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Dual single nucleotide polymorphisms typing of apolipoprotein E gene based on double restriction endonuclease with lambda exonuclease and triple helix molecular switch assistance.
Biosens Bioelectron
March 2025
Department of Pharmacy, ZhuJiang Hospital, Southern Medical University, Guangzhou, 510280, PR China. Electronic address:
Single nucleotide polymorphisms (SNPs) are critical determinants of disease susceptibility, pathogenesis, and drug response, underscoring the need for their accurate monitoring in clinical practice. In this study, we propose a novel apolipoprotein E (APOE) genotyping method for the rapid and precise identification of six genotypes (ε2/ε2, ε3/ε3, ε4/ε4, ε2/ε3, ε2/ε4, and ε3/ε4). The method utilizes restriction endonucleases AflIII and HaeII to selectively cleave the rs429358 and rs7412 sites, thereby generating distinct double-stranded DNA fragments.
View Article and Find Full Text PDFHLA-DQB1*03:01 and risk of Hepatitis B virus-related hepatocellular carcinoma.
Hepatology
March 2025
Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA.
Background Aims: The human leukocyte antigen (HLA) locus is implicated in hepatocellular carcinoma (HCC) among chronic hepatitis B virus (HBV) carriers. We investigated associations of HLA variants, amino acid polymorphisms, zygosity, and evolutionary divergence (HED) with HBV-related HCC in Han Chinese and explored biological mechanisms.
Approach Results: We examined the associations of HLA variants (imputed 4-digit classical alleles and amino acid polymorphisms), zygosity, and HED with HBV-related HCC in a discovery set (706 HBV-related HCC cases, 6,197 chronic HBV carriers in Taiwan).
Novel SCAR markers for accurate diagnosis of toxic and .
Food Chem (Oxf)
June 2025
Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand.
Toxic and are mistaken for wild edible mushroom species under the same genus, and those under . These species have similar morphological characteristics and occupy the same ecosystems. Accidental ingestion of and can lead to gastrointestinal syndromes including nausea, vomiting, and diarrhea.
View Article and Find Full Text PDFComparative analysis of genotype imputation strategies for SNPs calling from RNA-seq.
BMC Genomics
March 2025
State Key Laboratory of Swine and Poultry Breeding Industry, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
Background: RNA sequencing (RNA-seq) is a powerful tool for transcriptome profiling, enabling integrative studies of expression quantitative trait loci (eQTL). As it identifies fewer genetic variants than DNA sequencing (DNA-seq), reference panel-based genotype imputation is often required to enhance its utility.
Results: This study evaluated the accuracy of genotype imputation using SNPs called from RNA-seq data (RNA-SNPs).
Benchmarking long-read structural variant calling tools and combinations for detecting somatic variants in cancer genomes.
Sci Rep
March 2025
Department of Biological Sciences, Middle East Technical University, Universiteler Mah. Dumlupınar Bulvarı 1, 06800, Çankaya, Ankara, Turkey.
Cancer genomes have a complicated landscape of mutations, including large-scale rearrangements known as structural variants (SVs). These SVs can disrupt genes or regulatory elements, playing a critical role in cancer development and progression. Despite their importance, accurate identification of somatic structural variants (SVs) remains a significant bottleneck in cancer genomics.
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