Common SNP-Based Haplotype Analysis of the 4p16.3 Huntington Disease Gene Region

Abstract

Age at the onset of motor symptoms in Huntington disease (HD) is determined largely by the length of a CAG repeat expansion in HTT but is also influenced by other genetic factors. We tested whether common genetic variation near the mutation site is associated with differences in the distribution of expanded CAG alleles or age at the onset of motor symptoms. To define disease-associated single-nucleotide polymorphisms (SNPs), we compared 4p16.3 SNPs in HD subjects with population controls in a case:control strategy, which revealed that the strongest signals occurred at a great distance from the HD mutation as a result of "synthetic association" with SNP alleles that are of low frequency in population controls. Detailed analysis delineated a prominent ancestral haplotype that accounted for ∼50% of HD chromosomes and extended to at least 938 kb on about half of these. Together, the seven most abundant haplotypes accounted for ∼83% of HD chromosomes. Neither the extended shared haplotype nor the individual local HTT haplotypes were associated with altered CAG-repeat length distribution or residual age at the onset of motor symptoms, arguing against modification of these disease features by common cis-regulatory elements. Similarly, the 11 most frequent control haplotypes showed no trans-modifier effect on age at the onset of motor symptoms. Our results argue against common local regulatory variation as a factor influencing HD pathogenesis, suggesting that genetic modifiers be sought elsewhere in the genome. They also indicate that genome-wide association analysis with a small number of cases can be effective for regional localization of genetic defects, even when a founder effect accounts for only a fraction of the disorder.

Huntingtin Haplotypes Provide Prioritized Target Panels for Allele-specific Silencing in Huntington Disease Patients of European Ancestry

“…codon deletion present in exon 58 of HTT has been targeted for selective HTT silencing in vitro by siRNA, 27,28 but the frequency of this polymorphism among HD chromosomes varies from 59% in an American cohort 26 to 18.6% in Italy. 29 No study has examined the phased heterozygosity and haplotype relationship of all common alleles in the HTT transcript and it therefore remains unclear which HTT polymorphism, or combination of polymorphisms, would offer treatment for the greatest number of patients across different ancestry groups.…”

“…Exogenous suppression of full-length mutant HTT by ASO is also sufficient for rescue of transcriptional abnormalities in YAC128 mice 37 . While the pathogenic impact of the exon 1 transcript remains unclear in HD patients, the efficacious reversal of HD phenotypes by suppression of full-length HTT in transgenic models suggests that reduction of the exon 1 transcript may not be required to elicit therapeutic benefits of ASO treatment.Expansion of the CAG repeat has been shown to occur on multiple haplotypes in different Caucasian populations 24,26. Here we demonstrate that three intragenic HTT haplotypes, identical across four different populations of European ancestry, account for approximately 90% of HD chromosomes across these groups.…”

Identification of Genetic Factors that Modify Clinical Onset of Huntington’s Disease

“…We and others have reported that the remaining variance has a large heritable component, implicating the actions of other genetic variations in modifying HD pathogenesis and suggesting that the difference between predicted and observed age of onset could be used in genetic studies to identify modifiers (Djoussé et al, 2003; Wexler et al, 2004). Haplotype analysis of HTT in HD subjects indicates that common genetic variation at the locus is not a major source of disease modification (Lee et al, 2012a), and the length of the normal CAG repeat in heterozygotes shows no statistically significant modifier influence, either alone or in interaction with the expanded allele (Lee et al, 2012b). Indeed, there is also no effect of a second expanded CAG allele on age at onset, indicating that HD pathogenesis is not HTT dosage dependent but rather reflects the completely dominant effects of a single mutant allele.…”

“…Analysis of GWA1 (after QC: ~700,000 typed and ~8 million 1000 Genomes-imputed SNPs with MAF > 1%) did not reveal any genome-wide significant signals for association with the phenotype of “residual of age at motor onset” in a linear mixed model with covariates including ancestry characteristics and gender (see Experimental Procedures for details). GWA1 provided the basis for building SNP haplotypes of HTT that revealed that ~50% of European HD subjects share a haplotype indicative of a common ancestor, but the rest are consistent with mutation on multiple other chromosome backbones contributing to HD (Lee et al, 2012a). No effect of HTT haplotype on the age at onset phenotype was detected, permitting all HD subjects to be grouped for our GWA analyses.…”

Multivariate genotypic analyses that identify specific genotypes to characterize disease and control groups in ADNI

“…In the validation analysis, these effects were "ambiguous" in that we have not classified them as "risk" or "control" factors because they fall outside of our designated regions (i.e., ambiguous because effects were either in a region between CON and AD or between CON and MCI). LRMP has been reported both in Huntington's Disease [93] and with substantial down-regulation in HIV neuroblastoma cell lines [94]. PARVG has been associated with Parkinson's Disease [95] and neurodegeneration [96].…”