Chagas disease, caused by Trypanosoma cruzi, can reactivate and cause severe acute disease in immunocompromised patients such as those infected with human immunodeficiency virus (HIV). We conducted amplicon deep sequencing of a 327-bp fragment of the tcscd5 gene using an Ion Torrent PGM directly from clinical samples from HIV patients with high parasitemia. We describe the within-host diversity, both characterizing the discrete typing unit of the infections and confirming the presence of multistrain infections, directly from clinical samples. This method can rapidly provide information on the genetic diversity of T. cruzi infection, which can have direct impacts on clinical disease.
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http://dx.doi.org/10.1093/infdis/jiab350 | DOI Listing |
Nucleic Acids Res
January 2025
Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Biomedicinbyggnaden 6K och 6L, Umeå universitetssjukhus, 901 87, Umeå, Sweden.
Single-cell RNA-seq methods can be used to delineate cell types and states at unprecedented resolution but do little to explain why certain genes are expressed. Single-cell ATAC-seq and multiome (ATAC + RNA) have emerged to give a complementary view of the cell state. It is however unclear what additional information can be extracted from ATAC-seq data besides transcription factor binding sites.
View Article and Find Full Text PDFJBMR Plus
February 2025
Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland.
Hypophosphatemic rickets is a rare bone disease characterized by short stature, bone deformities, impaired bone mineralization, and dental problems. Most commonly, hypophosphatemic rickets is caused by pathogenic variants in the X-chromosomal gene, but autosomal dominant and recessive forms also exist. We investigated a Finnish family in which the son (index, 29 yr) and mother (56 yr) had hypophosphatemia since childhood.
View Article and Find Full Text PDFMol Oncol
January 2025
Division of Molecular Genome Analysis, German Cancer Research Center, Heidelberg, Germany.
Colorectal cancer (CRC) patients with microsatellite-stable (MSS) tumors are mostly treated with chemotherapy. Clinical benefits of targeted therapies depend on mutational states and tumor location. Many tumors carry mutations in KRAS proto-oncogene, GTPase (KRAS) or B-Raf proto-oncogene, serine/threonine kinase (BRAF), rendering them more resistant to therapies.
View Article and Find Full Text PDFCancer
February 2025
Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.
Background: This study aims to explore the genetic characteristics of biliary tract cancer (BTC), with a particular focus on the impact of DNA damage response and repair (DDR) genes on clinical outcomes.
Methods: A total of 180 patients with BTC and next-generation sequencing data were retrospectively analyzed. Clinical outcomes were compared between DDR-positive and DDR-negative groups.
Sci Rep
January 2025
Institute of Emerging Infectious Diseases, Korea University, Seoul, Republic of Korea.
This study aimed to evaluate the usefulness of amplicon-based real-time metagenomic sequencing applied to cerebrospinal fluid (CSF) for identifying the causative agents of bacterial meningitis. We conducted a 16S rRNA amplicon sequencing using a nanopore-based platform, alongside routine polymerase chain reaction (PCR) testing or bacterial culture, to compare its clinical performance in pathogen detection on CSF samples. Among 17 patients, nanopore-based sequencing, multiplex PCR, and bacterial culture detected potential bacterial pathogens in 47.
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