A5075682354- Cancer Genomics and Diagnostics
- Advanced Breast Cancer Therapies
- Bladder and Urothelial Cancer Treatments
- HER2/EGFR in Cancer Research
- Cancer Immunotherapy and Biomarkers
- Cancer Treatment and Pharmacology
- Prostate Cancer Treatment and Research
- Epigenetics and DNA Methylation
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Urinary and Genital Oncology Studies
- Breast Cancer Treatment Studies
- Lung Cancer Treatments and Mutations
- Single-cell and spatial transcriptomics
- RNA modifications and cancer
- Molecular Biology Techniques and Applications
- Esophageal Cancer Research and Treatment
- Colorectal Cancer Treatments and Studies
- Genetic factors in colorectal cancer
- Renal cell carcinoma treatment
- Lung Cancer Research Studies
- BRCA gene mutations in cancer
- Ferroptosis and cancer prognosis
- Glaucoma and retinal disorders
- Glioma Diagnosis and Treatment
Sichuan University
2025
Hefei University of Technology
2023-2024
Chengdu University
2024
Shanghai Medical Information Center
2024
Washington University in St. Louis
2023
University of Notre Dame
2022
Jiangnan University
2022
Genentech
2012-2015
Kaiser Permanente South San Francisco Medical Center
2013
Northwestern University
2006-2012
Illumina microarray is becoming a popular platform. The BeadArray technology from makes its preprocessing and quality control different other technologies. Unfortunately, most analyses have not taken advantage of the unique properties system, just incorporated methods originally designed for Affymetrix microarrays. lumi Bioconductor package especially to process data. It includes data input, control, variance stabilization, normalization gene annotation portions. In specific,...
High-throughput profiling of DNA methylation status CpG islands is crucial to understand the epigenetic regulation genes. The microarray-based Infinium assay by Illumina one platform for low-cost high-throughput profiling. Both Beta-value and M-value statistics have been used as metrics measure levels. However, there are no detailed studies their relations strengths limitations. We demonstrate that relationship between methods a Logit transformation, show method has severe heteroscedasticity...
A major problem for current peak detection algorithms is that noise in mass spectrometry (MS) spectra gives rise to a high rate of false positives. The positive especially problematic detecting peaks with low amplitudes. Usually, various baseline correction and smoothing methods are applied before attempting detection. This approach very sensitive the amount aggressiveness correction, which contribute making results inconsistent between runs, instrumentation analysis methods.Most simply...
Variance stabilization is a step in the preprocessing of microarray data that can greatly benefit performance subsequent statistical modeling and inference. Due to often limited number technical replicates for Affymetrix cDNA arrays, achieving variance be difficult. Although Illumina platform provides larger on each array (usually over 30 randomly distributed beads per probe), these have not been leveraged current log2 transformation process. We devised variance-stabilizing (VST) method...
Immunotherapy-based monotherapy treatment in metastatic pancreatic ductal adenocarcinoma (mPDAC) has shown limited benefit outside of the mismatch repair deficiency setting, while safety and efficacy combining dual-checkpoint inhibitor immunotherapy with chemotherapy remains uncertain. Here, we present results from CCTG PA.7 study (NCT02879318), a randomized phase II trial comparing gemcitabine nab-paclitaxel without immune checkpoint inhibitors durvalumab tremelimumab 180 patients mPDAC....
Background Uterine leiomyomas, or fibroids, represent the most common benign tumor of female reproductive tract. Fibroids become symptomatic in 30% all women and up to 70% African American age. Epigenetic dysregulation individual genes has been demonstrated leiomyoma cells; however, vivo genome-wide distribution such epigenetic abnormalities remains unknown. Principal Findings We characterized compared DNA methylation mRNA expression profiles uterine matched adjacent normal myometrial...
Abstract Background Hepatocellular carcinoma (HCC) is a heterogeneous disease with high mortality rate. Recent genomic studies have identified TP53 , AXIN1 and CTNNB1 as the most frequently mutated genes. Lower frequency mutations been reported in ARID1A ARID2 JAK1 . In addition, hepatitis B virus (HBV) integrations into human genome associated HCC. Results Here, we deep-sequence 42 HCC patients combination of whole genome, exome transcriptome sequencing to identify mutational landscape...
BackgroundMetastatic prostate cancer is a clonally heterogeneous disease state characterized by progressive somatic perturbations. The aim of this study was to identify cell free DNA- (cfDNA-) based alterations and their associations with outcomes in metastatic cancer.MethodsIn longitudinal prospective cohort plasma cfDNA/circulating tumor DNA (ctDNA) analyzed before, during, after androgen deprivation therapy (ADT) 4 independent patient groups ranging from untreated hormone sensitive...
Abstract Purpose: Clinical biomarkers to identify patients unlikely benefit from CDK4/6 inhibition (CDK4/6i) in combination with endocrine therapy (ET) are lacking. We implemented a comprehensive circulating tumor DNA (ctDNA) analysis genomic features for predicting and monitoring treatment resistance. Experimental Design: ctDNA was isolated 216 plasma samples collected 51 hormone receptor–positive (HR+)/HER2-negative (HER2−) metastatic breast cancer (MBC) on phase II trial of palbociclib...
Background and Purpose— The pathogenesis of intracranial aneurysms (IAs) remains elusive. Most studies have focused on individual genes, or a few interrelated genes products, at time in human IA. However, broad view pathologic mechanisms has not been investigated by identifying pathogenic their interaction networks. Our study aimed to analyze global gene expression patterns the IA wall. Methods— To our knowledge, group was first perform Illumina microarray analysis via comparison aneurysm...
Abstract Subjective methods have been reported to adapt a general-purpose ontology for specific application. For example, Gene Ontology (GO) Slim was created from GO generate highly aggregated report of the human-genome annotation. We propose statistical general purpose, OBO Foundry Disease (DO) identification gene-disease associations. Thus, we need simplified definition disease categories derived implicated genes. On basis assumption that DO terms having similar associated genes are...
Non-small cell lung cancers (NSCLC) comprise multiple distinct biologic groups with different prognoses. For example, patients epithelial-like tumors have a better prognosis and exhibit greater sensitivity to inhibitors of the epidermal growth factor receptor (EGFR) pathway than mesenchymal-like tumors. Here, we test hypothesis that NSCLCs can be distinguished from on basis global DNA methylation patterns.To determine whether phenotypic subsets defined their patterns, combined...
Abstract Although pesticides are subject to extensive carcinogenicity testing before regulatory approval, pesticide exposure has repeatedly been associated with various cancers. This suggests that may cause cancer via nonmutagenicity mechanisms. The present study provides evidence support the hypothesis pesticide‐induced be mediated in part by epigenetic We examined whether seven commonly used (i.e., fonofos, parathion, terbufos, chlorpyrifos, diazinon, malathion, and phorate) induces DNA...
We sought to identify predictive biomarkers for a novel nicotinamide phosphoribosyltransferase (NAMPT) inhibitor.We use NAMPT inhibitor, GNE-617, evaluate nicotinic acid rescue status in panel of more than 400 cancer cell lines. Using correlative analysis and RNA interference (RNAi), we specific biomarker status. next determine the mechanism regulation expression biomarker. Finally, develop immunohistochemical (IHC) DNA methylation assays tissue prevalence across indications.Nicotinate...
Genomic alterations in DNA damage response (DDR) genes are common metastatic castration-resistant prostate cancer (mCRPC). Understanding how these genomic events impact prognosis and/or treatment is vital for optimising clinical outcomes.
Oligonucleotide probes that are sequence identical may have different identifiers between manufacturers and even versions of the same company's microarray; sometimes identifier is reused represents a completely oligonucleotide, resulting in ambiguity potentially mis-identification genes hybridizing to probe.We devised unique, non-degenerate encoding scheme can be used as universal representation identify an oligonucleotide across manufacturers. We named encoded 'nuID', for nucleotide...
Disease and Gene Annotations database (DGA, http://dga.nubic.northwestern.edu) is a collaborative effort aiming to provide comprehensive integrative annotation of the human genes in disease network context by integrating computable controlled vocabulary Ontology (DO version 3 revision 2510, which has 8043 inherited, developmental acquired diseases), NCBI Reference Into Function (GeneRIF) molecular interaction (MIN). DGA integrates these resources together using semantic mappings build an set...
No AccessJournal of UrologyAdult Urology1 Oct 2021Urinary Molecular Pathology for Patients with Newly Diagnosed Urothelial Bladder CancerThis article is commented on by the following:Editorial CommentEditorial Comment Ruiyun Zhang, Jingyu Zang, Feng Xie, Yue Yiqiu Wang, Ying Jing, Yi Zhaoxiong Chen, Akezhouli Shahatiaili, Mei-Chun Cai, Zhixin Zhao, Pan Du, Shidong Jia, Guanglei Zhuang, and Haige Chen ZhangRuiyun Zhang Department Urology, Ren Ji Hospital, School Medicine, Shanghai Jiao Tong...
Intrinsic resistance to androgen receptor signalling inhibitors (ARSI) occurs in 20-30% of men with metastatic castration-resistant prostate cancer (mCRPC). Ceramide metabolism may have a role ARSI resistance. Our study's aim is investigate the association ceramide-sphingosine-1-phosphate (ceramide-S1P) axis mCRPC.Lipidomic analysis (∼700 lipids) was performed on plasma collected from 132 mCRPC, before commencing enzalutamide or abiraterone. AR gene aberrations 77 these were identified by...