Linkage and candidate gene studies of autism spectrum disorders in European populations

Abstract

Over the past decade, research on the genetic variants underlying susceptibility to autism and autism spectrum disorders (ASDs) has focused on linkage and candidate gene studies. This research has implicated various chromosomal loci and genes. Candidate gene studies have proven to be particularly intractable, with many studies failing to replicate previously reported associations. In this paper, we investigate previously implicated genomic regions for a role in ASD susceptibility, using four cohorts of European ancestry. Initially, a 384 SNP Illumina GoldenGate array was used to examine linkage at six previously implicated loci. We identify linkage approaching genome-wide suggestive levels on chromosome 2 (rs2885116, MLOD=1.89). Association analysis showed significant associations in MKL2 with ASD (rs756472, P=4.31 x 10(-5)) and between SND1 and strict autism (rs1881084, P=7.76 x 10(-5)) in the Finnish and Northern Dutch populations, respectively. Subsequently, we used a second 384 SNP Illumina GoldenGate array to examine the association in seven candidate genes, and evidence for association was found in RELN (rs362780, P=0.00165). Further increasing the sample size strengthened the association with RELN (rs362780, P=0.001) and produced a second significant result in GRIK2 (rs2518261, P=0.008). Our results strengthen the case for a more detailed study of the role of RELN and GRIK2 in autism susceptibility, as well as identifying two new potential candidate genes, MKL2 and SND1.

Figure 1

Results of linkage analyses of chromosomes 2, 3, 6, 7, 16 and 17. The blue line indicates results for the combined set of IMGSAC, PARIS and Finnish families, whereas the red line shows results when Finnish samples are excluded. Each locus is shown to the same scale. The regions covered are as follows (NCBI Build 36.1): chromosome 2, rs2320399 (133 458 918) → rs1020941 (194 183 515), 60 724 597 bp; chromosome 3, rs721729 (174 671 967) → rs725656 (186 008 902), 11 336 935 bp; chromosome 6, rs1590957 (89 867 130) → rs1378702 (113 107 351), 23 240 221 bp; chromosome 7, rs726820 (93 449 846) → rs273937 (137 230 419), 43 780 573 bp; chromosome 16, rs1424125 (6 002 554) → rs722075 (17 242 000), 11 239 446 bp; chromosome 17, rs719601 (25 755 541) → rs1990673 (50 405 024), 24 649 483 bp.

Figure 2

TDT association analysis of SNPs in previously reported regions of linkage using Finnish and Northern Dutch families. Association was tested for both strict autism and the broader phenotype of ASD in the Finnish and Northern Dutch families separately. Results are depicted as follows: Finnish strict autism=blue, Finnish ASD=black, Northern Dutch strict autism=red, Northern Dutch ASD=purple. Results are plotted as −log(P). Each locus is shown to the same scale. The regions covered are as follows (NCBI Build 36.1): chromosome 2, rs2320399 (133 458 918) → rs1020941 (194 183 515), 60 724 597 bp; chromosome 3, rs721729 (174 671 967) → rs725656 (186 008 902), 11 336 935 bp; chromosome 6, rs1590957 (89 867 130) → rs1378702 (113 107 351), 23 240 221 bp; chromosome 7, rs726820 (93 449 846) → rs273937 (137 230 419), 43 780 573 bp; chromosome 16, rs1424125 (6 002 554) → rs722075 (17 242 000), 11 239 446 bp; chromosome 17, rs719601 (25 755 541) → rs1990673 (50 405 024), 24 649 483 bp.

Figure 3

TDT meta-analysis of Illumina GoldenGate candidate gene data. Association with strict autism and the wider ASD phenotype was performed separately using combined data for the IMGSAC, PARIS and Finnish samples. Results for strict autism are plotted as blue triangles and for ASD as red circles. Results are plotted as −log(P). Each locus is shown to the same scale. The regions covered are as follows (NCBI Build 36.1): NOSTRIN, rs6433093 (169 367 190) → rs12993143 (169 427 746), 60 556 bp; GRIK2, rs2852512 (101 953 275) → rs2852620 (102 621 626), 668 351 bp; RELN, rs1978198 (102 896 685) → rs4298437 (103 413 113), 516 428 bp; PRKCB1, rs3760106 (23 753 297) → rs3729908 (24 138 749), 385 452 bp; SLC6A4, rs3813034 (25 548 930) → rs16965628 (25 579 551), 30 621 bp; SHANK3, rs2341009 (49 480 446) → rs756638 (49 518 559), 38 113 bp; ASMT, rs6588807 (1 708 581) → rs5949028 (1 715 666), 7085 bp.