Deep sequencing of the Nicastrin gene in pooled DNA, the identification of genetic variants that affect risk of Alzheimer's disease

Michelle K. Lupton, Petroula Proitsi, Makrina Danillidou, Magda Tsolaki, Gillian Hamilton, Richard Wroe, Megan Pritchard, Kathryn Lord, Belinda M. Martin, Iwona Kloszewska, Hilkka Soininen, Patrizia Mecocci, Bruno Vellas, Denise Harold, Paul Hollingworth, Simon Lovestone, John F. Powell

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Abstract

Nicastrin is an obligatory component of the gamma-secretase; the enzyme complex that leads to the production of Abeta fragments critically central to the pathogenesis of Alzheimer's disease (AD). Analyses of the effects of common variation in this gene on risk for late onset AD have been inconclusive. We investigated the effect of rare variation in the coding regions of the Nicastrin gene in a cohort of AD patients and matched controls using an innovative pooling approach and next generation sequencing. Five SNPs were identified and validated by individual genotyping from 311 cases and 360 controls. Association analysis identified a non-synonymous rare SNP (N417Y) with a statistically higher frequency in cases compared to controls in the Greek population (OR 3.994, CI 1.105-14.439, p = 0.035). This finding warrants further investigation in a larger cohort and adds weight to the hypothesis that rare variation explains some of genetic heritability still to be identified in Alzheimer's disease.
Original languageEnglish
Article numbere17298
JournalPLoS ONE
Volume6
Issue number2
DOIs
Publication statusPublished - 25 Feb 2011

Keywords

  • Alzheimer’s disease
  • genotyping
  • sequence alignment

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    Lupton, M. K., Proitsi, P., Danillidou, M., Tsolaki, M., Hamilton, G., Wroe, R., Pritchard, M., Lord, K., Martin, B. M., Kloszewska, I., Soininen, H., Mecocci, P., Vellas, B., Harold, D., Hollingworth, P., Lovestone, S., & Powell, J. F. (2011). Deep sequencing of the Nicastrin gene in pooled DNA, the identification of genetic variants that affect risk of Alzheimer's disease. PLoS ONE , 6(2), [e17298]. https://doi.org/10.1371/journal.pone.0017298