Long-read sequencing identifies copy-specific markers ofSMNgene conversion in spinal muscular atrophy

Abstract

AbstractThe complex 2 Mbsurvival motor neuron (SMN)locus on chromosome 5q13, including the spinal muscular atrophy (SMA)-causing geneSMN1and modifierSMN2, remains incompletely resolved due to numerous segmental duplications. Variation inSMN2copy number, presumably influenced bySMN1toSMN2gene conversion, affects disease severity, thoughSMN2copy number alone has insufficient prognostic value due to limited genotype-phenotype correlations. With advancements in newborn screening andSMN-targeted therapies, identifying genetic markers to predict disease progression and treatment response is crucial. Progress has thus far been limited by methodological constraints. To address this, we used targeted nanopore long-read sequencing to analyze copy-specific variation inSMNand neighboring genes. In 25 healthy controls, we identified single nucleotide variants (SNVs) specific toSMN1andSMN2haplotypes that could serve as gene conversion markers. In 31 SMA patients, 45% of haplotypes showed varyingSMN1toSMN2gene conversion breakpoints, serving as direct evidence of gene conversion as a common genetic characteristic in SMA and prompting further investigation into gene conversion markers as disease modifiers. Our findings illustrate that both methodological advances and the analysis of patient samples are required to advance our understanding of complex genetic loci and address critical clinical challenges.