Clustering of Juvenile Canavan disease in an Indian community due to population bottleneck and isolation: genomic signatures of a founder event

• Published in: European journal of human genetics : EJHG 2023-01, Vol.31 (1), p.73-80
• Main Authors: Kotambail, Ananthapadmanabha, Selvam, Pavalan, Muthusamy, Karthik, Thomas, Maya, Sudhakar, Sniya Valsa, Ghati, Chetan, Danda, Sumita, Arunachal, Gautham
• Format: Article
• Language: English
• Subjects: Age; Ataxia; Birth weight; Canavan disease; Canavan Disease - genetics; Cluster Analysis; Consanguinity; Founder Effect; Genetic screening; Genetics; Genetics, Population; Genomics; Genotyping; Haplotypes; Humans; Linkage disequilibrium; Mutation; Neurodegenerative diseases; Phenotypes; Population bottleneck; Population genetics; Population structure
• ISSN: 1018-4813; 1476-5438
• DOI: 10.1038/s41431-022-01198-4

Mild/juvenile Canavan disease (M/JCD) is less frequently reported in the literature and little is known about its pathogenetic mechanisms. We report a comprehensive investigation into the pathogenetic mechanism of a novel NM_000049.4(ASPA):c.526G>A variant in two families. The families belong to Telugu Devanga Chettiar community (TDC) from southern India. TDC has a complex history of migration from their historical origin centuries ago with high endogamy. TDC probably has the highest clustering M/JCD recorded historically (around 24 cases). The pathogenic variant was shown to cause non-classical splicing defect resulting in two different transcripts. The splicing aberration, a loss of function mechanism coupled with a milder missense effect can explain the milder phenotype compared to the infantile-onset CD. The high clustering of an extremely rare form of neurodegenerative disorder with reduced fitness, led us to speculate the possibility of a founder event. Genotyping array of TDC and multiple distinct populations of Indian origin for several population genetic parameters was performed. It yielded robust signatures of a founder event in TDC, such as a high fixation index, increased runs of homozygosity and identity-by-descent in the absence of consanguinity; a large haplotype with high linkage disequilibrium among markers comprising the pathogenic variant; a robust population structure; mutation dating, estimating the age of the potential founder of TDC at around 375 years; possibly a high carrier rate in TDC. This study has not only focused its attention on natural history and pathogenetics but also paves way for carrier screening programs in TDC and future therapeutic studies.