Patrick Kwok‐Shing Ng
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View article: A feasibility study of enzymatic methylation sequencing of cell-free DNA from cerebrospinal fluid of pediatric central nervous system tumor patients for molecular classification
A feasibility study of enzymatic methylation sequencing of cell-free DNA from cerebrospinal fluid of pediatric central nervous system tumor patients for molecular classification Open
Background Array-based DNA methylation profiling is the gold standard for central nervous system (CNS) tumor molecular classification, but requires over 100 ng input DNA from surgical tissue. Cell-free tumor DNA (cfDNA) in cerebrospinal fl…
View article: PATH-11. FEASIBILITY OF BRAIN TUMOR CLASSIFICATION BY ENZYMATIC DNA METHYLATION SEQUENCING ANALYSIS OF CELL-FREE DNA OBTAINED FROM CEREBROSPINAL FLUID
PATH-11. FEASIBILITY OF BRAIN TUMOR CLASSIFICATION BY ENZYMATIC DNA METHYLATION SEQUENCING ANALYSIS OF CELL-FREE DNA OBTAINED FROM CEREBROSPINAL FLUID Open
BACKGROUND Array-based DNA methylation profiling is the gold standard for molecular classification of brain tumors. However, it relies on significant amount of input DNA extracted from surgical tissue, thus limiting its use for tumors wher…
View article: Immunosuppressive tumor microenvironment of osteosarcoma
Immunosuppressive tumor microenvironment of osteosarcoma Open
Osteosarcoma is the most common malignant bone tumor in children, characterized by a high degree of genomic instability, resulting in copy-number alterations and genomic rearrangements without disease-defining recurrent mutations. Clinical…
RARE-04. DEVELOPMENT OF A PLATFORM TO PROFILE MICRORNA IN CEREBROSPINAL FLUID FROM PATIENTS WITH INTRACRANIAL GERM CELL TUMORS Open
BACKGROUND Current diagnosis of intracranial germ cell tumors (iGCTs) utilizes alpha fetoprotein (AFP) and chorionic gonadotropin (β-HCG) as biomarkers in the blood or cerebrospinal fluid (CSF). Two thirds of iGCTs are marker negative and …
View article: Supplementary Figures from Frequent Mutation of the PI3K Pathway in Head and Neck Cancer Defines Predictive Biomarkers
Supplementary Figures from Frequent Mutation of the PI3K Pathway in Head and Neck Cancer Defines Predictive Biomarkers Open
Supplementary Figures - PDF file 441K, Four figures as follows: SF1: decreased PTEN expression in HNSCC with PTEN loss. SFs 2-4: PIK3CA mutant HNSCC tumorgrafts treatment response characterization; PI3K inhibitors +/- cetuximab, tumor meas…
View article: Supplementary Tables from Frequent Mutation of the PI3K Pathway in Head and Neck Cancer Defines Predictive Biomarkers
Supplementary Tables from Frequent Mutation of the PI3K Pathway in Head and Neck Cancer Defines Predictive Biomarkers Open
Supplementary Tables - PDF file 207K, Five supplementary tables denoting clinical characteristics of tumors, statistical correlations between PI3K mutational status, HPV status, cancer gene mutation status, and significance of pathway and …
View article: Supplementary Text from Frequent Mutation of the PI3K Pathway in Head and Neck Cancer Defines Predictive Biomarkers
Supplementary Text from Frequent Mutation of the PI3K Pathway in Head and Neck Cancer Defines Predictive Biomarkers Open
Supplementary Text - PDF file 99K, Contains figure legends for supplemental figures 1-4, and text describing supplemental methodology
Data from Frequent Mutation of the PI3K Pathway in Head and Neck Cancer Defines Predictive Biomarkers Open
Genomic findings underscore the heterogeneity of head and neck squamous cell carcinoma (HNSCC). Identification of mutations that predict therapeutic response would be a major advance. We determined the mutationally altered, targetable mito…
View article: Supplementary Figures from Frequent Mutation of the PI3K Pathway in Head and Neck Cancer Defines Predictive Biomarkers
Supplementary Figures from Frequent Mutation of the PI3K Pathway in Head and Neck Cancer Defines Predictive Biomarkers Open
Supplementary Figures - PDF file 441K, Four figures as follows: SF1: decreased PTEN expression in HNSCC with PTEN loss. SFs 2-4: PIK3CA mutant HNSCC tumorgrafts treatment response characterization; PI3K inhibitors +/- cetuximab, tumor meas…
View article: Supplementary Text from Frequent Mutation of the PI3K Pathway in Head and Neck Cancer Defines Predictive Biomarkers
Supplementary Text from Frequent Mutation of the PI3K Pathway in Head and Neck Cancer Defines Predictive Biomarkers Open
Supplementary Text - PDF file 99K, Contains figure legends for supplemental figures 1-4, and text describing supplemental methodology
View article: Data from Frequent Mutation of the PI3K Pathway in Head and Neck Cancer Defines Predictive Biomarkers
Data from Frequent Mutation of the PI3K Pathway in Head and Neck Cancer Defines Predictive Biomarkers Open
Genomic findings underscore the heterogeneity of head and neck squamous cell carcinoma (HNSCC). Identification of mutations that predict therapeutic response would be a major advance. We determined the mutationally altered, targetable mito…
View article: Supplementary Tables from Frequent Mutation of the PI3K Pathway in Head and Neck Cancer Defines Predictive Biomarkers
Supplementary Tables from Frequent Mutation of the PI3K Pathway in Head and Neck Cancer Defines Predictive Biomarkers Open
Supplementary Tables - PDF file 207K, Five supplementary tables denoting clinical characteristics of tumors, statistical correlations between PI3K mutational status, HPV status, cancer gene mutation status, and significance of pathway and …
Efficacy of futibatinib, an irreversible fibroblast growth factor receptor inhibitor, in FGFR-altered breast cancer Open
The role of the fibroblast growth factor receptor (FGFR) gene alterations as therapeutic targets in breast cancer have not been well characterized. Futibatinib (TAS-120; Taiho) is a novel pan-FGFR inhibitor. We sought to determine the effi…
View article: Gene Novelties in Amphioxus Illuminate the Early Evolution of Cephalochordates
Gene Novelties in Amphioxus Illuminate the Early Evolution of Cephalochordates Open
Amphioxus is considered the best-known living proxy to the chordate ancestor and an irreplaceable model organism for evolutionary studies of chordates and deuterostomes. In this study, a high-quality genome of the Beihai amphioxus, Branchi…
A functional genomic approach to actionable gene fusions for precision oncology Open
Fusion genes represent a class of attractive therapeutic targets. Thousands of fusion genes have been identified in patients with cancer, but the functional consequences and therapeutic implications of most of these remain largely unknown.…
RAC1 Alterations Induce Acquired Dabrafenib Resistance in Association with Anaplastic Transformation in a Papillary Thyroid Cancer Patient Open
BRAF-activating mutations are the most frequent driver mutations in papillary thyroid cancer (PTC). Targeted inhibitors such as dabrafenib have been used in advanced BRAF-mutated PTC; however, acquired resistance to the drug is common and …
Cancer-associated mutations in the p85α N-terminal SH2 domain activate a spectrum of receptor tyrosine kinases Open
Significance Phosphoinositide 3-kinase activation typically occurs following stimulation by upstream receptor tyrosine kinases (RTKs), which alleviate p110α inhibition by p85α. p85α and p110α driver mutations have been reported to activate…
Molecular Landscape of BRAF-Mutant NSCLC Reveals an Association Between Clonality and Driver Mutations and Identifies Targetable Non-V600 Driver Mutations Open
In BRAF-mutant NSCLC, clonality is higher in known functional mutations and may allow identification of variants of unknown significance that are more likely to be oncogenic drivers. Our data indicate that certain non-V600 mutations are re…
Comprehensive assessment of computational algorithms in predicting cancer driver mutations Open
Background The initiation and subsequent evolution of cancer are largely driven by a relatively small number of somatic mutations with critical functional impacts, so-called driver mutations. Identifying driver mutations in a patient’s tum…
Additional file 10 of Comprehensive assessment of computational algorithms in predicting cancer driver mutations Open
Additional file 10. Performance metrics of 17 algorithms using default categorical predictions for benchmark 2.
Additional file 21 of Comprehensive assessment of computational algorithms in predicting cancer driver mutations Open
Additional file 21. Performance metrics of 33 algorithms using the median scores as threshold to make binary predictions for benchmark 5.
Additional file 14 of Comprehensive assessment of computational algorithms in predicting cancer driver mutations Open
Additional file 14. Performance metrics of 15 algorithms using default categorical predictions for benchmark 3. CanDrA and FATHMM-disease were not included in the list, since all TP53 mutations in this analysis were predicted as “drivers” …
Additional file 17 of Comprehensive assessment of computational algorithms in predicting cancer driver mutations Open
Additional file 17. Performance metrics of 33 algorithms using the median scores as threshold to make binary predictions for benchmark 4.
Additional file 1 of Comprehensive assessment of computational algorithms in predicting cancer driver mutations Open
Additional file 1. Default prediction categories of 17 algorithms.
Additional file 5 of Comprehensive assessment of computational algorithms in predicting cancer driver mutations Open
Additional file 5. Performance metrics of 33 algorithms using the median scores as threshold to make binary predictions for benchmark 1.
Additional file 18 of Comprehensive assessment of computational algorithms in predicting cancer driver mutations Open
Additional file 18. Performance metrics of 17 algorithms using default categorical predictions for benchmark 4.