Quang M. Trinh
A5072430983- Cancer Genomics and Diagnostics
- Colorectal Cancer Screening and Detection
- Genetic factors in colorectal cancer
- Bioinformatics and Genomic Networks
- Nutrition and Health in Aging
- Nutritional Studies and Diet
- Colorectal Cancer Treatments and Studies
- Plant-based Medicinal Research
- Gene expression and cancer classification
- Semantic Web and Ontologies
- Animal testing and alternatives
- Biomedical Text Mining and Ontologies
- Service-Oriented Architecture and Web Services
- Genomics and Phylogenetic Studies
- Acute Myeloid Leukemia Research
- Glioma Diagnosis and Treatment
- Radiomics and Machine Learning in Medical Imaging
- Cancer Research and Treatments
- Genomics and Rare Diseases
- Advanced Database Systems and Queries
- Cancer-related Molecular Pathways
- Genetics, Bioinformatics, and Biomedical Research
- Pancreatic and Hepatic Oncology Research
- Protein Degradation and Inhibitors
- RNA modifications and cancer
Ontario Institute for Cancer Research
2016-2025
Institute of Cancer Research
2016
University of Toronto
2013
University of Calgary
2006-2008
Glioblastoma is an incurable brain malignancy. By the time of clinical diagnosis, these tumours exhibit a degree genetic and cellular heterogeneity that provides few clues to mechanisms initiate drive gliomagenesis1,2. Here, explore early steps in gliomagenesis, we utilized conditional gene deletion lineage tracing tumour mouse models, coupled with serial magnetic resonance imaging, then closely track formation. We isolated labelled unlabelled cells at multiple stages—before first visible...
Mutations in human induced pluripotent stem cells (iPSCs) pose a risk for their clinical use due to preferential reprogramming of mutated founder cell and selection mutations during maintenance iPSCs culture. It is unknown, however, if are stress associated with oncogene expression reprogramming. We performed whole exome sequencing foreskin fibroblasts derived at two different passages. found that vitro passaging contributed 7% the iPSC coding point mutation load, ultradeep amplicon revealed...
Significance Noonan syndrome (NS) is one of several RASopathies, which are developmental disorders caused by mutations in genes encoding RAS-ERK pathway components. The cause 20–30% NS cases remains unknown, and distinguishing from other RASopathies related can be difficult. We used next-generation sequencing (NGS) to identify causative or candidate for 13 27 patients lacking known NS-associated mutations. Other harbor single variants potential genes, suggesting rare private genetic...
The nematode Caenorhabditis briggsae is a model for comparative developmental evolution with C. elegans . Worldwide collections of have implicated an intriguing history divergence among genetic groups separated by latitude, or restricted geography, that being exploited to dissect the basis adaptive and reproductive incompatibility; yet, genomic scope timing population unclear. We performed high-coverage whole-genome sequencing 37 wild isolates applied pairwise sequentially Markovian...
Colorectal cancer (CRC) is a biologically heterogeneous disease. To characterize its mutational profile, we conduct targeted sequencing of 205 genes for 2,105 CRC cases with survival data. Our data shows several findings in addition to enhancing the existing knowledge CRC. We identify PRKCI, SPZ1, MUTYH, MAP2K4, FETUB, and TGFBR2 as additional significantly mutated find that among hypermutated tumors, an increased mutation burden associated improved CRC-specific (HR = 0.42, 95% CI:...
Abstract Sonic hedgehog medulloblastoma encompasses a clinically and molecularly diverse group of cancers the developing central nervous system. Here, we use unbiased sequencing transcriptome across large cohort 250 tumors to reveal differences among molecular subtypes disease, demonstrate previously unappreciated importance non-coding RNA transcripts. We identify alterations within cAMP dependent pathway ( GNAS , PRKAR1A ) which converge on GLI2 activity show that 18% have genetic event...
Availability of lung cancer models that closely mimic human tumors remains a significant gap in research, as tumor cell lines and mouse may not recapitulate the spectrum heterogeneity seen patients. We aimed to establish patient-derived xenograft (PDX) resource from surgically resected non-small (NSCLC). Fresh tissue surgical resection was implanted grown subcutaneous pocket non-obese severe combined immune deficient (NOD SCID) gamma mice. Subsequent passages were NOD SCID A subset matched...
A key step in cancer genome analysis is the identification of somatic mutations tumor. This typically done by comparing tumor to reference sequence derived from a normal tissue taken same donor. However, there are variety common scenarios which matched not available for comparison. In this work, we describe an algorithm distinguish single nucleotide variants (SNVs) next-generation sequencing data germline polymorphisms absence samples using machine learning approach. Our was evaluated family...
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Abstract Carriers of germline biallelic pathogenic variants in the MUTYH gene have a high risk colorectal cancer. We test 5649 cancers to evaluate discriminatory potential tumor mutational signature specific for identifying carriers and classifying uncertain clinical significance (VUS). Using matched targeted multi-gene panel approach, our classifier identifies all known non-carriers an independent set 3019 (accuracy = 100% (95% confidence interval 99.87–100%)). All monoallelic are...
Human cerebral cancers are known to contain cell types resembling the varying stages of neural development. However, basis this association remains unclear. Here, we map development mouse cerebrum across developmental time-course, from embryonic day 12.5 postnatal 365, performing single-cell transcriptomics on >100,000 cells. By comparing reference atlas data >100 glial tumours adult and paediatric human cerebrum, find that tumour cells have an expression signature overlaps with temporally...
A locus on human chromosome 11q23 tagged by marker rs3802842 was associated with colorectal cancer (CRC) in a genome-wide association study; this finding has been replicated case-control studies worldwide. In order to identify biologic factors at that are related the etiopathology of CRC, we used microarray-based target selection methods, coupled next-generation sequencing, study 103 kb locus. We genotyped 369 putative variants from 1,030 patients CRC (cases) and 1,061 individuals without...
Abstract Background Obesity is an established risk factor for colorectal cancer (CRC), but the evidence association inconsistent across molecular subtypes of disease. Methods We pooled data on body mass index (BMI), tumor microsatellite instability status, CpG island methylator phenotype BRAF and KRAS mutations, Jass classification types 11 872 CRC cases 013 controls from observational studies. used multinomial logistic regression to estimate odds ratios (OR) 95% confidence intervals (CI)...
ABSTRACT Background and Aims The microbiome has long been suspected of a role in colorectal cancer (CRC) tumorigenesis. mutational signature SBS88 mechanistically links CRC development with the strain Escherichia coli harboring pks island that produces genotoxin colibactin, but genomic, pathological survival characteristics associated SBS88-positive tumors are unknown. Methods CRCs were identified from targeted sequencing data 5,292 17 studies tested for their association...
Abstract Background Waist circumference (WC) and its allometric counterpart, “a body shape index” (ABSI), are risk factors for colorectal cancer (CRC); however, it is uncertain whether associations with these measurements limited to specific molecular subtypes of the disease. Methods Data from 2,772 CRC cases 3,521 controls were pooled four cohort studies within Genetics Epidemiology Colorectal Cancer Consortium. Four markers (BRAF mutation, KRAS CpG island methylator phenotype,...
ABSTRACT MYC-driven (MYC+) cancers are aggressive and often fatal. MYC dysregulation is a key event in these cancers, but overexpression of alone not always enough to cause cancer. Plasmocytoma Variant Translocation 1 ( PVT1 ), long non-coding RNA (lncRNA) adjacent on chromosome 8 rearrangement hotspot many MYC+ cancers. In addition being co-amplified with MYC, the genomic at involves translocation, which has had obscure functional consequences. We report that translocation locus asymmetric...
<p>Association between waist circumference, proximal colon cancer, and its molecular subtypes.</p>
<p>Summary of study-specific assessment microsatellite instability (MSI) status.</p>
<p>Association between ABSI, colorectal cancer, and its molecular subtypes after conducting multiple imputation.</p>
<p>Association between waist circumference, colorectal cancer, and its molecular subtypes after conducting multiple imputation.</p>
<p>Association between waist circumference, distal colon cancer, and its molecular subtypes.</p>
<p>Association between A Body Shape Index (ABSI), distal colon cancer, and its molecular subtypes.</p>
<p>Association between A Body Shape Index (ABSI), proximal colon cancer, and its molecular subtypes.</p>
<p>Association between waist circumference, rectal cancer, and its molecular subtypes.</p>