Relative RLA of <i>IDE</i> putative functional variants and haplotypes.

<p>Relative RLA levels to pGL3P (RRLA), expressed as % pGL3P expression are tabulated for each variant comprising a–b) H1, c–d) H2, e–f) H6, g–h) H9. 0 = major allele, 1 = minor allele. H1 = the most common <i>IDE</i> haplotype comprising the major allele at each variant. The RRLA for each sequence comprising haplotypes H2, H6 and H9 are plotted relative to the sequence comprising H1, expressed as fold-change in RRLA relative to H1. “Haplotype RRLA” is the averaged % RRLA for the variants in each haplotype. All standard error of the mean RRLA <0.7. P-values resulting from paired t-tests comparing “Haplotype RRLA” values for H2, H6 or H9 vs H1 are also shown.</p

Summary of 17 <i>IDE</i> variants and haplotype composition.

<p>The variant ID (vID), rs number (where available), major (Maj) and minor (Min) allele, Chromosomal position, location within the gene, % conservation of surrounding sequence with mouse and rat genomes and minor allele frequency (MAF) are detailed for each variant. The allele composition of the three haplotypes studied here are defined as 0 = major allele, 1 = minor allele. The fold-difference (Δ) in cerebellar <i>IDE</i> mRNA levels are given for each individual variant and haplotype that demonstrated significance at the p<0.05 level only.</p

<i>IDE</i> variant specific primer sequences.

<p>Primers specific for sequences in <i>IDE</i> surrounding each variant were used to generate attB- tagged products for cloning; sequences were amplified from DNA taken from individuals known to be homozygous for the major and minor allele indicated in the “Major” and “Minor” columns; vID; variant identification number, rs number; dbSNP variant identifier, Size; PCR product size (base pairs), AT; annealing temperature used for the amplification of each sequence.</p

Functional effects of sequences surrounding five <i>IDE</i> variants on <i>in vitro</i> reporter gene expression.

<p>Relative Luciferase Activity (RLA; relative <i>Firefly:Renilla Luciferase</i> values) is shown for A) v685, B) v10, C) v315, D) v687 and E) v154 in Be(2)-C and HepG2 cell lines. Constructs containing sequence surrounding major allele are shown as white bars and those containing sequence surrounding minor allele are shown as shaded bars. <i>IDE</i> sequences were cloned either 5′ to the promoter or 3′ to <i>Firefly Luciferase</i>. Error bars represent standard error of the mean. * p = 0.05−0.01, ** p = 0.009−0.0001.</p

Proportion of carriers of the minor allele according to age in controls free of neurological disease.

<p>SNP = single nucleotide polymorphism. CI = confidence interval. *Chromosomal positions based on the February 2009 (GRCH37/hg19) genome assembly [<i>SNCA</i> is located at Chr4;90,645,251–90,759,447]. P-values result from logistic regression models adjusted for gender, where the outcome was presence of the minor allele of the given SNP, and the predictor variable was age as a continuous variable. Genotype call rates for all SNPs were >95%.</p

Single SNP associations with PD.

<p>PD = Parkinson's disease. SNP = single nucleotide polymorphism. MA = minor allele. OR = odds ratio. CI = confidence interval. *Chromosomal positions based on the February 2009 (GRCH37/hg19) genome assembly [<i>SNCA</i> is located at Chr4;90,645,251–90,759,447]. ORs, 95% CIs, and p-values result from logistic regression models adjusted for age and gender. ORs correspond to presence vs. absence of the minor allele.</p

Linkage disequilibrium between SNPs in controls as measured by pairwise r² values.

<p>Values are given as percentages out of a maximum of 100. Solid black boxes indicate an r² value of 100.</p

Exonic Re-Sequencing of the Chromosome 2q24.3 Parkinson’s Disease Locus

<div><p>Genome-wide association studies (GWAS) in Parkinson’s disease (PD) have identified over 20 genomic regions associated with disease risk. Many of these loci include several candidate genes making it difficult to pinpoint the causal gene. The locus on chromosome 2q24.3 encompasses three genes: <i>B3GALT1</i>, <i>STK39</i>, and <i>CERS6</i>. In order to identify if the causal variants are simple missense changes, we sequenced all 31 exons of these three genes in 187 patients with PD. We identified 13 exonic variants including four non-synonymous and three insertion/deletion variants (indels). These non-synonymous variants and rs2102808, the GWAS tag SNP, were genotyped in three independent series consisting of a total of 1976 patients and 1596 controls. Our results show that the seven identified 2q24.3 coding variants are not independently responsible for the GWAS association signal at the locus; however, there is a haplotype, which contains both rs2102808 and a <i>STK39</i> exon 1 6bp indel variant, that is significantly associated with PD risk (Odds Ratio [OR] = 1.35, 95% CI: 1.11–1.64, P = 0.003). This haplotype is more associated than each of the two variants independently (OR = 1.23, P = 0.005 and 1.10, P = 0.10, respectively). Our findings suggest that the risk variant is likely located in a non-coding region. Additional sequencing of the locus including promoter and regulatory regions will be needed to pinpoint the association at this locus that leads to an increased risk to PD.</p></div

Exonic variants detected by sequencing of 187 PD patients and validation in 376 controls.

<p>*Exon 1 of <i>B3GALT1</i> is non-coding, AA = amino acid, MAF = minor allele frequency, OR = Odds ratio, CI = confidence interval, P = P-value. Only non-synonymous and indel coding variants were genotyped in controls.</p><p>Exonic variants detected by sequencing of 187 PD patients and validation in 376 controls.</p

<i>STK39</i> exon 1 insertion/deletion variants.

<p>We detected three insertion/deletion (indels) variants in exon 1 of gene <i>STK39</i>. The indels are located in a proline/alanine rich protein domain called the PAPA box. The figure was created using the UCSC genome browser. (<a href="http://genome.ucsc.edu/" target="_blank">http://genome.ucsc.edu/</a>)</p