ComprehensiveSMN1andSMN2profiling for spinal muscular atrophy analysis using long-read PacBio HiFi sequencing

Abstract

AbstractSpinal muscular atrophy, a leading cause of early infant death, is caused by biallelic mutations of theSMN1gene. Sequence analysis ofSMN1is challenging due to high sequence similarity with its paralogSMN2. Both genes have variable copy numbers across populations. Furthermore, without pedigree information, it is impossible to identify silent carriers (2+0) with two copies ofSMN1on one chromosome and zero copies on the other. We developed Paraphase, an informatics method that identifies full-lengthSMN1andSMN2haplotypes, determines the gene copy numbers and calls phased variants using long-read PacBio HiFi data. TheSMN1andSMN2copy number calls by Paraphase are highly concordant with orthogonal methods (99.2% forSMN1and 100% forSMN2). We applied Paraphase to 438 samples across five ethnic populations to conduct a population-wide haplotype analysis of these highly homologous genes. We identified majorSMN1andSMN2haplogroups and characterized their co-segregation through pedigree-based analyses. We identified twoSMN1haplotypes that form a common two-copySMN1allele in African populations. Testing positive for these two haplotypes in an individual with two copies ofSMN1gives a silent carrier risk of 88.5%, which is significantly higher than the currently used marker (1.7-3.0%). Extending beyond simple copy number testing, Paraphase can detect pathogenic variants and enable potential haplotype-based screening of silent carriers through statistical phasing of haplotypes into alleles. Future analysis of larger population data will allow identification of more diverse haplotypes and genetic markers for silent carriers.