Quality control and quantification in IG/TR next-generation sequencing marker identification: protocols and bioinformatic functionalities by EuroClonality-NGS

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Quality control and quantification in IG/TR next-generation sequencing marker identification: protocols and bioinformatic functionalities by EuroClonality-NGS

Assessment of clonality, marker identification and measurement of minimal residual disease (MRD) of immunoglobulin (IG) and T cell receptor (TR) gene rearrangements in lymphoid neoplasms using next-generation sequencing (NGS) is currently under intensive development for use in clinical diagnostics. So far, however, there is a lack of suitable quality control (QC) options with regard to standardisation and quality metrics to ensure robust clinical application of such approaches. The EuroClonality-NGS Working Group has therefore established two types of QCs to accompany the NGS-based IG/TR assays. First, a central polytarget QC (cPT-QC) is used to monitor the primer performance of each of the EuroClonality multiplex NGS assays; second, a standardised human cell line-based DNA control is spiked into each patient DNA sample to work as a central in-tube QC and calibrator for MRD quantification (cIT-QC). Having integrated those two reference standards in the ARResT/Interrogate bioinformatic platform, EuroClonality-NGS provides a complete protocol for standardised IG/TR gene rearrangement analysis by NGS with high reproducibility, accuracy and precision for valid marker identification and quantification in diagnostics of lymphoid malignancies.This work was supported by Ministry of Health of the Czech Republic, grant no. 16-34272A; computational resources were provided by the CESNET LM2015042 and the CERIT Scientific Cloud LM2015085, provided under the programme “Projects of Large Research, Development, and Innovations Infrastructures”. Analyses in Prague (JT, EF and MS) were supported by Ministry of Health, Czech Republic, grant no. 00064203, and by PRIMUS/17/MED/11. Analyses in the Monza (Centro Ricerca Tettamanti, SS, AG and GC) laboratory were supported by the Italian Association for Cancer Research (AIRC) and Comitato Maria Letizia Verga

Detection of Rare Earth Elements (REEs) in mine waste applying destructive and spectral techniques: a chance to overcome the rising worldwide REEs demand?

he increasing demand of Rare Earth Elements (REE) in the industry and their economic relevance plays a crucial role in the mining exploration. In order to cover the worldwide demand unconventional deposits such as dumps and tailings from abandoned mines are being considered as a new source to recover REE bearing minerals. Purwadi et al. (2018) have investigated the concentration and visible and near-infrared reflectance spectroscopy of REEs-bearing tailings of a closed tin mine located on the Bangka Island (Indonesia) but detected no REEs bearing minerals due to their low abundance (<1wt.%). Our study investigates the sediments (quartz rich tailings) from this tin mine by means of Electron Microprobe (EMP). The measurements on 12 tailing samples have shown the occurrence of zircon ZrSiO4 and abundant REE bearing minerals such as monazite (Ce,La)PO4 , xenotime YPO4 , thorite (Th,U)SiO4, and uranite UO2. REEs bearing phases occur in quartz or at the grain boundaries, are approximately 5 to 50 μ large, and form relatively fresh (poorly altered) un-to subhedral grains providing suitable surfaces for EMP point analyses. Plotting the concentration of the REEs of monazite and xenotime in the chondrite normalized diagram they show the typical monazite decreasing and xenotime increasing pattern with no obvious anomaly. Chemically monazites are characterized by high thorium (up to 18% ThO - mainly as huttonite component) and very high yttrium and xenotime component (up to 3.5 wt. % Y2O3) indicating a high monazite formation temperature. More analyses including ICP-OES on selected samples are planned in the near future to investigate REE distribution in these type of deposits e.g. depleting and or enrichment triggered by fluids, weathering and alteration. The integration of spectral techniques and mineralogical-chemical investigations such as EMP and ICP-OES should play a crucial role in the future to characterize dumps, for the recovery of REEs and their signature in the deposits leading to a sustainable and economical extraction

Rare Earth Elements (REEs) in mine waste: a way to solve the rising worldwide REEs demand?

The increasing demand of Rare Earth Elements (REE) in the industry and their economic importance plays a crucial role in the mining exploration. More knowledge on unconventional deposits such as dumps and tailings should be gathered to recover REEs. Purwadi et al. (2018) studied the concentration and visible and near-infrared reflectance spectroscopy of REEs-bearing tailings of a closed tin mine located on the Bangka Island (Indonesia) but detected no REEs bearing minerals due to their low abundance (<1wt.%). Our study investigates quartz rich tailings from this tin mine by means of Electron Microprobe (EMP). The measurements on 12 samples have shown the occurrence of zircon ZrSiO4 and abundant REE bearing minerals such as monazite (Ce,La)PO4, xenotime YPO4, thorite (Th,U)SiO4, and uranite UO2. REEs bearing phases occur in quartz or at the grain boundaries, are approximately 5 to 50 µ large, and form relatively fresh (poorly altered) un-to subhedral grains suitable for EMP point analyses. Plotting the concentration of the monazite and xenotime REEs in the chondrite normalized diagram they show the typical monazite decreasing and xenotime increasing pattern with no obvious anomaly. Chemically monazites are characterized by high thorium (up to 18% ThO - mainly as huttonite component) and very high yttrium and xenotime component (up to 3.5 wt. % Y2O3) indicating a high monazite formation temperature. Additional ICP-OES analyses, elemental mappings and in situ dating on monazite, will show the REEs distribution, e.g. depleting and or enrichment triggered by fluids, and the geochemical signature of these tailings

Geothermal exploration in Indonesia based on Mineralogy and Hydrothermal Alteration

Indonesia with its large, but partially unexplored geothermal potential is one of the most interesting and suitable places in the world to conduct geothermal exploration research. This study focuses on geothermal exploration based on fluid-rock geochemistry/geomechanics and aims to compile an overview on geochemical data-rock properties from important geothermal fields in Indonesia. The research carried out in the field and in the laboratory is performed in the framework of the GEOCAP cooperation (Geothermal Capacity Building program Indonesia- the Netherlands). The application of petrology and geochemistry accounts to a better understanding of areas where operating power plants exist but also helps in the initial exploration stage of green areas. Because of their relevance and geological setting geothermal fields in Java (Wayang Windu, Tanguban Perahu) have been visited so far. Mount Salak, Gunung Slamet (Java) and Flores surveys are planned in the near future. Operators, universities and governmental agencies will benefit from this approach as it will be applied also to new green-field terrains. By comparing the characteristics of the fluids, the alteration petrology and the rock geochemistry we also aim to compile an overview of the geochemistry of several geothermal fields in Indonesia. The gathering of this information is the base for the geomechanical experiments on-going at TUD. At the same time the rock petrology and fluid geochemistry will be used as input data to model the reservoir fluid composition along with TP parameters with the geochemical workbench PHREEQC. The field and laboratory data are mandatory for both the implementation and validation of the model results. If successful, this approach can be applied in many geothermal fields characterized by steep terrain and tropical vegetation, which hampers the classical seismic-geophysical exploration methods