Multilaboratory Assessment of a New Reference Material for Quality Assurance of Cell-Free Tumor DNA Measurements.
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ABSTRACT:
SUBMITTER: He HJ
PROVIDER: S-EPMC6626992 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Duchenne and Becker muscular dystrophies (DMD/BMD) are allelic X-linked recessive disorders that affect approximately 1 in 3500 and 1 in 20,000 male individuals, respectively. Approximately 65% of patients with DMD have deletions, 7% to 10% have duplications, and 25% to 30% have point mutations in one or more of the 79 exons of the dystrophin gene. Most clinical genetics laboratories test for deletions, and some use technologies that can detect smaller mutations and duplications. Reference and quality control materials for DMD/BMD diagnostic and carrier genetic testing are not commercially available. To help address this need, the Centers for Disease Control and Prevention-based Genetic Testing Reference Material Coordination Program, in collaboration with members of the genetic testing and the DMD/BMD patient communities and the Coriell Cell Repositories, have characterized new and existing cell lines to create a comprehensive DMD/BMD reference material panel. Samples from 31 Coriell DMD cell lines from male probands and female carriers were analyzed using the Affymetrix SNP Array 6.0 and Multiplex Ligation-Dependent Probe Amplification (MRC-Holland BV, Amsterdam, the Netherlands), a multiplex PCR assay, and DNA sequence analysis. Identified were 16 cell lines with deletions, 9 with duplications, and 4 with point mutations distributed throughout the dystrophin gene. There were no discordant results within assay limitations. These samples are publicly available from Coriell Institute for Medical Research (Camden, NJ) and can be used for quality assurance, proficiency testing, test development, and research, and should help improve the accuracy of DMD testing.
| S-EPMC3128550 | biostudies-literature
Project description:TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies. Using only the sequenced reads and the assembly as input, we show that multiple common artifacts of de novo transcriptome assembly can be readily detected. These include chimeras, structural errors, incomplete assembly, and base errors. TransRate evaluates these errors to produce a diagnostic quality score for each contig, and these contig scores are integrated to evaluate whole assemblies. Thus, TransRate can be used for de novo assembly filtering and optimization as well as comparison of assemblies generated using different methods from the same input reads. Applying the method to a data set of 155 published de novo transcriptome assemblies, we deconstruct the contribution that assembly method, read length, read quantity, and read quality make to the accuracy of de novo transcriptome assemblies and reveal that variance in the quality of the input data explains 43% of the variance in the quality of published de novo transcriptome assemblies. Because TransRate is reference-free, it is suitable for assessment of assemblies of all types of RNA, including assemblies of long noncoding RNA, rRNA, mRNA, and mixed RNA samples.
| S-EPMC4971766 | biostudies-other
Project description:Recent long-read assemblies often exceed the quality and completeness of available reference genomes, making validation challenging. Here we present Merqury, a novel tool for reference-free assembly evaluation based on efficient k-mer set operations. By comparing k-mers in a de novo assembly to those found in unassembled high-accuracy reads, Merqury estimates base-level accuracy and completeness. For trios, Merqury can also evaluate haplotype-specific accuracy, completeness, phase block continuity, and switch errors. Multiple visualizations, such as k-mer spectrum plots, can be generated for evaluation. We demonstrate on both human and plant genomes that Merqury is a fast and robust method for assembly validation.
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Project description:RationaleThe stable carbon isotopic (δ13 C) reference material (RM) LSVEC Li2 CO3 has been found to be unsuitable for δ13 C standardization work because its δ13 C value increases with exposure to atmospheric CO2 . A new CaCO3 RM, USGS44, has been prepared to alleviate this situation.MethodsUSGS44 was prepared from 8 kg of Merck high-purity CaCO3 . Two sets of δ13 C values of USGS44 were determined. The first set of values was determined by online combustion, continuous-flow (CF) isotope-ratio mass spectrometry (IRMS) of NBS 19 CaCO3 (δ13 CVPDB = +1.95 milliurey (mUr) exactly, where mUr = 0.001 = 1‰), and LSVEC Li2 CO3 (δ13 CVPDB = -46.6 mUr exactly), and normalized to the two-anchor δ13 CVPDB-LSVEC isotope-delta scale. The second set of values was obtained by dual-inlet (DI)-IRMS of CO2 evolved by reaction of H3 PO4 with carbonates, corrected for cross contamination, and normalized to the single-anchor δ13 CVPDB scale.ResultsUSGS44 is stable and isotopically homogeneous to within 0.02 mUr in 100-μg amounts. It has a δ13 CVPDB-LSVEC value of -42.21 ± 0.05 mUr. Single-anchor δ13 CVPDB values of -42.08 ± 0.01 and -41.99 ± 0.02 mUr were determined by DI-IRMS with corrections for cross contamination.ConclusionsThe new high-purity, well-homogenized calcium carbonate isotopic reference material USGS44 is stable and has a δ13 CVPDB-LSVEC value of -42.21 ± 0.05 mUr for both EA/IRMS and DI-IRMS measurements. As a carbonate relatively depleted in 13 C, it is intended for daily use as a secondary isotopic reference material to normalize stable carbon isotope delta measurements to the δ13 CVPDB-LSVEC scale. It is useful in quantifying drift with time, determining mass-dependent isotopic fractionation (linearity correction), and adjusting isotope-ratio-scale contraction. Due to its fine grain size (smaller than 63 μm), it is not suitable as a δ18 O reference material. A δ13 CVPDB-LSVEC value of -29.99 ± 0.05 mUr was determined for NBS 22 oil.
| S-EPMC7816275 | biostudies-literature
Project description:The feasibility of the production of a reference material for pesticide residue analysis in a cucumber matrix was investigated. Cucumber was spiked at 0.075 mg/kg with each of the 15 selected pesticides (acetamiprid, azoxystrobin, carbendazim, chlorpyrifos, cypermethrin, diazinon, (α + β)-endosulfan, fenitrothion, imazalil, imidacloprid, iprodione, malathion, methomyl, tebuconazole and thiabendazole) respectively. Three different strategies were considered for processing the material, based on the physicochemical properties of the vegetable and the target pesticides. As a result, a frozen spiked slurry of fresh cucumber, a spiked freeze-dried cucumber powder and a freeze-dried cucumber powder spiked by spraying the powder were studied. The effects of processing and aspects related to the reconstitution of the material were evaluated by monitoring the pesticide levels in the three materials. Two separate analytical methods based on LC-MS/MS and GC-MS/MS were developed and validated in-house. The spiked freeze-dried cucumber powder was selected as the most feasible material and more exhaustive studies on homogeneity and stability of the pesticide residues in the matrix were carried out. The results suggested that the between-unit homogeneity was satisfactory with a sample intake of dried material as low as 0.1 g. A 9-week isochronous stability study was undertaken at -20 °C, 4 °C and 18 °C, with -70 °C designated as the reference temperature. The pesticides tested exhibited adequate stability at -20 °C during the 9-week period as well as at -70 °C for a period of 18 months. These results constitute a good basis for the development of a new candidate reference material for selected pesticides in a cucumber matrix.
| S-EPMC4383829 | biostudies-literature
Project description:PurposeTo develop and characterize an algorithm that mimics human expert visual assessment to quantitatively determine the quality of three-dimensional (3D) whole-heart MR images.Materials and methodsIn this study, 3D whole-heart cardiac MRI scans from 424 participants (average age, 57 years ± 18 [standard deviation]; 66.5% men) were used to generate an image quality assessment algorithm. A deep convolutional neural network for image quality assessment (IQ-DCNN) was designed, trained, optimized, and cross-validated on a clinical database of 324 (training set) scans. On a separate test set (100 scans), two hypotheses were tested: (a) that the algorithm can assess image quality in concordance with human expert assessment as assessed by human-machine correlation and intra- and interobserver agreement and (b) that the IQ-DCNN algorithm may be used to monitor a compressed sensing reconstruction process where image quality progressively improves. Weighted κ values, agreement and disagreement counts, and Krippendorff α reliability coefficients were reported.ResultsRegression performance of the IQ-DCNN was within the range of human intra- and interobserver agreement and in very good agreement with the human expert (R 2 = 0.78, κ = 0.67). The image quality assessment during compressed sensing reconstruction correlated with the cost function at each iteration and was successfully applied to rank the results in very good agreement with the human expert.ConclusionThe proposed IQ-DCNN was trained to mimic expert visual image quality assessment of 3D whole-heart MR images. The results from the IQ-DCNN were in good agreement with human expert reading, and the network was capable of automatically comparing different reconstructed volumes.Supplemental material is available for this article.© RSNA, 2020.
| S-EPMC8082371 | biostudies-literature
Project description:The National Drug File - Reference Terminology (NDF-RT) is a large and complex drug terminology consisting of several classification hierarchies on top of an extensive collection of drug concepts. These hierarchies provide important information about clinical drugs, e.g., their chemical ingredients, mechanisms of action, dosage form and physiological effects. Within NDF-RT such information is represented using tens of thousands of roles connecting drugs to classifications. In previous studies, we have introduced various kinds of Abstraction Networks to summarize the content and structure of terminologies in order to facilitate their visual comprehension, and support quality assurance of terminologies. However, these previous kinds of Abstraction Networks are not appropriate for summarizing the NDF-RT classification hierarchies, due to its unique structure. In this paper, we present the novel Ingredient Abstraction Network (IAbN) to summarize, visualize and support the audit of NDF-RT's Chemical Ingredients hierarchy and its associated drugs. A common theme in our quality assurance framework is to use characterizations of sets of concepts, revealed by the Abstraction Network structure, to capture concepts, the modeling of which is more complex than for other concepts. For the IAbN, we characterize drug ingredient concepts as more complex if they belong to IAbN groups with multiple parent groups. We show that such concepts have a statistically significantly higher rate of errors than a control sample and identify two especially common patterns of errors.
| S-EPMC5652327 | biostudies-literature
Project description:NIST standard reference material (SRM) 2373 was developed to improve the measurements of the HER2 gene amplification in DNA samples. SRM 2373 consists of genomic DNA extracted from five breast cancer cell lines with different amounts of amplification of the HER2 gene. The five components are derived from the human cell lines SK-BR-3, MDA-MB-231, MDA-MB-361, MDA-MB-453, and BT-474. The certified values are the ratios of the HER2 gene copy numbers to the copy numbers of selected reference genes DCK, EIF5B, RPS27A, and PMM1. The ratios were measured using quantitative polymerase chain reaction and digital PCR, methods that gave similar ratios. The five components of SRM 2373 have certified HER2 amplification ratios that range from 1.3 to 17.7. The stability and homogeneity of the reference materials were shown by repeated measurements over a period of several years. SRM 2373 is a well characterized genomic DNA reference material that can be used to improve the confidence of the measurements of HER2 gene copy number.
| S-EPMC4906140 | biostudies-literature
Project description:Comprehensive analysis of monoclonal antibody therapeutics involves an ever expanding cadre of technologies. Lifecycle-appropriate application of current and emerging techniques requires rigorous testing followed by discussion between industry and regulators in a pre-competitive space, an effort that may be facilitated by a widely available test metric. Biopharmaceutical quality materials, however, are often difficult to access and/or are protected by intellectual property rights. The NISTmAb, humanized IgG1? Reference Material 8671 (RM 8671), has been established with the intent of filling that void. The NISTmAb embodies the quality and characteristics of a typical biopharmaceutical product, is widely available to the biopharmaceutical community, and is an open innovation tool for development and dissemination of results. The NISTmAb lifecyle management plan described herein provides a hierarchical strategy for maintenance of quality over time through rigorous method qualification detailed in additional submissions in the current publication series. The NISTmAb RM 8671 is a representative monoclonal antibody material and provides a means to continually evaluate current best practices, promote innovative approaches, and inform regulatory paradigms as technology advances. Graphical abstract The NISTmAb Reference Material (RM) 8671 is intended to be an industry standard monoclonal antibody for pre-competitive harmonization of best practices and designing next generation characterization technologies for identity, quality, and stability testing.
| S-EPMC5830479 | biostudies-literature
Project description:BackgroundEvaluation of changes in tumor size from images acquired by ultrasound (US), computed tomography (CT) or magnetic resonance imaging (MRI) is a common measure of cancer chemotherapy efficacy. Tumor size measurement based on either the World Health Organization (WHO) criteria or the Response Evaluation Criteria in Solid Tumors (RECIST) is the only imaging biomarker for anti-cancer drug testing presently approved by the United States Food and Drug Administration (FDA). The aim of this paper was to design and test a quality assurance phantom with the capability of monitoring tumor size changes with multiple preclinical imaging scanners (US, CT and MRI) in order to facilitate preclinical anti-cancer drug testing.MethodsThree phantoms (Gammex/UTHSCSA Mark 1, Gammex/UTHSCSA Mark 2 and UTHSCSA multimodality tumor measurement phantom) containing tumor-simulating test objects were designed and constructed. All three phantoms were scanned in US, CT and MRI devices. The size of test objects in the phantoms was measured from the US, CT and MRI images. RECIST, WHO and volume analyses were performed.ResultsThe smaller phantom size, simplified design and better test object CT contrast of the UTHSCSA multimodality tumor measurement phantom allowed scanning of the phantom in preclinical US, CT and MRI scanners compared with only limited preclinical scanning capability of Mark 1 and Mark 2 phantoms. For all imaging modalities, RECIST and WHO errors were reduced for UTHSCSA multimodality tumor measurement phantom (≤1.69 ± 0.33%) compared with both Mark 1 (≤ -7.56 ± 6.52%) and Mark 2 (≤ 5.66 ± 1.41%) phantoms. For the UTHSCSA multimodality tumor measurement phantom, measured tumor volumes were highly correlated with NIST traceable design volumes for US (R2 = 1.000, p < 0.0001), CT (R2 = 0.9999, p < 0.0001) and MRI (R2 = 0.9998, p < 0.0001).ConclusionsThe UTHSCSA multimodality tumor measurement phantom described in this study can potentially be a useful quality assurance tool for verifying radiologic assessment of tumor size change during preclinical anti-cancer therapy testing with multiple imaging modalities.
| S-EPMC3206432 | biostudies-literature