C9orf72 Repeat Expansion Discordance in 6 Multigenerational Kindreds

Abstract

Background and objectives: A hexanucleotide repeat expansion in the noncoding region of the C9orf72 gene is the most common genetically identifiable cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia in populations of European ancestry. Pedigrees associated with this expansion exhibit phenotypic heterogeneity and incomplete disease penetrance, the basis of which is poorly understood. Relatives of those carrying the C9orf72 repeat expansion exhibit a characteristic cognitive endophenotype independent of carrier status. To examine whether additional shared genetic or environmental risks within kindreds could compel this observation, we have conducted a detailed cross-sectional study of the inheritance within multigenerational Irish kindreds carrying the C9orf72 repeat expansion.

Methods: One hundred thirty-one familial ALS pedigrees, 59 of which carried the C9orf72 repeat expansion (45.0% [95% CI 36.7-53.5]), were identified through the Irish population-based ALS register. C9orf72 genotyping was performed using repeat-primed PCR with amplicon fragment length analysis. Pedigrees were further investigated using SNP, targeted sequencing data, whole-exome sequencing, and whole-genome sequencing.

Results: We identified 21 kindreds where at least 1 family member with ALS carried the C9orf72 repeat expansion and from whom DNA was available from multiple affected family members. Of these, 6 kindreds (28.6% [95% CI 11.8-48.3]) exhibited discordant segregation. The C9orf72 haplotype was studied in 2 families and was found to segregate with the C9orf72-positive affected relative but not the C9orf72-negative affected relative. No other ALS pathogenic variants were identified within these discordant kindreds.

Discussion: Family members of kindreds associated with the C9orf72 repeat expansion may carry an increased risk of developing ALS independent of their observed carrier status. This has implications for assessment and counseling of asymptomatic individuals regarding their genetic risk.

Figure 1. Flowchart of Irish ALS Kindreds Carrying the C9orf72 Repeat Expansion

Figure 2. C9orf72 Discordant Families

(A) refers to Pedigree A, (B) to Pedigree B and (C) to Pedigree C. C9orf72+ indicates a carrier of the repeat expansion as confirmed with rpPCR in 2 independent laboratories. C9orf72- indicates the individual does not carry the pathogenic expansion. SNP indicates that there is SNP genotyping available. TNGS indicates that there is targeted sequencing data available. WES indicates that there is whole-exome sequencing data available. WGS indicates that there is whole-genome sequencing data available.

Figure 3. C9orf72 Haplotype Analysis for Pedigrees A and C

The yellow highlight indicates that the 2 positive samples carry the established elongated C9orf72 haplotype. The red highlight indicates 2 loci where the C9orf72-negative patients in pedigrees A and C are homozygous for the nonrisk allele indicating that they either did not inherit the haplotype or recombination occurred in the inherited haplotype. Both whole-genome sequencing (WGS) and SNP genotyping were available for individual II.XI in pedigree A. The presence of heterozygous genotypes eliminates the possibility that the observed haplotype is attributable to a large deletion in the region.