A5070458644- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- Bat Biology and Ecology Studies
- Genomic variations and chromosomal abnormalities
- Epigenetics and DNA Methylation
- Genetic factors in colorectal cancer
- Colorectal Cancer Treatments and Studies
- Lung Cancer Treatments and Mutations
- Pancreatic and Hepatic Oncology Research
- Genomics and Phylogenetic Studies
- Metastasis and carcinoma case studies
- Chromosomal and Genetic Variations
- Genomics and Chromatin Dynamics
- Gene expression and cancer classification
- Cancer-related molecular mechanisms research
- Cancer, Hypoxia, and Metabolism
- Plant Disease Resistance and Genetics
- Single-cell and spatial transcriptomics
- Cancer, Lipids, and Metabolism
- Genetic Syndromes and Imprinting
- Advanced biosensing and bioanalysis techniques
- CRISPR and Genetic Engineering
- thermodynamics and calorimetric analyses
- Cancer-related Molecular Pathways
- Cancer Research and Treatments
Sichuan University
2015-2025
West China Hospital of Sichuan University
2025
State Key Laboratory of Biotherapy
2018
Somatic structural variations (Somatic SVs) are critical genomic alterations with significant implications in cancer genomics. Although long-read sequencing (LRS) theoretically provides optimal resolution for detecting these variants due to its ability span large segments, current LRS - based methods, which derived from short read somatic SV detection algorithms, mainly rely on split information. The high error rate of long and the errors introduced by seed-and-chaining strategy mainstream...
Abstract Repetitive elements insertions (REIs), including tandem repeat (TRIs) and transposable element (TEIs), constitute >90% of large-scale (>50bp) somatic are linked to diseases cancer biomarkers. However, the genomic landscape REIs in pan-cancer has not been well-characterized due short-read sequencing limitations. Here, we detected 325 genomes across 12 types using long-read whole-genome customized algorithms. The diverse sequence patterns TRIs insertion mechanisms TEIs were...
Abstract Background The high lethal rate of pancreatic cancer is partly due to a lack efficient biomarkers for screening and early diagnosis. We attempted develop effective noninvasive methods using 5-methylcytosine (5mC) 5-hydroxymethylcytosine (5hmC) markers from circulating cell-free DNA (cfDNA) the detection ductal adenocarcinoma (PDAC). Results A 24-feature 5mC model that can accurately discriminate PDAC healthy controls (area under curve (AUC) = 0.977, sensitivity 0.824, specificity 1)...
Abstract Background Colorectal cancer (CRC) is a major type whose mechanism of metastasis remains elusive. Methods In this study, we characterised the evolutionary pattern metastatic CRC (mCRC) by analysing bulk and single-cell exome sequencing data primary tumours from 7 patients with liver metastases. Here, were analysed whole-exome (WES); 4 these also using sequencing. Results Despite low genomic divergence between paired cancers in data, WES (scWES) revealed rare mutations defined two...
Abstract Motivation Identifying chromatin accessibility is one of the key steps in studying regulation eukaryotic genomes. The combination exogenous methyltransferase and nanopore sequencing provides an strategy to identify open over long genomic ranges at single-molecule scale. However, endogenous methylation, non-open-chromatin-specific methylation base-calling errors limit accuracy hinders its application complex Results We systematically evaluated impact these three influence factors,...
Macaca fascicularis (M. fascicularis) is a primate model organism that played important role in studying human health. It vital to better understand the similarity and differences of gene regulation between M. human. Current comparative study two species are limited by low quality annotation lack regulatory element data on genome. In this study, we improved with 57 expression from multiple tissues and, more importantly, manual curation procedure. The new enabled us map identify location...
Abstract Transposable elements (TEs) serve as both insertional mutagens and regulatory in cells, their aberrant activity is increasingly being revealed to contribute diseases cancers. However, measuring the transcriptional consequences of nonreference young TEs at individual loci remains challenging with current methods, primarily due technical limitations, including short read lengths generated insufficient coverage target regions. Here, we introduce a long-read targeted RNA sequencing...
Single-nucleotide variant (SNV) detection in the genome of single cells is affected by DNA amplification artefacts, including imbalanced alleles and early PCR errors. Existing single-cell genotyper accuracy often depends on quality coordination both target external data, such as heterozygous profiles determined bulk data. In most studies, information from different sources not perfectly matched. High-accuracy SNV with a limited data source remains challenge. We developed new method, SCOUT...
<p>Supplementary Methods and Material</p>
<p>SF1:Supplementary Fig. S1, Somatic mutations of NSCLC patients related to 1; SF2:Supplementary S2, Data quality and subtyping NSCLC, Related Figure 2; SF3:Supplementary S3, Delineation single cell open chromatin signature patient LWQC; SF4:Supplementary S4, Distribution function broad regions, 4; SF5:Supplementary S5, The relationship between somatic CNV, peaks gene expression, 5; SF6:Supplementary S6, Characteristics eQTLs ATAC-QTLs, 6 7; SF7:Supplementary S7, Validation genomic...
<p>SF1:Supplementary Fig. S1, Somatic mutations of NSCLC patients related to 1; SF2:Supplementary S2, Data quality and subtyping NSCLC, Related Figure 2; SF3:Supplementary S3, Delineation single cell open chromatin signature patient LWQC; SF4:Supplementary S4, Distribution function broad regions, 4; SF5:Supplementary S5, The relationship between somatic CNV, peaks gene expression, 5; SF6:Supplementary S6, Characteristics eQTLs ATAC-QTLs, 6 7; SF7:Supplementary S7, Validation genomic...
<p>Supplementary Methods and Material</p>
<div>Abstract<p>Non–small cell lung carcinoma (NSCLC) is a major cancer type whose epigenetic alteration remains unclear. We analyzed open chromatin data with matched whole-genome sequencing and RNA-seq of 50 primary NSCLC cases. observed high interpatient heterogeneity profiles the degree correlated to several clinical parameters. Lung adenocarcinoma squamous (LUSC) exhibited distinct patterns. Beyond this, we uncovered that broadest peaks indicated key genes led less stable...
<div>Abstract<p>Non–small cell lung carcinoma (NSCLC) is a major cancer type whose epigenetic alteration remains unclear. We analyzed open chromatin data with matched whole-genome sequencing and RNA-seq of 50 primary NSCLC cases. observed high interpatient heterogeneity profiles the degree correlated to several clinical parameters. Lung adenocarcinoma squamous (LUSC) exhibited distinct patterns. Beyond this, we uncovered that broadest peaks indicated key genes led less stable...