Marcos Díaz‐Gay
A5086161793- Cancer Genomics and Diagnostics
- Genetic factors in colorectal cancer
- Epigenetics and DNA Methylation
- Colorectal Cancer Treatments and Studies
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Evolution and Genetic Dynamics
- Genomics and Rare Diseases
- DNA Repair Mechanisms
- Genomic variations and chromosomal abnormalities
- Molecular Biology Techniques and Applications
- Radiomics and Machine Learning in Medical Imaging
- Ubiquitin and proteasome pathways
- Peptidase Inhibition and Analysis
- Lung Cancer Treatments and Mutations
- PARP inhibition in cancer therapy
- Glycosylation and Glycoproteins Research
- Health, Environment, Cognitive Aging
- Colorectal Cancer Screening and Detection
- Biological Research and Disease Studies
- Melanoma and MAPK Pathways
- Clusterin in disease pathology
- Head and Neck Cancer Studies
- Cancer-related molecular mechanisms research
- BRCA gene mutations in cancer
La Jolla Bioengineering Institute
2020-2025
University of California, San Diego
2020-2025
Centro de Investigación del Cáncer
2025
Cancer Research Center
2025
Spanish National Cancer Research Centre
2025
Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas
2017-2022
Consorci Institut D'Investigacions Biomediques August Pi I Sunyer
2017-2022
Universitat de Barcelona
2017-2021
Moores Cancer Center
2021
Hospital Clínic de Barcelona
2017-2020
Mutational signature analysis is commonly performed in cancer genomic studies. Here, we present SigProfilerExtractor, an automated tool for
Analysis of mutational signatures is a powerful approach for understanding the mutagenic processes that have shaped evolution cancer genome. To evaluate operative in genome, one first needs to quantify their activities by estimating number mutations imprinted each signature.
Abstract International differences in the incidence of many cancer types indicate existence carcinogen exposures that have not yet been identified by conventional epidemiology make a substantial contribution to burden 1 . In clear cell renal carcinoma, obesity, hypertension and tobacco smoking are risk factors, but they do explain geographical variation its 2 Underlying causes can be inferred sequencing genomes cancers from populations with different rates detecting patterns somatic...
Mutational signatures have been proved as a valuable pattern in somatic genomics, mainly regarding cancer, with potential application biomarker clinical practice. Up to now, several bioinformatic packages address this topic developed different languages/platforms. MutationalPatterns has arisen the most efficient tool for comparison currently reported Catalogue of Somatic Mutations Cancer (COSMIC) database. However, analysis mutational is nowadays restricted small community experts. In work...
The somatic mutations found in a cancer genome are imprinted by different mutational processes. Each process exhibits characteristic signature, which can be affected the architecture. However, interplay between signatures and topographical genomic features has not been extensively explored. Here, we integrate from 5,120 whole-genome-sequenced tumors 40 types with 516 ENCODE to evaluate effect of nucleosome occupancy, histone modifications, CTCF binding, replication timing,...
PURPOSE Cancers with homologous recombination deficiency (HRD) can benefit from platinum salts and poly(ADP-ribose) polymerase inhibitors. Standard diagnostic tests for detecting HRD require molecular profiling, which is not universally available. METHODS We trained DeepHRD, a deep learning platform predicting hematoxylin eosin (H&E)–stained histopathological slides, using primary breast (n = 1,008) ovarian 459) cancers The Cancer Genome Atlas (TCGA). DeepHRD was compared four standard...
Somatic copy number alterations (CNAs) are a hallmark of cancer, but their role in tumorigenesis and clinical relevance remain largely unclear. Here, we developed CNApp, web-based tool that allows comprehensive exploration CNAs by using purity-corrected segmented data from multiple genomic platforms. CNApp generates genome-wide profiles, computes CNA scores for broad, focal global burdens, uses machine learning-based predictions to classify samples. We applied the TCGA pan-cancer dataset...
SUMMARY Mutational signature analysis is commonly performed in genomic studies surveying cancer and normal somatic tissues. Here we present SigProfilerExtractor, an automated tool for accurate de novo extraction of mutational signatures all types mutations. Benchmarking with a total 34 distinct scenarios encompassing 2,500 simulated operative more than 60,000 unique synthetic genomes 20,000 exomes demonstrates that SigProfilerExtractor outperforms thirteen other tools across datasets without...
Analysis of mutational signatures is a powerful approach for understanding the mutagenic processes that have shaped evolution cancer genome. Here we present SigProfilerAssignment, desktop and an online computational framework assigning all types to individual samples. SigProfilerAssignment first tool allows both analysis copy-number probabilistic assignment somatic mutations. As its engine, uses custom implementation forward stagewise algorithm sparse regression nonnegative least squares...
Tobacco smoke, alone or combined with alcohol, is the predominant cause of head and neck cancer (HNC). Here, we further explore how tobacco exposure contributes to development by mutational signature analysis 265 whole-genome sequenced HNC from eight countries. Six tobacco-associated signatures were detected, including some not previously reported. Differences in incidence between countries corresponded differences mutation burdens signatures, consistent dominant role causation. found burden...
// Clara Esteban-Jurado 1 , David Giménez-Zaragoza 2 Jenifer Muñoz Sebastià Franch-Expósito Miriam Álvarez-Barona 3 Teresa Ocaña Cuatrecasas 4 Sabela Carballal María López-Cerón Maria Marti-Solano 5 Marcos Díaz-Gay Tom van Wezel 6 Antoni Castells Luis Bujanda 7 Judith Balmaña 8 Victoria Gonzalo 9 Gemma Llort 10 Ruiz-Ponte Joaquín Cubiella 11 Francesc Balaguer Rosa Aligué Sergi Castellví-Bel Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer...
All cancers harbor somatic mutations in their genomes. In principle, affecting between one and fifty base pairs are generally classified as small mutational events. Conversely, large events affect more than pairs, and, most cases, they encompass copy-number structural variants many thousands of pairs. Prior studies have demonstrated that examining patterns can be leveraged to provide both biological clinical insights, thus, resulting an extensive repertoire tools for evaluating Recently,...
Mutations in somatic cells are inflicted by both extrinsic and intrinsic sources contribute over time to cancer. Tobacco smoke contains chemical carcinogens that have been causatively implicated with cancers of the lung head & neck 1,2 . APOBEC family DNA cytosine deaminases emerged as endogenous mutation cancer, hallmark mutational signatures (SBS2/SBS13) often co-occur tumors tobacco smokers an equally diagnostic signature (SBS4) 3,4 Here we challenge dogma processes thought occur...
ABSTRACT Colorectal cancer incidence rates vary geographically and have changed over time. Notably, in the past two decades, of early-onset colorectal cancer, affecting individuals under age 50 years, has doubled many countries. The reasons for this increase are unknown. Here, we investigate whether mutational processes contribute to geographic age-related differences by examining 981 genomes from 11 No major were found microsatellite unstable cancers, but variations mutation burden...
Understanding lung cancer evolution can identify tools for intercepting its growth. In a landscape analysis of 1024 adenocarcinomas (LUAD) with deep whole-genome sequencing integrated multiomic data, we identified 542 LUAD that displayed diverse clonal architecture. this group, observed an interplay between mobile elements, endogenous and exogenous mutational processes, distinct driver genes, epidemiological features. Our results revealed divergent evolutionary trajectories based on tobacco...
(Abstracted from J Clin Oncol 2024;42:3550–3560) The field of precision medicine attempts to treat conditions with combinations that are tailored the individual and disease; oncology uses techniques identify molecular defects in tumors them targeted interventions. For both breast ovarian cancers, previous literature has shown homologous recombination deficiency (HRD) can be treated poly(ADP-ribose) polymerase (PARP) inhibitors platinum salts.
Tobacco smoke, alone or combined with alcohol, is the predominant cause of head and neck cancer (HNC). We explore how tobacco exposure contributes to development by mutational signature analysis 265 whole-genome sequenced HNC samples from eight countries. Six tobacco-associated signatures were detected, including some not previously reported. Differences in incidence between countries corresponded differences mutation burdens signatures, consistent dominant role causation. found burden...
Lynch syndrome is the most common cause of hereditary colorectal cancer (CRC), and it characterized by DNA mismatch repair (MMR) deficiency. The term Lynch-like (LLS) used for patients with MMR-deficient tumors neither germline mutation in MLH1, MSH2, MSH6, PMS2, or EPCAM nor MLH1 somatic methylation. Biallelic inactivation cryptic MMR variants undetected during genetic testing have been proposed to be involved. Sixteen early-onset LLS CRC were selected tumor whole-exome sequencing. Two...
A significant proportion of colorectal cancer (CRC) cases have familial aggregation but little is known about the genetic factors that contribute to these cases. We performed an exhaustive functional characterization variants associated with CRC.We whole-exome sequencing analyses 75 patients from 40 families a history CRC (including early-onset cases) unknown germline basis (discovery cohort). also sequenced specific genes in DNA external replication cohort 473 families, including 488 tumors...
The serrated polyposis syndrome (SPS) is the most common and yet underdiagnosed colorectal syndrome. It characterized by multiple and/or large colonic polyps a higher associated risk for cancer (CRC). main objective of this study was to identify new candidate genes involved in germline predisposition SPS/CRC. Thirty-nine SPS patients from 16 families (≥2 per family) were recruited without alterations well-known hereditary CRC genes, somatic whole-exome sequencing performed. Germline rare...
Colorectal cancer (CRC) shows aggregation in some families but no alterations the known hereditary CRC genes. We aimed to identify new candidate genes which are potentially involved germline predisposition familial CRC. An integrated analysis of and tumor whole-exome sequencing data was performed 18 unrelated families. Deleterious single nucleotide variants (SNV), short insertions deletions (indels), copy number (CNVs) loss heterozygosity (LOH) were assessed as candidates for first or second...
ABSTRACT Breast and ovarian cancers harboring homologous recombination deficiencies (HRD) can benefit from platinum-based chemotherapies PARP inhibitors. Standard diagnostic tests for detecting HRD utilize molecular profiling, which is not universally available especially medically underserved populations. Here, we trained a deep learning approach predicting genomically derived scores routinely sampled hematoxylin eosin (H&E)-stained histopathological slides. For breast cancer, the was...