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SNPs, microarrays and pooled DNA:identification of four loci associated with mild mental impairment in a sample of 6000 children

Butcher, Lee M. and Meaburn, Emma and Knight, Jo and Sham, Pak C. and Schalkwyk, Leonard C. and Craig, Ian W. and Plomin, Robert (2005) SNPs, microarrays and pooled DNA:identification of four loci associated with mild mental impairment in a sample of 6000 children. Human Molecular Genetics, 14 (10). pp. 1315-1325. ISSN 0964-6906

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Abstract

Mild mental impairment (MMI) represents the low extreme of the quantitative trait of general intelligence and is highly heritable. Quantitative trait loci (QTLs) conferring susceptibility to MMI, as for most complex traits, are likely to be of small effect size. Using a novel approach we call SNP-MaP (SNP Microarrays and Pooling), we have identified four loci associated with MMI. These four loci have been replicated in two SNP-MaP studies and verified by individual genotyping. The two SNP-MaP studies conducted were a case versus control comparison (n = 515 and n = 1028, respectively) and a low versus high general intelligence extremes group comparison (n = 503 and n = 505, respectively). Each of the four groups consisted of five independent 'subpools', with each subpool assayed on a separate microarray. Twelve loci showing the largest significant differences in both SNP-MaP studies were individually genotyped on 6154 children. Of the four loci positively associated with MMI, the minor allele of each conferred the greater risk for MMI. Two of the loci are close to known genes and may be in linkage disequilibrium with them. One of the loci is between the candidate genes KLF7 and CREB1, but given possible long-range effects on expression and the unknown importance of untranslated elements such as micro-RNAs, all four loci deserve attention as candidates. Although each SNP accounts for a small amount of variance, their effects are additive and they can be combined in a 'SNP set' that can be used as a genetic risk index for MMI in behavioral genomic analyses.

Item Type: Article
Journal or Publication Title: Human Molecular Genetics
Uncontrolled Keywords: Child ; DNA ; Genetic Markers ; Humans ; Intellectual Disability ; Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide
Subjects:
Departments:
ID Code: 79914
Deposited By: ep_importer_pure
Deposited On: 07 Jun 2016 14:58
Refereed?: Yes
Published?: Published
Last Modified: 21 Sep 2017 01:35
Identification Number:
URI: http://eprints.lancs.ac.uk/id/eprint/79914

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