Hugues Sicotte
A5007577734- Pancreatic and Hepatic Oncology Research
- Chromatin Remodeling and Cancer
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Prostate Cancer Treatment and Research
- Mechanisms of cancer metastasis
- Cancer Genomics and Diagnostics
- Cancer, Lipids, and Metabolism
- Estrogen and related hormone effects
- Glioma Diagnosis and Treatment
- Cancer Research and Treatments
- Ovarian cancer diagnosis and treatment
- Molecular Biology Techniques and Applications
- Radiopharmaceutical Chemistry and Applications
- Genetic Associations and Epidemiology
- Cancer-related molecular mechanisms research
- RNA modifications and cancer
- Liver Disease Diagnosis and Treatment
- MicroRNA in disease regulation
- Epigenetics and DNA Methylation
- Cancer-related Molecular Pathways
- Gene expression and cancer classification
- Telomeres, Telomerase, and Senescence
- Atherosclerosis and Cardiovascular Diseases
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
Mayo Clinic
2014-2025
WinnMed
2014-2025
Mayo Clinic in Florida
2011-2024
Mayo Clinic in Arizona
2012-2022
University of Minnesota Rochester
2017
Jacksonville College
2016
University of California, San Francisco
2013-2014
Department of Medical Sciences
2014
Babol University of Medical Sciences
2014
Charlottesville Medical Research
2014
The prediction of clinical behavior, response to therapy, and outcome infiltrative glioma is challenging. On the basis previous studies tumor biology, we defined five molecular groups with use three alterations: mutations in TERT promoter, IDH, codeletion chromosome arms 1p 19q (1p/19q codeletion). We tested hypothesis that within based on these features, tumors would have similar variables, acquired somatic alterations, germline variants.We scored as negative or positive for each markers...
Although the costs of next generation sequencing technology have decreased over past years, there is still a lack simple-to-use applications, for comprehensive analysis RNA data. There no one-stop shop transcriptomic genomics. We developed MAP-RSeq, computational workflow that can be used obtaining genomic features from data, any genome. For optimization tools and parameters, MAP-RSeq was validated using both simulated real datasets. consists six major modules such as alignment reads,...
Abstract Background Stored biological samples with pathology information and medical records are invaluable resources for translational research. However, RNAs extracted from the archived clinical tissues often substantially degraded. RNA degradation distorts RNA-seq read coverage in a gene-specific manner, has profound influences on whole-genome gene expression profiling. Result We developed transcript integrity number (TIN) to measure degradation. When applied 3 independent datasets, we...
Abstract Background Glioblastoma (GBM) exhibits profound intratumoral genetic heterogeneity. Each tumor comprises multiple genetically distinct clonal populations with different therapeutic sensitivities. This has implications for targeted therapy and informed paradigms. Contrast-enhanced (CE)-MRI conventional sampling techniques have failed to resolve this heterogeneity, particularly nonenhancing populations. study explores the feasibility of using multiparametric MRI texture analysis...
Abstract Ovarian cancer is a clinically and molecularly heterogeneous disease. The driving forces behind this variability are unknown. Here, we report wide variation in the expression of DNA cytosine deaminase APOBEC3B, with elevated majority ovarian cell lines (three SDs above mean normal surface epithelial cells) high-grade primary cancers. APOBEC3B active nucleus several elicits biochemical preference for deamination cytosines 5′-TC dinucleotides. Importantly, examination whole-genome...
Triple-negative (TN) breast cancer is an aggressive subtype of associated with a unique set epidemiologic and genetic risk factors. We conducted two-stage genome-wide association study TN (stage 1: 1529 cases, 3399 controls; stage 2: 2148 1309 controls) to identify loci that influence risk. Variants in the 19p13.1 PTHLH showed significant associations (P < 5 × 10−8) 1 2 combined. Results also suggested substantial enrichment significantly variants among single nucleotide polymorphisms (SNPs)...
Abstract Purpose: Androgen receptor (AR) variant AR-V7 is a ligand-independent transcription factor that promotes prostate cancer resistance to AR-targeted therapies. Accordingly, efforts are under way develop strategies for monitoring and inhibiting in castration-resistant (CRPC). The purpose of this study was understand whether other AR variants may be coexpressed with promote Experimental Design: We utilized complementary short- long-read sequencing intact mRNA isoforms characterize...
We conducted a genome-wide association study to identify novel genes influencing diastolic blood pressure (BP) response hydrochlorothiazide, commonly prescribed thiazide diuretic preferred for the treatment of high BP. Affymetrix GeneChip Human Mapping 100K Arrays were used measure single nucleotide polymorphisms across 22 autosomes in 194 non-Hispanic black subjects and 195 white with essential hypertension selected from opposite tertiles race- sex-specific distributions age-adjusted BP...
Background: Breast cancer patients with residual disease after neoadjuvant chemotherapy (NAC) have increased recurrence risk. Molecular characterization, knowledge of NAC response, and simultaneous generation patient-derived xenografts (PDXs) may accelerate drug development. However, the feasibility this approach is unknown. Methods: We conducted a prospective study 140 breast treated performed tumor germline sequencing generated using core needle biopsies. Chemotherapy response was assessed...
Abstract Background Glioblastoma (GBM) represents an aggressive cancer type with a median survival of only 14 months. With fewer than 5% patients surviving 5 years, comprehensive profiling these rare could elucidate prognostic biomarkers that may confer better patient outcomes. We utilized multiple molecular approaches to characterize the largest cohort isocitrate dehydrogenase (IDH)–wildtype GBM long-term survivors (LTS) date. Methods Retrospective analysis was performed on 49 archived...
Background Expression level of many genes shows abundant natural variation in human populations. The variations gene expression are believed to contribute phenotypic differences. Emerging evidence has shown that microRNAs (miRNAs) one the key regulators expression. However, past studies have focused on miRNA target and used loss- or gain-of-function approach may not reflect association between mRNAs. Methodology/Principal Findings To examine regulatory effect global under endogenous...
Genomewide association studies ( GWAS ) and candidate‐gene have implicated single‐nucleotide polymorphisms SNP s) in at least 45 different genes as putative glioma risk factors. Attempts to validate these associations yielded variable results few genetic factors been consistently replicated. We conducted a case‐control study of Caucasian cases controls from the University California San Francisco (810 cases, 512 controls) Mayo Clinic (852 789 an attempt replicate previously reported for...
Abstract Motivation: Exome sequencing (exome-seq) data, which are typically used for calling exonic mutations, have also been utilized in detecting DNA copy number variations (CNVs). Despite the existence of several CNV detection tools, there is still a great need sensitive and an accurate CNV-calling algorithm with built-in QC steps, does not require paired reference each sample. Results: We developed novel method named PatternCNV, (i) accounts read coverage between exons while leveraging...
To determine early somatic changes in high-grade serous ovarian cancer (HGSOC), we performed whole genome sequencing on a rare collection of 16 low stage HGSOCs. The majority showed extensive structural alterations (one had an ultramutated profile), exhibited high levels p53 immunoreactivity, and harboured TP53 mutation, deletion or inactivation. BRCA1 BRCA2 mutations were observed two tumors, with nine showing evidence homologous recombination (HR) defect. Combined Analysis Cancer Genome...
Genome-wide association studies have implicated single nucleotide polymorphisms (SNPs) in 7 genes as glioma risk factors, including 2 (TERT, RTEL1) involved telomerase structure/function. We examined associations of these established loci with age at diagnosis among patients glioma. SNP genotype data were available for 2286 Caucasian from the University California, San Francisco (n = 1434) and Mayo Clinic 852). Regression analyses performed to test between "number alleles" "age diagnosis,"...
770 Background: Pancreatic ductal adenocarcinoma (PDAC) is associated with poor prognosis and limited treatment options. A 584 bp deletion in CTRB2 , which impairs chymotrypsin B2 function, has been linked to increased PDAC risk. This study investigates the impact of this on progression survival outcomes patients PDAC. Methods: There were 633 whom CTRB2ex6 was genotyped; 263 received chemotherapy had time (TTP) information. TTP calculated from diagnosis date until earliest 1) (event), 2)...