Mapping autism risk loci using genetic linkage and chromosomal rearrangements

Abstract

Autism spectrum disorders (ASDs) are common, heritable neurodevelopmental conditions. The genetic architecture of ASDs is complex, requiring large samples to overcome heterogeneity. Here we broaden coverage and sample size relative to other studies of ASDs by using Affymetrix 10K SNP arrays and 1,181 [corrected] families with at least two affected individuals, performing the largest linkage scan to date while also analyzing copy number variation in these families. Linkage and copy number variation analyses implicate chromosome 11p12-p13 and neurexins, respectively, among other candidate loci. Neurexins team with previously implicated neuroligins for glutamatergic synaptogenesis, highlighting glutamate-related genes as promising candidates for contributing to ASDs.

Figure 1

Linkage across the genome for all families and ancestries, based on levels of diagnostic certainty. Vertical reference lines separate chromosomes, which are ordered. The horizontal reference bar is given at a Zlr of 3.18, the threshold for suggestive linkage according to the Lander/Kruglyak criterion, which is roughly accurate in this setting (4.1 is the threshold for significant linkage). The suggestive threshold would be expected to be crossed by chance once per genome scan. It is crossed once, and the peak falls within 11p12 (Zlr = 3.57 at rs2421826).

Figure 2

Chromosome ideogram depicting 253 inferred CNVs found in 196 Autism patients These CNVs are derived from the highest stringency ‘filtered’ dataset, but many other true CNVs will also be found in the other analyses and should be examined further. Characteristics of the complete dataset are described in Table 2. Some of the larger changes could represent somatic artifacts or missed karyotypic anomalies. All data is also downloadable or viewed in Genome Browser format at the Autism Chromosome Rearrangement Database (http://projects.tcag.ca/autism/). As additional analyses and validation is performed the data will be posted at the same site.

Figure 3

Highlighted linkage results due to removing families in which affected individuals carry putative CNV. Results from all families (ignoring CNVs) noted by the cyan line; results from the filtered set, the orange line; results from the plate set, red line; and results from the batch set, black line. Families all fall in the broad diagnostic category. Complete results are in Supplementary Figure 2. For 11p12, the maximum occurs in 11p13 (Zlr = 3.33 at rs2421826). For chromosome 15, there are two up-crossings: the smaller peak occurs at in 15q23 (Zlr = 3.19 at rs1372828) and the larger in 15q25.3 (Zlr = 3.41 near rs1433452). For families removed versus retained, heterogeneity of estimated identity-by-descent was tested in the ± 5 cM linkage region surrounding each peak and reported as regional minimum heterogeneity p-value m-p (11p12-p13, m-p = 0.074; 15q23, m-p = 0.044; 15q25.3, m-p = 0.004).

Figure 4

Linkage peaks by MO/FC, based on levels of diagnostic certainty. For FC families and narrow diagnosis, peaks localize to 5p14.33 (Zlr = 3.41 at rs1968011; m-p = 0.141), 9p24.1 (Zlr = 3.21 at rs1340513; m-p = 0.0007), and 11p13 (Zlr = 3.77 at rs1358054; m-p = 0.008); for FC/Broad, to 9p24.1 (Zlr = 3.59 at rs722628; m-p = 0.006) and 11p13 (Zlr = 3.90 at rs1358054; m-p = 0.015); and for FC/All, to 11p12 (Zlr = 3.63 at rs1039205; m-p = 0.078). For all MO families, peaks localize to 5q12 (Zlr = 3.26 at rs673743; m-p = 0.019), 9q33.3 (Zlr = 3.30 at rs536861; m-p = 0.0005).

Figure 5

The effect on linkage of splitting families into FC and MO families while also removing families in which affected individuals putatively carry CNV. For FC families and filtered subset, peaks localize to 9p24.1 (Zlr = 3.32 at rs1575284; m-p = 0.105), and 11p12 (Zlr = 3.90 at rs1039205; m-p = 0.411); for FC/Plate, to 9p24.1 (Zlr = 3.28 at rs1821892; m-p = 0.295) and 11p12 (Zlr = 3.48 at rs1039205; m-p = 0.111); and for FC/Batch, to 11p13 (Zlr = 4.03 at rs1358054; m-p = 0.014) and 15q23 (Zlr = 3.30 at rs1433452; m-p = 0.044).