Peter W. Laird
A5025761663- Epigenetics and DNA Methylation
- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- Cancer-related gene regulation
- Genetic factors in colorectal cancer
- Lung Cancer Treatments and Mutations
- Genomics and Chromatin Dynamics
- Histone Deacetylase Inhibitors Research
- Ferroptosis and cancer prognosis
- Bladder and Urothelial Cancer Treatments
- Occupational and environmental lung diseases
- Colorectal Cancer Screening and Detection
- Medical Imaging and Pathology Studies
- Peptidase Inhibition and Analysis
- Nutrition, Genetics, and Disease
- Genetic Syndromes and Imprinting
- Colorectal Cancer Treatments and Studies
- Glioma Diagnosis and Treatment
- Cancer-related molecular mechanisms research
- Bioinformatics and Genomic Networks
- Protein Degradation and Inhibitors
- Estrogen and related hormone effects
- Radiomics and Machine Learning in Medical Imaging
- Cancer, Hypoxia, and Metabolism
- Pancreatic and Hepatic Oncology Research
Van Andel Institute
2016-2025
Edinburgh Napier University
2008-2024
University of Southern California
2009-2023
USC Norris Comprehensive Cancer Center
2003-2023
The University of Texas MD Anderson Cancer Center
2008-2018
Baylor College of Medicine
2017
Case Western Reserve University
2016
University Hospitals Cleveland Medical Center
2016
Albany Medical Center Hospital
2016
The University of Tokyo
2016
Infiltrating stromal and immune cells form the major fraction of normal in tumour tissue not only perturb signal molecular studies but also have an important role cancer biology. Here we describe 'Estimation STromal Immune MAlignant Tumours using Expression data' (ESTIMATE)—a method that uses gene expression signatures to infer samples. ESTIMATE scores correlate with DNA copy number-based purity across samples from 11 different types, profiled on Agilent, Affymetrix platforms or based RNA...
Diffuse low-grade and intermediate-grade gliomas (which together make up the lower-grade gliomas, World Health Organization grades II III) have highly variable clinical behavior that is not adequately predicted on basis of histologic class. Some are indolent; others quickly progress to glioblastoma. The uncertainty compounded by interobserver variability in diagnosis. Mutations IDH, TP53, ATRX codeletion chromosome arms 1p 19q (1p/19q codeletion) been implicated as clinically relevant...
Highlights•Alteration map of 10 signaling pathways across 9,125 samples from 33 cancer types•Reusable, curated pathway templates that include a catalogue driver genes•57% tumors have at least one potentially actionable alteration in these pathways•Co-occurrence alterations suggests combination therapy opportunitiesSummaryGenetic control cell-cycle progression, apoptosis, and cell growth are common hallmarks cancer, but the extent, mechanisms, co-occurrence differ between individual tumor...
We conducted comprehensive integrative molecular analyses of the complete set tumors in The Cancer Genome Atlas (TCGA), consisting approximately 10,000 specimens and representing 33 types cancer. performed clustering using data on chromosome-arm-level aneuploidy, DNA hypermethylation, mRNA, miRNA expression levels reverse-phase protein arrays, which all, except for revealed primarily organized by histology, tissue type, or anatomic origin. influence cell type was evident...
Determining how somatic copy number alterations (SCNAs) promote cancer is an important goal. We characterized SCNA patterns in 4,934 cancers from The Cancer Genome Atlas Pan-Cancer data set. Whole-genome doubling, observed 37% of cancers, was associated with higher rates every other type SCNA, TP53 mutations, CCNE1 amplifications and the PPP2R complex. SCNAs that were internal to chromosomes tended be shorter than telomere-bounded SCNAs, suggesting different mechanisms underlying their...
Cancer progression involves the gradual loss of a differentiated phenotype and acquisition progenitor stem-cell-like features. Here, we provide novel stemness indices for assessing degree oncogenic dedifferentiation. We used an innovative one-class logistic regression (OCLR) machine-learning algorithm to extract transcriptomic epigenetic feature sets derived from non-transformed pluripotent stem cells their progeny. Using OCLR, were able identify previously undiscovered biological mechanisms...
We report here on a quantitative technique called COBRA to determine DNA methylation levels at specific gene loci in small amounts of genomic DNA. Restriction enzyme digestion is used reveal methylationdependent sequence differences PCR products sodium bisulfite-treated as described previously. show that the original sample are represented by relative digested and undigested product linearly fashion across wide spectrum levels. In addition, we this can be reliably applied obtained from...
Papillary renal-cell carcinoma, which accounts for 15 to 20% of carcinomas, is a heterogeneous disease that consists various types renal cancer, including tumors with indolent, multifocal presentation and solitary an aggressive, highly lethal phenotype. Little known about the genetic basis sporadic papillary no effective forms therapy advanced exist.We performed comprehensive molecular characterization 161 primary using whole-exome sequencing, copy-number analysis, messenger RNA microRNA...
Cancer chromatin accessibility landscape The Genome Atlas (TCGA) provides a high-quality resource of molecular data on large variety human cancers. Corces et al. used recently modified assay to profile determine the accessible in 410 TCGA samples from 23 cancer types (see Perspective by Taipale). When were integrated with other omics available for same tumor samples, inherited risk loci predisposition revealed, transcription factors and enhancers driving subtypes patient survival differences...
<h2>Summary</h2> DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 types. Mutations with accompanying loss heterozygosity were observed in over 1/3 genes, including <i>TP53</i> <i>BRCA1/2</i>. Other prevalent included epigenetic silencing the direct genes <i>EXO5</i>, <i>MGMT</i>, <i>ALKBH3</i> ∼20% samples. Homologous recombination (HRD) was...
Polycomb group proteins (PCGs) are involved in repression of genes that required for stem cell differentiation. Recently, it was shown promoters PCG target (PCGTs) 12-fold more likely to be methylated cancer than non-PCGTs. Age is the most important demographic risk factor cancer, and we hypothesized its carcinogenic potential may referred by irreversibly stabilizing features. To test this, analyzed methylation status over 27,000 CpGs mapping ∼14,000 whole blood samples from 261...