A whole-genome massively parallel sequencing analysis of BRCA1 mutant oestrogen receptor-negative and -positive breast cancers

BRCA1 encodes a tumour suppressor protein that plays pivotal roles in homologous recombination (HR) DNA repair, cell-cycle checkpoints, and transcriptional regulation. BRCA1 germline mutations confer a high risk of early-onset breast and ovarian cancer. In more than 80% of cases, tumours arising in BRCA1 germline mutation carriers are oestrogen receptor (ER)-negative; however, up to 15% are ER-positive. It has been suggested that BRCA1 ER-positive breast cancers constitute sporadic cancers arising in the context of a BRCA1 germline mutation rather than being causally related to BRCA1 loss-of-function. Whole-genome massively parallel sequencing of ER-positive and ER-negative BRCA1 breast cancers, and their respective germline DNAs, was used to characterize the genetic landscape of BRCA1 cancers at base-pair resolution. Only BRCA1 germline mutations, somatic loss of the wild-type allele, and TP53 somatic mutations were recurrently found in the index cases. BRCA1 breast cancers displayed a mutational signature consistent with that caused by lack of HR DNA repair in both ER-positive and ER-negative cases. Sequencing analysis of independent cohorts of hereditary BRCA1 and sporadic non-BRCA1 breast cancers for the presence of recurrent pathogenic mutations and/or homozygous deletions found in the index cases revealed that DAPK3, TMEM135, KIAA1797, PDE4D, and GATA4 are potential additional drivers of breast cancers. This study demonstrates that BRCA1 pathogenic germline mutations coupled with somatic loss of the wild-type allele are not sufficient for hereditary breast cancers to display an ER-negative phenotype, and has led to the identification of three potential novel breast cancer genes (ie DAPK3, TMEM135, and GATA4).

Multicenter Blinded Analysis of RT-PCR Detection Methods for Paramyxoviruses in Relation to Paget's Disease of Bone

Conflicting results have been reported on the detection of paramyxovirus transcripts in Paget's disease, and a possible explanation is differences in the sensitivity of RT-PCR methods for detecting virus. In a blinded study, we found no evidence to suggest that laboratories that failed to detect viral transcripts had less sensitive RT-PCR assays, and we did not detect measles or distemper transcripts in Paget's samples using the most sensitive assays evaluated.

Introduction: There is conflicting evidence on the possible role of persistent paramyxovirus infection in Paget's disease of bone (PDB). Some workers have detected measles virus (MV) or canine distemper virus (CDV) transcripts in cells and tissues from patients with PDB, but others have failed to confirm this finding. A possible explanation might be differences in the sensitivity of RT-PCR methods for detecting virus. Here we performed a blinded comparison of the sensitivity of different RT-PCR-based techniques for MV and CDV detection in different laboratories and used the most sensitive assays to screen for evidence of viral transcripts in bone and blood samples derived from patients with PDB.

Materials and Methods: Participating laboratories analyzed samples spiked with known amounts of MV and CDV transcripts and control samples that did not contain viral nucleic acids. All analyses were performed on a blinded basis.

Results: The limit of detection for CDV was 1000 viral transcripts in three laboratories (Aberdeen, Belfast, and Liverpool) and 10,000 transcripts in another laboratory (Manchester). The limit of detection for MV was 16 transcripts in one laboratory (NIBSC), 1000 transcripts in two laboratories (Aberdeen and Belfast), and 10,000 transcripts in two laboratories (Liverpool and Manchester). An assay previously used by a U.S.-based group to detect MV transcripts in PDB had a sensitivity of 1000 transcripts. One laboratory (Manchester) detected CDV transcripts in a negative control and in two samples that had been spiked with MV. None of the other laboratories had false-positive results for MV or CDV, and no evidence of viral transcripts was found on analysis of 12 PDB samples using the most sensitive RT-PCR assays for MV and CDV.

Conclusions: We found that RT-PCR assays used by different laboratories differed in their sensitivity to detect CDV and MV transcripts but found no evidence to suggest that laboratories that previously failed to detect viral transcripts had less sensitive RT-PCR assays than those that detected viral transcripts. False-positive results were observed with one laboratory, and we failed to detect paramyxovirus transcripts in PDB samples using the most sensitive assays evaluated. Our results show that failure of some laboratories to detect viral transcripts is unlikely to be caused by problems with assay sensitivity and highlight the fact that contamination can be an issue when searching for pathogens by sensitive RT-PCR-based techniques.

Genome scan meta-analysis of schizophrenia and bipolar disorder, part II:Schizophrenia

Schizophrenia is a common disorder with high heritability and a 10-fold increase in risk to siblings of probands. Replication has been inconsistent for reports of significant genetic linkage. To assess evidence for linkage across studies, rank-based genome scan meta-analysis (GSMA) was applied to data from 20 schizophrenia genome scans. Each marker for each scan was assigned to 1 of 120 30-cM bins, with the bins ranked by linkage scores (1 = most significant) and the ranks averaged across studies (R(avg)) and then weighted for sample size (N(sqrt)[affected casess]). A permutation test was used to compute the probability of observing, by chance, each bin's average rank (P(AvgRnk)) or of observing it for a bin with the same place (first, second, etc.) in the order of average ranks in each permutation (P(ord)). The GSMA produced significant genomewide evidence for linkage on chromosome 2q (PAvgRnk

A fluorescence model of the C3 radical in comets

Theoretical resonance fluorescence calculations are presented of the triatomic C3 radical and are compared with observations of the C3 emission in comets Hale-Bopp and de Vico. A theoretical model of the C3 vibration-rotational structure in the A1Piu - X1Sigmag + electronic system is introduced. The model takes into account the detailed structure of the bending mode nu2 which is responsible for the emission of the 4050 Å group. A total of 1959 levels are considered, with 515 levels in the ground state. The main effort is to model high-resolution spectra of the 4050 Å emission in comets C/1995 O1 Hale-Bopp and 122P/1995 S1 de Vico. The agreement between observed and theoretical spectra is good for a value of the dipole moment derivative of dmu/dr ~ 2.5 Debye Å-1. The modeled C3 emission exhibits a pronounced Swings effect. Based on observations made with William Herschel Telescope operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias, and on observations made at the McDonald Observatory, which is operated by the University of Texas at Austin, USA.

Sher 25: pulsating but apparently alone

The blue supergiant Sher 25 is surrounded by an asymmetric, hourglass-shaped circumstellar nebula, which shows similarities to the triple-ring structure seen around SN 1987A. From optical spectroscopy over six consecutive nights, we detect periodic radial velocity variations in the stellar spectrum of Sher 25 with a peak-to-peak amplitude of ~ 12 km s^-1 on a time-scale of about 6 d, confirming the tentative detection of similar variations by Hendry et al. From consideration of the amplitude and time-scale of the signal, coupled with observed line profile variations, we propose that the physical origin of these variations is related to pulsations in the stellar atmosphere, rejecting the previous hypothesis of a massive, short-period binary companion. The radial velocities of two other blue supergiants with similar bipolar nebulae, SBW1 and HD 168625, were also monitored over the course of six nights, but these did not display any significant radial velocity variations. 

Identification of diagnostic biomarkers for infection in premature neonates

Infection is a leading cause of neonatal morbidity and mortality worldwide. Premature neonates are particularly susceptible to infection because of physiologic immaturity, comorbidity, and extraneous medical interventions. Additionally premature infants are at higher risk of progression to sepsis or severe sepsis, adverse outcomes, and antimicrobial toxicity. Currently initial diagnosis is based upon clinical suspicion accompanied by nonspecific clinical signs and is confirmed upon positive microbiologic culture results several days after institution of empiric therapy. There exists a significant need for rapid, objective, in vitro tests for diagnosis of infection in neonates who are experiencing clinical instability. We used immunoassays multiplexed on microarrays to identify differentially expressed serum proteins in clinically infected and non-infected neonates. Immunoassay arrays were effective for measurement of more than 100 cytokines in small volumes of serum available from neonates. Our analyses revealed significant alterations in levels of eight serum proteins in infected neonates that are associated with inflammation, coagulation, and fibrinolysis. Specifically P- and E-selectins, interleukin 2 soluble receptor alpha, interleukin 18, neutrophil elastase, urokinase plasminogen activator and its cognate receptor, and C-reactive protein were observed at statistically significant increased levels. Multivariate classifiers based on combinations of serum analytes exhibited better diagnostic specificity and sensitivity than single analytes. Multiplexed immunoassays of serum cytokines may have clinical utility as an adjunct for rapid diagnosis of infection and differentiation of etiologic agent in neonates with clinical decompensation.

Broad balmer wings in BA Hyper/Supergiants distorted by diffuse interstellar bands: five examples in the 30 Doradus Region from the VLT-Flames Tarantula Survey

Extremely broad emission wings at Hβ and Hα have been found in VLT-FLAMES Tarantula Survey data for five very luminous BA supergiants in or near 30 Doradus in the Large Magellanic Cloud. The profiles of both lines are extremely asymmetrical, which we have found to be caused by very broad diffuse interstellar bands (DIBs) in the longward wing of Hβ and the shortward wing of Hα. These DIBs are well known to interstellar but not to many stellar specialists, so that the asymmetries may be mistaken for intrinsic features. The broad emission wings are generally ascribed to electron scattering, although we note difficulties for that interpretation in some objects. Such profiles are known in some Galactic hyper/supergiants and are also seen in both active and quiescent Luminous Blue Variables (LBVs). No prior or current LBV activity is known in these 30 Dor stars, although a generic relationship to LBVs is not excluded; subject to further observational and theoretical investigation, it is possible that these very luminous supergiants are approaching the LBV stage for the first time. Their locations in the HRD and presumed evolutionary tracks are consistent with that possibility. The available evidence for spectroscopic variations of these objects is reviewed, while recent photometric monitoring does not reveal variability. A search for circumstellar nebulae has been conducted, with an indeterminate result for one of them.