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Association analysis of mild mental impairment using DNA pooling to screen 432 brain-expressed single-nucleotide polymorphisms


We hypothesize that mild mental impairment (MMI) represents the low extreme of the same quantitative trait loci (QTLs) that operate throughout the distribution of intelligence. To detect QTLs of small effect size, we employed a direct association strategy by genotyping 432 presumably functional nonsynonymous single-nucleotide polymorphisms (nsSNPs) identified from public databases on DNA pools of 288 cases and 1025 controls. In total, 288 MMI cases were identified by in-home administration of McCarthy Scales of Children's Abilities to 836 twin pairs selected from a community sample of more than 14 000 children previously screened for nonverbal cognitive delay using parentally administered tests. Controls were selected from the community sample representing the full range of nonverbal intelligence. SNPs showing at least 7% allele frequency differences between case and control DNA pools were tested for their association with the full range of nonverbal intelligence using five DNA subpools, each representing quintiles of the normal quantitative trait scores from the 1025 controls. SNPs showing linear associations in the expected direction across quintiles using pooled DNA were individually genotyped for the 288 cases and 1025 controls and analyzed using standard statistical methods. One SNP (rs1136141) in HSPA8 met these criteria, yielding a significant (P=0.036) allelic frequency difference between cases and controls for individual genotyping and a significant (P=0.013) correlation within the control group that accounts for 0.5% of the variance. The present SNP strategy combined with DNA pooling and large samples represents a step towards identifying QTLs of small effect size associated with complex traits in the postgenomic era when all functional polymorphisms will be known.

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  1. Inlow JK, Restifo LL . Molecular and comparative genetics of mental retardation. Genetics 2004; 166: 835–881.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Plomin R, DeFries JC, McClearn GE, McGuffin P . Behavioral Genetics, 4th edn. Worth Publishers: New York, 2001.

    Google Scholar 

  3. Knight SJL, Regan R, Nicod A, Horsley SW, Kearney L, Homfray T et al. Subtle chromosomal rearrangements in children with unexplained mental retardation. Lancet 1999; 354: 1676–1681.

    Article  CAS  PubMed  Google Scholar 

  4. Winnepenninckx B, Rooms L, Kooy RF . Mental retardation: a review of the genetic causes. Br J Dev Disab 2003; 49: 29–44.

    Article  Google Scholar 

  5. Plomin R . Genetic research on general cognitive ability as a model for mild mental retardation. Int Rev Psychiatry 1999; 11: 34–36.

    Article  Google Scholar 

  6. Gottfredson LS . G, jobs and life. In: Nyborg H (ed) The Scientific Study of General Intelligence. Pergamon: Amsterdam, 2003; 293–342.

    Chapter  Google Scholar 

  7. Nichols PL . Familial mental retardation. Behav Genet 1984; 14: 161–170.

    Article  CAS  PubMed  Google Scholar 

  8. Reed EW, Reed SC . Mental Retardation: a Family Study. Saunders: Philadelphia, 1965.

    Google Scholar 

  9. Spinath F, Harlaar N, Ronald A, Plomin R . Substantial genetic influence on mild mental impairment in early childhood. Am J Ment Retard 2004; 109: 34–43.

    Article  PubMed  Google Scholar 

  10. Plomin R, Owen MJ, McGuffin P . The genetic basis of complex human behaviors. Science 1994; 264: 1733–1739.

    Article  CAS  PubMed  Google Scholar 

  11. Carlson CS, Eberle MA, Kruglyak L, Nickerson DA . Mapping complex disease loci in whole-genome association studies. Nature 2004; 429: 446–452.

    Article  CAS  PubMed  Google Scholar 

  12. Kruglyak L . Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 1999; 22: 139–144.

    Article  CAS  PubMed  Google Scholar 

  13. Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ et al. Linkage disequilibrium in the human genome. Nature 2001; 411: 199–204.

    CAS  PubMed  Google Scholar 

  14. Botstein D, Risch N . Discovering genotypes underlying human phenotypes: past successes for Mendelian disease, future approaches for complex disease. Nat Genet 2003; 33: 228–237.

    Article  CAS  PubMed  Google Scholar 

  15. Sunyaev S, Ramensky V, Bork P . Towards a structural basis of human non-synonymous single nucleotide polymorphisms. Trends Genet 2000; 16: 198–200.

    Article  CAS  PubMed  Google Scholar 

  16. Chang H, Fujita T . PicSNP: a browsable catalog of nonsynonymous single nucleotide polymorphisms in the human genome. Biochem Biophys Res Commun 2001; 287: 288–291.

    Article  CAS  PubMed  Google Scholar 

  17. Sherry ST, Ward M, Sirotkin K . dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Res 1999; 9: 677–679.

    CAS  PubMed  Google Scholar 

  18. Norton N, Williams NM, Williams HJ, Spurlock G, Kirov G, Morris DW et al. Universal, robust, highly quantitative SNP allele frequency measurement in DNA pools. Human Genet 2002; 110: 471–478.

    Article  CAS  Google Scholar 

  19. Sham P, Bader JS, Craig I, O'Donovan M, Owen M . DNA pooling: a tool for large-scale association studies. Nat Rev Genet 2002; 3: 862–871.

    Article  CAS  PubMed  Google Scholar 

  20. Trouton A, Spinath FM, Plomin R . Twins Early Development Study (TEDS): a multivariate, longitudinal genetic investigation of language, cognition and behaviour problems in childhood. Twin Res 2002; 5: 444–448.

    Article  PubMed  Google Scholar 

  21. Colledge E, Bishop DVM, Dale P, Koeppen-Schomerus G, Price TS, Happé F et al. The structure of language abilities at 4 Years: a twin study. Dev Psychol 2002; 38: 749–757.

    Article  PubMed  Google Scholar 

  22. Oliver B, Dale PS, Saudino K, Petrill SA, Pike A, Plomin R . The validity of parent-based assessment of non-verbal cognitive abilities of three-year olds. Early Child Dev Care 2002; 172: 337–348.

    Article  Google Scholar 

  23. Saudino KJ, Dale PS, Oliver B, Petrill SA, Richardson V, Rutter M et al. The validity of parent-based assessment of the cognitive abilities of two-year-olds. Br J Dev Psychol 1998; 16: 349–363.

    Article  Google Scholar 

  24. McCarthy D . McCarthy Scales of Children's Abilities. The Psychological Corporation: New York, 1972.

    Google Scholar 

  25. Viding E, Price TS, Spinath FM, Bishop DV, Dale PS, Plomin R . Genetic and environmental mediation of the relationship between language and nonverbal impairment in 4-year-old twins. J Speech, Lang Hear Res 2003; 46: 1271–1282.

    Article  Google Scholar 

  26. Rozen S, Skaletsky HJ . Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics Methods in Molecular Biology. Humana Press: New Jersey, 2000; 365–386.

    Google Scholar 

  27. Freeman B, Smith N, Curtis C, Huckett L, Mill J, Craig I . DNA from buccal swabs recruited by mail: evaluation of storage effects on long-term stability and suitability for multiplex polymerase chain reaction genotyping. Behav Genet 2003; 33: 67–72.

    Article  CAS  PubMed  Google Scholar 

  28. Hoogendoorn B, Norton N, Kirov G, Williams N, Hamshere ML, Spurlock G et al. Cheap, accurate and rapid allele frequency estimation of single nucleotide polymorphisms by primer extension and DHPLC in DNA pools. Hum Genet 2000; 107: 488–493.

    Article  CAS  PubMed  Google Scholar 

  29. Liu Q, Thorland EC, Sommer SS . Inhibition of PCR amplification by a point mutation downstream of a primer. Biotechniques 1997; 22: 292–300.

    Article  CAS  PubMed  Google Scholar 

  30. Barnard R, Futo V, Pecheniuk N, Slattery M, Walsh T . PCR bias toward the wild-type k-ras and p53 sequences: implications for PCR detection of mutations and cancer diagnosis. Biotechniques 1998; 25: 684–691.

    Article  CAS  PubMed  Google Scholar 

  31. Le Hellard S, Ballereau SJ, Visscher PM, Torrance HS, Pinson J, Morris SW et al. SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi automated method for data storage and analysis. Nucleic Acids Res 2002; 30: e74.

    Article  PubMed  PubMed Central  Google Scholar 

  32. Tavaria M, Gabriele T, Anderson RL, Mirault ME, Baker E, Sutherland G et al. Localization of the gene encoding the human heat shock cognate protein, HSP73, to chromosome 11. Genomics 1995; 29: 266–268.

    Article  CAS  PubMed  Google Scholar 

  33. Plomin R, DeFries JC, Craig IW, McGuffin P . Behavioral genetics. In: Plomin R, DeFries JC, Craig IW, McGuffin P (eds). Behavioral Genetics in the Postgenomic Era. American Psychological Association: Washington, DC, 2003; 3–15.

    Chapter  Google Scholar 

  34. Cohen J . Statistical Power Analysis for the Behavioral Sciences, 2nd edn. Hillsdale, Lawrence Erlbaum Associates: New Jersey, 1988.

    Google Scholar 

  35. Zou G, Zhao H . The impacts of errors in individual genotyping and DNA pooling on association studies. Genet Epidemiol 2004; 26: 1–10.

    Article  PubMed  Google Scholar 

  36. Eddy SR . Non-coding RNA genes and the modern RNA world. Nat Rev Genet 2001; 2: 919–929.

    Article  CAS  PubMed  Google Scholar 

  37. Butcher LM, Meaburn E, Liu L, Hill L, Al-Chalabi A, Plomin R et al. Genotyping pooled DNA on microarrays: a systematic genome screen of thousands of SNPs in large samples to detect QTLs for complex traits. Behav Genet 2004; 4: 549–555.

    Article  Google Scholar 

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We thank all the parents and twins who have contributed time and effort to the Twins Early Development Study (TEDS) for making this study possible. We are also grateful to KBiosciences, UK for their proficient individual genotyping efforts. This work was supported in part by UK Medical Research Council grant G9424799.

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Correspondence to L M Butcher.

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Butcher, L., Meaburn, E., Dale, P. et al. Association analysis of mild mental impairment using DNA pooling to screen 432 brain-expressed single-nucleotide polymorphisms. Mol Psychiatry 10, 384–392 (2005).

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