A5080345196- Genomics and Rare Diseases
- Cancer Genomics and Diagnostics
- Genomic variations and chromosomal abnormalities
- BRCA gene mutations in cancer
- Genetic factors in colorectal cancer
- DNA Repair Mechanisms
- Genomics and Phylogenetic Studies
- Genomics and Chromatin Dynamics
- Colorectal Cancer Treatments and Studies
Centro de Investigación Biomédica en Red de Cáncer
2020-2024
Institut d'Investigació Biomédica de Bellvitge
2020-2024
Institut Català d'Oncologia
2019-2024
Instituto de Salud Carlos III
2020-2024
Institute of Predictive and Personalized Medicine of Cancer
2019-2021
Institut d'Investigació Biomèdica de Girona
2020
Instituto Oncológico Dr. Rosell
2020
Abstract Although germline copy-number variants (CNVs) are the genetic cause of multiple hereditary diseases, detecting them from targeted next-generation sequencing data (NGS) remains a challenge. Existing tools perform well for large CNVs but struggle with single and multi-exon alterations. The aim this work is to evaluate CNV calling working on gene panel NGS their suitability as screening step before orthogonal confirmation in diagnostics strategies. Five (DECoN, CoNVaDING, panelcn.MOPS,...
Fanconi anemia (FA) is caused by biallelic mutations in FA genes. Monoallelic five of these genes (BRCA1, BRCA2, PALB2, BRIP1 and RAD51C) increase the susceptibility to breast/ovarian cancer are used clinical diagnostics as bona-fide hereditary Increasing evidence suggests that monoallelic other could predispose tumor development, especially breast cancer. The objective this study assess mutational spectrum 14 additional (FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM,...
CHEK2 variants are associated with intermediate breast cancer risk, among other cancers. We aimed to comprehensively describe in a Spanish hereditary (HC) cohort and adjust the American College of Medical Genetics Genomics Association for Molecular Pathology (ACMG-AMP) guidelines their classification. First, three frequent were screened retrospective Hereditary Breast Ovarian Cancer 516 patients. After, whole coding region was analyzed by next-generation sequencing 1848 prospective patients...
Only a small fraction of hereditary breast and/or ovarian cancer (HBOC) cases are caused by germline variants in the high-penetrance 1 and 2 genes (BRCA1 BRCA2). BRCA1-associated ring domain (BARD1), nuclear partner BRCA1, has been suggested as potential HBOC risk gene, although its prevalence penetrance variable according to populations type tumor. We aimed investigate BARD1 truncating cohort patients with clinical suspicion HBOC. A comprehensive screening multigene panel analysis was...
Abstract Motivation Germline variant classification allows accurate genetic diagnosis and risk assessment. However, it is a tedious iterative process integrating information from several sources types of evidence. It should follow gene-specific (if available) or general updated international guidelines. Thus, the main burden incorporation next-generation sequencing into clinical setting. Results We created vaRiants in HC (vaRHC) R package to assist hereditary cancer by: (i) collecting...
Accurate classification of genetic variants is crucial for clinical decision-making in hereditary cancer. In Spain, diagnostic laboratories have traditionally approached this task independently due to the lack a dedicated resource. Here we present SpadaHC, web-based database sharing cancer genes Spanish population. SpadaHC implemented using three-tier architecture consisting relational database, web tool and bioinformatics pipeline. Contributing can share variant classifications from...
Introduction Germline CNVs are important contributors to hereditary cancer. In genetic diagnostics, multiplex ligation-dependent probe amplification (MLPA) is commonly used identify them. However, MLPA time-consuming and expensive if applied many genes, hence routine laboratories test only a subset of genes interest. Methods results We evaluated next-generation sequencing (NGS)-based CNV detection tool (DECoN) as first-tier screening decrease costs turnaround time expand analysis all...
Germline copy-number variants (CNVs) are relevant mutations for multiple genetics fields, such as the study of hereditary diseases. However, available benchmarks show that all next-generation sequencing (NGS) CNV calling tools produce false positives. We developed CNVfilteR, an R package uses single-nucleotide variant calls usually obtained in germline NGS pipelines to identify those The can detect both deletions and duplications. evaluated CNVfilteR performance on callsets generated by 13...
Abstract Germline copy number variants (CNVs) play a significant role in hereditary diseases. However, the accurate detection of CNVs from targeted next-generation sequencing (NGS) gene panel data remains challenging task. Several tools for calling within this context have been published to date, but available benchmarks suffer limitations, including testing on simulated data, small datasets, and subset tools. In work, we conducted comprehensive benchmarking 12 (Atlas-CNV, ClearCNV, ClinCNV,...
ABSTRACT Motivation Although germline copy number variants (CNVs) are the genetic cause of multiple hereditary diseases, detecting them from targeted next-generation sequencing data (NGS) remains a challenge. Existing tools perform well for large CNVs but struggle with single and multi-exon alterations. The aim this work is to evaluate CNV calling working on gene panel NGS up single-exon resolution their suitability as screening step before orthogonal confirmation in diagnostics strategies....