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Incontinentia pigmenti (IP) is caused by loss-of-function variants in IKBKG, with molecular genetic diagnosis complicated by a pseudogene. We describe seven individuals from three families with IP but negative clinical genetic testing in whom long-read …
Read PDFTemple syndrome is an imprinting disorder resulting from abnormal genomic or epigenomic aberrations of chromosome 14 including maternal uniparental disomy (matUPD), paternal deletion of 14q32, or aberrant methylation of the imprinting control regions at 14q32. …
Read PDF5-Methylcytosine (5mC) is the most common DNA modification in the human genome. Bisulfite conversion combined with short-read sequencing captures this modification at single-nucleotide resolution but introduces PCR duplication bias and limits co-methylation analysis between distant …
Read PDFHomologous recombination rearranges genetic information during meiosis, creating new combinations of the genome while also introducing mutations, and influencing GC content. Here we report direct detection of recombination events using highly accurate long-read sequencing from …
Read PDFColorectal cancer (CRC) is driven by a complex spectrum of somatic mutations and structural variants that contribute to tumor heterogeneity and therapy resistance. In this study, we performed a comparative analysis of short-read Illumina and …
Read PDF<h4>Background</h4>Upper tract urothelial carcinoma (UTUC), including renal pelvic urothelial carcinoma and ureter urothelial carcinoma, accounts for 10% of urothelial carcinoma (UC). Poorer outcomes and different genetic characteristics of UTUC were reported compared to urothelial carcinoma …
Read PDFDNA methylation can give rise to robust biomarkers of aging, yet most studies profile it at the bulk tissue level, which masks cell type-specific alterations that may follow distinct aging trajectories. Long-read sequencing technology enables …
Read PDF<h4>Introduction</h4>Faulty DNA repair and epigenetic regulation contribute to neurodegeneration in Alzheimer's disease. Long-read sequencing enables analysis of "dark regions" that are difficult to study via traditional sequencing methodologies.<h4>Methods</h4>Using nanopore whole-genome DNA sequencing of post mortem …
Read PDFAlthough next-generation sequencing has emerged as a powerful tool for diagnosing rare diseases (RD), many cases of inherited metabolic diseases (IMD) remain unsolved, hindering the diagnosis, clinical and therapeutic management of the patients. The primary …
Read PDF<h4>Background</h4>The detection of 5-methylcytosine (5mC) patterns in the human genome is relevant for the diagnosis of various genetic conditions. Genome-wide methylation episignatures provide a new approach for resolving variants of uncertain significance. Whole-genome DNA methylation …
Read PDF<h4>Background</h4>Potato (Solanum tuberosum) breeding is severely hindered by its highly heterozygous autotetraploid genome, where complex allelic interactions impede precise trait selection. Reconstructing complete haplotype-resolved assemblies is crucial for genome-assisted breeding. However, current assembly methods for …
Read PDFDecorus tungting is a vulnerable, endemic cyprinid species of conservation significance, historically abundant in Dongting Lake but now suffering severe population declines due to overfishing and river modifications. However, no genome assembly has been reported …
Read PDFTrichomonas vaginalis is a flagellated protozoan parasite and the causative agent of trichomoniasis, the most prevalent non-viral sexually transmitted infection, with significant impact on public health and economy. Here, we present a chromosome-level genome of …
Read PDFThe wrentit (Chamaea fasciata) is a chaparral and scrub specialist bird found from coastal Oregon to northern Baja California. We generated a draft reference assembly for the species using PacBio HiFi long read and Omni-C …
Read PDFThe white-spotted sawyer, Monochamus scutellatus (Say) (Coleoptera: Cerambycidae), is an important vector of pinewood nematode (PWN), Bursaphelenchus xylophilus (Steiner and Buhrer) Nickle, in North America. While Monochamus species from the Palearctic region have been extensively …
Read PDFFontitrygon garouaensis (Smooth Freshwater Stingray) is an evolutionarily distinct and globally endangered species and is currently the only stingray known to be strictly adapted to African freshwater systems. Lack of a reference genome has limited …
Read PDFBACKGROUND: The soil-dwelling Rhabdocoela flatworm, Luticola nematophagus, recently identified as a specialized predator of plant-parasitic nematodes such as Meloidogyne incognita, demonstrates considerable potential as a biocontrol agent for agricultural nematode diseases. This study presents the …
Read PDFThe giant pangasius (Pangasius sanitwongsei) is a critically endangered freshwater species with considerable ecological and economic significance in Southeast Asia and southern China. However, the lack of a high-quality reference genome has limited studies on …
Read PDF<h4>Motivation</h4>Understanding the bacterial epigenome is increasingly recognised as essential for uncovering key mechanisms of gene regulation, host-pathogen interactions, and adaptation to environmental changes. Third-generation sequencing technologies, such as Oxford Nanopore, now enable the direct detection …
Read PDFSolanum verrucosum is a wild diploid potato species notable for carrying the uncharacterized Rpi-ver1 gene conferring resistance to Phytophthora infestans, possessing unusually structured centromeres, and exhibiting the rare trait of self-compatibility, the genetic basis of …
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