Low-level constitutional mosaicism of BRCA1 in two women with young onset ovarian cancer.

Germline pathogenic variants in BRCA1 and BRCA2 cause hereditary breast and ovarian cancer. The vast majority of these variants are inherited from a parent. De novo constitutional pathogenic variants are rare. Even fewer cases of constitutional mosaicism have been reported and these have mostly been described in women with breast cancer. Here we report low-level constitutional mosaicism identified by Next Generation Sequencing in two women with ovarian cancer. A BRCA1 c.5074G > A p.(Asp1692Asn) variant detected in the first female at 42 years, classed as likely pathogenic, was found in ~ 52% of reads in DNA extracted from tumour, ~ 10% of reads in DNA extracted from peripheral blood leukocytes and ~ 10% of reads in DNA extracted from buccal mucosa. The second BRCA1 c.2755_2758dupCCTG p.(Val920AlafsTer6) variant was detected in a female aged 53 years, classed as pathogenic, and was found in ~ 59% of reads in DNA extracted from tumour, ~ 14% of reads in DNA extracted from peripheral blood leukocytes and similarly in ~ 14% of reads in both DNA extracted from buccal mucosa and urine sample. Sanger sequencing confirmed the presence of these variants at a corresponding low level consistent with mosaicism that may not have been detected by this method alone. This report demonstrates the clinical benefit for two women of BRCA1/BRCA2 germline NGS testing at a depth that can detect low-level mosaicism. As well as informing appropriate treatments, tumour sequencing results may facilitate the detection and interpretation of low-level mosaic variants in the germline. Both results have implications for other cancer risks and for relatives when providing a family cancer risk assessment and reproductive risk. The implications for laboratory practice, clinical genetics management and genetic counselling for constitutional mosaicism of BRCA1/BRCA2 are discussed.

Modeling Contaminant Microbes in Rivers During Both Baseflow and Stormflow.

Rivers transport contaminant microorganisms (including fecal indicator bacteria and human pathogens) long distances downstream of diffuse and point sources, posing a human health risk. We present a mobile-immobile model that incorporates transport as well as immobilization and remobilization of contaminant microbes and other fine particles during baseflow and stormflow. During baseflow conditions, hyporheic exchange flow causes particles to accumulate in streambed sediments. Remobilization of stored particles from streambed sediments occurs slowly during baseflow via hyporheic exchange flow, while remobilization is vastly increased during stormflow. Model predictions are compared to observations over a range of artificial and natural flood events in the dairy contaminated Topehaehae Stream, New Zealand. The model outputs closely matched timing and magnitude of E. coli and turbidity observations through multiple high-flow events. By accounting for both state-of-flow and hyporheic exchange processes, the model provides a valuable framework for predicting particle and contaminant microbe behavior in streams.

Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes.

PURPOSE: Where multiple in silico tools are concordant, the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) framework affords supporting evidence toward pathogenicity or benignity, equivalent to a likelihood ratio of ~2. However, limited availability of "clinical truth sets" and prior use in tool training limits their utility for evaluation of tool performance. METHODS: We created a truth set of 9,436 missense variants classified as deleterious or tolerated in clinically validated high-throughput functional assays for BRCA1, BRCA2, MSH2, PTEN, and TP53 to evaluate predictive performance for 44 recommended/commonly used in silico tools. RESULTS: Over two-thirds of the tool-threshold combinations examined had specificity of <50%, thus substantially overcalling deleteriousness. REVEL scores of 0.8-1.0 had a Positive Likelihood Ratio (PLR) of 6.74 (5.24-8.82) compared to scores <0.7 and scores of 0-0.4 had a Negative Likelihood Ratio (NLR) of 34.3 (31.5-37.3) compared to scores of >0.7. For Meta-SNP, the equivalent PLR = 42.9 (14.4-406) and NLR = 19.4 (15.6-24.9). CONCLUSION: Against these clinically validated "functional truth sets," there was wide variation in the predictive performance of commonly used in silico tools. Overall, REVEL and Meta-SNP had best balanced accuracy and might potentially be used at stronger evidence weighting than current ACMG/AMP prescription, in particular for predictions of benignity.

Revisiting peak serum cortisol response to insulin-induced hypoglycemia in children.

PURPOSE: To evaluate factors that could potentially affect the hypothalamic-pituitary adrenal (HPA) axis response to insulin-induced hypoglycemia in children without history or symptoms of adrenal insufficiency and to propose a cut-off value to define a normal response in this population. METHODS: Exploratory single-center study involving 78 children that prospectively underwent insulin tolerance test (ITT) for suspected growth hormone (GH) deficiency. METHODS: Glucose, cortisol, GH, adrenocorticotrophic hormone (ACTH), epinephrine and norepinephrine levels were measured at baseline and after insulin-induced hypoglycemia. Serum cortisol was measured using Access automated immunoassay. RESULTS: Mean (range) basal morning serum cortisol of 8 (2.2-19.5) µg/dL/222 (61-542) nmol/L increased after hypoglycemia to 20.5 (14.6-29.5) µg/dL/570 nmol/L (405-819) nmol/L. Peak serum cortisol levels of 14.6 µg/dL (405 nmol/L) and 15.4 µg/dL (428 nmol/L) corresponded to the 2.5th and 5th percentiles, respectively. Peak serum cortisol correlated with peak plasma epinephrine (r = 0.367; P = 0.0014) but did not correlate with age, BMI-SD or peak serum GH. Children with intact and abnormal GH responses presented similar mean peak serum cortisol levels (20.0 vs. 20.6 µg/dL/555 vs. 572 nmol/L; P = 0.21). CONCLUSION: Our data indicate that the current cut-off to define normal HPA axis response in children after insulin-induced hypoglycemia warrants reevaluation to avoid over-diagnosis of adrenal insufficiency. Our results suggest that peak serum cortisol levels ≥ 15.4 µg/dL (428 nmol/L) in children undergoing ITT might represent a normal cortisol response to stress, regardless of age, BMI or GH secretory capacity.

All-Order Amplitudes at any Multiplicity in the Multi-Regge Limit.

We propose an all-loop expression for scattering amplitudes in planar N=4 super Yang-Mills theory in multi-Regge kinematics valid for all multiplicities, all helicity configurations, and arbitrary logarithmic accuracy. Our expression is arrived at from comparing explicit perturbative results with general expectations from the integrable structure of a closely related collinear limit. A crucial ingredient of the analysis is an all-order extension for the central emission vertex that we recently computed at next-to-leading logarithmic accuracy. As an application, we use our all-order formula to prove that all amplitudes in this theory in multi-Regge kinematics are single-valued multiple polylogarithms of uniform transcendental weight.

Cryptosporidium oocyst persistence in agricultural streams -a mobile-immobile model framework assessment.

Rivers are a means of rapid and long-distance transmission of pathogenic microorganisms from upstream terrestrial sources. Pathogens enter streams and rivers via overland flow, shallow groundwater discharge, and direct inputs. Of concern is the protozoal parasite, Cryptosporidium, which can remain infective for weeks to months under cool and moist conditions, with the infectious stage (oocysts) largely resistant to chlorination. We applied a mobile-immobile model framework to assess Cryptosporidium transport and retention in streams, that also accounts for inactivation. The model is applied to California's Central Valley where Cryptosporidium exposure can be at higher risk due to agricultural and wildlife nonpoint sources. The results demonstrate that hyporheic exchange is an important process to include in models characterizing pathogen dynamics in streams, delaying downstream transmission and allowing for immobilization processes, such as reversible filtration in the sediments, to occur. Although in-stream concentrations decrease relatively quickly (within hours), pathogen accumulation of up to 66% of the inputs due to immobilization processes in the sediments and slower moving surface water could result in long retention times (months to years). The model appropriately estimates baseflow pathogen accumulation and can help predict the potential loads of resuspended pathogens in response to a storm event.

Evaluation of universal immunohistochemical screening of sebaceous neoplasms in a service setting.

BACKGROUND: Muir-Torre syndrome (MTS) is a subtype of Lynch syndrome, which encompasses the combination of sebaceous skin tumours or keratoacanthomas and internal malignancy, due to mutations in DNA mismatch repair genes. Sebaceous neoplasms (SNs) may occur before other malignancies, and may lead to the diagnosis, which allows testing of other family members, cancer surveillance, risk-reducing surgery or prevention therapies. AIM: To evaluate the efficacy of universal immunohistochemistry (IHC) screening of SNs in a service setting. METHODS: Patients with SNs were ascertained by a regional clinical pathology service over a 3-year period. Results of tumour IHC, clinical genetics notes and germline genetic testing were retrospectively reviewed. RESULTS: In total, 62 patients presented with 71 SNs; 9 (15%) of these patients had previously diagnosed MTS. Tumour IHC was performed for 50 of the 53 remaining patients (94%); 26 (52%) had loss of staining of one or more mismatch repair proteins. Fifteen patients were referred to the Clinical Genetics department, and 10 patients underwent germline genetic testing. Two had a new diagnosis of MTS confirmed, with heterozygous pathogenic mutations detected in the MSH2 and PMS2 genes (diagnostic yield 20%). The PMS2 mutation was identified in a 57-year-old woman with a sebaceous adenoma and history of endometrial cancer; to our knowledge, this is the first time a PMS2 mutation has been reported in MTS. CONCLUSIONS: Universal IHC screening of SNs is an effective method to identify cases for further genetic evaluation. Rates of referral to clinical genetics were only moderate (58%). Increased awareness of MTS could help improve the rate of onward referral.

Cell-specific abnormalities of glutamate transporters in schizophrenia: sick astrocytes and compensating relay neurons?

Excitatory amino-acid transporters (EAATs) bind and transport glutamate, limiting spillover from synapses due to their dense perisynaptic expression primarily on astroglia. Converging evidence suggests that abnormalities in the astroglial glutamate transporter localization and function may underlie a disease mechanism with pathological glutamate spillover as well as alterations in the kinetics of perisynaptic glutamate buffering and uptake contributing to dysfunction of thalamo-cortical circuits in schizophrenia. We explored this hypothesis by performing cell- and region-level studies of EAAT1 and EAAT2 expression in the mediodorsal nucleus of the thalamus in an elderly cohort of subjects with schizophrenia. We found decreased protein expression for the typically astroglial-localized glutamate transporters in the mediodorsal and ventral tier nuclei. We next used laser-capture microdissection and quantitative polymerase chain reaction to assess cell-level expression of the transporters and their splice variants. In the mediodorsal nucleus, we found lower expression of transporter transcripts in a population of cells enriched for astrocytes, and higher expression of transporter transcripts in a population of cells enriched for relay neurons. We confirmed expression of transporter protein in neurons in schizophrenia using dual-label immunofluorescence. Finally, the pattern of transporter mRNA and protein expression in rodents treated for 9 months with antipsychotic medication suggests that our findings are not due to the effects of antipsychotic treatment. We found a compensatory increase in transporter expression in neurons that might be secondary to a loss of transporter expression in astrocytes. These changes suggest a profound abnormality in astrocyte functions that support, nourish and maintain neuronal fidelity and synaptic activity.

Retention and remobilization dynamics of fine particles and microorganisms in pastoral streams.

Both microbial metabolism and pathogen retention and remobilization are dependent on downstream transport of fine particles, which migrate in a series of deposition and resuspension events. All fine particles, including clay minerals, particulate organic carbon, nutrients and microbes, are often considered to be transported similarly in the environment because of a lack of specific observations comparing their relative transport. We conducted a tracer injection study to compare the transport and retention of the fecal indicator bacterium Escherichia coli, synthetic inert fluorescent fine particles, and a dissolved conservative tracer. We found that the fluorescent fine particles and bacteria were transported similarly, with both having greater retention than the solute tracer. We used a stochastic model to evaluate in-stream retention and migration of the solute, fluorescent particles, and E. coli. The best-fit model parameters indicate that different stream reaches had varied retention characteristics, but always showed greater retention of fluorescent particles and E. coli compared to the solute tracer. Direct measurements within known retention areas after the injection showed that the majority of the fluorescent particles and E. coli were retained near the sediment-water interface in macrophyte stands or filtered within the top 3 cm of the streambed sediment. Both the tracer particles and E. coli were retained within these regions for multiple months following the injection experiment. The stochastic model properly captured the wide range of storage timescales and processes we observed in the stream. Our results demonstrate the importance of the streambed sediment and in-stream macrophytes as short- and long-term reservoirs for fine organic particles and microbes in streams.

Exoplanet detection. A terrestrial planet in a ~1-AU orbit around one member of a ~15-AU binary.

Using gravitational microlensing, we detected a cold terrestrial planet orbiting one member of a binary star system. The planet has low mass (twice Earth's) and lies projected at ~0.8 astronomical units (AU) from its host star, about the distance between Earth and the Sun. However, the planet's temperature is much lower, <60 Kelvin, because the host star is only 0.10 to 0.15 solar masses and therefore more than 400 times less luminous than the Sun. The host itself orbits a slightly more massive companion with projected separation of 10 to 15 AU. This detection is consistent with such systems being very common. Straightforward modification of current microlensing search strategies could increase sensitivity to planets in binary systems. With more detections, such binary-star planetary systems could constrain models of planet formation and evolution.

Incorporating new materials and techniques into clinical practice.

This article outlines the subjects presented and discussed at the December 2012 IADR Dental Materials Innovation Workshop held at King's College London. Incorporating new materials and techniques into clinical practice was considered from 4 perspectives: (1) Accelerating the "research to regulatory approval" process was presented with current developments in the United States, with the National Institutes of Health/Food and Drug Administration process as a working example; (2) intellectual property and regulatory requirements were discussed across the well-established US and EU frameworks, as well as the more recently developed procedures across Brazil, Russia, India, and China; (3) the challenges and opportunities of incorporating innovations into dental education were considered with reference to the future needs of both students and faculty; and (4) the key but difficult and unpredictable step of translating such innovations into routine dental practice was then explored. Constructive and far-ranging discussion among the broadly based Workshop participants (from dental research, education, practice, and industry, as well as environmental organizations and the World Health Organization) mapped out key issues for the future. The focus was on facilitating the more timely adoption of improvements in both materials and techniques to improve patient health and health systems, while minimizing environmental impact.

Cyclical vomiting syndrome in children: a prospective study.

BACKGROUND: Cyclical vomiting syndrome (CVS) is a disorder that affects all ages and is characterized by episodes of severe nausea and vomiting with symptom-free intervals between episodes. The incidence in children is 3.15/100 000 children per year. Our objective was to evaluate the natural history of CVS and examine factors that predict symptom resolution. METHODS: Thirty newly diagnosed children (mean 9.15 years, SD 3.31 range 3.5-15.7) were enrolled. All children had a follow-up interview at 3 months, 27/30 at 6 months, and 22/30 at 9 months. KEY RESULTS: Following diagnosis of CVS, only 5/22(22.7%) children had no further episodes of vomiting at 9 months, whereas 17/22 (77.3%) continued to vomit. In the year prior to diagnosis, 15/30 (50%) children were admitted to hospital. Of the 22 children with follow-up for 9 months, only one child required hospital admission. Children who continued to vomit had higher internalizing scores on CBCL compared with those who stopped vomiting (P = NS). The Pediatric Quality-of-Life Score suggested those who continued to vomit had a poorer quality of life at diagnosis compared with those who stopped vomiting (P < 0.05). CONCLUSIONS & INFERENCES: Making a positive diagnosis of CVS and providing families with information is very important in the management of CVS. Although 75% of children reported regular episodes of vomiting 9 months after diagnosis, there was a significant reduction in the frequency and severity of symptoms in addition to a marked reduction in the use of medical services.