Samirkumar B. Amin
A5057939952- Cancer Genomics and Diagnostics
- Epigenetics and DNA Methylation
- Multiple Myeloma Research and Treatments
- MicroRNA in disease regulation
- Genomics and Chromatin Dynamics
- Cancer Mechanisms and Therapy
- RNA modifications and cancer
- Glioma Diagnosis and Treatment
- Genomics and Phylogenetic Studies
- Ubiquitin and proteasome pathways
- Protein Degradation and Inhibitors
- Circular RNAs in diseases
- Cancer-related molecular mechanisms research
- Molecular Biology Techniques and Applications
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Cancer Research and Treatments
- RNA Research and Splicing
- Evolution and Genetic Dynamics
- Single-cell and spatial transcriptomics
- Histone Deacetylase Inhibitors Research
- Genetic factors in colorectal cancer
- DNA Repair Mechanisms
- Prostate Cancer Treatment and Research
- Chromosomal and Genetic Variations
Montreal General Hospital
2024
Jackson Laboratory
2017-2023
Baylor College of Medicine
2017-2023
The University of Texas MD Anderson Cancer Center
2015-2023
Yale University
2023
Quantitative BioSciences
2020-2022
Somerset NHS Foundation Trust
2015
National Institutes of Health
2015
Musgrove Park Hospital
2015
Taunton & Somerset NHS Foundation Trust
2015
Abstract Somatic mutations in cancer genomes are caused by multiple mutational processes, each of which generates a characteristic signature 1 . Here, as part the Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium 2 International Cancer Genome (ICGC) and The Atlas (TCGA), we characterized signatures using 84,729,690 somatic from 4,645 whole-genome 19,184 exome sequences that encompass most types cancer. We identified 49 single-base-substitution, 11 doublet-base-substitution, 4...
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...
The discovery of drivers cancer has traditionally focused on protein-coding genes
Abstract Transcript alterations often result from somatic changes in cancer genomes 1 . Various forms of RNA have been described cancer, including overexpression 2 , altered splicing 3 and gene fusions 4 ; however, it is difficult to attribute these underlying genomic owing heterogeneity among patients tumour types, the relatively small cohorts for whom samples analysed by both transcriptome whole-genome sequencing. Here we present, our knowledge, most comprehensive catalogue...
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 Here, as part of the Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium, for which whole-genome and—for a subset—whole-transcriptome sequencing data from 2,658 cancers across 38 tumor types was aggregated, we systematically investigated potential viral pathogens using consensus approach that integrated three independent pipelines. Viruses were detected in 382 genome and 68 transcriptome datasets. We found high prevalence known tumor-associated viruses such Epstein–Barr virus...
Gene fusion represents a class of molecular aberrations in cancer and has been exploited for therapeutic purposes. In this paper we describe TumorFusions, data portal that catalogues 20 731 gene fusions detected 9966 well characterized samples 648 normal specimens from The Cancer Genome Atlas (TCGA). spans 33 types TCGA. Fusion transcripts were identified via uniform pipeline, including filtering against list 3838 transcript panel non-neoplastic samples. Fusions mapped to somatic DNA...
Abstract In cancer, the primary tumour’s organ of origin and histopathology are strongest determinants its clinical behaviour, but in 3% cases a patient presents with metastatic tumour no obvious primary. Here, as part ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium , we train deep learning classifier to predict cancer type based on patterns somatic passenger mutations detected whole genome sequencing (WGS) 2606 tumours representing 24 common types produced by PCAWG...
Abstract Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for resource lncRNAs with validated roles. Furthermore, it remains debated whether mutated can drive tumorigenesis, and such functions could be conserved during evolution. Here, as part ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium, we introduce Cancer LncRNA Census (CLC), compilation 122 GENCODE causal roles in phenotypes. In contrast to existing databases, CLC requires...
Multi-omics datasets represent distinct aspects of the central dogma molecular biology. Such high-dimensional profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple using statistical fusion, rationalizes contributing evidence highlights associated genes. As part ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing from...
Oncogenic extrachromosomal DNA elements (ecDNA) play an important role in tumor evolution, but our understanding of ecDNA biology is limited. We determined the distribution single-cell copy number across patient tissues and cell line models observed how cell-to-cell frequency varies greatly. The exceptional intratumoral heterogeneity suggested ecDNA-specific replication propagation mechanisms. To evaluate transfer genetic material from parental to offspring cells during mitosis, we...
Abstract Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic respond poorly to therapy. Pan-cancer hallmarks tumour hypoxia remain understood, with limited comprehension its associations specific mutational processes, non-coding driver genes evolutionary features. Here, as part the ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 types, we quantify in 1188 spanning 27 cancer...
Abstract Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, most cancers outside the sex organs. Efforts to link these clinical specific molecular features focused on somatic mutations within coding regions genome. Here we report a pan-cancer analysis whole genomes 1983 tumours 28 subtypes as part ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium. We both confirm results exome studies, also uncover previously undescribed...