ArticleAmerican journal of human genetics2023
Comprehensive SMN1 and SMN2 profiling for spinal muscular atrophy analysis using long-read PacBio HiFi sequencing.
Article in American journal of human genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- Article
- SMN1 mutation spectrum and functional analysis of novel SMN1 variants in a Chinese spinal muscular atrophy cohort.Journal of human genetics · 2026Article
- Characterisation of the SMN1/2 locus using a highly specific variant caller on whole-genome sequence data from 500,000 individuals.European journal of human genetics : EJHG · 2026Article
- Structural variant discovery and diagnostic impact in rare diseases from short-read and long-read sequencing.medRxiv : the preprint server for health sciences · 2026Article
- Ensilication preserves high-molecular weight native DNA for clinical long-read sequencing.Genome biology · 2026Article
- Characterizing SMN1 hybrid and deletion alleles using large-scale SNP array-based SMA carrier screening.BMC medical genomics · 2026Article
- Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes.Nature communications · 2026Article
- Multimodal characterisation of the SMN locus in SMA: copy number quantification and hybrid gene identification.NPJ genomic medicine · 2026Article
- Determinants of haplotype phasing accuracy in long-read human genome sequencing.bioRxiv : the preprint server for biology · 2026Article
- Exploring the phenotypic and genotypic spectrum of spinal muscular atrophy in Bangladeshi children.BMC neurology · 2026Article
- Integrative analysis of in silico predictions and clinical evidence to delineate the capability of HiFi long-read sequencing in paralogous genes.NPJ genomic medicine · 2026Article
- MLDP-AS: an optimized next-generation sequencing assay for enhanced detection of technically challenging variants in expanded carrier screening.Journal of translational medicine · 2026Article
- Multiplatform comparisons and annotation of structural variants highlight the utility of the T2T reference genome in human diagnostics.GigaScience · 2026Article
- Long-read genome sequencing enhances diagnostics of pediatric neurological disorders.Genome medicine · 2026Article
- Clinical application of long-read sequencing in newborn genetic screening for congenital adrenal hyperplasia.Frontiers in genetics · 2026Article
- Evolutionary hotspots of structural variation drive inter-individual differences in the expression of fusion transcripts in the human brain.Nucleic acids research · 2025Article
- Validation on the First-Tier Fully Automated High-ThroughputInternational journal of neonatal screening · 2025Article
- Hybridization capture long-read sequencing and de novo assembly of homologous haplotypes: a comprehensive hemophilia test.Blood advances · 2025Article
- Advancements in Prenatal Genetic Screening and Testing: Emerging Technologies and Evolving Applications.Diagnostics (Basel, Switzerland) · 2025Review
- Structural variation in nebulin and its impact on phenotype and inheritance: establishing a dominant distal phenotype caused by large deletions.European journal of human genetics : EJHG · 2025Review
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Authors and funding
10 authors.
Funding
Abstract
Spinal muscular atrophy, a leading cause of early infant death, is caused by bi-allelic mutations of SMN1. Sequence analysis of SMN1 is challenging due to high sequence similarity with its paralog SMN2. Both genes have variable copy numbers across populations. Furthermore, without pedigree information, it is currently not possible to identify silent carriers (2+0) with two copies of SMN1 on one chromosome and zero copies on the other. We developed Paraphase, an informatics method that identifies full-length SMN1 and SMN2 haplotypes, determines the gene copy numbers, and calls phased variants using long-read PacBio HiFi data. The SMN1 and SMN2 copy-number calls by Paraphase are highly concordant with orthogonal methods (99.2% for SMN1 and 100% for SMN2). We applied Paraphase to 438 samples across 5 ethnic populations to conduct a population-wide haplotype analysis of these highly homologous genes. We identified major SMN1 and SMN2 haplogroups and characterized their co-segregation through pedigree-based analyses. We identified two SMN1 haplotypes that form a common two-copy SMN1 allele in African populations. Testing positive for these two haplotypes in an individual with two copies of SMN1 gives 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.
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