Objective: To perform targeted resequencing of the SNCA locus to identify novel variants in the Indian patients with Parkinsons’s disease (PD).

Background: To date, most genetic loci implicated in familial Parkinson’s disease (PD) have been identified in the European population with little transferability to other ethnically diverse populations. Several rare variants from the SNCA gene encoding alpha-synuclein protein are causal for autosomal dominant PD.

Method: A total of 298 cases and 301 age-matched controls of Indian ancestry were included in the study. The raw sequence reads were analyzed using an in-house analysis pipeline, involving detection of small variants using Freebayes, and structural variants using Manta. To find novel PD variants, we filtered the detected variants using two main criteria: (1) must be a missense variant or nonsense variant; and (2) not present in the 1000 genomes or gnomAD population variant databases.

Results: The average re-sequencing depth was 244X. On average, 97.85% of the 366-kbp target region was covered with at least 20X depth. Of the 599 samples (298 cases and 301 controls), ten samples of low quality (average target region read depth of less than 50× or more than 93% of the target region covered by less than 20×). A further three samples that were duplicated, were excluded from further analysis. Thus, a total of 288 PD cases and 298 controls were available for the variant analysis.
No novel missense and/or structural variants were identified in the Indian patients with PD

Conclusion: This is the first comprehensive screening of the SNCA gene in the Indian population. It reveals that variants in the SNCA gene might be irrelevant for the Indian PD population, suggesting a need for identifying other loci in the under-represented populations

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MDS Abstracts - https://www.mdsabstracts.org/abstract/resequencing-of-the-complete-snca-locus-in-indian-patients-with-parkinsons-disease/