Restriction Enzyme Generated Next-Generation Sequencing Libraries and Genetic Risk Modifiers of BRCA1 Mutation Carriers

Next-generation sequencing (NGS) is a high throughput technique used to sequence large amounts of DNA in a short amount of time. However, a limitation to NGS is that the generated data is in a single consensus sequence without distinguishing between variants on homologous chromosomes. Separating or phasing the variants from the maternal and paternal chromosomes can provide information about the genetic origin of disease and information about how DNA nucleotide alterations interact in cis. This dissertation explores a new technical method of using restriction enzymes during NGS library preparation and its ability to increase the amount of phasing information that can be derived from NGS data. This study provides evidence that increasing the fragment size of NGS libraries can increase the amount of variant phasing information derived from NGS data. BRCA1 is a well-known tumor suppressor that, when mutated, predisposes the mutation carrier to breast cancer. BRCA1 mutation carriers have a 44-75% risk of developing breast cancer by age 70. In this study, we used next-generation sequencing data to identify germline genetic variants that modify the risk of breast cancer in BRCA1 mutation carriers. With the use of both biological and statistical filters, five variants were identified that changed breast cancer risk in BRCA1 mutation carriers. Furthermore, it was shown that two of the affected genes alter the growth of BRCA1 mutation breast cell lines. Perhaps, more importantly, the two variants were shown to alter the function of the affected genes. This is the first study to provide functional evidence on how common genetic variants can modify the risk of breast cancer in BRCA1 mutation carriers

Exome-based Variant Detection in Core Promoters.

Core promoter controls the initiation of transcription. Core promoter sequence change can disrupt transcriptional regulation, lead to impairment of gene expression and ultimately diseases. Therefore, comprehensive characterization of core promoters is essential to understand normal and abnormal gene expression in biomedical studies. Here we report the development of EVDC (Exome-based Variant Detection in Core promoters) method for genome-scale analysis of core-promoter sequence variation. This method is based on the fact that exome sequences contain the sequences not only from coding exons but also from non-coding region including core promoters generated by random fragmentation in exome sequencing process. Using exome data from three cell types of CD4+ T cells, CD19+ B cells and neutrophils of a single individual, we characterized the features of core promoter-mapped exome sequences, and analysed core-promoter variation in this individual genome. We also compared the core promoters between YRI (Yoruba in Ibadan, Nigeria) and the CEU (Utah residents of European decedent) populations using the exome data generated by the 1000 Genome project, and observed much higher variation in YRI population than in CEU population. Our study demonstrates that the EVDC method provides a simple but powerful means for genome-wile de novo characterization of core promoter sequence variation

Prevalence and spectrum of BRCA germline variants in mainland Chinese familial breast and ovarian cancer patients.

Germline mutations in BRCA1 and BRCA2 are the most penetrating genetic predispositions for breast and ovarian cancer, and their presence is largely ethnic-specific. Comprehensive information about the prevalence and spectrum of BRCA mutations has been collected in European and North American populations. However, similar information is lacking in other populations, including the mainland Chinese population despite its large size of 1.4 billion accounting for one fifth of the world\u27s population. Herein, we performed an extensive literature analysis to collect BRCA variants identified from mainland Chinese familial breast and ovarian cancer patients. We observed 137 distinct BRCA1 variants in 409 of 3,844 and 80 distinct BRCA2 variants in 157 of 3,024 mainland Chinese patients, with an estimated prevalence of 10.6% for BRCA1 and 5.2% for BRCA2. Of these variants, only 40.3% in BRCA1 and 42.5% in BRCA2 are listed in current Breast Cancer Information Core database. We observed higher frequent variation in BRCA1 exons 11A, 11C, 11D, and 24 and BRCA2 exon 10 in Chinese patients than in the patients of other populations. The most common pathogenic variant in BRCA1 wasc.981_982delAT in exon 11A, and in BRCA2 c.3195_3198delTAAT in exon 11B and c.5576_5579delTTAA in exon 11E; the most common novel variant in BRCA1 was c.919A\u3eG in exon 10A, and in BRCA2 c.7142delC in exon 14. None of the variants overlap with the founder mutations in other populations. Our analysis indicates that the prevalence of BRCA variation in mainland Chinese familial breast and ovarian cancer patients is at a level similar to but the spectrum is substantially different from the ones of other populations

Quiet Supersonic Flights 2018 (QSF18) Test: Galveston, Texas Risk Reduction for Future Community Testing with a Low-Boom Flight Demonstration Vehicle

The Quiet Supersonic Flights 2018 (QSF18) Program was designed to develop tools and methods for demonstration of overland supersonic flight with an acceptable sonic boom, and collect a large dataset of responses from a representative sample of the population. Phase 1 provided the basis for a low amplitude sonic boom testing in six different climate regions that will enable international regulatory agencies to draft a noise-based standard for certifying civilian supersonic overland flight. Phase 2 successfully executed a large scale test in Galveston, Texas, developed well documented data sets, calculated dose response relationships, yielded lessons, and identified future risk reduction activities

Miniature Exercise Device-2 (MED-2): Preliminary ISS Evaluation Results for a Compact Motorized Resistive and Aerobic Rowing Exercise Device

Future human missions beyond Low Earth Orbit (LEO) will require onboard equipment to provide exercise capabilities for the crew to counter the adverse physiological effects of long-duration microgravity. To accomplish this within the physical constraints of a space vehicle or transit module, a single miniature device that provides both resistive and aerobic exercise modalities is required. To meet this need, Johnson Space Centers (JSC) Software, Robotics, and Simulation Division (ER) developed the Miniature Exercise Device-2 (MED-2). MED-2 integrates a torque-controlled servomotor and a series-elastic actuator to provide highly-controllable load profiles and a large magnitude output performance in a very small package. This innovative technology is derived from years of JSC/ER design, development and operational experience with cutting-edge robotics, motor controllers, software and actuator/sensor miniaturization, including Robonaut 2 and MED-1. MED-2 was presented at the 2016 ISS R&D Conference. This is an update now that the last of six crewmembers will have completed planned MED-2 sessions on the International Space Station (ISS) in May 2018.Current state-of-the-art ISS exercise equipment consists of two treadmills, a resistive exercise device and two cycle ergometers with a total mass of several thousand pounds and a total volume of several cubic yards. This equipment has proven vital to mitigate the musculoskeletal and cardiovascular degradation effects of microgravity. However, due to the large operational volume and mass of these ISS devices, tailoring them for smaller vehicles, such as Orion, is not possible. In addition, each of the current ISS devices targets a single specific modality. Compared to the existing spaceflight (and even terrestrial) exercise equipment, MED-2 is a new archetype altogether. The combined features of compact size, multi-modality and high-performance is attributable to its innovative series elastic actuator and motor controller. Following its arrival on ISS in 2016, MED-2 was evaluated in two parts. The first and shorter evaluation was an engineering functional checkout of the hardware. As this was a novel exercise device previously never used on ISS, the initial checkout assessed the operation of the hardware and ensured the motion and dynamic range of the crew did not present any collision or other hazards. The second portion of the study collected the heart rates, kinematics and utilized operational volumes of six astronauts to determine the quality of both the resistive and aerobic exercise modalities as delivered by MED-2. Investigators from JSC Biomedical Research and Environmental Science Division (SK) and Glenn Research Center are currently evaluating the data and preparing preliminary results. For the resistive exercise modality, MED-2 demonstrated a range of constant resistive loads from 10-150 lbf. With a displacement range of 84 inches, the MED-2 accommodates users from 5th percentile Japanese female through 95th percentile American male for all of its certified exercises. The displacement measurement accuracy has also been verified within 2.5 percent full range. The crew was able to successfully perform all prescribed resistive exercises, except Goblet Squats which were not feasible with a constant load profile. For the aerobic exercise modality, MED-2 simulated a rowing motion with prescribed and user-selected resistance levels. It has demonstrated rates up to 60 strokes per minute on the ground. MED-2 loads and displacements performance are the same as those cited for the resistive modality. Although each of the crew was able to perform the prescribed aerobic rowing sets, there was considerable variability in the rowing motion among different crewmembers. Also, as expected, the crew was unable to get the full benefits of a typical terrestrial rowing stroke because the current configuration does not allow the user to reach past their feet. These observations have already informed the requirements for other microgravity rowing devices currently in development. One of the unique features of the MED-2 device is the intuitive touch-screen control system. This One Portal graphical user interface (GUI) was developed based on JSC/ERs heritage knowledge and experience of developing and sustaining the current ISS exercise equipment. Through this interface, the crew easily performed prepared prescriptions as well as had the ability to adjust exercise modality, load and other exercise details such as number of repetitions and number of sets. This touch-screen and GUI fulfilled the MED-2 project goal to simplify the interaction between the user and the device. Furthermore, the extent to which MED-2 utilizes a touchscreen and GUI to control exercise equipment is unmatched among the existing ISS exercise devices. As a motorized device, MED-2 technology can provide a customizable force profile that can be varied as a function of strap displacement, strap velocity or a combination of these and other variables. During 2017, JSC/ER developed and flight-certified a resistive exercise algorithm that mimics the 1-G inertial effects of free-weights and enables adjustable eccentric-to-concentric loading ratios. Subsequent development will explore varying the load profiles and incorporating additional exercises beyond the current list of certified movements

Family-specific, novel, deleterious germline variants provide a rich resource to identify genetic predispositions for BRCAx familial breast cancer

BACKGROUND: Genetic predisposition is the primary risk factor for familial breast cancer. For the majority of familial breast cancer, however, the genetic predispositions remain unknown. All newly identified predispositions occur rarely in disease population, and the unknown genetic predispositions are estimated to reach up to total thousands. Family unit is the basic structure of genetics. Because it is an autosomal dominant disease, individuals with a history of familial breast cancer must carry the same genetic predisposition across generations. Therefore, focusing on the cases in lineages of familial breast cancer, rather than pooled cases in disease population, is expected to provide high probability to identify the genetic predisposition for each family. METHODS: In this study, we tested genetic predispositions by analyzing the family-specific variants in familial breast cancer. Using exome sequencing, we analyzed three families and 22 probands with BRCAx (BRCA-negative) familial breast cancer. RESULTS: We observed the presence of family-specific, novel, deleterious germline variants in each family. Of the germline variants identified, many were shared between the disease-affected family members of the same family but not found in different families, which have their own specific variants. Certain variants are putative deleterious genetic predispositions damaging functionally important genes involved in DNA replication and damaging repair, tumor suppression, signal transduction, and phosphorylation. CONCLUSIONS: Our study demonstrates that the predispositions for many BRCAx familial breast cancer families can lie in each disease family. The application of a family-focused approach has the potential to detect many new predispositions

Relation between cathodoluminescence and trace-element distribution of magmatic topaz from the Ary-Bulak massif, Russia

In order to define the cathodoluminescence (CL) properties of magmatic topaz and its relation with traceelement composition, we studied topaz phenocrysts from the Ary-Bulak ongonite massif, Russia using a wide array of analytical techniques. Scanning electron microscopy CL panchromatic images reveal strong variations, which define micrometre-scale euhedral growth textures. Several truncations of these growth textures occur in single grains implying multiple growth and resorption events. The CL spectra of both CLbright and -dark domains have a major peak in the near-ultraviolet centred at 393 nm. Cathodoluminescence images taken after several minutes of electron bombardment show decreasing emission intensity. Electron microprobe analyses indicate high F concentrations (average OH/(OH + F) = 0.04 calculated by difference, 100 wt.% – total from electron probe microanalyses), consistent with what has been found previously in topaz-bearing granites, and the OH stretching vibration (~3653 cm-1) was detected in Raman spectra. Laser ablation inductively-coupled plasma mass spectrometry traverses performed across the CL textures detected trace elements at ppm to thousands of ppm levels, including: Fe, Mn, Li, Be, B, P, Nb, Ta, W, Ti, Ga, light rare-earth elements, Th and U. Lithium,W, Nb and Ta appear to be correlated with CL intensity, suggesting a role for some of these elements in the activation of CL in topaz. In contrast, no clear correlation was found between CL intensity and F contents, despite the fact that the replacement of OH for F is known to affect the cell parameters of topaz

Quiet Supersonic Flights 2018 (QSF18) Test: Galveston, Texas Risk Reduction for Future Community Testing with a Low-Boom Flight Demonstration Vehicle

The Quiet Supersonic Flights 2018 (QSF18) Program was designed to develop tools and methods for demonstration of overland supersonic flight with an acceptable sonic boom, and collect a large dataset of responses from a representative sample of the population. Phase 1 provided the basis for a low amplitude sonic boom testing in six different climate regions that will enable international regulatory agencies to draft a noise-based standard for certifying civilian supersonic overland flight. Phase 2 successfully executed a large scale test in Galveston, Texas, developed well documented data sets, calculated dose response relationships, yielded lessons, and identified future risk reduction activities

Geologic history of Martian regolith breccia Northwest Africa 7034: Evidence for hydrothermal activity and lithologic diversity in the Martian crust

The timing and mode of deposition for Martian regolith breccia Northwest Africa (NWA) 7034 were determined by combining petrography, shape analysis, and thermochronology. NWA 7034 is composed of igneous, impact, and brecciated clasts within a thermally annealed submicron matrix of pulverized crustal rocks and devitrified impact/volcanic glass. The brecciated clasts are likely lithified portions of Martian regolith with some evidence of past hydrothermal activity. Represented lithologies are primarily ancient crustal materials with crystallization ages as old as 4.4 Ga. One ancient zircon was hosted by an alkali-rich basalt clast, confirming that alkalic volcanism occurred on Mars very early. NWA 7034 is composed of fragmented particles that do not exhibit evidence of having undergone bed load transport by wind or water. The clast size distribution is similar to terrestrial pyroclastic deposits. We infer that the clasts were deposited by atmospheric rainout subsequent to a pyroclastic eruption(s) and/or impact event(s), although the ancient ages of igneous components favor mobilization by impact(s). Despite ancient components, the breccia has undergone a single pervasive thermal event at 500–800°C, evident by groundmass texture and concordance of ~1.5 Ga dates for bulk rock K-Ar, U-Pb in apatite, and U-Pb in metamict zircons. The 1.5 Ga age is likely a thermal event that coincides with rainout/breccia lithification. We infer that the episodic process of regolith lithification dominated sedimentary processes during the Amazonian Epoch. The absence of pre-Amazonian high-temperature metamorphic events recorded in ancient zircons indicates source domains of static southern highland crust punctuated by episodic impact modification

Ablative therapy for people with localised prostate cancer : a systematic review and economic evaluation

The research reported in this issue of the journal was funded by the HTA programme as project number 10/136/01. The contractual start date was in April 2012. The draft report began editorial review in October 2013 and was accepted for publication in April 2014. The authors have been wholly responsible for all data collection, analysis and interpretation, and for writing up their work. The HTA editors and publisher have tried to ensure the accuracy of the authors’ report and would like to thank the reviewers for their constructive comments on the draft document. However, they do not accept liability for damages or losses arising from material published in this report. Acknowledgements We thank l the people recruited from the local UCAN for providing valuable consumer insight and advice through their participation as members of the project focus group: - Mark Emberton (Professor of Interventional Oncology), Damian Greene (consultant urologist), Axel Heidenreich (Professor and Director of Department of Urology), Christoph von Klot (specialist in brachytherapy), Roger Kockelbergh (BAUS chairman and Clinical Director of Urology) and Axel Merserburger (Deputy Clinical Director of Urology and Urologic Oncology) for providing their clinical expertise as members of the project advisory group - Edgar Paez (consultant urologist) and Gill Lawrence (Head of Radiotherapy Physics) for providing a list of staff time by grade and specialty involved in EBRT - Debbie Bennett (Radiotherapy Service Manager) for providing estimates for the expected number of uses for EBRT - Ian Pedley (clinical director/clinical oncologist) and Gill Lawrence for providing a list of all resource inputs relevant to brachytherapy - Steve Locks (Consultant Clinical Scientist in Radiotherapy) for providing a list of reusable equipment and consumables used during brachytherapy, along with their unit costs - Sue Asterling (urology research nurse) and Mark Kelly (Acting Divisional General Manager – Theatres) for providing a list of all resource inputs relevant to cryotherapy - Lara Kemp for providing secretarial support. The Health Services Research Unit is core funded by the Chief Scientist Office of the Scottish Government Health Directorates.Peer reviewedPublisher PD