delay

Background:

Autism is highly influenced by genetic factors. Genome-wide linkage and more recently association approaches have been used to identify autism genes. Two independent studies reported evidence for linkage to a region on chromosome 3p25 and a third association between a micro-satellite marker and autism in the same region. We performed a linkage scan in families from the AGRE collection and confirm linkage to this region on chromosome 3p25.

Objectives:

Identify the gene(s) underlying the replicated linkage signal on chromosome 3p25 using a high density, SNP genotyping and association study approach.

Methods:

228 SNPs were selected for genotyping. SNPs were selected with a MAF≥ 0.1 according to CEU-HAPMAP data. SNPs were genotyped using the SNPLex assay (Applied Biosystems). Initially we performed an association analysis in 493 autism families from the AGRE collection followed by a replication study of the positive markers in an independent sample of 323 families from Italy.

Results:

Six markers located in the ATP2B2 gene showed positive p-values. The strongest evidence for association was obtained for markers rs3774180 (p= 0.002) and rs2278556 (p= 0.004). All six positive markers were genotyped in the Italian replication set. All but one also showed positive association with the same allele, again rs3774180 and rs2278556 providing the strongest results (p= 0.002 and p= 0.006 respectively). The joint analysis of the 816 families resulted in strong evidence for association of the ATP2B2 gene with autism (rs3774180, p= 3.4x10^-5, and rs 2278556, p= 1.4x10^-4).

ATP2B2 codes for the brain specific calcium pump PMCA2. Calcium transport plays a major role in synaptic signal transmission and pathways associated with autism have been shown to depend on intra-cellular calcium concentrations. ATP2B2 is also expressed in the inner ear and has been shown to be involved in the modulation of hearing impairment. We therefore investigated if the association with autism could be more specifically linked with endophenotypes that may be dependent on hearing or the correct interpretation of sounds (e.g. language). We selected the ADIR-scores correlated with onset of language DEVT, AWORD and APHRASE. As this information was available only in the AGRE data only the 493 AGRE families were included in this sub-analysis. The family set was split into two for initial analysis and replication respectively (278 and 215 families). For DEVT a total of eight SNP markers showed significant p-values in the first family set, including all but one from the primary autism analysis. The strongest signal was obtained for markers rs6442169 (p= 0.003), which was moderately positive in the in the initial analysis and rs3774180 (p= 0.0039). Only one marker and two markers respectively showed positive association with APHRASE and AWORD. Marker rs6442169 replicated for DEVT in the 208 additional AGRE families. In the combined set the p-value was p= 1.9x10^-4.

Conclusions:

We replicated a linkage signal on chromosome 3p25. SNP analyses in a total sample of 816 families provides strong evidence for association of the ATP2B2 gene with autism. More specifically, our results show that ATP2B2 may be involved in language delay in autism.