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In this study, we validated recombinant adeno-associated viral integration analysis (RAAVioli), a previously published computational method for the comprehensive analysis of adeno-associated virus vector (AAV) integration sites (ISs) and vector rearrangements across both long- and …
Read PDFPURPOSE: Hereditary angioedema due to C1-inhibitor deficiency (HAE-C1INH) is caused by heterozygous pathogenic variants in the SERPING1 gene. Structural variants (SVs) account for 10–15% of cases, and while many can be identified using conventional diagnostic …
Read PDFSomatic structural variants (SVs) are the predominant source of cancer driver mutations and play a critical role in oncogenesis. Comprehensive characterization of somatic SVs is critical for elucidating the mechanisms underlying tumorigenesis and for identifying …
Read PDFGenome sequencing (GS) has emerged as a transformative tool in the diagnosis of rare diseases with complex phenotypes. This technology uncovers structural, intronic, non-coding, and mitochondrial variants that traditional methods might miss, thereby facilitating the …
Read PDF<h4>Background</h4>Integrating short- and long-read sequencing technologies has become a promising approach for achieving accurate and comprehensive genomic analysis. Although short-read sequencing (Illumina, etc.) offers high base accuracy and cost efficiency, it struggles with structural variant …
Read PDFAlthough numerous algorithms have been developed to identify structural variations (SVs) in genomic sequences, there is a dearth of approaches that can be used to evaluate their results. This is significant as the accurate identification …
Read PDFSpeciation is a key driver of biodiversity and understanding its genomic underpinnings can be important for predicting and managing biodiversity. Structural variants (SVs) are large-scale (> 50 bp) changes in the genome and have been …
Read PDFThe model woody plant <i>Populus trichocarpa</i> displays an atypical alkene-diverse wax cuticle likely driven by copy number variation (CNV) of <i>3-ketoacyl-CoA synthases</i> (<i>KCS</i>), which has been difficult to confirm with short-read assemblies. Long-read sequencing enables …
Read PDFPiperacillin-tazobactam (TZP) resistance in <i>Klebsiella pneumoniae</i> involves diverse mechanisms with unclear prevalence and phenotypic impact. To elucidate these mechanisms, we analyzed <i>K. pneumoniae</i> clinical isolates resistant to TZP but susceptible to cefotaxime and cefepime. Among …
Read PDFThe 2q31 region is commonly associated with pathogenic alleles of the HOXD cluster leading to various clinical phenotypes related to skeletal development. We present a proband with tetralogy of Fallot and multiple congenital anomalies. Genomic …
Read PDF<h4>Background</h4>Identifying the genetic basis of hypotonia and muscle weakness is critical for patient management and family counseling. However, diagnosis is often hindered by diverse genomic alterations, including repeat expansions, structural variants (SVs), and methylation defects. …
Read PDF<h4>Background</h4>Structural variants (SVs) in human genomes are implicated in a variety of human diseases. Long-read sequencing delivers much longer read lengths than short-read sequencing and may greatly improve SV detection. However, due to the relatively …
Read PDF<h4>Background</h4>TANGO2 deficiency disorder (TDD) is a rare autosomal recessive condition characterized by neurodevelopmental delay, epilepsy, and metabolic crises, mainly caused by recurrent deletions in <i>TANGO2</i>. This study reports the identification of TDD in 2 unrelated …
Read PDF<h4>Background</h4>Accurate typing of the D antigen is critical to provide guidance for blood transfusion and safe management of Rh-incompatible pregnancies. RHD genotyping assays have been widely adopted to improve D variant detection, especially for common …
Read PDFStructural variants (SVs), including duplications, deletions, inversions, translocations, and insertions, play major roles in human phenotypic diversity but remain difficult to detect because of variable size and structural complexity. Optical genome mapping (OGM) uses ultra-high …
Read PDFRapid advances in short-read DNA sequencing technologies have revolutionized population genomic studies, but there are genomic regions where this technology reaches its limits. Limitations mostly arise due to the difficulties in assembly or alignment to …
Read PDFLong-read sequencing technologies have contributed greatly to comparative genomics among species and can also be applied to study genomics within a species. In this study, to determine how substantial genomic changes are generated and tolerated …
Read PDFStructural variation (SV) is typically defined as variation within the human genome that exceeds 50 base pairs (bp). SV may be copy number neutral or it may involve duplications, deletions, and complex rearrangements. Recent studies …
Read PDFMutation of o2 doubles maize endosperm lysine content, but it causes an inferior kernel phenotype. Developing quality protein maize (QPM) by introgressing o2 modifiers (Mo2s) into the o2 mutant benefits millions of people in developing …
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