Background/Purpose:   Although there are >50 rheumatoid arthritis (RA) risk loci that contain common variants, there are no known genomic loci that harbor rare mutations that influence RA risk in a Mendelian fashion. Here, we perform whole exome sequencing to search for rare, causal mutations in a 4-generation, 48-person consanguineous Syrian pedigree in which 8 individuals were affected with seropositive rheumatoid arthritis (RA). 

Methods:   We performed GWAS genotyping on 16 family members (affected and unaffected) and genome-wide exome sequencing in 4 CCP+ RA cases. To search for rare causal mutations, we developed a novel non-parametric linkage analysis we term “Loss-of-co-Homozygosity” (LOcH) mapping that extends homozygosity mapping to include any type of inheritance mode. The fundamental principal underlying LOcH is that a disease-causing mutation in a pedigree resides on a single ancestral haplotype, and that affected individuals will carry at least one copy of the mutation – but are never homozygous for the non-mutated allele. We used LOcH mapping to search the genome for regional stretches that lose one or both homozygous genotypes (i.e., lose “co-homozygosity”) in affected cases, which serve as candidate regions harboring rare causal mutations. Within the detected LOcH stretches, we performed imputation of mutations identified by exome sequencing.  We evaluated the presence of the LOcH stretches in other non-exome-sequenced subjects, and calculated a P-value for association with case-control status using Fisher’s exact test.

Results:   Using GWAS data and LOcH mapping, we identified ~12% of the genome in which the same ancestral haplotype was shared among all RA cases. Within these regions, we identified 13 nonsense or missense mutations shared among all cases but not observed in dbSNP, the 1000 Genomes Project, or the Exome Sequencing Project. We imputed these 13 candidate mutations in all unaffected family members, and found that 1 mutation preferentially segregated in cases compared to controls: all 4 RA cases inherited this mutation, but only 3/12 controls were heterozygous for the mutation (P = 0.02). The mutated gene is phospholipase B1 (PLB1), which has been implicated in human epidermal barrier function but not yet implicated in RA or other autoimmune diseases.

Conclusion:   While additional investigation of this mutation is required to confirm the association with risk of RA, the approach highlights a novel method of statistical analysis of genome-wide sequence data.

ACR Meeting Abstracts - https://acrabstracts.org/abstract/loss-of-co-homozygosity-mapping-and-exome-sequencing-of-a-syrian-pedigree-identified-the-candidate-causal-mutation-associated-with-rheumatoid-arthritis/