A high-density SNP genome-wide linkage scan in a large autism extended pedigree

Department of Psychiatry, University of Utah, Salt Lake City, UT, USA.
Molecular Psychiatry (Impact Factor: 14.5). 03/2008; 14(6):590-600. DOI: 10.1038/mp.2008.14
Source: PubMed


We performed a high-density, single nucleotide polymorphism (SNP), genome-wide scan on a six-generation pedigree from Utah with seven affected males, diagnosed with autism spectrum disorder. Using a two-stage linkage design, we first performed a nonparametric analysis on the entire genome using a 10K SNP chip to identify potential regions of interest. To confirm potentially interesting regions, we eliminated SNPs in high linkage disequilibrium (LD) using a principal components analysis (PCA) method and repeated the linkage results. Three regions met genome-wide significance criteria after controlling for LD: 3q13.2-q13.31 (nonparametric linkage (NPL), 5.58), 3q26.31-q27.3 (NPL, 4.85) and 20q11.21-q13.12 (NPL, 5.56). Two regions met suggestive criteria for significance 7p14.1-p11.22 (NPL, 3.18) and 9p24.3 (NPL, 3.44). All five chromosomal regions are consistent with other published findings. Haplotype sharing results showed that five of the affected subjects shared more than a single chromosomal region of interest with other affected subjects. Although no common autism susceptibility genes were found for all seven autism cases, these results suggest that multiple genetic loci within these regions may contribute to the autism phenotype in this family, and further follow-up of these chromosomal regions is warranted.

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    • "LSAMP (OMIM #603241) encodes a limbic system-associated membrane protein (LAMP) and has been shown to regulate anxiety-like phenotypes in mice [7]. GAP43 (OMIM #162060) is almost exclusively expressed in neuronal tissue and is a candidate gene for ASD [8]. "
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