Biomedical subjects

Xiaonan Zhao

Publications and source records attributed to Xiaonan Zhao.

4 recordsLinked to original sources

PubMed2026

Computational strategies for copy number variation detection, disease association, and beyond.

Copy number variations (CNVs) are key structural variations that contribute to human genetic diversity, evolution, and disease susceptibility. Advances in sequencing technologies and computational methods have improved CNV detection, yet association studies remain challenged by methodological limitations and a lack of standardisation. This review provides an overview of computational strategies for germline CNV detection and disease association. We highlight the value of CNV analysis for uncovering genetic contributions to complex traits and disease risk and outline an analysis workflow including key benchmarking methods. We also discuss current challenges and future directions for advancing CNV detection and association analysis.

Humans↗

PubMed2026

Targeted reflex RNA sequencing for enhanced variant classification on exome and genome sequencing improves patient outcomes.

RNA sequencing (RNA-seq) has been utilized to provide functional evidence regarding the impact of splicing variants. This study explores the utility of targeted reflex RNA-seq to inform classification of predicted splicing variants identified through clinical exome sequencing (ES) and genome sequencing (GS). A retrospective analysis was conducted on consecutive ES/GS cases completed at a single center in which targeted reflex RNA-seq was performed following identification of eligible variants. There were 131 cases (4.1%) that had at least one RNA-seq eligible variant reported, with eight of these cases having two unique eligible variants. Of the 139 eligible variants, 125 were classified as variants of uncertain significance (VUS). Sixty-four cases had targeted reflex RNA-seq completed with 27 cases having at least one variant reclassified (42.2%). After reclassification, 23 cases had positive results, and two cases had a likely diagnosis of an autosomal recessive condition. Clinical outcomes data regarding positive RNA-seq cases showed that 71% (10/14) had clinical management changes and 43% (6/14) had treatment changes. Incorporation of targeted reflex RNA-seq analysis into the diagnostic pipeline of rare diseases enhances variant classification and resolves uncertainty regarding predicted splice variants, leading to an estimated 1.6% increase in diagnostic yield of clinical ES/GS.

Journal Article↗

PubMed2025

ABCD-type phage cocktail targeting distinct LPS receptor sites demonstrates superior efficacy against multidrug-resistant Salmonella.

The narrow host range of phages poses a limitation in addressing multidrug-resistant bacteria, whereas phage cocktail therapy, targeting multiple bacterial receptors, broadens the phage host spectrum. This study establishes a comprehensive Salmonella phages repository through nationwide surveillance in China, isolating 242 phages classified into 29 genera, with genome sizes ranging from 5.4 to 350.3 Kb. Based on LPS specificity, phages were categorized into four types A-D. Here, we developed an ABCD-Type phage cocktail targeting four distinct LPS recognition sites, demonstrating superior efficacy versus single phages or phage cocktail with different receptors (CCR-Type). In vitro, ABCD-Type phage cocktail treatment sustained bactericidal activity > 36 h versus CCR's 8 h, effectively controlling Salmonella in lettuce, milk, and Galleria mellonella infection models. Moreover, ABCD-Type phage cocktail effectively cleared Salmonella biofilms and showed promising results in the treatment of animal infections, significantly reducing bacterial loads in infected chicks and improving their survival rates. Resistant mutants predominantly harbored mutations in the btuB gene and LPS biosynthesis genes. These mutants showed increased antibiotic sensitivity and attenuated virulence. Collectively, these findings underscore the therapeutic potential of Salmonella phages, specifically ABCD-Type phage cocktail formulations which contain the phages PJNS014, PJNS023, PJNS036, and PJNS038, for controlling Salmonella infections. This work provides a foundation for developing advanced phage-based therapeutics.

Salmonella Phages↗

PubMed2025

DNA methylation and machine learning: challenges and perspective toward enhanced clinical diagnostics.

DNA methylation is an epigenetic modification that regulates gene expression by adding methyl groups to DNA, affecting cellular function and disease development. Machine learning, a subset of artificial intelligence, analyzes large datasets to identify patterns and make predictions. Over the past two decades, advances in bioinformatics technologies for arrays and sequencing have generated vast amounts of data, leading to the widespread adoption of machine learning methods for analyzing complex biological information for medical problems. This review explores recent advancements in DNA methylation studies that leverage emerging machine learning techniques for more precise, comprehensive, and rapid patient diagnostics based on DNA methylation markers. We present a general workflow for researchers, from clinical research questions to result interpretation and monitoring. Additionally, we showcase successful examples in diagnosing cancer, neurodevelopmental disorders, and multifactorial diseases. Some of these studies have led to the development of diagnostic platforms that have entered the global healthcare market, highlighting the promising future of this field.

Humans↗