Miranda P G Zalusky | Search PubMed

PubMed2026

needLR: long-read structural variant annotation with population-scale frequency estimation.

SUMMARY: We present needLR, a structural variant (SV) annotation tool that can be used for filtering and prioritization of candidate pathogenic SVs from long-read sequencing data using population allele frequencies, annotations for genomic context, and gene-phenotype associations. When using population data from 500 presumably healthy individuals to evaluate nine test cases with known pathogenic SVs, needLR assigned allele frequencies to over 97.5% of all detected SVs and reduced the average number of novel genic SVs to 121 per case while retaining all known pathogenic variants. AVAILABILITY AND IMPLEMENTATION: needLR is implemented in bash with dependencies including Truvari v4.2.2, BEDTools v2.31.1, and BCFtools v1.19. Source code, documentation, and pre-computed population allele frequency data are freely available at https://github.com/jgust1/needLR under an MIT license and archived on Zenodo at https://zenodo.org/records/19463479.

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PubMed2025

Long-read DNA sequencing resolves a rare case of alloimmune hemolysis mimicking autoimmune hemolysis.

BACKGROUND: Immune hemolytic anemia poses a significant challenge in transfusion medicine, as identification of underlying alloantibodies can be masked by warm and/or cold autoantibodies. This increases the risk of transfusing incompatible blood, which can precipitate or exacerbate hemolysis. Identifying alloantibodies in the presence of autoantibodies remains difficult with standard serologic and genotypic methods, often delaying accurate diagnosis and appropriate transfusion strategies. CASE REPORT: We describe a 63-year-old woman with autoimmune hemolytic anemia who suffered near-fatal hemolysis following transfusion. Despite extensive serologic and genotypic testing, the cause of her hemolytic transfusion reactions remained elusive. Given her clinical course and transfusion history, we hypothesized that her acute hemolytic transfusion reactions could be due to immune sensitization to a high-incidence RBC antigen. Research whole-genome long-read sequencing (LRS) revealed homozygosity for a rare KEL*02N.16 allele, consistent with a rare Ko phenotype, which was validated by Sanger sequencing. Retrospective serologic testing with Ko RBCs further confirmed alloimmunization within the Kell system. CONCLUSION: This case highlights the limitations of conventional serologic and genotypic methods in detecting rare blood group phenotypes, and emphasizes the diagnostic power of long-read sequencing in transfusion medicine. Early molecular testing in complex hemolytic cases can facilitate targeted transfusion strategies, reduce the risk of severe hemolysis, and improve patient outcomes. As sequencing technologies become more accessible, they have the potential to revolutionize blood group typing and alloimmunization risk assessment in clinical practice.

Humans↗