Timothy A. Beck
A5010213541- Cancer Genomics and Diagnostics
- Genomics and Phylogenetic Studies
- Radiomics and Machine Learning in Medical Imaging
- AI in cancer detection
- Cancer-related molecular mechanisms research
- RNA modifications and cancer
- Cell Image Analysis Techniques
- Pancreatic and Hepatic Oncology Research
- Genetic factors in colorectal cancer
- Genomics and Rare Diseases
- Evolution and Genetic Dynamics
- Molecular Biology Techniques and Applications
- Prostate Cancer Treatment and Research
- Mitochondrial Function and Pathology
- Genomic variations and chromosomal abnormalities
- Single-cell and spatial transcriptomics
- Cancer Cells and Metastasis
- Bioinformatics and Genomic Networks
- RNA Research and Splicing
- Genetics, Bioinformatics, and Biomedical Research
- Nutrition, Genetics, and Disease
- Prostate Cancer Diagnosis and Treatment
- Chromosomal and Genetic Variations
- High Altitude and Hypoxia
- Video Analysis and Summarization
Ontario Institute for Cancer Research
2012-2023
Human Longevity (United States)
2019-2020
University of California, Davis
2016
Abstract Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation this variation at whole-genome scale 1–3 . Here we report integrative analysis 2,658 whole-cancer genomes their matching normal tissues across 38 tumour types from Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium International Genome (ICGC) The Atlas (TCGA). We describe generation PCAWG resource, facilitated international data sharing using compute clouds. On...
Mitochondria are essential cellular organelles that play critical roles in cancer. Here, as part of the International Cancer Genome Consortium/The Atlas Pan-Cancer Analysis Whole Genomes Consortium, which aggregated whole-genome sequencing data from 2,658 cancers across 38 tumor types, we performed a multidimensional, integrated characterization mitochondrial genomes and related RNA data. Our analysis presents most definitive mutational landscape identifies several hypermutated cases....
Abstract As whole-genome sequencing for cancer genome analysis becomes a clinical tool, full understanding of the variables affecting output is required. Here using tumour-normal sample pairs from two different types cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct benchmarking exercise within context International Cancer Genome Consortium. We compare methods, pipelines validation methods. show that PCR-free methods increasing depth to ∼100 × shows benefits, as long...
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 As next-generation sequencing becomes a clinical tool, full understanding of the variables affecting analysis output is required. Through International Cancer Genome Consortium (ICGC), we compared pipelines at five independent centers (CNAG, DKFZ, OICR, RIKEN and WTSI) using single tumor-blood DNA pair. Analyses by each center with one standardized algorithm revealed significant discrepancies. Although most performed well for coding mutations, library preparation methods coverage...
Abstract The emergence of next generation DNA sequencing technology is enabling high-resolution cancer genome analysis. Large-scale projects like the International Cancer Genome Consortium (ICGC) are systematically scanning genomes to identify recurrent somatic mutations. Second sequencing, however, still an evolving and procedures, both experimental analytical, constantly changing. Thus research community defining a set best practices for data analysis, with no single protocol emerging...
Accurate detection of somatic single nucleotide variants and small insertions deletions from DNA sequencing experiments tumour-normal pairs is a challenging task. Tumour samples are often contaminated with normal cells confounding the available evidence for variants. Furthermore, tumours heterogeneous so sub-clonal observed at reduced allele frequencies. We present here cell-line titration series dataset that can be used to evaluate variant calling pipelines goal reliably true mutations low...
Abstract Genomic rearrangements are a hallmark of cancer biology and progression, allowing cells to rapidly transform through alterations in regulatory structures, changes expression patterns, reprogramming signaling pathways, creation novel transcripts via gene fusion events. Though functional fusions encoding oncogenic proteins the most dramatic outcomes genomic rearrangements, we investigated relationship between evidenced by local using transcriptome data alone. 9,953 predictions from...
Abstract Genomic instability is one of the hallmarks cancer, leading to widespread copy number variations, chromosomal fusions, and other structural variations in many cancers. The breast cancer cell line SK-BR-3 an important model for HER2+ cancers, which are among most aggressive forms disease affect five cases. Through short read sequencing, arrays, technologies, genome known be highly rearranged with including approximately twenty-fold amplification HER2 oncogene, along numerous...
Abstract Men with localized prostate cancer vary widely in clinical outcome, a 30-50% failure rate after primary treatment. There is thus significant interest developing genomically refined prognostic groups. We sought to evaluate the extent of genetic heterogeneity, both between patients (inter-prostate) and within individual glands (intra-prostate) assess impact heterogeneity on risk stratification tight cohort. Copy number aberrations (CNAs) from 75 Gleason 7 were determined by OncoScan...
Abstract Intermediate risk prostate cancer (CaP) with Gleason score (GS) of 7 show up to 100x variability in genetic instability. As CaP is multifocal and likely multiclonal, there a need characterize heterogeneity for patient stratification, which would increase the ability act on genomic information by adding adjuvant therapies offset systemic occult metastases that currently limit cure ∼30% patients. Individual portraits could be used improve combined clinical-molecular staging criteria....
Five to ten percent of pancreatic cancer (PC) clusters within families. Epidemiologic studies suggest that Familial Pancreas Cancer (FPC) is caused by highly penetrant germline mutations, but less than 20% these genes have been identified. Characterizing the remaining genetic basis FPC should improve outcomes through molecularly tailored prevention, screening and treatment protocols. Exome sequencing (ES) a powerful new approach for detecting causes disease. However, causal mutation often...