Does multilocus inherited neoplasia alleles syndrome have severe clinical expression?

Síndromes de càncer; Panell genètic; Proves genètiquesSíndromes de cáncer; Panel de genes; Prueba genéticaCancer syndromes; Gene panel; Genetic testingImportance Genetic testing of hereditary cancer using comprehensive gene panels can identify patients with more than one pathogenic mutation in high and/or moderate-risk-associated cancer genes. This phenomenon is known as multilocus inherited neoplasia alleles syndrome (MINAS), which has been potentially linked to more severe clinical manifestations. Objective To determine the prevalence and clinical features of MINAS in a large cohort of adult patients with hereditary cancer homogeneously tested with the same gene panel. Patients and methods A cohort of 1023 unrelated patients with suspicion of hereditary cancer was screened using a validated panel including up to 135 genes associated with hereditary cancer and phakomatoses. Results Thirteen (1.37%) patients harbouring two pathogenic mutations in dominant cancer-predisposing genes were identified, representing 5.7% (13/226) of patients with pathogenic mutations. Most (10/13) of these cases presented clinical manifestations associated with only one of the mutations identified. One case showed mutations in MEN1 and MLH1 and developed tumours associated with both cancer syndromes. Interestingly, three of the double mutants had a young age of onset or severe breast cancer phenotype and carried mutations in moderate to low-risk DNA damage repair-associated genes; two of them presented biallelic inactivation of CHEK2. We included these two patients for the sake of their clinical interest although we are aware that they do not exactly fulfil the definition of MINAS since both mutations are in the same gene. Conclusions and relevance Genetic analysis of a broad cancer gene panel identified the largest series of patients with MINAS described in a single study. Overall, our data do not support the existence of more severe manifestations in double mutants at the time of diagnosis although they do confirm previous evidence of severe phenotype in biallelic CHEK2 and other DNA repair cancer-predisposing genes.Contract grant sponsor: Supported by the Carlos III National Health Institute and Ministerio de Educación y Ciencia funded by FEDER funds–a way to build Europe (PI16/00563, PI16/01363, SAF2015-68016-R and CIBERONC); the Government of Catalonia (Pla estratègic de recerca i innovació en salut (PERIS), 2017SGR1282 and 2017SGR496); and the scientific foundation Asociación Española Contra el Cáncer

BARD1 Pathogenic Variants Are Associated with Triple-Negative Breast Cancer in a Spanish Hereditary Breast and Ovarian Cancer Cohort

BARD1; Càncer hereditari de mama i ovari; Risc moderat de càncerBARD1; Cáncer de mama y ovario hereditario; Riesgo de cáncer moderadoBARD1; Hereditary breast and ovarian cancer; Moderate cancer riskOnly a small fraction of hereditary breast and/or ovarian cancer (HBOC) cases are caused by germline variants in the high-penetrance breast cancer 1 and 2 genes (BRCA1 and BRCA2). BRCA1-associated ring domain 1 (BARD1), nuclear partner of BRCA1, has been suggested as a potential HBOC risk gene, although its prevalence and penetrance are variable according to populations and type of tumor. We aimed to investigate the prevalence of BARD1 truncating variants in a cohort of patients with clinical suspicion of HBOC. A comprehensive BARD1 screening by multigene panel analysis was performed in 4015 unrelated patients according to our regional guidelines for genetic testing in hereditary cancer. In addition, 51,202 Genome Aggregation Database (gnomAD) non-Finnish, non-cancer European individuals were used as a control population. In our patient cohort, we identified 19 patients with heterozygous BARD1 truncating variants (0.47%), whereas the frequency observed in the gnomAD controls was 0.12%. We found a statistically significant association of truncating BARD1 variants with overall risk (odds ratio (OR) = 3.78; CI = 2.10–6.48; p = 1.16 × 10−5). This association remained significant in the hereditary breast cancer (HBC) group (OR = 4.18; CI = 2.10–7.70; p = 5.45 × 10−5). Furthermore, deleterious BARD1 variants were enriched among triple-negative BC patients (OR = 5.40; CI = 1.77–18.15; p = 0.001) compared to other BC subtypes. Our results support the role of BARD1 as a moderate penetrance BC predisposing gene and highlight a stronger association with triple-negative tumors.Contract grant sponsor: Supported by the Carlos III National Health Institute funded by FEDER funds—a way to build Europe—(PI19/00553; PI16/00563; PI16/01898; PI16/11363; PI15/00355; PI12/02585; SAF2015-68016-R and CIBERONC); the Government of Catalonia (Pla estratègic de recerca i innovació en salut (PERIS_MedPerCan and URDCat projects), 2017SGR1282 and 2017SGR496); and CERCA Programa/Generalitat de Catalunya for institutional support. GCAT is supported by Acción de Dinamización del ISCIII-MINECO (ADE 10/00026), by the Ministry of Health of the Generalitat of Catalunya and by Agència de Gestió d’Ajuts Universitaris i de Recerca (AGAUR) (2017-SGR 529) and GCAT Cession Research Project PI-2018-09 GCAT_CM

Unravelling the skills and motivations of Magdalenian artists in the depths of Atxurra Cave (Northern Spain)

Atxurra cave has a decorated assemblage composed of more than a hundred engraved animal depictions. All of them are located in deep parts of the cave and most of them are hidden in raised areas, away from the main path. The main sector is the “Ledge of the Horses”, located at 330 m from the entrance of the cave. It is a space of 12 m long and 1.5 m wide, elevated 4 m above the cave floor. This area includes almost fifty engraved and painted animals accompanied by a dozen flint tools, three fireplaces, and around one hundred charcoal fragments from torches. This extraordinary archaeological record allows us to value the complexity of the artistic production inside the caves during the Upper Palaeolithic. Our study has confirmed that there is planning prior to artistic production, both in terms of the iconographic aspects (themes, techniques, formats), its location (visibility, capacity), and the lighting systems. Furthermore, the data indicates the panel was decorated to be seen by third parties from different positions and was expressly illuminated for this purpose. This evidence supports the role of rock art as a visual communication system in Upper Palaeolithic societies.The authors wish to thank the Cultural Heritage Service of the Diputación Foral de Bizkaia for funding the 4-year multidisciplinary study project (2016–2020) “Study of rock art in Atxurra cave” directed by Dr Diego Garate. The present study has been carried out within the framework of the research project "Before art: social investment in symbolic expressions during the Upper Palaeolithic in the Iberian Peninsula” (PID2019-107262GB-I00), PI: Diego Garate, funded by the Ministerio de Ciencia, Innovación y Universidades (Spain), the research projet “Scientific virtual reality for the study and dissemination of the scenarios of artistic creation in Palaeolithic caves (RealCaveART)” (PDC2022-133124-I00), PI: Diego Garate, funded by MCIN/AEI/10.13039/501100011033 and the European Union Next Generation EU/PRTR, and the research project “Creation and perception in Anatomically Modern Humans: analysis of the biological, cognitive and social skills linked to the production of Paleolithic art (ArtMindHuman)” (PID2021-125166OB-I00), PI: Olivia Rivero, funded by the Ministerio de Ciencia, Innovación y Universidades (Spain). I. Intxaurbe’s PhD research is funded by a grant for the training of research personnel (PIF 2019) at the University of the Basque Country (UPV/EHU). M.A. Median-Alcaide developpes lighting system analyses inside the framework of her “A-Light” project of the HORIZON-MSCA-2021-PF-01-01 (101066376)

BARD1 Pathogenic Variants are Associated with Triple-Negative Breast Cancer in a Spanish Hereditary Breast and Ovarian Cancer Cohort

Only a small fraction of hereditary breast and/or ovarian cancer (HBOC) cases are caused by germline variants in the high-penetrance breast cancer 1 and 2 genes (BRCA1 and BRCA2). BRCA1-associated ring domain 1 (BARD1), nuclear partner of BRCA1, has been suggested as a potential HBOC risk gene, although its prevalence and penetrance are variable according to populations and type of tumor. We aimed to investigate the prevalence of BARD1 truncating variants in a cohort of patients with clinical suspicion of HBOC. A comprehensive BARD1 screening by multigene panel analysis was performed in 4015 unrelated patients according to our regional guidelines for genetic testing in hereditary cancer. In addition, 51,202 Genome Aggregation Database (gnomAD) non-Finnish, non-cancer European individuals were used as a control population. In our patient cohort, we identified 19 patients with heterozygous BARD1 truncating variants (0.47%), whereas the frequency observed in the gnomAD controls was 0.12%. We found a statistically significant association of truncating BARD1 variants with overall risk (odds ratio (OR) = 3.78; CI = 2.10-6.48; p = 1.16 x 10(-5)). This association remained significant in the hereditary breast cancer (HBC) group (OR = 4.18; CI = 2.10-7.70; p = 5.45 x 10(-5)). Furthermore, deleterious BARD1 variants were enriched among triple-negative BC patients (OR = 5.40; CI = 1.77-18.15; p = 0.001) compared to other BC subtypes. Our results support the role of BARD1 as a moderate penetrance BC predisposing gene and highlight a stronger association with triple-negative tumors

Exploring the Role of Mutations in Fanconi Anemia Genes in Hereditary Cancer Patients

Fanconi anemia (FA) is caused by biallelic mutations in FA genes. Monoallelic mutations in five of these genes (BRCA1, BRCA2, PALB2, BRIP1 and RAD51C) increase the susceptibility to breast/ovarian cancer and are used in clinical diagnostics as bona-fide hereditary cancer genes. Increasing evidence suggests that monoallelic mutations in other FA genes could predispose to tumor development, especially breast cancer. The objective of this study is to assess the mutational spectrum of 14 additional FA genes (FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, FANCP, FANCQ, FANCR and FANCU) in a cohort of hereditary cancer patients, to compare with local cancer-free controls as well as GnomAD. A total of 1021 hereditary cancer patients and 194 controls were analyzed using our next generation custom sequencing panel. We identified 35 pathogenic variants in eight genes. A significant association with the risk of breast cancer/breast and ovarian cancer was found for carriers of FANCA mutations (odds ratio (OR) = 3.14 95% confidence interval (CI) 1.4-6.17, p = 0.003). Two patients with early-onset cancer showed a pathogenic FA variant in addition to another germline mutation, suggesting a modifier role for FA variants. Our results encourage a comprehensive analysis of FA genes in larger studies to better assess their role in cancer risk

Large scale multifactorial likelihood quantitative analysis of BRCA1 and BRCA2 variants: An ENIGMA resource to support clinical variant classification

The multifactorial likelihood analysis method has demonstrated utility for quantitative assessment of variant pathogenicity for multiple cancer syndrome genes. Independent data types currently incorporated in the model for assessing BRCA1 and BRCA2 variants include clinically calibrated prior probability of pathogenicity based on variant location and bioinformatic prediction of variant effect, co-segregation, family cancer history profile, co-occurrence with a pathogenic variant in the same gene, breast tumor pathology, and case-control information. Research and clinical data for multifactorial likelihood analysis were collated for 1,395 BRCA1/2 predominantly intronic and missense variants, enabling classification based on posterior probability of pathogenicity for 734 variants: 447 variants were classified as (likely) benign, and 94 as (likely) pathogenic; and 248 classifications were new or considerably altered relative to ClinVar submissions. Classifications were compared with information not yet included in the likelihood model, and evidence strengths aligned to those recommended for ACMG/AMP classification codes. Altered mRNA splicing or function relative to known nonpathogenic variant controls were moderately to strongly predictive of variant pathogenicity. Variant absence in population datasets provided supporting evidence for variant pathogenicity. These findings have direct relevance for BRCA1 and BRCA2 variant evaluation, and justify the need for gene-specific calibration of evidence types used for variant classification

Large scale multifactorial likelihood quantitative analysis of BRCA1 and BRCA2 variants: An ENIGMA resource to support clinical variant classification

Abstract The multifactorial likelihood analysis method has demonstrated utility for quantitative assessment of variant pathogenicity for multiple cancer syndrome genes. Independent data types currently incorporated in the model for assessing BRCA1 and BRCA2 variants include clinically calibrated prior probability of pathogenicity based on variant location and bioinformatic prediction of variant effect, co-segregation, family cancer history profile, co-occurrence with a pathogenic variant in the same gene, breast tumor pathology, and case-control information. Research and clinical data for multifactorial likelihood analysis were collated for 1395 BRCA1/2 predominantly intronic and missense variants, enabling classification based on posterior probability of pathogenicity for 734 variants: 447 variants were classified as (likely) benign, and 94 as (likely) pathogenic; 248 classifications were new or considerably altered relative to ClinVar submissions. Classifications were compared to information not yet included in the likelihood model, and evidence strengths aligned to those recommended for ACMG/AMP classification codes. Altered mRNA splicing or function relative to known non-pathogenic variant controls were moderately to strongly predictive of variant pathogenicity. Variant absence in population datasets provided supporting evidence for variant pathogenicity. These findings have direct relevance for BRCA1 and BRCA2 variant evaluation, and justify the need for gene-specific calibration of evidence types used for variant classification. This article is protected by copyright. All rights reserved.Peer reviewe

Genetic approaches to improve hereditary cancer diagnosis based on next-generation sequencing data

Programa de Doctorat en Biomedicina / Tesi realitzada a l'Institut d'Investigació Biomèdica de Bellvitge (IDIBELL) i a l'Institut Català d'Oncologia (ICO)The overarching aim of the present thesis project is to implement new testing strategies and develop new tools that will contribute to improve the genetic diagnosis of hereditary cancer, with the ultimate goal of individualizing the risk estimations of patients and their families in order to personalize prevention, follow-up, treatment and prophylactic recommendations. This study has been mainly focused on the two most prevalent HC syndromes: hereditary breast and ovarian cancer and hereditary colorectal cancer, although data on other less prevalent cancer syndromes are also presented. Specific aims 1. To elucidate the role of new candidate cancer-predisposing genes and to devise new genotype-phenotype correlations. 2. To improve the classification of VUS. 3. To increase the mutation detection rate of the studied genes, following two different approaches: 3.1. Implementation of somatic testing in unsolved hereditary cancer patients with two goals: to assess the prevalence of mosaicism and to evaluate the frequency of double somatic hits among Lynch-like syndrome patients. 3.2. Implementation of new testing strategies complementary to DNA-based sequencing to address mutational discovery in previously unexplored regions

Genetic approaches to improve hereditary cancer diagnosis based on next-generation sequencing data

[eng] he overarching aim of the present thesis project is to implement new testing strategies and develop new tools that will contribute to improve the genetic diagnosis of hereditary cancer, with the ultimate goal of individualizing the risk estimations of patients and their families in order to personalize prevention, follow-up, treatment and prophylactic recommendations. This study has been mainly focused on the two most prevalent HC syndromes: hereditary breast and ovarian cancer and hereditary colorectal cancer, although data on other less prevalent cancer syndromes are also presented. Specific aims 1. To elucidate the role of new candidate cancer-predisposing genes and to devise new genotype-phenotype correlations. 2. To improve the classification of VUS. 3. To increase the mutation detection rate of the studied genes, following two different approaches: 3.1. Implementation of somatic testing in unsolved hereditary cancer patients with two goals: to assess the prevalence of mosaicism and to evaluate the frequency of double somatic hits among Lynch-like syndrome patients. 3.2. Implementation of new testing strategies complementary to DNA-based sequencing to address mutational discovery in previously unexplored regions

RNA assay identifies a previous misclassification of BARD1 c.1977A>G variant

Case-control studies have shown an association of BARD1 with hereditary breast and/or ovarian cancer (HBOC) predisposition. BARD1 alternatively spliced isoforms are abundant and some are highly expressed in different cancer types. In addition, a number of BARD1 germline pathogenic variants have been reported among HBOC patients. In previous reports, BARD1 c.1977A>G variant has been classified as pathogenic since it produces a frameshift transcript lacking exons 2 to 9. In the present study, we sought to validate the mRNA splicing results previously published and to contribute with new evidence to refine the classification of this substitution according to ACMG/AMP guidelines. The presence of the variant was screened in patients and controls. RT-PCR was performed in order to compare the transcriptional profiles of two variant carriers and ten non-carrier controls. In addition, allele-specific expression was assessed. No differences in variant frequency were detected between patients and controls. The RNA assay confirmed the presence of the shorter transcript lacking exons 2-9, but it was detected both in carriers and non-carriers. Furthermore, allelic imbalance was discarded and no significant differences in the proportion of full-length and shorter transcript were detected between carriers and controls. The shorter transcript detected corresponds to BARD1 isoform η, constituted by exons 1, 10 and 11. Our results support that this transcript is a constitutive splicing product rather than an aberrant transcript caused by BARD1 c.1977A>G variant, and for this reason this variant should be considered as likely benign following ACMG/AMP guidelines