The C9ORF72 expansion mutation is a common cause of ALS+/-FTD in Europe and has a single founder

Abstract

A massive hexanucleotide repeat expansion mutation (HREM) in C9ORF72 has recently been linked to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here we describe the frequency, origin and stability of this mutation in ALS+/-FTD from five European cohorts (total n=1347). Single-nucleotide polymorphisms defining the risk haplotype in linked kindreds were genotyped in cases (n=434) and controls (n=856). Haplotypes were analysed using PLINK and aged using DMLE+. In a London clinic cohort, the HREM was the most common mutation in familial ALS+/-FTD: C9ORF72 29/112 (26%), SOD1 27/112 (24%), TARDBP 1/112 (1%) and FUS 4/112 (4%) and detected in 13/216 (6%) of unselected sporadic ALS cases but was rare in controls (3/856, 0.3%). HREM prevalence was high for familial ALS+/-FTD throughout Europe: Belgium 19/22 (86%), Sweden 30/41 (73%), the Netherlands 10/27 (37%) and Italy 4/20 (20%). The HREM did not affect the age at onset or survival of ALS patients. Haplotype analysis identified a common founder in all 137 HREM carriers that arose around 6300 years ago. The haplotype from which the HREM arose is intrinsically unstable with an increased number of repeats (average 8, compared with 2 for controls, P<10(-8)). We conclude that the HREM has a single founder and is the most common mutation in familial and sporadic ALS in Europe.

Figure 1

Details of the 82-SNP risk haplotype defined by rs1 05 11 816 (2 74 68 461 hg19) to rs7 34 40 960 (2 75 78 647 hg19), covering 110 kb region between MOB3B and C9ORF72. The top row represents the background haplotype on which the expansion arose (r), with the founder expansion directly below it (R). An additional 12 recombined HREM haplotypes are also shown along with their representation within the case cohort. The non-risk allele is highlighted in red.

Figure 2

(a) Multiple alignment of the region surrounding the HREM from various mammals, showing the polymorphism in chimpanzees. Digits in identifiers refer to NCBI Trace Archive (ti) accession numbers, for example, ti 26 82 35 684. (b) Phylogeny of the unique haplotypes observed within our sample set, showing how the HREM occurs only within a single, distinct, clade of risk-associated haplotypes. Identifiers with an X contain the expanded HREM allele (highlighted in red). Digits after the underscore indicate the number of chromosomes in which the haplotype was observed. The phylogram was constructed from the consensus of 3807 best-scoring trees produced by the phylip 3.69 dnapars algorithm (Felsenstein, 1989), rooted using an unweighted consensus from all 139 unique haplotypes. To retain clarity, only those haplotypes with the HREM or those without but seen five or more times are shown. Additionally, nine haplotypes that had undergone major recombination events were also removed. Four of these contained the expansion (4 chromosomes) and five did not (33 chromosomes). (c) Figures showing repeat allele frequencies for risk and non-risk haplotypes. The repeat sizes are smaller for the non-risk haplotypes, consistent with the hypothesis that the risk haplotype predisposes to repeat instability. The difference in repeat allele frequency distribution for the two haplotype patterns is highly significant (P≪10^–8).

Figure 3

Bar chart showing how the frequency of the founder risk haplotype varies across continents and populations (data from the 1000 Genomes project, www.1000genomes.org), and how it is most prevalent in Europeans. Percentages indicate the number of chromosomes on which the haplotype was observed.