Scientific Publications
Search results for "Hirst M"
2013/08/01
Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm.DNA methylation plays key roles in diverse biological processes such as X chromosome inactivation, transposable element repression, genomic imprinting, and tissue-specific gene expression. Sequencing-...
2013/08/01
Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods.Recent advancements in sequencing-based DNA methylation profiling methods provide an unprecedented opportunity to map complete DNA methylomes. These include whole-genome bisulfite sequencing (WGBS, Me...
2013/07/04
Comprehensive molecular characterization of clear cell renal cell carcinoma.Genetic changes underlying clear cell renal cell carcinoma (ccRCC) include alterations in genes controlling cellular oxygen sensing (for example, VHL) and the maintenance of chromatin states (for exam...
2013/07/01
DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape.Transposable element (TE)-derived sequences comprise half of the human genome and DNA methylome and are presumed to be densely methylated and inactive. Examination of genome-wide DNA methylation statu...
2013/07/01
Complete genomic landscape of a recurring sporadic parathyroid carcinoma.Parathyroid carcinoma is a rare endocrine malignancy with an estimated incidence of less than 1 per million population. Excessive secretion of parathyroid hormone, extremely high serum calcium level, ...
2013/06/30
Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells.DNA methylation is a heritable epigenetic modification involved in gene silencing, imprinting, and the suppression of retrotransposons. Global DNA demethylation occurs in the early embryo and the germ...
2013/06/07
Complete genomic landscape of a recurring sporadic parathyroid carcinoma.Parathyroid carcinoma is a rare endocrine malignancy with an estimated incidence of less than 1 per million population. Excessive secretion of parathyroid hormone, extremely high serum calcium level, ...
2013/05/30
Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia.BACKGROUND: Many mutations that contribute to the pathogenesis of acute myeloid leukemia (AML) are undefined. The relationships between patterns of mutations and epigenetic phenotypes are not yet c...
2013/05/26
DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape.Transposable element (TE)-derived sequences comprise half of the human genome and DNA methylome and are presumed to be densely methylated and inactive. Examination of genome-wide DNA methylation statu...
2013/05/16
The shaping and functional consequences of the microRNA landscape in breast cancer.MicroRNAs (miRNAs) show differential expression across breast cancer subtypes, and have both oncogenic and tumour-suppressive roles. Here we report the miRNA expression profiles of 1,302 breast tumour...
2013/04/01
The genetic landscape of high-risk neuroblastoma.Neuroblastoma is a malignancy of the developing sympathetic nervous system that often presents with widespread metastatic disease, resulting in survival rates of less than 50%. To determine the spectr...
2013/02/01
Epigenomics: sequencing the methylome.DNA methylation patterns are increasingly surveyed through methods that utilize massively parallel sequencing. Sequence-based assays developed to detect DNA methylation can be broadly divided into tho...
2012/11/01
Spark: A navigational paradigm for genomic data exploration.Biologists possess the detailed knowledge critical for extracting biological insight from genome-wide data resources, and yet they are increasingly faced with nontrivial computational analysis challen...
2012/10/07
DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution.DNA rearrangements such as sister chromatid exchanges (SCEs) are sensitive indicators of genomic stress and instability, but they are typically masked by single-cell sequencing techniques. We develope...
2012/10/01
Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer.Loss of heterozygosity (LOH) and copy number alteration (CNA) feature prominently in the somatic genomic landscape of tumors. As such, karyotypic aberrations in cancer genomes have been studied extens...
2012/09/01
Use of mutation profiles to refine the classification of endometrial carcinomas.The classification of endometrial carcinomas is based on pathological assessment of tumour cell type; the different cell types (endometrioid, serous, carcinosarcoma, mixed, undifferentiated, and clear...
2012/08/16
Mutation discovery in regions of segmental cancer genome amplifications with CoNAn-SNV: a mixture model for next generation sequencing of tumors.Next generation sequencing has now enabled a cost-effective enumeration of the full mutational complement of a tumor genome-in particular single nucleotide variants (SNVs). Most current computational ...
2012/08/14
Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia.Genomic profiling has identified a subtype of high-risk B-progenitor acute lymphoblastic leukemia (B-ALL) with alteration of IKZF1, a gene expression profile similar to BCR-ABL1-positive ALL and poor ...
2012/05/01
Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer.Next-generation sequencing is making sequence-based molecular pathology and personalized oncology viable. We selected an individual initially diagnosed with conventional but aggressive prostate adenoc...
2012/04/04
The clonal and mutational evolution spectrum of primary triple-negative breast cancers.Primary triple-negative breast cancers (TNBCs), a tumour type defined by lack of oestrogen receptor, progesterone receptor and ERBB2 gene amplification, represent approximately 16% of all breast cance...
2012/04/01
JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data.MOTIVATION: Identification of somatic single nucleotide variants (SNVs) in tumour genomes is a necessary step in defining the mutational landscapes of cancers. Experimental designs for genome-wide as...
2012/03/01
Next generation sequencing of prostate cancer from a patient identifies a deficiency of methylthioadenosine phosphorylase, an exploitable tumor target.Castrate-resistant prostate cancer (CRPC) and neuroendocrine carcinoma of the prostate are invariably fatal diseases for which only palliative therapies exist. As part of a prostate tumor sequencing p...
2012/01/19
Recurrent somatic DICER1 mutations in nonepithelial ovarian cancers.BACKGROUND: Germline truncating mutations in DICER1, an endoribonuclease in the RNase III family that is essential for processing microRNAs, have been observed in families with the pleuropulmonary ...
2012/01/15
Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data.MOTIVATION: The study of cancer genomes now routinely involves using next-generation sequencing technology (NGS) to profile tumours for single nucleotide variant (SNV) somatic mutations. However, s...
2012/01/12
Identification and characterization of Hoxa9 binding sites in hematopoietic cells.The clustered homeobox proteins play crucial roles in development, hematopoiesis, and leukemia, yet the targets they regulate and their mechanisms of action are poorly understood. Here, we identified ...
2012/01/01
Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers.Oligodendroglioma is characterized by unique clinical, pathological, and genetic features. Recurrent losses of chromosomes 1p and 19q are strongly associated with this brain cancer but knowledge of th...