Identification and optimization of parameters for accurate quantification of RNA by RT-dPCR.

Reverse transcription-digital PCR (RT-dPCR) is attracting attention as a method that enables SI-traceable RNA quantification without calibration, but its accuracy and bias have not been thoroughly studied. In this study, the accurate quantification of RNA by the RT-dPCR method was investigated using NMIJ CRM 6204-b, an RNA certified reference material whose certified value was assigned by orthogonal chemical measurement methods. Moreover, a two-step RT-dPCR method was adopted to examine in detail the conditions for the RT reaction process, which was expected to be the major uncertainty component in the RT-dPCR measurement. Optimization experiments revealed that the type of reverse transcriptase, the concentration of template RNA, and the type and concentration of primers in the RT reaction affected the value quantified by RT-dPCR. Under the optimal conditions, the value quantified by RT-dPCR, 76.4 ng/µL ± 6.7 ng/µï»¿L (the quantified value ± expanded uncertainty (k = 2)), was consistent with the certified value, 68.2 ng/µï»¿L ± 5.8 ng/µï»¿L, of NMIJ CRM 6204-b RNA 1000-A within the expanded uncertainty. From the results of the uncertainty evaluation, the relative combined uncertainty of the RT-dPCR method was 4.42%, and the major uncertainty components in the RT-dPCR method were the preparation of RT solution (3.68%), the inter-day difference (1.80%), and the RT reaction (1.30%). Together, the results suggested that the contribution of the RT reaction process to the total uncertainty was greater than that of the dPCR process.

Limited frequency of malignant change in lobular endocervical glandular hyperplasia.

INTRODUCTION: Although lobular endocervical glandular hyperplasia is a benign disorder of the uterine cervix, its potential as a precursor of minimal deviation adenocarcinoma has been reported. However, the natural history of the disease and the frequency of malignant change are not fully understood. We evaluated the frequency of malignant change of clinical lobular endocervical glandular hyperplasia and explored useful parameters indicating malignant change. METHODS: The clinical courses of 175 patients with cervical multi-cystic lesions who visited Shinshu University Hospital between June 1995 and June 2019 were retrospectively analyzed. We examined the results of follow-up and outcomes of the patients diagnosed with lobular endocervical glandular hyperplasia and investigated the frequency of malignant transformation. RESULTS: Of the 175 patients, 15, 84, and 76 were clinically diagnosed with suspected malignancy, suspected lobular endocervical glandular hyperplasia, and suspected nabothian cyst, respectively. Of these patients, 69 patients with suspected lobular endocervical glandular hyperplasia were followed, and 12 underwent hysterectomy after a mean follow-up of 57.1 (range: 3-154) months due to lesion enlargement (increase in tumor diameter of >20%) and/or worsening cytology. Of these 12 patients, two had lobular endocervical glandular hyperplasia with atypia and one had minimal deviation adenocarcinoma. Of 69 patients, the rate of malignant change was 1.4% (1/69). The growth rates of the lesions for these three patients during follow-up were significantly higher than those of nine patients who underwent surgery with lobular endocervical glandular hyperplasia without atypia and 48 follow-up cases of suspected lobular endocervical glandular hyperplasia. The cut-off value of the growth rate suggesting malignant transformation was 38.1% (84.6% sensitivity and 100% specificity). Tumor size and cytology did not change in the remaining 57 cases continuing follow-up. CONCLUSION: An increase in tumor size and worsening cytology are important parameters for detecting malignant transformation of lobular endocervical glandular hyperplasia during follow-up. However, the frequency of malignant change of this disease may be limited. These results suggest that conservative management may be an option for clinical lobular endocervical glandular hyperplasia.

Proficiency testing by the National Metrology Institute of Japan for quantification of pesticide residues in grain samples from 2012 to 2018.

From 2012 to 2018, proficiency testings (PTs) were carried out to support the analytical skill development of participants. Grains were sprayed with various target pesticides and used as material samples for PTs. It was found that 27-56% and 10-43% of participants used the Japanese official multiresidue method and a solid-phase extraction technique with the Quick, Easy, Cheap, Effective, Rugged, and Safe (modified QuEChERS, known as "STQ" in Japan) method, respectively. Reported results were evaluated using two types of z-scores: one was based on consensus values calculated from the analytical results reported by the participants, and the other was based on values obtained by the National Metrology Institute of Japan (NMIJ). Acceptable z-scores based on the consensus values and NMIJ reference values were achieved by 78-95% and 67-94% of the participants, respectively. Many laboratories improved their z-scores by continuing participation in our PT.

Whole-exome sequencing of lobular endocervical glandular hyperplasia.

Lobular endocervical glandular hyperplasia (LEGH) was first reported as a benign proliferative disorder of the uterine cervix. However, it currently remains unclear whether it has the biological characteristics of pyloric metaplasia or precursor of minimal deviation adenocarcinoma (MDA)/gastric-type mucinous cervical adenocarcinoma (GAS). Therefore, in the present study we performed whole-exome sequencing on three cases of LEGH collected by laser-microdissection from the frozen tissue sections of surgically removed uteri. Analysis of the results identified 50 somatic variants. After several filtering processes, we identified 13 functional variants, including 12 missense and one insertion-deletion variants. Of these mutations, keratinocyte proline-rich protein, olfactory receptor M4 and zinc finger protein 645 mutations were found in the Catalogue Of Somatic Mutations In Cancer but were not related to carcinogenic diseases. We did not detect any significant copy number alterations or signatures. Although this was a limited case series, we did not identify any variants relevant to the tumorigenesis of LEGH to MDA/GAS, suggesting a metaplastic aspect of LEGH.

Certification and stability assessment of recombinant human growth hormone as a certified reference material for protein quantification.

A certified reference material (CRM) for the quantification of protein, essential to manage quality control and quality assurance in protein-related works, has been developed. Amino acid analysis with conventional acid hydrolysis and isotope dilution HPLC-MS was used to establish an SI-traceable absolute protein quantification method using recombinant human growth hormone (hGH) as a model protein. The certification method was verified by comparative studies between 1) different methods of protein quantification based on microwave-assisted hydrolysis, and 2) different labs as part of the Asian Collaboration on Reference Material project with Japan, China, and Korea. Certification, evaluation of measurement uncertainty, homogeneity testing, and stability testing were carried out, after which the candidate CRM for hGH quantification was successfully certified with excellent agreement within the certified value in the two comparative studies. Although the quantification value of hGH by amino acid analysis showed good robustness in various conditions, results of intact protein analysis showed degradation profiles in temperatures higher than 4 °C. Consequently, storage and dissemination conditions should be set in accordance with stability tests. Based on the results, this method is believed to be suitable for accurate quantification of hGH. Additionally, it can also be used as a guide to preparation of CRM, and instructions for quality management of protein work for other similar proteins.

Development of certified reference material NMIJ CRM 6205-a for the validation of DNA quantification methods: accurate mass concentrations of 600-bp DNA solutions having artificial sequences.

Two 600-bp DNA solutions (DNA600-G and DNA600-T) were developed as certified reference material, NMIJ CRM 6205-a, for the validation of DNA quantification methods. Both DNA600-G and DNA600-T are ideal as "spike-in control" because these materials have artificial nucleic acid sequences. The certified values were determined as the mass concentration of total DNA (whole DNA materials in sample solution regardless of sequence) at 25 °C by formic acid hydrolysis/liquid chromatography-isotope dilution mass spectrometry (LC-IDMS) and inductively coupled plasma-mass spectrometry (ICP-MS) based on the amount of phosphorus. DNAs were synthesized, and plasmids including the synthesized DNAs were cloned into Escherichia coli DH5α. The amplified plasmids were digested with a restriction enzyme and highly purified. Then, the purified DNAs were diluted with water to approximately 1 ng/µL. By using the CRM-validated methods in fields where DNA quantification is required, the reliability of DNA quantification could be improved. Graphical abstract.

Characterization of scallop midgut gland certified reference material for quantification of diarrhetic shellfish toxins.

A scallop midgut gland certified reference material, NMIJ CRM 7520-a, was developed for validation and quality assurance during the inspection of shellfish for diarrhetic shellfish toxins. The candidate material was prepared by using naturally-toxic and nontoxic boiled midgut glands spiked with okadaic acid (OA). The homogeneity and stability of the material were found to be appropriate. For the characterization of OA and dinophysistoxin-1 (DTX1), nine participants were involved in a co-laboratory study based on the Japanese Official Testing Method, where the compounds were assayed by liquid chromatography-tandem mass spectrometry following alkaline hydrolysis. The analytical values were obtained by the standard addition method with a standard spiking solution calibrated using the standard-solution certified reference materials OA and DTX1. The certified concentrations with expanded uncertainties (coverage factor k = 2, approximate 95% confidence interval) were determined to be (0.205 ±â€¯0.061) mg/kg for OA and (0.45 ±â€¯0.11) mg/kg for DTX1.

Amino Acid Analysis by Hydrophilic Interaction Chromatography Coupled with Isotope Dilution Mass Spectrometry.

Here, we describe an amino acid analysis that is based on the use of hydrophilic interaction liquid chromatography coupled with isotope dilution mass spectrometry for the accurate quantification of underivatized amino acids from hydrolyzed peptide/protein. Twelve underivatized amino acids were separated and detected during an 88-min runtime. The absolute limits of detection and limits of quantification (on column) of the four amino acids (isoleucine, phenylalanine, proline, and valine) were in the range of 6-80 and 20-200 fmol, respectively. As little as 25 pmol of peptide or protein hydrolysate is sufficient for determining absolute content.

Evaluation of the impact of matrix effects in LC/MS measurement on the accurate quantification of neonicotinoid pesticides in food by isotope-dilution mass spectrometry.

The use of isotope-labeled internal standards is the most widely accepted approach to overcome the matrix effects on quantification of pesticides in food by LC/MS. We evaluated the impact of the matrix effects on quantification of six neonicotinoid pesticides, acetamiprid, clothianidin, dinotefuran, imidacloprid, thiacloprid, and thiamethoxam, in food by using deuterated internal standards. The calibration curves for each pesticide were obtained by using matrix-free and matrix-matched calibration solutions with blank brown rice, carrot, and green onion extracts. For brown rice and carrot, the matrix effects were not observed. In contrast, the slopes of calibration curves for each pesticide were influenced by presence of green onion extracts in calibration solutions (variability of the slopes was 4-9%), because the ratios of peak area for native pesticide to those for internal standards were influenced by matrix. The spike-and-recovery test with green onion was also performed. The analytical values obtained by using matrix-free calibration solution were biased from the spiked concentration, whereas those obtained by using matrix-matched calibration solution were comparable to the spiked concentration. These results indicate that matrix-matched calibration solution should be used for accurate quantification of neonicotinoid pesticides in food by LC/MS using deuterated internal standards.

Interlaboratory comparison of liquid chromatography-tandem mass spectrometry quantification of diarrhetic shellfish toxins in scallop midgut glands.

An interlaboratory comparison (ILC) was organized as a measure of the analytical competency in the liquid chromatography-tandem mass spectrometry quantification of okadaic acid (OA) and dinophysistoxin-1 (DTX1) in scallop midgut gland samples. The test sample was prepared using boiled midgut glands of naturally contaminated scallops with DTX1 and its esters by spiking with OA, and homogeneity and stability of this test sample was assessed to be appropriate. Twenty laboratories participated in the ILC based on the Japanese official testing method; they submitted two sets of analytical concentrations of target analytes along with the details of their analytical protocols. For assessing these data, assigned values were established from another ILC where ten participants quantified the target analytes by the standard addition method. The mean analytical results of the former ILC showed good agreement with the assigned values, and the corresponding relative reproducibility standard deviations met the criterion of CODEX STAN 292. Meanwhile, the results of more than half of the participants were out of the uncertainty range of the assigned values; these participants were encouraged to investigate their protocols to improve their analytical capability.

Effects of the pH and Concentration on the Stability of Standard Solutions of Proteinogenic Amino Acid Mixtures.

To prepare metrologically traceable amino acid mixed standard solutions, it is necessary to determine the stability of each amino acid present in the mixed solutions. In the present study, we prepared amino acid mixed solutions using certified reference standards of 17 proteinogenic amino acids, and examined the stability of each of these amino acids in 0.1 N HCl. We found that the concentration of glutamic acid decreased significantly during storage. LC/MS analysis indicated that the instability of glutamic acid was due to the partial degradation of glutamic acid to pyroglutamic acid in 0.1 N HCl. Using accelerated degradation tests, we investigated several solvent compositions to improve the stability of glutamic acid in amino acid mixed solution, and determined that the change of the pH by diluting the mixed solution improved the stability of glutamic acid.

Isotope-dilution liquid chromatography-tandem mass spectrometry for sensitive quantification of human insulin in serum using derivatization-technique.

An isotope-dilution mass spectrometry (IDMS) method for measuring insulin levels in human serum was developed using C-terminal-derivatization method coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). The carboxyl groups of Glu-C-cleavage products were derivatized with 1-(2-pyrimidinyl)piperazine to increase MS/MS sensitivity and IDMS quantification, resulting in increases in LC-MS/MS peak areas of derivatized Glu-C-cleavage products of human insulin by ∼23-(A5-17 peptide) to 49-fold(B14-21 peptide), respectively, as compared with results observed in the absence of derivatization. Separation was achieved on a C18 column by gradient elution at 0.3 mL/min, with a mobile phase composed of 0.1% formic acid in acetonitrile and water. Validation studies of target peptides (B1-13 peptide and B14-21 peptide) revealed a linear response in the range of 0.05 ng/mL to 10 ng/mL (regression coefficient, r2 = 0.9987 and 0.9988, respectively), a relative standard deviation within and between days of <8.6%, and spike and recovery test results indicating mean recoveries ranging from 100.2% to 106.6%. Comparison with an established commercial immunoassay showed high correlation (r2 = 0.9943 and 0.9944, B1-13 peptide and B14-21 peptide, respectively) at serum concentrations of between 0.20 ng/mL and 1.51 ng/mL. These findings suggested that this IDMS-based approach was able to quantify human serum insulin with high sensitivity and precision in the reference interval and indicated a potential for determining serum-insulin reference-measurement procedures to allow traceable measurement.

Implementing a Reference Measurement System for C-Peptide: Successes and Lessons Learned.

BACKGROUND: Assessment of endogenous insulin secretion by measuring C-peptide concentrations is widely accepted. Recent studies have shown that preservation of even small amounts of endogenous C-peptide production in patients with type 1 diabetes reduces risks for diabetic complications. Harmonization of C-peptide results will facilitate comparison of data from different research studies and later among clinical laboratory results at different sites using different assay methods. CONTENT: This review provides an overview of the general process of harmonization and standardization and the challenges encountered with implementing a reference measurement system for C-peptide. SUMMARY: Efforts to harmonize C-peptide results are described, including those by the National Institute of Diabetes and Digestive and Kidney Diseases-led C-peptide Standardization Committee in the US, activities in Japan, efforts by the National Institute for Biological Standards and Control in the UK, as well as activities led by the Bureau International des Poids et Mesures and the National Metrology Institute in China. A traceability scheme is proposed along with the next steps for implementation. Suggestions are made for better collaboration to optimize the harmonization process for other measurands.

Concentration Measurement of Amino Acid in Aqueous Solution by Quantitative 1H NMR Spectroscopy with Internal Standard Method.

We describe a procedure to determine concentrations of amino acid standard solutions by quantitative NMR spectroscopy using an internal standard. The measurement samples were prepared by solvent exchange to remove any intense solvent signal in the 1H NMR spectra. The method was demonstrated on valine aqueous solutions of different concentrations. The accuracy of the measured concentrations that fell well within the range of the expanded uncertainty is also discussed. All of the results are in good agreement with the preparation values. We believe that this approach should be useful to determine the concentrations of standard solutions whose solute components are difficult to weigh because of extremely small amount or hygroscopicity.

High transport efficiency of nanoparticles through a total-consumption sample introduction system and its beneficial application for particle size evaluation in single-particle ICP-MS.

In order to facilitate reliable and efficient determination of both the particle number concentration (PNC) and the size of nanoparticles (NPs) by single-particle ICP-MS (spICP-MS) without the need to correct for the particle transport efficiency (TE, a possible source of bias in the results), a total-consumption sample introduction system consisting of a large-bore, high-performance concentric nebulizer and a small-volume on-axis cylinder chamber was utilized. Such a system potentially permits a particle TE of 100 %, meaning that there is no need to include a particle TE correction when calculating the PNC and the NP size. When the particle TE through the sample introduction system was evaluated by comparing the frequency of sharp transient signals from the NPs in a measured NP standard of precisely known PNC to the particle frequency for a measured NP suspension, the TE for platinum NPs with a nominal diameter of 70 nm was found to be very high (i.e., 93 %), and showed satisfactory repeatability (relative standard deviation of 1.0 % for four consecutive measurements). These results indicated that employing this total consumption system allows the particle TE correction to be ignored when calculating the PNC. When the particle size was determined using a solution-standard-based calibration approach without an NP standard, the particle diameters of platinum and silver NPs with nominal diameters of 30-100 nm were found to agree well with the particle diameters determined by transmission electron microscopy, regardless of whether a correction was performed for the particle TE. Thus, applying the proposed system enables NP size to be accurately evaluated using a solution-standard-based calibration approach without the need to correct for the particle TE.

Prenatal sonographic diagnosis of fetal valproate syndrome: a case report.

BACKGROUND: Prenatal exposure of mother to valproate (VPA) causes teratogenic effects in the fetus, namely fetal valproate syndrome (FVS). We report a case of fetal valproate syndrome rarely diagnosed by prenatal sonographic examination. CASE PRESENTATION: Our patient was a female infant who was born to a 27-year-old nulliparous Japanese woman with epilepsy. The mother was diagnosed with infantile epilepsy at 1 year of age and had been using three antiepileptic drugs, including valproate, but preconceptional counseling was not performed. At 25 weeks of gestation, contracture of the fetal right wrist joint suggestive of a radial ray defect was observed by transabdominal ultrasonography. The fetus demonstrated growth retardation starting from 32 weeks of gestation. In addition, saddle nose as a facial anomaly was detected by three-dimensional ultrasound at 37 weeks of gestation. Accordingly, we suspected that the fetus had fetal valproate syndrome. At 39 weeks of gestation, the mother delivered an infant weighing 2056 g. The neonate had characteristic features of fetal valproate syndrome, such as facial configuration, slight muscular hypotonia of the whole body, breathing problems, right-hand articular contracture accompanied by radial ray defect, and cardiovascular malformation. CONCLUSIONS: When obstetricians manage epileptic pregnant women without enough preconceptional counseling or adjustment for antiepileptic drugs, careful sonographic observation of the fetus is mandatory.

Quantitative Nuclear Magnetic Resonance Spectroscopy Based on PULCON Methodology: Application to Quantification of Invaluable Marine Toxin, Okadaic Acid.

ERETIC2 (Electronic Reference To access In vivo Concentrations 2) based on PULCON (Pulse Length-based Concentration determination) methodology is a quantitative NMR (qNMR) using an external standard. The performance of the PULCON method was assessed using maleic acid (MA). Quantification of the diarrhetic shellfish toxin and okadaic acid by PULCON was successfully consistent with that obtained by a conventional internal standard method, demonstrating that the PULCON method is useful for the quantification of invaluable marine toxins without any contaminations by an internal standard.

Usefulness of a management protocol for patients with cervical multicystic lesions: A retrospective analysis of 94 cases and the significance of GNAS mutation.

AIM: The proper preoperative diagnosis and management of cervical proliferative disorders presenting with multiple cysts, including minimal deviation adenocarcinoma (MDA), lobular endocervical glandular hyperplasia (LEGH), and nabothian cyst (NC), have not been fully established. We previously proposed a management protocol comprising a diagnostic approach using cytology, magnetic resonance imaging, and gastric-type mucin and subsequent treatment. We herein evaluate the usefulness of this protocol and implications of GNAS mutations in LEGH. METHODS: The clinical courses of 94 patients with cervical multicystic lesions who visited our hospital between June 1995 and September 2014 were retrospectively analyzed. GNAS mutations were investigated in 10 LEGH, five LEGH with atypia, and two MDA cases. RESULTS: Of the 94 patients, the conditions of 10, 59, and 25 were clinically diagnosed as suspicious of MDA or carcinoma (S/O MDA-Ca), suspicious of LEGH (S/O LEGH), and NC, respectively. Ten patients each with S/O MDA-Ca and S/O LEGH underwent hysterectomy, and the correct ratio for diagnosis was 90% (18/20). Of the 42 S/O LEGH cases followed-up for more than 12 months, three showed an increase in tumor size. After hysterectomy, two were LEGH with atypia while one was NC. The GNAS mutation was detected in two cases of LEGH with atypia, one of which showed an increase in tumor size during follow-up. CONCLUSION: The management protocol we propose herein will be useful. An increase in tumor size is important to detect potentially malignant LEGH. GNAS mutations may be involved in the tumorigenesis of potentially malignant LEGH.

Formic acid hydrolysis/liquid chromatography isotope dilution mass spectrometry: An accurate method for large DNA quantification.

Liquid chromatography-isotope dilution mass spectrometry (LC-IDMS) with formic acid hydrolysis was established for the accurate quantification of λDNA. The over-decomposition of nucleobases in formic acid hydrolysis was restricted by optimizing the reaction temperature and the reaction time, and accurately corrected by using deoxynucleotides (dNMPs) and isotope-labeled dNMPs as the calibrator and the internal standard, respectively. The present method could quantify λDNA with an expanded uncertainty of 4.6% using 10fmol of λDNA. The analytical results obtained with the present method were validated by comparing with the results of phosphate-base quantification by inductively coupled plasma-mass spectrometry (ICP-MS). The results showed good agreement with each other. We conclude that the formic acid hydrolysis/LC-IDMS method can quantify λDNA accurately and is promising as the primary method for the certification of DNA as reference material.

Quantification of peptides using N-terminal isotope coding and C-terminal derivatization for sensitive analysis by micro liquid chromatography-tandem mass spectrometry.

Stable isotope-coding coupled with mass spectrometry is a popular method for quantitative proteomics and peptide quantification. However, the efficiency of the derivatization reaction at a particular functional group, especially in complex structures, can affect accuracy. Here, we present a dual functional-group derivatization of bioactive peptides followed by micro liquid chromatography-tandem mass spectrometry (LC-MS/MS). By separating the sensitivity-enhancement and isotope-coding derivatization reactions, suitable chemistries can be chosen. The peptide amino groups were reductively alkylated with acetaldehyde or acetaldehyde-d4 to afford N-alkylated products with different masses. This process is simple, quick and high-yield, and accurate comparative analysis can be achieved for the mass-differentiated peptides. Then, the carboxyl groups were derivatized with 1-(2-pyrimidinyl)piperazine to increase MS/MS sensitivity. Angiotensins I-IV, bradykinin and neurotensin were analyzed after online solid phase extraction by micro LC-MS/MS. In all instances, a greater than 17-fold increase in sensitivity was achieved, compared with the analyses of the underivatized peptides. Furthermore, the values obtained from the present method were in agreement with the result from isotope dilution quantification using isotopically labeled angiotensin I [Asp-Arg-(Val-d8 )-Tyr-Ile-His-Pro-(Phe-d8 )-His-Leu]. Copyright © 2016 John Wiley & Sons, Ltd.