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

Lupton MK, Proitsi P, Danillidou M, Tsolaki M, Hamilton G, Wroe R, Pritchard M, Lord K, Martin BM, Kloszewska I, Soininen H, Mecocci P, Vellas B, Harold D, Hollingworth P, Lovestone S, Powell JF - PLoS ONE (2011)

Bottom Line: 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.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).

View Article: PubMed Central - PubMed

Affiliation: MRC Centre for Neurodegeneration Research, Institute of Psychiatry, King's College London, London, United Kingdom.

ABSTRACT
Nicastrin is an obligatory component of the γ-secretase; the enzyme complex that leads to the production of Aβ 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.

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Related in: MedlinePlus

Depth of coverage.A: The depth of coverage at each position where the X axis shows the genomic position on chromosome 1 (hg18, Mar. 2006). B: Locations of the PCR products aligned to the X axis. C: Locations of the Exons of Nicastrin aligned to the X axis.
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pone-0017298-g001: Depth of coverage.A: The depth of coverage at each position where the X axis shows the genomic position on chromosome 1 (hg18, Mar. 2006). B: Locations of the PCR products aligned to the X axis. C: Locations of the Exons of Nicastrin aligned to the X axis.

Mentions: The sequencing of the case and control pools generated 307005 and 302171 reads respectively. For the case and control pools 87.1% and 87.0% of reads respectively mapped to the reference sequence. This resulted in a mean coverage of 228 reads per position for each individual in the case pool (114 per allele) and 197 reads per position for each individual in the control pool (98 reads per allele). Fig. 1A shows the distribution of read coverage. Using the cut off for variant calling described in the methods we were able to identify SNPs at a frequency of 3–8 variants in the pool, depending on the transition type. For example in the case pool the error distribution allowed the identification of a G-A transversion with a frequency of 3 variants, but for a A-C transition the error distribution was higher only allowing the identification of variants with a frequency as low as 7.


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

Lupton MK, Proitsi P, Danillidou M, Tsolaki M, Hamilton G, Wroe R, Pritchard M, Lord K, Martin BM, Kloszewska I, Soininen H, Mecocci P, Vellas B, Harold D, Hollingworth P, Lovestone S, Powell JF - PLoS ONE (2011)

Depth of coverage.A: The depth of coverage at each position where the X axis shows the genomic position on chromosome 1 (hg18, Mar. 2006). B: Locations of the PCR products aligned to the X axis. C: Locations of the Exons of Nicastrin aligned to the X axis.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3045431&req=5

pone-0017298-g001: Depth of coverage.A: The depth of coverage at each position where the X axis shows the genomic position on chromosome 1 (hg18, Mar. 2006). B: Locations of the PCR products aligned to the X axis. C: Locations of the Exons of Nicastrin aligned to the X axis.
Mentions: The sequencing of the case and control pools generated 307005 and 302171 reads respectively. For the case and control pools 87.1% and 87.0% of reads respectively mapped to the reference sequence. This resulted in a mean coverage of 228 reads per position for each individual in the case pool (114 per allele) and 197 reads per position for each individual in the control pool (98 reads per allele). Fig. 1A shows the distribution of read coverage. Using the cut off for variant calling described in the methods we were able to identify SNPs at a frequency of 3–8 variants in the pool, depending on the transition type. For example in the case pool the error distribution allowed the identification of a G-A transversion with a frequency of 3 variants, but for a A-C transition the error distribution was higher only allowing the identification of variants with a frequency as low as 7.

Bottom Line: 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.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).

View Article: PubMed Central - PubMed

Affiliation: MRC Centre for Neurodegeneration Research, Institute of Psychiatry, King's College London, London, United Kingdom.

ABSTRACT
Nicastrin is an obligatory component of the γ-secretase; the enzyme complex that leads to the production of Aβ 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.

Show MeSH
Related in: MedlinePlus