Quantitative copy number analysis by Multiplex Ligation-dependent Probe Amplification (MLPA) of BRCA1-associated breast cancer regions identifies BRCAness

Our group has previously employed array Comparative Genomic Hybridization (aCGH) to assess the genomic patterns of BRCA1-mutated breast cancers. We have shown that the so-called BRCA1-like(aCGH) profile is also present in about half of all triple-negative sporadic breast cancers and is predictive for benefit from intensified alkylating chemotherapy. As aCGH is a rather complex method, we translated the BRCA1(aCGH) profile to a Multiplex Ligation-dependent Probe Amplification (MLPA) assay, to identify both BRCA1-mutated breast cancers and sporadic cases with a BRCA1-like(aCGH) profile. The most important genomic regions of the original aCGH based classifier (3q22-27, 5q12-14, 6p23-22, 12p13, 12q21-23, 13q31-34) were mapped to a set of 34 MLPA probes. The training set consisted of 39 BRCA1-like(aCGH) breast cancers and 45 non-BRCA1-like(aCGH) breast cancers, which had previously been analyzed by aCGH. The BRCA1-like(aCGH) group consisted of germline BRCA1-mutated cases and sporadic tumours with low BRCA1 gene expression and/or BRCA1 promoter methylation. We trained a shrunken centroids classifier on the training set and validation was performed on an independent test set of 40 BRCA1-like(aCGH) breast cancers and 32 non-BRCA1-like(aCGH) breast cancer tumours. In addition, we validated the set prospectively on 69 new triple-negative tumours. BRCAness in the training set of 84 tumours could accurately be predicted by prediction analysis of microarrays (PAM) (accuracy 94%). Application of this classifier on the independent validation set correctly predicted BRCA-like status of 62 out of 72 breast tumours (86%). Sensitivity and specificity were 85% and 87%, respectively. When the MLPA-test was subsequently applied to 46 breast tumour samples from a randomized clinical trial, the same survival benefit for BRCA1-like tumours associated with intensified alkylating chemotherapy was shown as was previously reported using the aCGH assay. Since the MLPA assay can identify BRCA1-deficient breast cancer patients, this method could be applied both for clinical genetic testing and as a predictor of treatment benefit. BRCA1-like tumours are highly sensitive to chemotherapy with DNA damaging agents, and most likely to poly ADP ribose polymerase (PARP)-inhibitors. The MLPA assay is rapid and robust, can easily be multiplexed, and works well with DNA derived from paraffin-embedded tissue

Ethnic differences in the mother-son relationship of incarcerated and non-incarcerated male adolescents in the Netherlands

<p>Abstract</p> <p>Background</p> <p>In the Netherlands, youths of Moroccan origin account for a disproportionately large percentage of the population in juvenile justice institutions. Previous research showed that Moroccan adolescents in pre-trial arrest are characterized by less serious offending behavior (i.e., primarily property-based) and lower levels of mental health problems than native Dutch adolescents in pre-trial arrest. To date, little is known about the parent-child relationship of these adolescents. This study examines the mother-son relationships of Moroccan and native Dutch delinquent adolescents and their association with adolescent delinquency.</p> <p>Methods</p> <p>In the present study, differences in the mother-son relationship characteristics between families of incarcerated <it>(N = 129) </it>and non-incarcerated <it>(N = 324) </it>adolescents were examined, and it was analyzed if these differences between incarcerated and non-incarcerated adolescents were the same for Moroccans and native Dutch. Data collection for the incarcerated sample took place from 2006 to 2008. Comparison data were used of interviews conducted with mothers originating from former larger studies in the general Dutch population. Latent Class Analysis was performed in order to identify types of mother-son relationship. Logistic regression analyses were used to identify the relationships between mother-son relationship types, incarceration and ethnicity.</p> <p>Results</p> <p>A three class model of mother-son relationship types was found: a low-conflict mother-son relationship type, a high-conflict mother-son relationship type, and a neglectful mother-son relationship type. Compared to the native Dutch adolescents, Moroccans (both in the incarcerated and non-incarcerated population) more often showed a neglectful mother-son relationship type. For Moroccans, no differences in mother-son relationship types were found between the incarcerated and non-incarcerated adolescents, whereas considerable differences occurred between the native Dutch incarcerated and non-incarcerated adolescents.</p> <p>Conclusions</p> <p>Our findings indicate that mother-son relationship types of incarcerated Moroccan adolescents and non-incarcerated Moroccan adolescents are rather comparable. These findings are in line with previous studies which revealed the less problematic profile of Moroccan adolescents in pre-trial arrest in the Netherlands compared to native Dutch adolescents in pre-trial arrest.</p

Deficient Signaling via Alk2 (Acvr1) Leads to Bicuspid Aortic Valve Development

Bicuspid aortic valve (BAV) is the most common congenital cardiac anomaly in humans. Despite recent advances, the molecular basis of BAV development is poorly understood. Previously it has been shown that mutations in the Notch1 gene lead to BAV and valve calcification both in human and mice, and mice deficient in Gata5 or its downstream target Nos3 have been shown to display BAVs. Here we show that tissue-specific deletion of the gene encoding Activin Receptor Type I (Alk2 or Acvr1) in the cushion mesenchyme results in formation of aortic valve defects including BAV. These defects are largely due to a failure of normal development of the embryonic aortic valve leaflet precursor cushions in the outflow tract resulting in either a fused right- and non-coronary leaflet, or the presence of only a very small, rudimentary non-coronary leaflet. The surviving adult mutant mice display aortic stenosis with high frequency and occasional aortic valve insufficiency. The thickened aortic valve leaflets in such animals do not show changes in Bmp signaling activity, while Map kinase pathways are activated. Although dysfunction correlated with some pro-osteogenic differences in gene expression, neither calcification nor inflammation were detected in aortic valves of Alk2 mutants with stenosis. We conclude that signaling via Alk2 is required for appropriate aortic valve development in utero, and that defects in this process lead to indirect secondary complications later in life

HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.

Approximately 1-5% of breast cancers are attributed to inherited mutations in BRCA1 or BRCA2 and are selectively sensitive to poly(ADP-ribose) polymerase (PARP) inhibitors. In other cancer types, germline and/or somatic mutations in BRCA1 and/or BRCA2 (BRCA1/BRCA2) also confer selective sensitivity to PARP inhibitors. Thus, assays to detect BRCA1/BRCA2-deficient tumors have been sought. Recently, somatic substitution, insertion/deletion and rearrangement patterns, or 'mutational signatures', were associated with BRCA1/BRCA2 dysfunction. Herein we used a lasso logistic regression model to identify six distinguishing mutational signatures predictive of BRCA1/BRCA2 deficiency. A weighted model called HRDetect was developed to accurately detect BRCA1/BRCA2-deficient samples. HRDetect identifies BRCA1/BRCA2-deficient tumors with 98.7% sensitivity (area under the curve (AUC) = 0.98). Application of this model in a cohort of 560 individuals with breast cancer, of whom 22 were known to carry a germline BRCA1 or BRCA2 mutation, allowed us to identify an additional 22 tumors with somatic loss of BRCA1 or BRCA2 and 47 tumors with functional BRCA1/BRCA2 deficiency where no mutation was detected. We validated HRDetect on independent cohorts of breast, ovarian and pancreatic cancers and demonstrated its efficacy in alternative sequencing strategies. Integrating all of the classes of mutational signatures thus reveals a larger proportion of individuals with breast cancer harboring BRCA1/BRCA2 deficiency (up to 22%) than hitherto appreciated (∼1-5%) who could have selective therapeutic sensitivity to PARP inhibition

Comorbidity of physical and mental disorders and the effect on work-loss days

Objective: To examine the association between physical and mental disorders and the separate and joint effect of physical and mental disorders on work-loss. Method: Data was derived from the Netherlands Mental Health Survey and Incidence Study. This was a general population study in which 7076 adults, aged between 18 and 64 years, were assessed using the Composite International Diagnostic Interview. Medically treated physical disorders and work-loss were assessed using self-reports. Results: All physical disorders, except injury caused by accident, were significantly related to anxiety and mood disorders, but only weakly related to substance use disorders. Both physical and mental disorders were significantly related to work-loss; mental disorders more so than physical disorders. Physical-mental (PM) comorbidity leads to a mainly additive increase in work-loss. Conclusion: PM comorbidity is very common in the general population and leads to a greater absenteeism from work than pure disorders that also cause personal and social problems