1. Volume 23, Issue 11, Pages 1759-1771 (November 2015)
Huntingtin Haplotypes Provide Prioritized Target Panels for Allele-specific Silencing in Huntington Disease Patients of European Ancestry 
Chris Kay, Jennifer A Collins, Niels H Skotte, Amber L Southwell, Simon C Warby, Nicholas S Caron, Crystal N Doty, Betty Nguyen, Annamaria Griguoli, Colin J Ross, Ferdinando Squitieri, Michael R Hayden 
Molecular Therapy 
Volume 23, Issue 11, Pages (November 2015)
DOI: /mt
Copyright © 2015 American Society of Gene & Cell Therapy Terms and Conditions

2. Figure 1
SNPs across HTT represent specific gene-spanning haplotypes. (a) Single-nucleotide polymorphisms (SNPs) across HTT belong to gene-spanning haplotypes representing three major haplogroups A, B, and C. Transcribed (intragenic) SNPs are shaded gray. The primary Huntington disease (HD) haplotype, A1, is defined by rs The secondary HD haplotype A2 is defined by rs and rs One SNP (rs ) distinguishes the A haplogroup from the B and C haplogroups (black box). In our panel, 8 of 51 intragenic SNPs exclusively distinguish the A and B haplogroups from the C haplogroup (bold). (b) Pairwise linkage disequilibrium (LD) of SNP genotypes (r2) reveals a complex haplotype structure across the HTT gene region (black, r2 = 1; shades of gray, 1 > r2 > 0; white, r2 = 0). Alleles present on similar haplotypes are in high pairwise LD across HTT, such as A2-defining rs and rs Haplotype A1-defining SNP rs is not in LD with any other variant in our initial 63-SNP panel. Positions correspond to GRCh37. Representative extragenic crossover sequences are colored according to the most likely originating haplotype.
Molecular Therapy  , DOI: ( /mt )
Copyright © 2015 American Society of Gene & Cell Therapy Terms and Conditions

3. Figure 2
A1, A2, and A3a are the most common gene-spanning HD haplotypes. (a) In the UBC HD BioBank, the expanded CAG repeat (CAG > 35) is found on the A1 haplotype in 48.1% of phased, unrelated Canadian Huntington disease (HD) chromosomes. Intragenic recombinant haplotypes (X) are rare (3.0% of controls) whereas >95% of HTT haplotypes show no evidence of recombination within the transcribed gene sequence. C1 is the most common intragenic haplotype among Canadian control chromosomes, representing 29.8%. (b) The most common HD haplotype, A1, is uniquely defined by three transcribed polymorphisms in high pairwise linkage disequilibrium (LD) across HTT. The 4 bp indel rs represents a novel polymorphism associated with the CAG expansion (bold). The second most common HD haplotype, A2, is defined by five intragenic single-nucleotide polymorphisms (SNPs), three of which are novel (bold). HD-associated A3a, the third most common HD haplotype, is specifically marked by the novel SNP rs (c) Pairwise LD plot (r2) of A1 and A2 haplotype-defining polymorphisms as calculated from 700 phased haplotypes of European Caucasians.
Molecular Therapy  , DOI: ( /mt )
Copyright © 2015 American Society of Gene & Cell Therapy Terms and Conditions

4. Figure 3
In four European Huntington disease (HD) cohorts, distinct distributions of HD haplotypes are observed. As in Canada, A1 is the most frequent HD haplotype in Finland (60%) and Sweden (51%), and France (45%). In contrast, A2 is the most frequent HD haplotype in Italy (58%).
Molecular Therapy  , DOI: ( /mt )
Copyright © 2015 American Society of Gene & Cell Therapy Terms and Conditions

5. Figure 4
Cumulative treatment coverage of Huntington disease (HD) patients by A1, A2, and A3a allele-specific HTT silencing targets in four patient populations of European ancestry. Targeting one A1 allele (among three) and one A2 allele (among five) would permit selective HTT silencing treatment in 68% of HD patients in the Canadian cohort. In combination, A1 + A2 + A3a targets would permit selective silencing of an average of 80% of HD patients across all four populations.
Molecular Therapy  , DOI: ( /mt )
Copyright © 2015 American Society of Gene & Cell Therapy Terms and Conditions

6. Figure 5
ASOs targeting ΔACTT (rs ) potently and selectively silence A1 HTT mRNA and protein in human cells. (a) Design of antisense oligonucleotide (ASO) gapmers selectively targeting mutant HTT A1 mRNA at the ΔACTT sequence. (b) Transfection of patient-derived lymphoblasts (44/18 CAG) with ΔACTT-complementary ASOs selectively reduces mutant HTT mRNA. Patient lymphoblasts transfected with 5-9-5, 5-7-5, and LNA gapmers show dose-dependent reduction of mutant HTT mRNA relative to untreated controls, falling to 21.5% mutant HTT mRNA at the highest dose. Wild-type HTT mRNA levels do not fall below untreated levels at any tested dose of or LNA gapmer. (c) Dose-dependent reduction of mutant HTT protein relative to untreated controls, sparing wtHTT at all tested and LNA gapmer doses. ** and *** represent P = 0.01 and P = by analysis of variance with Bonferroni post hoc. LNA, locked nucleic acid.
Molecular Therapy  , DOI: ( /mt )
Copyright © 2015 American Society of Gene & Cell Therapy Terms and Conditions