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Adenosine-to-inosine (A-to-I) RNA editing leads to transcriptome diversity and is important for normal brain function. To date, only a handful of functional sites have been identified in mammals. We developed an unbiased assay to screen more than 36,000 computationally predicted nonrepetitive A-to-I sites using massively parallel target capture and DNA sequencing. A comprehensive set of several hundred human RNA editing sites was detected by comparing genomic DNA with RNAs from seven tissues of

Although prime editors are a powerful tool for genome editing, which can generate various types of mutations such as nucleotide substitutions, insertions, and deletions in the genome without double-strand breaks or donor DNA, the conventional prime editors are still limited to their target scopes because of the PAM preference of the Streptococcus pyogenes Cas9 (spCas9) protein. Here, we describe the engineered prime editors to expand the range of their target sites using various PAM-flexible Cas

BACKGROUND: The extent to which metastatic tumors further evolve by accumulating additional mutations is unclear and has yet to be addressed extensively using next-generation sequencing of high-grade serous ovarian cancer. METHODS: Eleven spatially separated tumor samples from the primary tumor and associated metastatic sites and two normal samples were obtained from a Stage IIIC ovarian cancer patient during cytoreductive surgery prior to chemotherapy. Whole exome sequencing and copy number ana

Utilizing the full power of next-generation sequencing often requires the ability to perform large-scale multiplex enrichment of many specific genomic loci in multiple samples. Several technologies have been recently developed but await substantial improvements. We report the 10,000-fold improvement of a previously developed padlock-based approach, and apply the assay to identifying genetic variations in hypermutable CpG regions across human chromosome 21. From approximately 3 million reads deri

Resection of recurrent adenocarcinoma of the colon and rectum at the anastomotic site was performed in 30 patients. In the majority of the patients, the recurrence was apparent within two years of the initial operation. In 27 patients, the recurrence was diagnosed based upon persistent signs and symptoms or if the tumor was clinically palpable. In 15 patients, complete resection of the recurrent tumor was feasible, and the median survival time was 59 months, with a five year survival rate of 49

BACKGROUND: Nontuberculous mycobacterium (NTM) species are ubiquitous microorganisms. NTM pulmonary disease (NTM-PD) is thought to be caused not by human-to-human transmission but by independent environmental acquisition. However, recent studies using next-generation sequencing (NGS) have reported trans-continental spread of Mycobacterium abscessus among patients with cystic fibrosis. RESULTS: We investigated NTM genomes through NGS to examine transmission patterns in three pairs of co-habiting

Molecular inversion probe (MIP)-based capture is a scalable and effective target-enrichment technology that can use synthetic single-stranded oligonucleotides as probes. Unlike the straightforward use of synthetic oligonucleotides for low-throughput target capture, high-throughput MIP capture has required laborious protocols to generate thousands of single-stranded probes from DNA microarray because of multiple enzymatic steps, gel purifications and extensive PCR amplifications. Here, we develop

More than one-fifth of patients had an inconsistent blood eosinophil level after the 1-year follow-up, and the AE-COPD rate according to ICS differed based on variability in eosinophils. Regular follow-up of blood eosinophils is required for COPD patients.

A case of interstitial pneumonitis secondary to mitomycin C and DTIC combination therapy in a 58-year-old male with metastatic adenocarcinoma of the rectum is reported. Dry cough and dyspnea, especially on exertion, were presenting symptoms. Arterial blood gas analysis was compatible with severe impairment in pulmonary diffusion capacity. Chest x-ray showed a diffuse increase in interstitial markings in both lung fields consistent with interstitial pneumonia. Histologically, prominence of type I

Our ML-based feature selection from proteomic data reveals ferroptosis to be the most distinctive feature of cultured COPD epithelial cells compared to non-COPD epithelial cells upon exposure to smoke extract.

Poly(ADP-ribose) polymerase inhibitors have been shown dramatic responses in patients with BRCAness. However, clinical studies have been limited to breast cancer patients with germline mutations. Here, we describe a patient with metastatic breast cancer who had a rare BRCA1 somatic mutation (BRCA1 c.4336G>T (p.E1446*)) detected by cell-free DNA analysis after failing standard therapies. This tier III variant of unknown significance was predicted to be a pathogenic variant in our assessment, lead

Abstract Background : Nontuberculous mycobacterium (NTM) species are ubiquitous microorganisms. NTM pulmonary disease (NTM-PD) is thought to be caused not by human-to-human transmission but by independent environmental acquisition. However, recent studies using next-generation sequencing (NGS) have reported trans-continental spread of Mycobacterium abscessus among patients with cystic fibrosis. Results : We investigated NTM genomes through NGS to examine transmission patterns in three pairs of c

Two novel pink-pigmented bacteria, designated strains MA0201 T and ID0610 T , were isolated from a car air conditioning system. The isolates were Gram-stain-negative, aerobic, non-spore-forming, rod-shaped and facultatively methylotrophic. Cells of strains MA0201 T and ID0610 T are motile with polar flagella (lophotrichous) and a polar flagellum (monotrichous), respectively. Both strains indicated catalase- and oxidase-positive activities. The growth of strain MA0201 T was observed at 15–35 °C,

Additional file 1: Table S1. Characteristics on environmental specimens. The numbers of collected specimens, culture-positive, morphologically distinct isolates from each habitat. Table S2. NTM species Identified and Sequencing Results. Description on the source of each sample and its sequencing quality (total read counts, mean depth, 20x coverage, number of SNPs), species, clonality, and morphologic feature.