PHIP - a novel candidate breast cancer susceptibility locus on 6q14.1

Most non-BRCA1/2 breast cancer families have no identified genetic cause. We used linkage and haplotype analyses in familial and sporadic breast cancer cases to identify a susceptibility locus on chromosome 6q. Two independent genome-wide linkage analysis studies suggested a 3 Mb locus on chromosome 6q and two unrelated Swedish families with a LOD > 2 together seemed to share a haplotype in 6q14.1. We hypothesized that this region harbored a rare high-risk founder allele contributing to breast cancer in these two families. Sequencing of DNA and RNA from the two families did not detect any pathogenic mutations. Finally, 29 SNPs in the region were analyzed in 44,214 cases and 43,532 controls from BCAC, and the original haplotypes in the two families were suggested as low-risk alleles for European and Swedish women specifically. There was also some support for one additional independent moderate-risk allele in Swedish familial samples. The results were consistent with our previous findings in familial breast cancer and supported a breast cancer susceptibility locus at 6q14.1 around the PHIP gene.Peer reviewe

Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus.

BACKGROUND: Multiple recent genome-wide association studies (GWAS) have identified a single nucleotide polymorphism (SNP), rs10771399, at 12p11 that is associated with breast cancer risk. METHOD: We performed a fine-scale mapping study of a 700 kb region including 441 genotyped and more than 1300 imputed genetic variants in 48,155 cases and 43,612 controls of European descent, 6269 cases and 6624 controls of East Asian descent and 1116 cases and 932 controls of African descent in the Breast Cancer Association Consortium (BCAC; http://bcac.ccge.medschl.cam.ac.uk/ ), and in 15,252 BRCA1 mutation carriers in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Stepwise regression analyses were performed to identify independent association signals. Data from the Encyclopedia of DNA Elements project (ENCODE) and the Cancer Genome Atlas (TCGA) were used for functional annotation. RESULTS: Analysis of data from European descendants found evidence for four independent association signals at 12p11, represented by rs7297051 (odds ratio (OR) = 1.09, 95 % confidence interval (CI) = 1.06-1.12; P = 3 × 10(-9)), rs805510 (OR = 1.08, 95 % CI = 1.04-1.12, P = 2 × 10(-5)), and rs1871152 (OR = 1.04, 95 % CI = 1.02-1.06; P = 2 × 10(-4)) identified in the general populations, and rs113824616 (P = 7 × 10(-5)) identified in the meta-analysis of BCAC ER-negative cases and BRCA1 mutation carriers. SNPs rs7297051, rs805510 and rs113824616 were also associated with breast cancer risk at P < 0.05 in East Asians, but none of the associations were statistically significant in African descendants. Multiple candidate functional variants are located in putative enhancer sequences. Chromatin interaction data suggested that PTHLH was the likely target gene of these enhancers. Of the six variants with the strongest evidence of potential functionality, rs11049453 was statistically significantly associated with the expression of PTHLH and its nearby gene CCDC91 at P < 0.05. CONCLUSION: This study identified four independent association signals at 12p11 and revealed potentially functional variants, providing additional insights into the underlying biological mechanism(s) for the association observed between variants at 12p11 and breast cancer risk.UK funding includes Cancer Research UK and NIH.This is the final version of the article. It first appeared from BioMed Central via http://dx.doi.org/10.1186/s13058-016-0718-

The BRCA2 c.68-7T > A variant is not pathogenic : A model for clinical calibration of spliceogenicity

Although the spliceogenic nature of the BRCA2 c.68-7T > A variant has been demonstrated, its association with cancer risk remains controversial. In this study, we accurately quantified by real-time PCR and digital PCR (dPCR), the BRCA2 isoforms retaining or missing exon 3. In addition, the combined odds ratio for causality of the variant was estimated using genetic and clinical data, and its associated cancer risk was estimated by case-control analysis in 83,636 individuals. Co-occurrence in trans with pathogenic BRCA2 variants was assessed in 5,382 families. Exon 3 exclusion rate was 4.5-fold higher in variant carriers (13%) than controls (3%), indicating an exclusion rate for the c.68-7T > A allele of approximately 20%. The posterior probability of pathogenicity was 7.44x10(-115). There was neither evidence for increased risk of breast cancer (OR 1.03; 95% CI 0.86-1.24) nor for a deleterious effect of the variant when co-occurring with pathogenic variants. Our data provide for the first time robust evidence of the nonpathogenicity of the BRCA2 c.68-7T > A. Genetic and quantitative transcript analyses together inform the threshold for the ratio between functional and altered BRCA2 isoforms compatible with normal cell function. These findings might be exploited to assess the relevance for cancer risk of other BRCA2 spliceogenic variants.Peer reviewe

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

Physical activity, sedentary time and breast cancer risk: a Mendelian randomisation study

Objectives: Physical inactivity and sedentary behaviour are associated with higher breast cancer risk in observational studies, but ascribing causality is difficult. Mendelian randomisation (MR) assesses causality by simulating randomised trial groups using genotype. We assessed whether lifelong physical activity or sedentary time, assessed using genotype, may be causally associated with breast cancer risk overall, pre/post-menopause, and by case-groups defined by tumour characteristics. Methods: We performed two-sample inverse-variance-weighted MR using individual-level Breast Cancer Association Consortium case-control data from 130 957 European-ancestry women (69 838 invasive cases), and published UK Biobank data (n=91 105–377 234). Genetic instruments were single nucleotide polymorphisms (SNPs) associated in UK Biobank with wrist-worn accelerometer-measured overall physical activity (nsnps=5) or sedentary time (nsnps=6), or accelerometer-measured (nsnps=1) or self-reported (nsnps=5) vigorous physical activity. Results: Greater genetically-predicted overall activity was associated with lower breast cancer overall risk (OR=0.59; 95% confidence interval (CI) 0.42 to 0.83 per-standard deviation (SD;~8 milligravities acceleration)) and for most case-groups. Genetically-predicted vigorous activity was associated with lower risk of pre/perimenopausal breast cancer (OR=0.62; 95% CI 0.45 to 0.87,≥3 vs. 0 self-reported days/week), with consistent estimates for most case-groups. Greater genetically-predicted sedentary time was associated with higher hormone-receptor-negative tumour risk (OR=1.77; 95% CI 1.07 to 2.92 per-SD (~7% time spent sedentary)), with elevated estimates for most case-groups. Results were robust to sensitivity analyses examining pleiotropy (including weighted-median-MR, MR-Egger). Conclusion: Our study provides strong evidence that greater overall physical activity, greater vigorous activity, and lower sedentary time are likely to reduce breast cancer risk. More widespread adoption of active lifestyles may reduce the burden from the most common cancer in women

Breast cancer risk genes: association analysis in more than 113,000 women

BACKGROUNDGenetic testing for breast cancer susceptibility is widely used, but for many genes, evidence of an association with breast cancer is weak, underlying risk estimates are imprecise, and reliable subtype-specific risk estimates are lacking.METHODSWe used a panel of 34 putative susceptibility genes to perform sequencing on samples from 60,466 women with breast cancer and 53,461 controls. In separate analyses for protein-truncating variants and rare missense variants in these genes, we estimated odds ratios for breast cancer overall and tumor subtypes. We evaluated missense-variant associations according to domain and classification of pathogenicity.RESULTSProtein-truncating variants in 5 genes (ATM, BRCA1, BRCA2, CHEK2, and PALB2) were associated with a risk of breast cancer overall with a P value of less than 0.0001. Protein-truncating variants in 4 other genes (BARD1, RAD51C, RAD51D, and TP53) were associated with a risk of breast cancer overall with a P value of less than 0.05 and a Bayesian false-discovery probability of less than 0.05. For protein-truncating variants in 19 of the remaining 25 genes, the upper limit of the 95% confidence interval of the odds ratio for breast cancer overall was less than 2.0. For protein-truncating variants in ATM and CHEK2, odds ratios were higher for estrogen receptor (ER)-positive disease than for ER-negative disease; for protein-truncating variants in BARD1, BRCA1, BRCA2, PALB2, RAD51C, and RAD51D, odds ratios were higher for ER-negative disease than for ER-positive disease. Rare missense variants (in aggregate) in ATM, CHEK2, and TP53 were associated with a risk of breast cancer overall with a P value of less than 0.001. For BRCA1, BRCA2, and TP53, missense variants (in aggregate) that would be classified as pathogenic according to standard criteria were associated with a risk of breast cancer overall, with the risk being similar to that of protein-truncating variants.CONCLUSIONSThe results of this study define the genes that are most clinically useful for inclusion on panels for the prediction of breast cancer risk, as well as provide estimates of the risks associated with protein-truncating variants, to guide genetic counseling. (Funded by European Union Horizon 2020 programs and others.)Molecular tumour pathology - and tumour geneticsMTG1 - Moleculaire genetica en pathologie van borstkanke

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

Neuroimmagini e profilo neuropsicologico nell’adrenoleucodistrofia legata all’X

Background scientifico: L'adrenoleucodistrofia a trasmissione recessiva legata all'X (ALD-X) è una patologia neurodegenerativa severa associata ad una progressiva demielinizzazione del sistema nervoso centrale e periferico, insufficienza surrenale (malattia di Addison) ed un accumulo di acidi grassi a catena molto lunga (VLCFA) nel plasma, nei fibroblasti e nei tessuti. Nell'8% dei casi origina da nuove mutazioni. Le forme parieto-occipitali sono le più frequenti. Scopo: I primi sintomi consistono in difficoltà cognitive, a livello visuomotorio e visuospaziale. Il Nostro scopo è quello di valutare se vi sia una discrepanza tra neuroimmagini e profilo neuropsicologico nell'ALD-X. Metodologie e soggetti: Riportiamo il caso di un bambino di 8,6 anni che giunge al pronto soccorso per un episodio simil-comiziale insorto in apiressia, al risveglio, con perdita di urine e seguito da ipotonia generalizzata, rallentamento nei movimenti e nell'eloquio ed amnesia retrograda. Effettuate EEGvv, TAC e RMN encefalo si sospetta ALD. Il bambino viene inviato presso il Reparto Degenze del Nostro Dipartimento. In anamnesi presente astenia e problemi uditivi da circa sei mesi per cui ha effettuato un videat ORL risultato nella norma. La gravidanza è normodecorsa, con sviluppo psicomotorio normale. Genitori non consanguinei entrambi italiani. Il bambino durante il ricovero è stata effettuata: misurazione degli VLCFA e dell'ACTH nel plasma, cortisolemia, esame del campo visivo centrale cromatico, EEGvv, RMN encefalo in spettroscopia, PEV, SEP, BAER, Sensory NCS, Motor NCS, F Wave. Lui, la madre ed il fratello minore effettuano l'analisi molecolare del gene ABCD1. Inoltre, il bambino è stato sottoposto ad una valutazione neuropsicologica. Una volta confermata la diagnosi e valutata l'estensione della lesione che non permetteva di effettuare il trapianto di midollo osseo, il bambino inizia terapia sostitutiva con idrocortisone ed Olio di Lorenzo; da circa sei mesi è entrato a far parte di un protocollo sperimentale per una nuova terapia. Attualmente abbiamo un follow-up di due anni. Risultati e discussioni: Si rilevano un aumento dei valori degli VCLFA e dell'ACTH. Il bambino presenta una mutazione puntiforme de novo per il gene ABCD1 (c.346G>A); la madre ed il fratello sono sani. All'EEGvv si evidenziano anomalie lente posteriori. Risultano nella norma: cortisolemia, PEV, SEP, BAER, Sensory NCS, Motor NCS, F Wave. All'esame del campo visivo centrale cromatico si evidenzia un restringimento irregolare della soglia differenziale visiva per tutti gli stimoli bilateralmente, prevalente per quello rosso. Alla RMN si rileva una diffusa, simmetrica e marcata demielinizzazione predominante a livello parietale. Alla spettroscopia si evidenzia un'elevazione del picco di colina con riduzione del picco del NAA e comparsa del picco del Lattato. L'esame trattografico dimostra rarefazione delle fibre mieliniche nella sostanza bianca occipito-parietale bilateralmente. Tutte queste alterazioni permangono stabili nel tempo. Dalla Nostra valutazione sono state registrate oscillazioni nel profilo neuropsicologico del bambino nelle varie età, con andamento non omogeneo, soprattutto in quei test che valutano le capacità motorie e di integrazione visuomotorie e nei test che valutano gli apprendimenti scolastici (soprattutto della letto-scrittura e della matematica). Queste oscillazioni, non coincidono con il quadro neuroradiologico rimasto invariato nei due anni di follow-up dimostrando così una discrepanza esistente tra neuroimmagini e profilo neuropsicologico. Tutto ciò ci porta a mettere in evidenza quanto sia importante, nei paziente affetti da ALD, integrare le indagini neuroradiologiche con una approfondita valutazione anche a livello neuropsicologico

Strengthening the Evidence-Based Approach to Guiding Effective Influenza Vaccination Policies

none10The availability of several effective and safe vaccines enables health systems to counteract annual influenza epidemics. However, the criteria of appropriateness and sustainability require that each citizen should receive the right vaccine. The value of each vaccine can be assessed within well-known frameworks, such as the Health Technology Assessment (HTA), a step that is fundamental to the process of allocating resources to vaccination strategies. The paper describes how HTA has been incorporated as an evidence-based tool to support the definition of Italian vaccination strategies, reports the results of the HTA report on the most recently available influenza vaccine in Italy (cell-based quadrivalent vaccine (QIVc)-Flucelvax® Tetra) and elaborates on current and future recommendations in the field of influenza vaccination. Recommendations issued by the Italian Ministry of Health foster the appropriate use of influenza vaccines from 2018-2019 onwards. Evidence of the value of newly available vaccines will hopefully support future decisions and promote the appropriate use of these vaccines on the basis of the characteristics of the target population. However, the success of influenza vaccination will also depend on citizens' empowerment and engagement in the decision-making process.noneCalabrò, Giovanna Elisa; Specchia, Maria Lucia; Boccalini, Sara; Panatto, Donatella; Rizzo, Caterina; Merler, Stefano; Ferriero, Anna Maria; Di Pietro, Maria Luisa; Bonanni, Paolo; de Waure, ChiaraCalabrò, Giovanna Elisa; Specchia, Maria Lucia; Boccalini, Sara; Panatto, Donatella; Rizzo, Caterina; Merler, Stefano; Ferriero, Anna Maria; Di Pietro, Maria Luisa; Bonanni, Paolo; de Waure, Chiar