Our genome-wide association study of Finnish ALS patients and controls identified loci on chromosomes 9p21 and 21q22 that represent the most significant association signals identified in a GWAS of ALS to date.2–9
The homozygous D90A allele of the SOD1
gene is a well-known cause of ALS within the Scandinavian population15
, and family-based linkage studies have previously identified the chromosome 9p13.2–21.3 region as being relevant to the pathogenesis of ALS.16–21
An earlier GWAS study reported by van Es et al gave suggestive evidence of association in the same chromosomal region, though the p-value in that study did not achieve genome-wide significance (uncorrected p for rs3849942 = 1·58×10−6
compared to a threshold of 1·7×10−7
for genome-wide significance based on 293,768 SNPs analyzed in that study).9
Published contemporaneously with our study, a GWAS of 599 UK ALS cases and 4,144 controls also replicated the association signal on chromosome 9p21 (rs903603, p-value = 8.9×10−8
Joint analysis involving these UK samples and an additional 3,713 cases and 3,986 controls that included US, Italian and Irish samples genotyped at our laboratory2–4
yielded a p-value of 6.64×10−10
While this cannot be considered to be an independent replication because of the sample overlap with the van Es et al GWAS9
, these data support the notion that the 9p21 locus is important across multiple populations.
Our data highlight the utility of performing GWA studies in population isolates with a high incidence of a particular disease. Compared to outbred European ancestry cohorts, the genetic homogeneity of the Finnish population increased our power to detect associated loci by decreasing both genetic variability (i.e. the number of genes in a population that cause disease), and allelic heterogeneity (i.e. the number of mutant alleles within a causative gene).10
Indeed, of the 36 monogenic diseases that are highly enriched in the Finnish population (known as the Finnish Disease Heritage), a single founder mutation accounts for 70–100% of these disease alleles.13,14,29
A comparison of epidemiological studies of ALS found the incidence of the disease in Finland to be 8·2 per 100,000 of the population among the 50 to 79 age-group, representing the highest occurrence of motor neuron degeneration outside of the Pacific Rim.11,12
Our study demonstrates that a sizeable proportion of this excess occurrence stems from an overrepresentation of the chromosome 9p21 risk haplotype and homozygous D90A SOD1
mutations within the Finnish population. In particular, the chromosome 9p21 risk haplotype was found in 44 out of 93 familial cases (47·3%), representing a larger proportion than was explained by the known D90A SOD1
allele (27 out of 93 cases, 29·0%). This scenario of a small number of loci underlying a disease arises from the unique history of Finland with a small founder population limited to several thousand individuals, and multiple population bottlenecks over the last few millennia, where a significant percentage of a population is killed or prevented from reproducing.13,14
Although homozygous D90A SOD1
allele is relatively uncommon outside of Scandinavia and Russia, a recent study has shown that the chromosome 9p21 locus accounts for a sizeable proportion of French ALS cases.20
However, because referral bias is known to occur in clinic-based cohorts of ALS patients30
, additional longitudinal, population-based genetic studies are required to determine if our results are generalizable to the entire Finnish ALS population. Furthermore, the lack of age- and gender-matching between the cases and controls included in this study may have lead to overestimation of the contribution of the identified loci in the pathogenesis of ALS in Finland, though this impact was likely mitigated by the close matching of genetic ancestry (see webappendix p 2).31
Our data dramatically narrow the region of interest within the chromosome 9p21 ALS locus from the known 3.58Mb minimum overlap region based on published linkage studies down to a 232Kb block of linkage disequilibrium (LD). Within this LD block, we identified a 42-SNP haplotype that was significantly associated with ALS, and which serves as a marker for the underlying founder mutation. The chromosome 9p21 ALS locus most likely represents a monogenic form of disease, as the association signal was strongest in an analysis restricted to familial ALS cases, and the original identification of the region was based on linkage studies of ALS families.16–21
The high odds ratio associated with carrying the 42-SNP risk haplotype is also consistent with monogenic, high penetrance inheritance. Although this 232Kb LD block encodes only four genes, mutation screening of these coding regions in our Finnish ALS cases failed to identify a pathogenic amino acid altering variant. This is consistent with reports from other groups who have similarly failed to identify a coding variant in the larger region, and suggests that the genetic factor underlying chromosome 9p21-related ALS may lie in an intronic or intergenic region, and may give rise to disease either by abnormally altering splicing, or by influencing gene expression.
A recently published GWAS of patients diagnosed with FTD detected a tentative association signal in the same LD block on chromosome 9p21 as found in our study of ALS patients.27
Furthermore, the partial risk haplotype reported in the FTD study was identical to that identified in our cohort of Finnish ALS patients.27
This observation is consistent with growing clinical, epidemiological, and genetic evidence indicating that ALS and FTD form a spectrum of disease, characterized neuropathologically by TDP-43 staining ubiquitin neuronal inclusions.32
In our study, ~4% of the patients linked to the chromosome 9p21 locus presenting with motor neuron dysfunction ultimately developed cognitive changes consistent with frontal lobe degeneration. Taken together, these data strongly suggest that the chromosome 9p21 locus represents a single founder mutation that underlies any combination of motor neuron and frontal cortex degeneration (i.e. pure ALS, pure FTD, ALS-FTD, and FTD with motor neuron disease). It is noteworthy that the prevalence rate of FTD in Scandinavia is among the highest in the world33
, suggesting an underlying genetic predisposition within this geographical region. Further studies will be required to confirm that the increased occurrence of FTD in Finland is also due to the chromosome 9p21 mutation.
In summary, our genome-wide study of the genetically homogeneous Finnish population identified the strongest associations signals of any ALS GWAS reported to date. Together, the chromosome 9p21 locus and the D90A allele of the SOD1
gene account for a large proportion of the excess incidence of ALS cases in Finland, and our observations further demonstrate the utility of performing GWAS in isolated populations. Furthermore, our data define a 42-SNP haplotype on chromosome 9p21 that significantly increased the risk of developing ALS, and which was identical to the risk haplotype recently tentatively suggested in FTD cases. The high frequency of this risk haplotype in the Finnish ALS population, as well as its identification in a recent FTD GWAS, suggests that chromosome 9p21-related disease arose from a single founder mutation with the highest frequency in Northern Europe, and which has subsequently disseminated throughout other European populations. Despite the inability to identify the specific genetic variant underlying this locus, our data make it feasible to identify chromosome 9p21-linked ALS cases by sequencing samples for this risk haplotype.20
Our future studies will continue to exploit the unique genetic structure of the Finnish population to understand the specific genetic factor underlying the chromosome 9p21 locus and to identify additional loci important in the pathogenesis of this fatal neurodegenerative disorder.