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Item Metadata only Rapid diagnosis of intra-amniotic infection using nanopore-based sequencing(2022-01-01) Chaemsaithong P.; Romero R.; Pongchaikul P.; Vivithanaporn P.; Lertrut W.; Jaovisidha A.; Mongkolsuk P.; Nitayanon P.; Pongsuktavorn K.; Kamlungkuea T.; Jung E.; Suksai M.; Singhsnaeh A.; Jenjaroenpun P.; Thaipisuttikul I.; Wongsurawat T.; Mahidol UniversityEarly diagnosis and treatment of intra-amniotic infection is crucial. Rapid pathogen identification allows for a definite diagnosis and enables proper management. We determined whether the 16S amplicon sequencing performed by a nanopore sequencing... technique make possible rapid bacterial identification at the species level in intra-amniotic infection. Five cases of confirmed intra-amniotic infection, determined by either cultivation or 16S rDNA polymerase chain reaction (PCR) Sanger sequencing, and 10Item Metadata only Ultrarapid and high-resolution HLA class I typing using transposase-based nanopore sequencing applied in pharmacogenetic testing(2023-01-01) Anukul N.; Jenjaroenpun P.; Sirikul C.; Wankaew N.; Nimsamer P.; Roothumnong E.; Pithukpakorn M.; Leetrakool N.; Wongsurawat T.; Mahidol UniversityNanopore sequencing has been examined as a method for rapid and high-resolution human leukocyte antigen (HLA) typing in recent years. We aimed to apply ultrarapid nanopore-based HLA typing for HLA class I alleles associated with drug..., an imbalance in the PCR amplification of different haplotypes could affect the accuracy of typing results. This work demonstrates the ability of transposase-based sequencing to report 3-field HLA alleles and its potential for race- and population-independentItem Metadata only Targeted sequencing analysis pipeline for species identification of human pathogenic fungi using long-read nanopore sequencing(2023-12-01) Langsiri N.; Worasilchai N.; Irinyi L.; Jenjaroenpun P.; Wongsurawat T.; Luangsa-ard J.J.; Meyer W.; Chindamporn A.; Mahidol UniversityAmong molecular-based techniques for fungal identification, Sanger sequencing of the primary universal fungal DNA barcode, the internal transcribed spacer (ITS) region (ITS1, 5.8S, ITS2), is commonly used in clinical routine laboratories due to its... technologies have been explored. The nanopore-based technology is now one of the most promising long-read sequencing technologies on the market as it has the potential to sequence the full-length ITS region in a single read. In this study, we established aItem Metadata only Comparative evaluation of commercial DNA isolation approaches for nanopore-only bacterial genome assembly and plasmid recovery(2024-11-12) Kruasuwan W.; Sawatwong P.; Jenjaroenpun P.; Wankaew N.; Arigul T.; Yongkiettrakul S.; Lunha K.; Sudjai A.; Siludjai D.; Skaggs B.; Wongsurawat T.; Kruasuwan W.; Mahidol UniversityThe advent of Oxford Nanopore Technologies has undergone significant improvements in terms of sequencing costs, accuracy, and sequencing read lengths, making it a cost-effective, and readily accessible approach for analyzing microbial genomes. A... major challenge for bacterial whole genome sequencing by Nanopore technology is the requirement for a higher quality and quantity of high molecular weight DNA compared to short-read sequencing platforms. In this study, using eight pathogenic bacteria, weItem Metadata only CAIM: coverage-based analysis for identification of microbiome(2024-07-25) Acheampong D.A.; Jenjaroenpun P.; Wongsurawat T.; Kurilung A.; Pomyen Y.; Kandel S.; Kunadirek P.; Chuaypen N.; Kusonmano K.; Nookaew I.; Acheampong D.A.; Mahidol UniversityAccurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species... resolution through a whole shotgun metagenomic approach. In this study, we developed a new bioinformatics tool, coverage-based analysis for identification of microbiome (CAIM), for accurate taxonomic classification and quantification within both longItem Metadata only Optimizing fungal DNA extraction and purification for Oxford Nanopore untargeted shotgun metagenomic sequencing from simulated hemoculture specimens(2025-06-17) Langsiri N.; Meyer W.; Irinyi L.; Worasilchai N.; Pombubpa N.; Wongsurawat T.; Jenjaroenpun P.; Luangsa-Ard J.J.; Chindamporn A.; Langsiri N.; Mahidol UniversityDNA barcode (Internal Transcribed Spacer (ITS) region). However, DNA extraction for long-read sequencing-based fungal identification poses a significant challenge, as obtaining long and intact fungal DNA is imperative. Comparing different lysis methods...Long-read metagenomics provides a promising alternative approach to fungal identification, circumventing methodological biases, associated with DNA amplification, which is a prerequisite for DNA barcoding/metabarcoding based on the primary fungalItem Metadata only Exploiting nanopore sequencing for characterization and grading of IDH-mutant gliomas(2023-01-01) Wongsurawat T.; Mahidol Universityof a nanopore-based copy-number variation sequencing (nCNV-seq) approach to simultaneously identify deletions of CDKN2A/B and 1p/19q. The nCNV-seq approach was initially evaluated on three distinct glioma cell lines and then applied to 19 IDH-mutant... gliomas (8 astrocytomas and 11 oligodendrogliomas) from patients. The whole-arm 1p/19q codeletion was detected in all oligodendrogliomas with high concordance among nCNV-seq, FISH, DNA methylation profiling, and whole-genome sequencing. For the CDKN2A/BItem Metadata only Native RNA or cDNA Sequencing for Transcriptomic Analysis: A Case Study on Saccharomyces cerevisiae(2022-04-12) Wongsurawat T.; Jenjaroenpun P.; Wanchai V.; Nookaew I.; Mahidol UniversityDirect sequencing of single molecules through nanopores allows for accurate quantification and full-length characterization of native RNA or complementary DNA (cDNA) without amplification. Both nanopore-based native RNA and cDNA approaches involve... complex transcriptome procedures at a lower cost. However, there are several differences between the two approaches. In this study, we perform matched native RNA sequencing and cDNA sequencing to enable relevant comparisons and evaluation. UsingItem Metadata only GLIMMERS: glioma molecular markers exploration using long-read sequencing(2024-01-01) Thongrattana W.; Arigul T.; Suktitipat B.; Pithukpakorn M.; Sathornsumetee S.; Wongsurawat T.; Jenjaroenpun P.; Thongrattana W.; Mahidol Universityand specialized resources that are necessary. To address this problem and help clinicians classify and grade brain tumors, we developed GLIMMERS: glioma molecular markers exploration using long-read sequencing, an open-access tool that automatically analyzes... nanopore-based CNV data and generates simplified reports. Availability and implementation: GLIMMERS is available at https://gitlab.com/silol_public/glimmers under the terms of the MIT license.Item Metadata only Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae(2023-12-01) Wanichthanarak K.; Nookaew I.; Pasookhush P.; Wongsurawat T.; Jenjaroenpun P.; Leeratsuwan N.; Wattanachaisaereekul S.; Visessanguan W.; Sirivatanauksorn Y.; Nuntasaen N.; Kuhakarn C.; Reutrakul V.; Ajawatanawong P.; Khoomrung S.; Mahidol University. Sanger sequencing was used to correct for differences in lengths and nucleotide bases between inverted repeats because of the homopolymers. The phylogenetic trees reconstructed using prevalent methods for phylogenetic inference were topologically similar...Background: Massive parallel sequencing technologies have enabled the elucidation of plant phylogenetic relationships from chloroplast genomes at a high pace. These include members of the family Rhamnaceae. The current Rhamnaceae phylogenetic tree
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