Carriership of two copies of C9orf72 hexanucleotide repeat intermediate-length alleles is a risk factor for ALS in the Finnish population

Abstract

The hexanucleotide repeat expansion in intron 1 of the C9orf72 gene causes amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. In addition to the effects of the pathogenic expansion, a role of intermediate-length alleles has been suggested in ALS, corticobasal degeneration and Parkinson’s disease. Due to the rarity of intermediate-length alleles with over 20 repeats and the geographical variability in their frequency, large studies that account for population stratification are needed to elucidate their effects. To this aim, we used repeat-primed PCR and confirmatory PCR assays to determine the C9orf72 repeat allele lengths in 705 ALS patients and 3958 controls from Finland. After exclusion of expansion carriers (25.5% of the ALS patients and 0.2% of the controls), we compared the frequency of intermediate-length allele carriers of 525 ALS cases and 3950 controls using several intermediate-length allele thresholds (7–45, 17–45, 21–45, 24–45 and 24–30). The carriership of an intermediate-length allele did not associate with ALS (Fisher’s test, all p ≥ 0.15) nor was there any association with survival (p ≥ 0.33), when we divided our control group into three age groups (18–65, 66–84 and 85–105 years). Carriership of two intermediate-length alleles was associated with ALS, when the longer allele was ≥ 17 repeats (p = 0.002, OR 5.32 95% CI 2.02–14.05) or ≥ 21 repeats (p = 0.00016, OR 15.21 95% CI 3.79–61.0). Our results show that intermediate-length alleles are a risk factor of ALS when present in both alleles, whereas carrying just one intermediate-length allele was not associated with ALS or survival.

C9orf72 Intermediate Repeats Confer Genetic Risk for Severe COVID-19 Pneumonia Independently of Age

“…Genetic analysis for C9orf72 HREs in the 240 COVID-19 patients did not reveal the presence of large (>30 repeats) expansions. Alleles with 2, 5, and 8 repeat units were the most frequent HREs in both sub-cohorts (Figure 1), as previously reported in several populations of both ALS patients and healthy controls [1,2,[4][5][6][7][8][9][10][11][12][47][48][49][50].…”

“…Demographic data of all patients are describ No differences in sex, age and ethnicity were found between the two sub-co Genetic analysis for C9orf72 HREs in the 240 COVID-19 patients did n presence of large (>30 repeats) expansions. Alleles with 2, 5, and 8 repeat u most frequent HREs in both sub-cohorts (Figure 1), as previously reported in ulations of both ALS patients and healthy controls [1,2,[4][5][6][7][8][9][10][11][12][47][48][49][50]. Based on a preliminary size cut-off of >8 and ≤30 repeat units to define lengths, which was determined on the basis of previous studies [12] (see M Methods section for more details), we found C9orf72 intermediate HREs in (16.25%) hospitalized COVID-19 patients and 8 out of 93 (8.60%) ALS pat Based on a preliminary size cut-off of >8 and ≤30 repeat units to define intermediate lengths, which was determined on the basis of previous studies [12] (see Materials and Methods section for more details), we found C9orf72 intermediate HREs in 39 out of 240 (16.25%) hospitalized COVID-19 patients and 8 out of 93 (8.60%) ALS patients, with a trend towards a higher prevalence of intermediate expansions in hospitalized COVID-19 vs. ALS patients, despite comparable average, median number and range of repeat units (Table 1).…”

“…In order to explore our hypothesis, we compared C9orf72 repeat size, allele distribution and frequency with those observed in a historical cohort of genetically characterized patients with ALS (n = 93), harboring no C9orf72 pathogenic large expansions, without clinically defined disorders related to immune dysfunctions, mostly Caucasian and from the same geographical region (Lombardy, Italy) of COVID-19 patients. Indeed, no significant differences in the distribution of repeat size, allele distribution and frequency have been observed between C9orf72 expansion-negative ALS cases and healthy controls in published studies [1,2,4,8,[47][48][49][50], while the length of the HRE may depend on the genetic ancestry, being expansions of more than 8 repeats linked to the chromosome 9 Finnish founder ALS risk haplotype that is common in individuals of Northern Europe ancestry [33]. Therefore, the cohort of C9orf72 expansion-negative ALS patients from the same geographical area of COVID-19 patients can be considered as representative of the population of that region regarding the genetic background relative to the C9orf72 gene and used to compare COVID-19 patients.…”

“…No significant differences between ALS cases without large C9orf72 HRE and healthy subjects have been thoroughly described regarding distribution, range and median repeat number [1,2,4,8,[47][48][49][50]. Nonetheless, differences in the prevalence of large C9orf72 pathogenic expansions have been described between people from Southern and Northern Europe and both large (>30 repeat units) and intermediate (>8 but ≤30 repeat units) expansions are linked to the chromosome 9 Finnish founder ALS risk haplotype, that is common in individuals of Northern European ancestry [33].…”

A Novel Genetic Marker for the C9orf72 Repeat Expansion in the Finnish Population

“…Thus, based on genotype data obtained from a global screening array, SNP association analysis was performed in a well-characterized iNPH patient cohort, comprising intermediate (15-30) and full-length (> 60 repeats) C9exp carriers (n = 41) who were compared to non-carriers (< 15 repeats, n = 801). Previous studies have suggested a pathological threshold of >30 units [3], [6] or >45 units [20] for the C9exp. However, intermediate repeats of <30 units may also associate with disease [4], [6], [7], [20].…”