Benchmarking whole exome sequencing in the German Network for Personalized Medicine

Introduction Whole Exome Sequencing (WES) has emerged as an efficient tool in clinical cancer diagnostics to broaden the scope from panel-based diagnostics to screening of all genes and enabling robust determination of complex biomarkers in a single analysis. Methods To assess concordance, six formalin-fixed paraffin-embedded (FFPE) tissue specimens and four commercial reference standards were analyzed by WES as matched tumor-normal DNA at 21 NGS centers in Germany, each employing local wet-lab and bioinformatics investigating somatic and germline variants, copy-number alteration (CNA), and different complex biomarkers. Somatic variant calling was performed in 494 diagnostically relevant cancer genes. In addition, all raw data were re-analyzed with a central bioinformatic pipeline to separate wet- and dry-lab variability. Results The mean positive percentage agreement (PPA) of somatic variant calling was 76% and positive predictive value (PPV) 89% compared a consensus list of variants found by at least five centers. Variant filtering was identified as the main cause for divergent variant calls. Adjusting filter criteria and re-analysis increased the PPA to 88% for all and 97% for clinically relevant variants. CNA calls were concordant for 82% of genomic regions. Calls of homologous recombination deficiency (HRD), tumor mutational burden (TMB), and microsatellite instability (MSI) status were concordant for 94%, 93%, and 93% respectively. Variability of CNAs and complex biomarkers did not increase considerably using the central pipeline and was hence attributed to wet-lab differences. Conclusion Continuous optimization of bioinformatic workflows and participating in round robin tests are recommend

Evaluating the value of subordinate standard spectra

The purpose of this work is to investigate if a subordinate reference spectra in addition to the main standard spectra for different atmospheric conditions can enable an intuitive and more direct comparison of solar energy components. The main criterion for the evaluations of the value of the spectra is the change of the plant components efficiency with the spectra. As the number of subordinate spectra should be as small as possible and only as high as needed the spectra is investigate for similarities. The applicability of the subordinate standard spectra and the possible improvement of quick product comparisons is tested and discussed based on time series of spectral data from five exemplary sites that are of interest for solar energy plants. These time series are created from ground measurements of broadband solar irradiance, aerosol optical depth, perceptible water vapor and other auxiliary parameters. A model to derive DNI spectra based on this input is enhanced so that also GTI can be derived. If the intuitive selection of a subordinate spectrum based only on the average atmospheric parameters for the example sites leads to more accurate estimation of the components efficiency (e.g. responsivity, absorptance, transmittance etc.), this suggests that this concept has some practical value. On the other hand, if this is not the case for some of the exemplary sites, it proofs that there are sites where this concept or at least the suggested 8 subordinate spectra are not applicable

Calibration Methods for Rotating Shadowband Irradiometers - Comparison to Calibration of Thermopile Sensors and Evaluation of Calibration Duration

Concentrated Solar Power (CSP) projects require accurate assessment and monitoring of the available direct beam resource. To this end, ground measurements on site are inexpendable. Pyrheliometers with thermopile sensors as speci�ed in [ISO 9060] are the standard instruments for �eld measurements of direct beam irradiance. During long-term deployment however, their comparatively high accuracy can only be maintained if the window through which the direct beam enters the instrument is cleaned frequently [Geuder a. Quaschning, 2006]. In the case of long-term solar resource assessments on site this can pose a problem in terms of logistics and maintenance costs. This is particularly relevant, if the measuring site is in a remote location. Rotating Shadowband Irradiometers (RSI) on the other hand have a lower accuracy to start with due to systematic errors of its photodiode sensor. However, they are less a�ected by soiling [Geuder a. Quaschning, 2006] and provide higher accuracy in long-term measuring campaigns at sites where cleaning is not possible on a daily basis. Furthermore, they are comparatively inexpensive and do not require as much additional equipment i.e. a tracking system. A solar panel is su�cient for power supply. The systematic errors of the sensor used in RSIs are caused by cosine and temperature e�ects and its spectral non-uniform responsivity. A number of correction functions can be employed to reduce these errors signi�cantly. Additionally, a thorough calibration of the sensor with application of the correction functions can further improve the quality of measurements. The calibration procedures of thermopile pyranometers and pyrheliometers are well documented in standards such as [ISO 9059], [ISO 9846] and [ISO 9847]. Because these standards are not applicable to RSIs due to their inherent characteristics speci�c calibration procedures for this type of instrument were developed by the German Aerospace Center (Deutsches Zentrum f�ur Luft- und Raumfahrt e.V., DLR). This work shall discuss the di�erences between calibration procedures for thermopile irradiometers and RSI and aspects which can be transferred from the existing standards to RSI calibration. Calibration methods developed by DLR have been successfully employed for a number of years. However, a thorough assessment of the necessary calibration duration with multiple measurements from several instruments has not been carried out before this thesis. Therefore, besides the comparison of calibration methods this work examines to which extend the RSI calibration results actuate in dependence on the duration of the calibration measuring period and furthermore provide a basis on which to choose the most suitable duration

Best Practices for Solar Irradiance Measurements with Rotating Shadowband Irradiometers

Large-scale solar plant projects require diligent solar resource assessments. For concentrating solar technologies the focus of the resource assessment lies on direct beam irradiation. Unfortunately, high accuracy irradiance data are scarcely available in regions which are attractive for solar energy applications. Satellite data can only be used in combination with ground data to estimate inter-annual variability and long-term mean values. Hence, new ground measurements have to be collected for solar plant projects. Ground measurement data usually show significantly higher accuracies than satellite derived irradiance data, when general guidelines regarding site selection and preparation, instrument selection and maintenance and data quality monitoring are respected. These best practices for Rotating Shadowband Irradiometers (RSIs) are presented in this document. Appropriate irradiance sensors for ground measurements must be selected in consideration of general surrounding conditions for equipment and maintenance to gain and maintain the necessary accuracy over the entire operation period. Thermopile instruments like pyrheliometers as specified in ISO standard 9060 [ISO9060 1990] are severely affected by soiling [Pape2009] and also require expensive and maintenance- intensive support devices such as solar trackers and power supply. Thus, the uncertainty of resource assessment with pyrheliometers depends heavily on the maintenance personnel and cannot be determined accurately in many cases. Due to their low soiling susceptibility, low power demand, and comparatively lower cost, Rotating Shadowband Irradiometers (RSI) show significant dvantages over the thermopile sensors when operated under the measurement conditions of remote weather stations. RSIs are also known as RSP (Rotating Shadowband Pyranometers) or RSR™ (Rotating Shadowband Radiometers). Here we use the notation RSI to refer to either instrument measuring irradiance by use of a rotating shadowband following the decision of the International expert group in IEA Solar Heating and Cooling Task 46, subtask B. The initially lower accuracy of RSIs, which can yield deviations of 5 to 10 % and more, is notably improved with proper calibration of the sensors and corrections of the systematic deviations of its response. Main causes of the systematic deviations are the limited spectral sensitivity and temperature dependence of the Si-photodiode commonly used in most RSIs. Besides the systematic deviations of the sensor response, a significant contribution to the measurement inaccuracy originates from the sensor calibration at the manufacturer, where no corrections are applied. For proper calibration however, the proposed corrections need yet to be considered in the calibration procedure. While well documented standards exist for the calibration of pyrheliometers and pyranometers ([ISO9059 1990], [ISO9846 1993], [ISO9847, 1992]) they cannot be applied to RSIs and no corresponding standards exist for RSIs This document contains RSI specific best practices for the following tasks: - Requirements on the selection of a location for a measurement station - Installation, operation and maintenance of a measurement station, including the case of remote sites - Documentation and quality control of the measurements - Correction of systematic errors & instrument calibration: procedure and frequency Also the performance and accuracy of RSIs are described

A Two-Stage Method for Measuring the Heliostat Offset

The conventional method of initial heliostat calibration by sequentially pointing the heliostats one by one onto a target is a very slow process. The use of unmanned airborne vehicles (UAVs) is a possible approach to developing a less time consuming procedure for the initial setup of the field control system and elimination of offset in light beam pointing. This paper presents a UAV based method for measuring the heliostat offset in two stages. The first stage, preliminary and less accurate, creates a three-dimensional model of the mirror facet corners in order to estimate the heliostat orientation. The estimated orientation from the first stage is a prerequisite for the second stage of measurement, in which the highly accurate heliostat orientation is derived from deflectometrically measuring the mirror shape. While work is still ongoing to fully implement the final steps of the second stage, the measuring principles has been demonstrated and partially validated for the first stage

Calibration methods for rotating shadowband irradiometers and optimizing the calibration duration

Resource assessment for concentrated solar power (CSP) needs accurate direct normal irradiance (DNI) measurements. An option for such measurement campaigns is the use of thoroughly calibrated rotating shadowband irradiometers (RSIs). Calibration of RSIs and Si-sensors is complex because of the inhomogeneous spectral response of these sensors and incorporates the use of several correction functions. One calibration for a given atmospheric condition and air mass might not be suitable under different conditions. This paper covers procedures and requirements of two calibration methods for the calibration of rotating shadowband irradiometers. The necessary duration of acquisition of test measurements is examined with regard to the site-specific conditions at Plataforma Solar de Almería (PSA) in Spain. Seven data sets of long-term test measurements were collected. For each data set, calibration results of varying durations were compared to its respective long-term result. Our findings show that seasonal changes of environmental conditions are causing small but noticeable fluctuation of calibration results. Calibration results within certain periods (i.e. November to January and April to May) show a higher likelihood of deviation. These effects can partially be attenuated by including more measurements from outside these periods. Consequently, the duration of calibrations at PSA can now be selected depending on the time of year in which measurements commence

Calibration methods for rotating shadowband irradiometers and optimizing the calibration duration

Resource assessment for concentrated solar power (CSP) needs accurate direct normal irradiance (DNI) measurements. An option for such measurement campaigns is the use of thoroughly calibrated rotating shadowband irradiometers (RSIs). Calibration of RSIs and Si-sensors is complex because of the inhomogeneous spectral response of these sensors and incorporates the use of several correction functions. One calibration for a given atmospheric condition and air mass might not be suitable under different conditions. This paper covers procedures and requirements of two calibration methods for the calibration of rotating shadowband irradiometers. The necessary duration of acquisition of test measurements is examined with regard to the site-specific conditions at Plataforma Solar de Almería (PSA) in Spain. Seven data sets of long-term test measurements were collected. For each data set, calibration results of varying durations were compared to its respective long-term result. Our findings show that seasonal changes of environmental conditions are causing small but noticeable fluctuation of calibration results. Calibration results within certain periods (i.e. November to January and April to May) show a higher likelihood of deviation. These effects can partially be attenuated by including more measurements from outside these periods. Consequently, the duration of calibrations at PSA can now be selected depending on the time of year in which measurements commence

Calibration methods for rotating shadowbankd irradiometers and evaluation of calibration duration

Resource assessment for Concentrated Solar Power (CSP) needs accurate Direct Normal Irradiance (DNI) measurements. An option for such measurement campaigns are Rotating Shadowband Irradiometers (RSIs) with a thorough calibration. Calibration of RSIs and Si-sensors in general is complex because of the inhomogeneous spectral response of such sensors and incorporates the use of several correction functions. A calibration for a given atmospheric condition and air mass might not work well for a different condition. This paper covers procedures and requirements for two calibration methods for the calibration of Rotating Shadowband Irradiometers. The necessary duration of acquisition of test measurements is examined in regard to the site specific conditions at Plataforma Solar de Almeria (PSA) in Spain. Data sets of several long-term calibration periods from PSA are used to evaluate the deviation of results from calibrations with varying duration from the long-term result. The findings show that seasonal changes of environmental conditions are causing small but noticeable fluctuation of calibration results. Certain periods (i.e. November to January and April to May) show a higher likelihood of particularly adverse calibration results. These effects can partially be compensated by increasing the inclusions of measurements from outside these periods