A5059943023- Molecular Biology Techniques and Applications
- Cancer Genomics and Diagnostics
- Gene expression and cancer classification
- Cancer-related molecular mechanisms research
- RNA modifications and cancer
- BRCA gene mutations in cancer
- RNA Research and Splicing
- Multiple Myeloma Research and Treatments
- Pancreatic and Hepatic Oncology Research
- Genomic variations and chromosomal abnormalities
- Chemotherapy-induced cardiotoxicity and mitigation
- Epigenetics and DNA Methylation
- Genetic Associations and Epidemiology
- Nutrition, Genetics, and Disease
- CRISPR and Genetic Engineering
- Ferroptosis and cancer prognosis
- Chromosomal and Genetic Variations
- MicroRNA in disease regulation
- Receptor Mechanisms and Signaling
- Genetic Mapping and Diversity in Plants and Animals
- Protein Degradation and Inhibitors
- Cancer Treatment and Pharmacology
- Heart Failure Treatment and Management
- Pharmacogenetics and Drug Metabolism
- Circular RNAs in diseases
Tempus Labs (United States)
2020-2024
Icahn School of Medicine at Mount Sinai
2018-2021
Genomic Health (United States)
2019-2021
University of Liège
2013-2019
Mount Sinai Hospital
2018-2019
Mount Sinai Hospital
2018
Centre Hospitalier Universitaire de Liège
2015-2017
Background: Over time, the chance of cure after diagnosis breast cancer has been increasing, as a consequence earlier diagnosis, improved diagnostic procedures and more effective treatment options.However, oncologists are concerned by risk long term side effects, including congestive heart failure (CHF).Methods: In this study, we evaluated innovative circulating cardiac biomarkers during anthracycline-based neoadjuvant chemotherapy (NAC) in patients.Levels cardiac-specific troponins T...
Abstract Background Endocrine-resistant HR+/HER2- breast cancer (BC) and triple-negative BC (TNBC) are of interest for molecularly informed treatment due to their aggressive natures limited profiles. Patients African Ancestry (AA) experience higher rates TNBC mortality than European (EA) patients, despite lower overall incidence. Here, we compare the molecular landscapes AA EA patients with in a real-world cohort promote equity precision oncology by illuminating heterogeneity potentially...
// Pierre Frères 1, 2, * , Stéphane Wenric Meriem Boukerroucha 2 Corinne Fasquelle Jérôme Thiry Nicolas Bovy 3 Ingrid Struman Geurts 4 Joëlle Collignon 1 Hélène Schroeder Frédéric Kridelka 5 Eric Lifrange 6 Véronique Jossa 7 Vincent Bours Claire Josse Guy Jerusalem University Hospital (CHU), Department of Medical Oncology, Liège, Belgium GIGA-Research, Laboratory Human Genetics, Molecular Angiogenesis, EE and CS,...
Whole transcriptome studies typically yield large amounts of data, with expression values for all genes or transcripts the genome. The search interest in a particular study setting can thus be daunting task, usually relying on automated computational methods. Moreover, most biological questions imply that such should performed multivariate setting, to take into account inter-genes relationships. Differential analysis commonly yields lists deemed significant, even after adjustment multiple...
Non-coding RNAs (ncRNA) represent 1/5 of the mammalian transcript number, and 90% genome length is transcribed. Many ncRNAs play a role in cancer. Among them, non-coding natural antisense transcripts (ncNAT) are RNA sequences that complementary overlapping to those either protein-coding (PCT) or transcripts. Several ncNATs were described as regulating protein coding gene expression on same loci, they expected act more frequently cis compared other commonly function trans. In this work, 22...
The BRCA1 gene plays a key role in triple negative breast cancers (TNBCs), which its expression can be lost by multiple mechanisms: germinal mutation followed deletion of the second allele; regulation promoter methylation; or miRNA-mediated silencing. This study aimed to establish correlation among BRCA1-related molecular parameters, tumor characteristics and clinical follow-up patients find new prognostic factors. protein mRNA was quantified situ TNBCs 69 patients. methylation status...
Abstract Understanding population health disparities is an essential component of equitable precision efforts. Epidemiology research often relies on definitions race and ethnicity, but these labels may not adequately capture disease burdens specific to sub-populations. Here we propose a framework for repurposing data from Electronic Health Records (EHRs) in concert with genomic explore enrichment within Using diverse biobank New York City, genetically identified 17 sub-populations, noted the...
Abstract Background: PDAC is a highly morbid disease with no validated biomarkers for first-line (1L) treatment selection. The PurIST single-sample molecular subtyping gene signature, initially described by Rashid et al. (Clin. Cancer Res., 2020), classifies tumors as basal or classical. Prior work showed that these subtypes are associated prognosis and subtype patients have significantly lower objective response rate to FOLFIRINOX (FFX) compared classical patients. This suggests potential...
Abstract Background Pancreatic ductal adenocarcinoma (PDAC) is amongst the deadliest cancers, with few modern tools to inform patient prognosis and help guide treatment options. Transcriptome-based molecular subtyping one emerging technology that has been employed patients optimize available therapeutic approaches. Here we retrospectively demonstrate clinical validity of PurIST (Purity Independent Subtyping Tumors), an RNA-based classifier divides PDAC into two subtypes differential...
The genomic profile of multiple myeloma (MM) has prognostic value by dividing patients into a good prognosis hyperdiploid group and bad nonhyperdiploid with higher incidence IGH translocations. This classification, however, is inadequate many other parameters like mutations, epigenetic modifications, heterogeneity may influence the prognosis. We performed study array-based comparative hybridization on cohort 162 to evaluate frequency gains losses. identified high X chromosome alterations...
Abstract Background: PDAC is a particularly fatal condition lacking established biomarkers for the choice of first-line treatment (1L). The PurIST algorithm gene signature (Rashid et al. Clin. Cancer Res., 2020) that categorizes tumors into basal or classical molecular subtypes and has been previously validated in patient cohort advanced (N=258). In this post-hoc analysis study, we examine whether can distinguish patients likely to respond FOLFIRINOX (FFX) versus Gemcitabine + nab-paclitaxel...
Abstract Whole transcriptome studies typically yield large amounts of data, with expression values for all genes or transcripts the genome. The search interest in a particular study setting can thus be daunting task, usually relying on automated computational methods. Moreover, most biological questions imply that such should performed multivariate setting, to take into account inter-genes relationships. Differential analysis commonly yields lists deemed significant, even after adjustment...
Abstract The emergence of genomic data in biobanks and health systems offers new ways to derive medically important phenotypes, including acute phenotypes occurring during inpatient clinical care. Here we study the genetic underpinnings rapid response phenylephrine, an α1-adrenergic receptor agonist commonly used treat hypotension anesthesia surgery. We quantified this by extracting blood pressure (BP) measurements 5 min before after administration phenylephrine. Based on derived phenotype,...
ABSTRACT An increasing number of bioinformatic tools designed to detect CNVs (copy variants) in tumor samples based on paired exome data where a matched healthy tissue constitutes the reference have been published recent years. The idea using pool unrelated DNA as has previously formulated but not thoroughly validated. As today, gold standard for CNV calling is still aCGH there an interest detecting by sequencing. We propose design metric allowing comparison two profiles, independently...
Abstract Non-coding RNAs (ncRNA) represent at least 1/5 of the mammalian transcript amount, and about 90% genome length is actively transcribed. Many ncRNAs have been demonstrated to play a role in cancer. Among them, natural antisense transcripts (NAT) are RNA sequences which complementary overlapping those protein-coding (PCT). NATs were punctually described as regulating gene expression, expected act more frequently cis than other that commonly function trans . In this work, 22 breast...
e13507 Background: Recent advances in transcriptomics have resulted the emergence of several publicly available breast cancer RNA-Seq datasets, such as TCGA, SCAN-B, and METABRIC. However, molecular predictors cannot be applied across datasets without correction batch differences. In this study, we demonstrate a homogenization algorithm that allows transfer subtype from one cohort to another. The only uses cohort-level summary statistics, therefore, does not require joint normalization both...
Reproducibility of results obtained using ribonucleic acid (RNA) data across labs remains a major hurdle in cancer research. Often, molecular predictors trained on one dataset cannot be applied to another due differences RNA library preparation and quantification, which inhibits the validation labs. While current correction algorithms reduce these differences, they require simultaneous access patient-level from all datasets, necessitates sharing training for when predictors. Here, we...
Finding informative predictive features in high-dimensional biological case-control datasets is challenging. The Extreme Pseudo-Sampling (EPS) algorithm offers a solution to the challenge of feature selection via combination deep learning and linear regression models. First, using variational autoencoder, it generates complex latent representations for samples. Second, classifies cases controls logistic regression. Third, new samples (pseudo-samples) around extreme model. Finally, trains...
Abstract The reproducibility of results obtained using RNA data across labs is a major hurdle in cancer research. Difference library preparation methods and gene expression quantification platforms prevent the application trained models to new labs. SpinAdapt novel unsupervised domain adaptation algorithm that enables transfer existing molecular technological platforms, without requiring re-training or calibration for future prospective data. Furthermore, uses summary statistics (independent...