Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays

A Pooled Genome-Wide Association Study of Asperger Syndrome

Asperger Syndrome (AS) is a neurodevelopmental condition characterized by impairments in social interaction and communication, alongside the presence of unusually repetitive, restricted interests and stereotyped behaviour. Individuals with AS have no delay in cognitive and language development. It is a subset of Autism Spectrum Conditions (ASC), which are highly heritable and has a population prevalence of approximately 1%. Few studies have investigated the genetic basis of AS. To address this gap in the literature, we performed a genome-wide pooled DNA association study to identify candidate loci in 612 individuals (294 cases and 318 controls) of Caucasian ancestry, using the Affymetrix GeneChip Human Mapping version 6.0 array. We identified 11 SNPs that had a p-value below 1x10^-5. These SNPs were independently genotyped in the same sample. Three of the SNPs (rs1268055, rs7785891 and rs2782448) were nominally significant, though none remained significant after Bonferroni correction. Two of our top three SNPs (rs7785891 and rs2782448) lie in loci previously implicated in ASC. However, investigation of the three SNPs in the ASC genome-wide association dataset from the Psychiatric Genomics Consortium indicated that these three SNPs were not significantly associated with ASC. The effect sizes of the variants were modest, indicating that our study was not sufficiently powered to identify causal variants with precision.

FUT2: filling the gap between genes and environment in Behçet's disease?

OBJECTIVES

To identify new susceptibility loci for Behçet's disease (BD), we performed a genome-wide association study (GWAS) using DNA pooling.

METHODS

Two replicate pools of 292 Iranian BD cases and of 294 age- and sex-matched controls were allelotyped in quadruplicate on the Affymetrix Genome-Wide Human SNP Array 6.0. Of the 51 top markers, 47 were technically validated through individually genotyping. Replication of validated single nucleotide polymorphisms (SNPs) was performed in an independent Iranian dataset (684 cases and 532 controls).

RESULTS

In addition to the well-established HLA-B locus, rs7528842 in a gene desert on chromosome 1p21.2, and rs632111 at the 3'UTR of FUT2 were associated in both the discovery and replication datasets (individually and in combination). However, only the FUT2 SNP was associated in a previous GWAS for BD in Turkish people. Fine-mapping of FUT2 in the full Iranian dataset showed additional associations in five coding SNPs (2.97E-06

CONCLUSIONS

This study suggests for the first time a putative link between a specific gene and environment in the aetiopathogenesis of BD. The non-secretor phenotype affects mucosal glycosylation, which may explain its known association with dysbiosis and altered susceptibility to infections. A different antigenic stimulation in early life and consequent increased propensity for autoimmunity and inflammation may contribute to BD development.

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MESH Headings

• 3' Untranslated Regions/genetics
• Adult
• Behcet Syndrome/genetics
• Case-Control Studies
• Chromosomes, Human, Pair 1/genetics
• Female
• Fucosyltransferases/genetics
• Genome-Wide Association Study
• HLA-B Antigens/genetics
• Humans
• Iran
• Male
• Middle Aged
• Polymorphism, Single Nucleotide
• White People/genetics
• Galactoside 2-alpha-L-fucosyltransferase

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Affiliation(s)

Joana M Xavier Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal Instituto Gulbenkian de Ciência, Oeiras, Portugal
Farhad Shahram Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
Inês Sousa Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal Instituto Gulbenkian de Ciência, Oeiras, Portugal
Fereydoun Davatchi Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
Mafalda Matos Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal Instituto Gulbenkian de Ciência, Oeiras, Portugal
Bahar Sadeghi Abdollahi Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
João Sobral Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal Instituto Gulbenkian de Ciência, Oeiras, Portugal
Abdolhadi Nadji Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
Manuela Oliveira Centro de Investigação Matemática e Aplicaçóes - CIMA, Universidade de Évora, Évora, Portugal
Fahmida Ghaderibarim Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
Niloofar Mojarad Shafiee Rheumatology Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
Sofia A Oliveira Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal Instituto Gulbenkian de Ciência, Oeiras, Portugal

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A genome wide association study of mathematical ability reveals an association at chromosome 3q29, a locus associated with autism and learning difficulties: a preliminary study

Mathematical ability is heritable, but few studies have directly investigated its molecular genetic basis. Here we aimed to identify specific genetic contributions to variation in mathematical ability. We carried out a genome wide association scan using pooled DNA in two groups of U.K. samples, based on end of secondary/high school national academic exam achievement: high (n = 419) versus low (n = 183) mathematical ability while controlling for their verbal ability. Significant differences in allele frequencies between these groups were searched for in 906,600 SNPs using the Affymetrix GeneChip Human Mapping version 6.0 array. After meeting a threshold of p<1.5×10⁻⁵, 12 SNPs from the pooled association analysis were individually genotyped in 542 of the participants and analyzed to validate the initial associations (lowest p-value 1.14 ×10⁻⁶). In this analysis, one of the SNPs (rs789859) showed significant association after Bonferroni correction, and four (rs10873824, rs4144887, rs12130910 rs2809115) were nominally significant (lowest p-value 3.278 × 10⁻⁴). Three of the SNPs of interest are located within, or near to, known genes (FAM43A, SFT2D1, C14orf64). The SNP that showed the strongest association, rs789859, is located in a region on chromosome 3q29 that has been previously linked to learning difficulties and autism. rs789859 lies 1.3 kbp downstream of LSG1, and 700 bp upstream of FAM43A, mapping within the potential promoter/regulatory region of the latter. To our knowledge, this is only the second study to investigate the association of genetic variants with mathematical ability, and it highlights a number of interesting markers for future study.