Candidate glutamatergic and dopaminergic pathway gene variants do not influence Huntington’s disease motor onset

Huntington’s disease (HD) is a neurodegenerative disorder characterized by motor, cognitive, and behavioral disturbances. It is caused by the expansion of the HTT CAG repeat, which is the major determinant of age at onset (AO) of motor symptoms. Aberrant function of N-methyl-D-aspartate receptors and/or overexposure to dopamine has been suggested to cause significant neurotoxicity, contributing to HD pathogenesis. We used genetic association analysis in 1,628 HD patients to evaluate candidate polymorphisms in N-methyl-D-aspartate receptor subtype genes (GRIN2A rs4998386 and rs2650427, and GRIN2B rs1806201) and functional polymorphisms in genes in the dopamine pathway (DAT1 3′ UTR 40-bp variable number tandem repeat (VNTR), DRD4 exon 3 48-bp VNTR, DRD2 rs1800497, and COMT rs4608) as potential modifiers of the disease process. None of the seven polymorphisms tested was found to be associated with significant modification of motor AO, either in a dominant or additive model, after adjusting for ancestry. The results of this candidate-genetic study therefore do not provide strong evidence to support a modulatory role for these variations within glutamatergic and dopaminergic genes in the AO of HD motor manifestations

Population stratification may bias analysis of PGC-1α as a modifier of age at Huntington disease motor onset

Huntington’s disease (HD) is an inherited neurodegenerative disorder characterized by motor, cognitive and behavioral disturbances, caused by the expansion of a CAG trinucleotide repeat in the HD gene. The CAG allele size is the major determinant of age at onset (AO) of motor symptoms, although the remaining variance in AO is highly heritable. The rs7665116 SNP in PPARGC1A, encoding the mitochondrial regulator PGC-1α, has been reported to be a significant modifier of AO in three European HD cohorts, perhaps due to affected cases from Italy. We attempted to replicate these findings in a large collection of (1,727) HD patient DNA samples of European origin. In the entire cohort, rs7665116 showed a significant effect in the dominant model (p value = 0.008) and the additive model (p value = 0.009). However, when examined by origin, cases of Southern European origin had an increased rs7665116 minor allele frequency (MAF), consistent with this being an ancestry-tagging SNP. The Southern European cases, despite similar mean CAG allele size, had a significantly older mean AO (p < 0.001), suggesting population-dependent phenotype stratification. When the generalized estimating equations models were adjusted for ancestry, the effect of the rs7665116 genotype on AO decreased dramatically. Our results do not support rs7665116 as a modifier of AO of motor symptoms, as we found evidence for a dramatic effect of phenotypic (AO) and genotypic (MAF) stratification among European cohorts that was not considered in previously reported association studies. A significantly older AO in Southern Europe may reflect population differences in genetic or environmental factors that warrant further investigation

SNPs revealed by exome sequencing in chromatin remodeling genes of the index patient.

<p>Bolded are the genes mutated in Coffin- Siris Syndrome. Standard nomenclatures for cDNA and protein variations (hg19) with their dbSNP reference numbers are listed. Genotypes variations from the reference hg19 genome sequence are indicated as 0/1 and 1/1 for heterozygous and homozygous variants, respectively. The effect of each SNP, denoted as single nucleotide variation (SNV), is shown as either synonymous (syn) or non-synonymous (nonsyn). Minor allele frequencies (MAF) are taken from the 1000 Genomes Project. N/A denotes non-available information.</p

Representative fluorescent <i>in situ</i> hybridization (FISH) patterns of DNA probes onto chromosomes 7, 22 der(7) and der(22) from this patient’s chromosome spreads.

<p>(<b>A</b>) Schematic drawing of normal chromosomes 7 and 22 and derivative chromosomes der(7) and der(22), showing the translocated chromosomal regions. The three panels below depict each the typical hybridization of a probe located (<b>B</b>) on chromosomes 7, der(7), (<b>C</b>) on chromosomes 7, der(7), der(22) and (<b>D</b>) chromosomes 7 and der(22).</p

Copy number variation (CNV) identified by array CGH in the patient.

<p>Shown are the CNV coordinates in hg18 (Build 36.3) for the gains and losses of DNA sequences on the listed chromosomes (Chr.) The number of individuals or occurrence in the Watson genome are indicated in the frequency data, which are derived from the Toronto Database of Genomic Variants (DGV).</p

FISH maps of YAC and BAC DNA clones from chromosome 7q31.1 in and around the duplicated region.

<p>The hg19 genomic coordinates of each marker and gene are indicated next to its designated name. The centromeric (CEN) and telomeric (TEL) directions are specified for orientation on the chromosome. Clones are denoted by their clone names, plate coordinates or/and Genbank designations. Each clone or restriction fragment is also denoted by its hybridization onto the patient’s chromosomes 7, der(7) and/or der(22). (<b>A</b>) FISH map of a 12.9 Mb region of chromosome 7 extending from the CFTR to the CPA1 genes. The denoted YAC probes represent three distinct areas of hybridization relative to the chromosome 7 translocation breakpoint, namely distal (7, der22), at or around the breakpoint (7, der7, der22) and proximal to the breakpoint (7, der7). (<b>B</b>) FISH map of BAC clones at and proximal to the 434,682 bp duplicated region, spanning the tail end of <i>C7orf58</i> and the entire <i>WNT16</i> and <i>FAM3C</i> genes. Note that all BAC clones within the duplicated region map to 7,d7,d22. (<b>C</b>) Bam HI restriction map, except for two designated Hind III (H) sites, of BAC 146J04 showing the FISH mapping of Bam HI and Hind III restriction fragments, indicating hybridization to 7,der(7) and der(22). The sizes in bp of each restriction fragment are shown and the exons in each gene displayed with solid boxes. The initiation (ATG) and termination (TGA, TAA) codons denote the gene boundaries except for C7orf58, which is only spanned by its last exon and part of the adjacent intron.</p