Haplotype-based stratification of Huntington's disease

Abstract

Huntington's disease (HD) is an autosomal dominant neurodegenerative disease caused by expansion of a CAG trinucleotide repeat in HTT, resulting in an extended polyglutamine tract in huntingtin. We and others have previously determined that the HD-causing expansion occurs on multiple different haplotype backbones, reflecting more than one ancestral origin of the same type of mutation. In view of the therapeutic potential of mutant allele-specific gene silencing, we have compared and integrated two major systems of HTT haplotype definition, combining data from 74 sequence variants to identify the most frequent disease-associated and control chromosome backbones and revealing that there is potential for additional resolution of HD haplotypes. We have used the large collection of 4078 heterozygous HD subjects analyzed in our recent genome-wide association study of HD age at onset to estimate the frequency of these haplotypes in European subjects, finding that common genetic variation at HTT can distinguish the normal and CAG-expanded chromosomes for more than 95% of European HD individuals. As a resource for the HD research community, we have also determined the haplotypes present in a series of publicly available HD subject-derived fibroblasts, induced pluripotent cells, and embryonic stem cells in order to facilitate efforts to develop inclusive methods of allele-specific HTT silencing applicable to most HD patients. Our data providing genetic guidance for therapeutic gene-based targeting will significantly contribute to the developments of rational treatments and implementation of precision medicine in HD.

Figure 1

Definitions and sequence relationships of HTT haplotypes. (a) Twenty SNPs, one 3 bp indel (rs149109767, alleles R-reference and D-deletion) and the CAG repeat polymorphism are shown at their genomic locations relative to that of the HTT RefSeq transcript (NM_002111). Genotype at each marker on each of 16 HTT haplotypes, defined in the text, is shown above the marker. Haplotypes are ordered based upon a neighbor-joining method (p-distance model) in a dendrogram with two main branches, each with different sizes of sub-clusters. Alleles in red represent differences from hap.01, the most frequent haplotype on CAG-expanded HD chromosomes. (b) Consensus alleles of 10 exon SNPs and 10 intron SNPs that showed the biggest cumulative heterozygosity were determined for each haplotype based on 1000 Genomes Project data. A consensus allele for a given SNP site represents the most frequent allele among a collection of chromosomes with same haplotype. Since hap.10 is not present in 1000 Genomes data (Phase 1), hap.10 was excluded in this analysis. Subsequently, alleles of SNPs that show variable alleles in 15 haplotypes and alleles of two exon SNPs that were used to define the haplotypes are indicated. SNPs in orange and black font colors represent SNPs on exons and introns of RefSeq NM_002111, respectively.

Figure 2

Correspondences of haplotypes and haplogroups. Based on Supplementary Table 4, correspondences of haplotypes to haplogroups were summarized. ‘hap.other’ and ‘Other’ were excluded to focus on distinct haplotypes. Thickness of an arrow represents relative proportion of a specific haplotype-haplogroup correspondence for a given haplotype. For example, most of hap.02 is classified as haplogroup A2b, and a small portion of hap.02 is classified as haplogroup A2a. Actual haplotype-haplogroup correspondence data can be found in Supplementary Table 4.

Figure 3

Frequencies of haplotypes in HD disease and normal chromosomes. HD subjects carrying one expanded and one normal chromosome were included in this analysis to estimate overall frequencies of haplotypes. From haplotypes probabilistically determined based on a union set of 74 SNPs, we used our haplotype definitions to classify each chromosome. Subsequently, frequencies of our haplotypes in HD disease chromosomes (a) and normal chromosomes in HD subjects (b) were calculated and summarized.