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<i>Staphylococcus epidermidis</i> ATCC 12228 was sequenced using a long-read method to generate a complete genome sequence, including some plasmid sequences. Some differences from the previously generated short-read sequence of this nonpathogenic and non-biofilm-forming strain were …
Read PDFThe killer cell immunoglobulin-like receptor (KIR) region of human chromosome 19 contains up to 16 genes for natural killer (NK) cell receptors that recognize human leukocyte antigen (HLA)/peptide complexes and other ligands. The KIR proteins …
Read PDF<h4>Background</h4>Singleton short-read genome sequencing (GS) is increasingly used as a first-line genetic test for childhood neurological disorders (such as intellectual disability, neurodevelopmental delay, motor delay, and hypotonia) with diagnostic yields from 26 to 35%, typically …
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 PDFConventional genome mapping-based approaches systematically overlook genetic variation, particularly in regions that substantially differ from the reference. To explore this hidden variation, here we examine unmapped and poorly mapped reads from the genomes of 640 …
Read PDFPine siskins (Spinus pinus) are irruptive migratory songbirds of biological interest in studies of endocrine regulation, immune function, and behavioral flexibility. Here, we present a chromosome-level reference genome from a female pine siskin, assembled de …
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 PDFHere, we present the complete genome sequence of a porcine endogenous retrovirus determined by Pacific Biosciences sequencing. A comparison of the genome of this isolate with those of other strains revealed the operation of a …
Read PDFA genetic diagnosis of autosomal-dominant polycystic kidney disease (ADPKD) is challenging due to allelic heterogeneity, high GC content, and homology of the PKD1 gene with six pseudogenes. Short-read next-generation sequencing approaches, such as whole-genome sequencing …
Read PDFDespite the key role of the human ribosome in protein biosynthesis, little is known about the extent of sequence variation in ribosomal DNA (rDNA) or its pre-rRNA and rRNA products. We recovered ribosomal DNA segments …
Read PDFAAV integration has become an important safety consideration in gene therapy. However, accurately determining integration sites remains challenging due to biases introduced by library preparation methods, sequencing technologies, and bioinformatic pipelines. In this study, we …
Read PDFNumerous proteins display pleiotropic functions in different clinical contexts. However, the molecular mechanism underlying such effects is rarely understood. Speckle-type POZ protein (<i>SPOP</i>) is a typical example, exhibiting tumor-suppressing or tumor-promoting effects in different tumor …
Read PDF<h4>Background</h4>Many neurodegenerative diseases are caused by nucleotide repeat expansions, but most expansions, like the C9orf72 'GGGGCC' (G<sub>4</sub>C<sub>2</sub>) repeat that causes approximately 5-7% of all amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) cases, are too …
Read PDFAmplification of DNA is required as a mandatory step during library preparation in most targeted sequencing protocols. This can be a critical limitation when targeting regions that are highly repetitive or with extreme guanine-cytosine (GC) …
Read PDFLong-read sequencing technologies are transforming our ability to assemble highly complex genomes. Realizing their full potential is critically reliant on extracting high-quality, high-molecular-weight (HMW) DNA from the organisms of interest. This is especially the case …
Read PDFAccurate and comprehensive characterization of genetic variation is essential for deciphering the genetic basis of diseases and other phenotypes. A vast amount of genetic variation stems from large-scale sequence changes arising from the duplication, deletion, …
Read PDFIGH@ proto-oncogene translocation is a common oncogenic event in lymphoid lineage cancers such as B-ALL, lymphoma and multiple myeloma. Here, to investigate the interplay between IGH@ proto-oncogene translocation and IGH allelic exclusion, we perform long-read …
Read PDFDespite the high accuracy of short read sequencing (SRS), there are still issues with attaining accurate single nucleotide polymorphism (SNP) genotypes at low sequencing coverage and in highly duplicated genomes due to misalignment. Long read …
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