Series Of Reference Materials Research Articles

Abstract 445: A validated genomic reference material with known content applicable to panel assays requiring low frequency variant allele detection

Abstract Prospective and GCP testing of tumors for important somatic variants in cancer is becoming more commonplace. Currently, there is a lack of a reliable and perpetual publicly available genomic material that can be used across a wide range of genomic testing methods for assessing the potential accuracy of a given test. A great variety of the next-gen sequencing (NGS) methods and processes currently in place now or in the future will have heterogeneous genomic targets, limits of detection, input material, and cost requirements. The variety of these tests extends from small panels (targeting 10 or more genes) to larger panels (targeting > 100 genes) to comprehensive tests (several hundred genes or WES/WGS). There is considerable variability in the sensitivity requirements of various assays with some designed to detect variant allele frequencies (VAF) of 10% or more while others wish to detect VAF < 1%. In addition, the testing itself has several layers of complexity: 1) the size and complex nature of the human genome; 2) the additional complexity of the damaged genome in cancer cells; 3) the amount and origin of the input material; and 4) the complex instruments and software algorithms necessary to proficiently perform the tests. The SEQC2 consortium has extensively evaluated and documented a pooled cell line reference material that has > 40,000 known variants with the great majority having allele frequencies < 10% in the standard pool. This effort evaluated DNA pooled from 11 cell lines, 10 of which are from distinct cancers, used for generating RNA material for the Universal Human Reference RNA (UHRR). This consortium defined ground truth (primarily SNVs, Indels) for each cell line using related and orthogonal genomic testing methods (multiple platforms, enrichment methods, and software algorithms) so that the content of various standardized admixtures and pools of the material will be known. The final results were validated by additional sequencing of the individual pools and through ddPCR testing of a large number of identified variants. The result is a series of reference materials with a large number and variety of validated variants at various VAF, suitable for a wide range of testing, including variants with VAF < 1%. These materials can be used as an ongoing reference material when developing new assays, conducting proficiency and reproducibility tests, or for quality control purposes when running regulated assays (positive and negative control variants). Citation Format: Wendell Jones, Joshua Xu, Binsheng Gong, Onco-panel Working Group of the Sequencing QualityControl Phase 2 (SEQC2) Consortium. A validated genomic reference material with known content applicable to panel assays requiring low frequency variant allele detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 445.

Determination of Rhenium in Geological Samples by Isotope Dilution–Multicollector–Inductively Coupled Plasma-Mass Spectrometry with Novel Chromatographic Separation

ABSTRACTA method was developed to determine rhenium contents in geological samples using multicollector–inductively coupled plasma-mass spectrometry (MC–ICP-MS) and extraction with an ion-exchange resin. Samples were digested in Carius tubes and osmium was converted into volatile OsO4, which was purified by distillation and microdistillation. The purified Os contents and isotopic ratios were determined using negative thermal ionization mass spectrometry. After the distillation of Os, the samples were treated with HF, then 1.2 M HCl, and loaded on ion-exchange resin columns. Re was eluted using 0.75 M HNO3 and directly determined by MC–ICP-MS. This method was validated using a series of reference materials and the analytical Re data are consistent with the literature values. This method precision (relative standard deviation) ranged from 0.8 to 6%. The procedural blank and detection limit (3σ) of Re were 1.1 pg and 0.5 pg/g (for a sample size of 2g), respectively. These results indicate that the proposed method can be applied to determine trace Re in geological samples. Using Carius tube digestion combined with HF desilicification and redissolution, the Re and Os contents found in the soluble and insoluble phases of several reference materials indicated that the distributions of Re and Os were homogeneous and heterogeneous, respectively.

Development of a WD-XRF analysis method of minor and trace elements in liquid petroleum products

This paper describes a methodology for the analysis of minor and trace elements in liquid petroleum products, with varying oxygen content between 0% w/w and 3.4% w/w and varying C/H ratio between 7 and 9, by wavelength-dispersive X-ray fluorescence (WD-XRF) spectrometry, necessary to determine the properties that indicate the function and performance of the product in service.There are a number of standard methods of chemical analysis by WD-XRF, atomic absorption spectrophotometry (AAS) or inductively coupled plasma atomic emission spectrometry (ICP-OES) that apply to one type of petroleum product. However, there is not a standard that applies to any kind of liquid petroleum products in a huge range of concentrations with low detection limits and uncertainties, that allow to control a great number of products in a huge range of concentrations of an elevate number of elements.In order to obtained a rapid an accurate methodology that allows the analysis of different materials in a huge range of concentrations, a WD-XRF method of measuring a set of elements: Al, Ba, Ca, Cr, Cu, Fe, Mg, Mn, Ni, P, Pb, S, Si, Ti, V and Zn, in a series of liquid petroleum products was developed being fine-tuned by optimising the measurement conditions and calculating the detection and quantification limits. The validation was carried out by using a series of reference materials and the uncertainty of the method was calculated.The analysis of sulphur was also performed by elemental analysis in addition to WD-XRF and the results obtained by both techniques were compared. The matrix of the different samples analysed and the standards used was also analysed by determining C, H, N and O.

Development and Application of Reference Materials of Series of Copper Cathode

In accordance with the requirements of the reference materials technical specifications, refer to some countries’ existing standards of chemical composition of copper Cathode products, design the chemical composition of each reference materials. Using proper methods of batching, smelting technique and extrusion processes etc., developed a set of reference materials of copper Cathode. Determine the content of the various elements using a variety of methods by several laboratories. These samples are mainly used for the determination of Pb, Fe, Bi, Sb, As, Sn, Ni,, Zn, P, S in copper cathode and parts of copper by photoelectric direct reading spectrometry, plasma spectroscopy and various methods of chemical analysis, these samples can also act as control samples for the control analysis of the relevant elements separately. The series of reference materials have advantages of accurate value, good uniformity and precision and linear, more reasonable distribution of elements.

Analysis of lignin-derived phenols in standard reference materials and ocean dissolved organic matter by gas chromatography/tandem mass spectrometry

A series of reference materials are proposed for intercomparison and quality control purposes during the quantification of lignin oxidation products (LOP) from diverse environmental matrices. These materials are all easily accessible and certified for diverse organic constituents (NIST and IHSS). They represent a suite of natural environmental matrices (from solids to aqueous) and are characterized by a wide range of organic carbon and lignin concentrations with abundant proportions of all major LOP. The variability of LOP concentrations and signatures for all these materials averages 3–5% and does not exceed 10%. Using these standards, a new quantification method was developed and validated for the determination of low-level CuO oxidation products using capillary gas chromatography–tandem mass spectrometry (GC/MS–MS). Tandem mass spectrometry provides both the high sensitivity and selectivity required for the identification and quantification of trace levels of dissolved lignin. The method is particularly useful for removing interference from co-eluting isotopes generated from the DOM matrix and during glucose amendment procedures of low-carbon samples. Such glucose amendment is not necessary, however, when the CuO to organic carbon weight-to-weight ratio can be kept at a value < 200–300.

Fundamental parameters analysis of RoHS elements in plastics

European Community Directive 2002∕95∕EC restricts the use of certain hazardous substances in electrical and electronic equipment. In particular, restrictions are placed on lead, mercury, cadmium, hexavalent chromium, and bromine (in polybrominated biphenyls or polybrominated diphenyl ethers). XRF is a convenient method for detecting the presence and measuring the amounts of these elements. Reliably quantifying all of these elements in plastics typically requires a large number of standards that are not yet readily available. Because of the light element matrix, using a “standardless” fundamental parameters method requires some reliance on the primary beam scatter, complicating the analysis algorithm and increasing the uncertainty. We have tested a simplified fundamental parameters method that determines the matrix via difference, requiring only one standard. The method was tested on a series of reference materials containing all of the regulated elements in a variety of plastic resins. One multi-element reference standard was used. It was necessary to include all of the additives in the specimens to achieve good quantitative accuracy. In addition, the scattered primary intensity was used in one set of tests to compensate for variations in specimen thickness. This thickness compensation was necessary to get acceptable results for Cd. Results were very promising, with average relative errors and relative standard deviations of about 10%.

Methodology and Application of GC‐MS to Study Altered Organic Binding Media from Objects of the Kunsthistorisches Museum, Vienna

Within the Kunsthistorisches Museum (KHM), Vienna, three off-line GC-MS analytical procedures for the identification of natural organic media have been refined, tested, and validated on a series of reference materials (partly artificially aged) to apply this knowledge for investigations of original, historic works of art from the museum's collections. At first, a set of artificially aged mockups has been prepared and a reference database has been built up for the identification of drying oils, resins, waxes, proteins and polysaccharides. Some interesting observations concerning the alteration of the composition of these organic media during different ageing steps are presented in the following text. In addition, some selected examples for the application of the refined techniques for the analysis of real samples from various museum objects are shown.

BCR certified reference materials for reactor neutron dosimetry

A series of reference materials intended for use as activation or fission monitors for neutron fluence rate measurements has been prepared by the Joint Research Centre of the European Commission. Certification has been carried out by expert European laboratories and distribution of the certified reference materials (CRMs) is through the BCR programme of the Commission. The list (18 CRMs) includes materials to cover the complete energy spectrum, and suitable for different irradiation times. Fission monitors are 238UO2 or 237NpO2 in the form of microspheres. Activation monitors are high purity metals (Ni, Cu, Al, Fe, Nb, Rh, or Ti), certified for interfering trace impurities, or dilute aluminium-based alloys, where aluminium is chosen as a suitable matrix for reducing the neutron self-shielding effect. Newly certified materials are IRMM-530R Al-0.1%Au, replacing the exhausted IRMM-530 material, used as comparator for k0-standardization, and three new Al-Co alloys (0.01-1%Co). Two others, in the process of certification are Al-0.1%Ag and Al-2%Sc for thermal and epithermal fluence rate measurements. Other candidate reference materials currently being certified are two uranium-doped glass intended for dosimetry by the fission-track technique.

Determination of components in refractories containing zirconia by x‐ray fluorescence spectrometry

For the purpose of proposing the use of a series of reference materials (SeRMs) for x-ray fluorescence spectrometry (XRFS) of refractories containing zirconia, we examined several methods of chemical analysis, and completed two Japanese Industrial Standard (JIS) methods of analysis for zircon and/or zirconia (ZS) and alumina, zirconia and silica (AZS) and two SeRMs of Japanese Refractory Reference Materials (JRRM) (10 samples per series). Inductively coupled plasma atomic emission spectrometry and XRFS were employed for the determination of HfO2. For XRFS analysis especially, a ZrO2 HfO2 binary calibration curve is employed using synthetic standard samples (with Hf Mα as an analysis line). The compositions of both series, 3–92 mass% for ZrO2 and 0.2–46 mass% for SiO2, cover a wide range of values. A high-precision calibration curve could be produced from these SeRMs. The content of HfO2, which has rarely undergone analysis to date, was 1.6 mass% for zirconia and 1.3–1.4 mass% for zircon. These SeRMs are also registered in the Code d'Indexation des Materiaux de Reference (COMAR). Copyright © 2000 John Wiley & Sons, Ltd.

Determination of components in refractories containing zirconia by x-ray fluorescence spectrometry

For the purpose of proposing the use of a series of reference materials (SeRMs) for x-ray fluorescence spectrometry (XRFS) of refractories containing zirconia, we examined several methods of chemical analysis, and completed two Japanese Industrial Standard (JIS) methods of analysis for zircon and/or zirconia (ZS) and alumina, zirconia and silica (AZS) and two SeRMs of Japanese Refractory Reference Materials (JRRM) (10 samples per series). Inductively coupled plasma atomic emission spectrometry and XRFS were employed for the determination of HfO2. For XRFS analysis especially, a ZrO2 HfO2 binary calibration curve is employed using synthetic standard samples (with Hf Mα as an analysis line). The compositions of both series, 3–92 mass% for ZrO2 and 0.2–46 mass% for SiO2, cover a wide range of values. A high-precision calibration curve could be produced from these SeRMs. The content of HfO2, which has rarely undergone analysis to date, was 1.6 mass% for zirconia and 1.3–1.4 mass% for zircon. These SeRMs are also registered in the Code d'Indexation des Materiaux de Reference (COMAR). Copyright © 2000 John Wiley & Sons, Ltd.

Partial leaching as an aid to slurry nebulization for the analysis of soils by ICP-MS with flow injection and mixed-gas plasmas

Acid leaching (with 1 mol dm-3 HNO3) was combined with slurry nebulization in inductively coupled plasma mass spectrometry, with mixed-gas plasmas and flow injection, in an attempt to facilitate the quantitative analysis of heterogeneous materials such as soils. Matrices analyzed ranged from marine sediment to metal-contaminated soil, and were chosen for their variety in elemental composition and matrix structure. Slurries were prepared by first grinding the material to less than 3 μm in high-purity water and then diluting to 0.1% (w/v) with 1 mol dm-3 HNO3, which served as both a dispersing and a leaching agent. The resulting slurries were injected (0.25 cm3) into a deionized distilled water carrier. Under these conditions, the sensitivity was about 85% of that achieved by continuous nebulization. Multivariate optimization of the nitrogen percentage, forward torch power, and aerosol carrier gas flow rate was conducted to find conditions maintaining sensitivity constant between different slurries. Since no set of conditions was optimal for all elements, a compromise set was selected, which resulted in accurate results for La and Pb in a series of reference materials, by calibrating with aqueous standards. On the other hand, the results for V and Cr were almost systematically low, indicating that the compromise plasma conditions did not allow complete atomization/ionization of these elements.Key words: inductively coupled plasma mass spectrometry, slurry nebulization, flow injection, mixed-gas plasma.

Partial leaching as an aid to slurry nebulization for the analysis of soils by ICP-MS with flow injection and mixed-gas plasmas

Acid leaching (with 1 mol dm-3 HNO3) was combined with slurry nebulization in inductively coupled plasma mass spectrometry, with mixed-gas plasmas and flow injection, in an attempt to facilitate the quantitative analysis of heterogeneous materials such as soils. Matrices analyzed ranged from marine sediment to metal-contaminated soil, and were chosen for their variety in elemental composition and matrix structure. Slurries were prepared by first grinding the material to less than 3 μm in high-purity water and then diluting to 0.1% (w/v) with 1 mol dm-3 HNO3, which served as both a dispersing and a leaching agent. The resulting slurries were injected (0.25 cm3) into a deionized distilled water carrier. Under these conditions, the sensitivity was about 85% of that achieved by continuous nebulization. Multivariate optimization of the nitrogen percentage, forward torch power, and aerosol carrier gas flow rate was conducted to find conditions maintaining sensitivity constant between different slurries. Since no set of conditions was optimal for all elements, a compromise set was selected, which resulted in accurate results for La and Pb in a series of reference materials, by calibrating with aqueous standards. On the other hand, the results for V and Cr were almost systematically low, indicating that the compromise plasma conditions did not allow complete atomization/ionization of these elements.Key words: inductively coupled plasma mass spectrometry, slurry nebulization, flow injection, mixed-gas plasma.

Interlaboratory study to improve the quality of trace element determinations in groundwater†

In order to control the quality of trace element determinations in groundwater, the Standards, Measurements and Testing Programme (formerly BCR) of the European Commission has started a project of which the final aim is to certify groundwater reference materials for their contents of a range of trace elements (Al, As, Br, Cd, Cu, I, Ni and Pb). The first part of this project consisted of an interlaboratory study which aimed to test the feasibility of preparation of candidate groundwater reference materials and to detect and remove most of the pitfalls observed in trace element determinations. This paper presents the main results of this interlaboratory study carried out prior to the certification campaign of a series of reference materials.