Certified DNA Reference Materials to Compare HER2 Gene Amplification Measurements Using Next-Generation Sequencing Methods

The National Institute of Standards and Technology (NIST) Standard Reference Materials 2373 is a set of genomic DNA samples prepared from five breast cancer cell lines with certified values for the ratio of the HER2 gene copy number to the copy numbers of reference genes determined by real-time quantitative PCR and digital PCR. Targeted-amplicon, whole-exome, and whole-genome sequencing measurements were used with the reference material to compare the performance of both the laboratory steps and the bioinformatic approaches of the different methods using a range of amplification ratios. Although good reproducibility was observed in each next-generation sequencing method, slightly different HER2 copy numbers associated with platform-specific biases were obtained. This study clearly demonstrates the value of Standard Reference Materials 2373 as reference material and as a calibrator for evaluating assay performance as well as for increasing confidence in reporting HER2 amplification for clinical applications

Development of NIST standard reference material 2373: Genomic DNA standards for HER2 measurements

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

Stress and Fatigue on Educators in Residential Treatment Centres: How does this impact restraint & seclusion?

Les mesures de contention et d’isolement (MCI) en centre de réadaptation pour jeunes en difficultés sont controversées et employées sur une base régulière. Bien que l’utilisation des MCI soit balisée par des lois, le stress ou la fatigue de l’éducateur est susceptible de teinter le processus décisionnel menant à leur application. Considérant les effets iatrogènes physiques et psychologiques pour le jeune et l’intervenant liés à cette pratique, il est pertinent d’approfondir la recherche à ce sujet. L’objectif de cette étude longitudinale prospective est d’examiner les liens associatifs entre le niveau de stress perçu, de fatigue aiguë, de fatigue chronique ainsi que la récupération des éducateurs et leurs recours aux contentions et isolements. Les 155 éducateurs composant l’échantillon final ont rempli des questionnaires à huit reprises sur une base hebdomadaire. Les données ont fait l’objet d’analyses en décalage croisé. Aucune des hypothèses n’a été confirmée. Les résultats ont toutefois révélé que le stress de l’éducateur était associé négativement aux MCI au temps subséquent. De plus, l’utilisation de MCI était associée positivement avec la fatigue aigüe, négativement avec la récupération et positivement à une utilisation de MCI dans les semaines suivantes.Restraints and seclusions (R&S) in youth residential treatment centers (RTCs) are used regularly even though their use is controversial. Although R&S are meant to be used within a legal framework, their application in the day-to-day operations can be influenced by the caregiver’s stress and fatigue. Considering the physical and psychological iatrogenic effects of R&S for both youth and educators, it is highly relevant to widen the current knowledge on the matter. Our objective was to examine, via a prospective longitudinal design, the associative links between the level of perceived stress, acute fatigue, chronic fatigue and intershift recovery on the use of R&S in youth RTCs. Our sample of 155 educators working in RTCs completed eight weekly diaries and cross-lagged analyses were conducted. None of the hypothesis were confirmed. However, results showed that the educator’s stress was negatively associated with R&S at a later time. Moreover, the use of R&S was positively associated with acute fatigue, negatively with recovery and positively with a subsequent use of R&S

Stress et fatigue chez les éducateurs en centre de réadaptation pour jeunes : influence sur leur recours aux contentions et isolements

Les mesures de contention et d’isolement (MCI) en centre de réadaptation pour jeunes en difficultés sont controversées et employées sur une base régulière. Bien que l’utilisation des MCI soit balisée par des lois, le stress ou la fatigue de l’éducateur est susceptible de teinter le processus décisionnel menant à leur application. Considérant les effets iatrogènes physiques et psychologiques pour le jeune et l’intervenant liés à cette pratique, il est pertinent d’approfondir la recherche à ce sujet. L’objectif de cette étude longitudinale prospective est d’examiner les liens associatifs entre le niveau de stress perçu, de fatigue aiguë, de fatigue chronique ainsi que la récupération des éducateurs et leurs recours aux contentions et isolements. Les 155 éducateurs composant l’échantillon final ont rempli des questionnaires à huit reprises sur une base hebdomadaire. Les données ont fait l’objet d’analyses en décalage croisé. Aucune des hypothèses n’a été confirmée. Les résultats ont toutefois révélé que le stress de l’éducateur était associé négativement aux MCI au temps subséquent. De plus, l’utilisation de MCI était associée positivement avec la fatigue aigüe, négativement avec la récupération et positivement à une utilisation de MCI dans les semaines suivantes.Restraints and seclusions (R&S) in youth residential treatment centers (RTCs) are used regularly even though their use is controversial. Although R&S are meant to be used within a legal framework, their application in the day-to-day operations can be influenced by the caregiver’s stress and fatigue. Considering the physical and psychological iatrogenic effects of R&S for both youth and educators, it is highly relevant to widen the current knowledge on the matter. Our objective was to examine, via a prospective longitudinal design, the associative links between the level of perceived stress, acute fatigue, chronic fatigue and intershift recovery on the use of R&S in youth RTCs. Our sample of 155 educators working in RTCs completed eight weekly diaries and cross-lagged analyses were conducted. None of the hypothesis were confirmed. However, results showed that the educator’s stress was negatively associated with R&S at a later time. Moreover, the use of R&S was positively associated with acute fatigue, negatively with recovery and positively with a subsequent use of R&S

Cooperation in publicly funded reference material production

The meeting was organized by the European Commission's Joint Research Centre, and held at the JRC-Geel site on 22-23 February, 2018. It was a follow-up of a similar meeting held in 2009. The objective of the meeting was to exchange information about ongoing publicly funded reference material (RM) production, identify areas of interest for future specific RMs, including Certified Reference Material (CRM) developments, investigate potential areas of collaboration, and to identify areas which may be of a lower importance in the future for a specific RM-producer. The benefit of exchanging such information is to avoid duplication of efforts in RM production, make better use of public funds by potentially matching competencies, and to address problems that are common to publicly funded RM-producers. Attendees included representatives of the following organisations: Bundesanstalt für Materialforschung und –prüfung (BAM), Germany; IAEA Environment Laboratories , Monaco; the Joint Research Centre (JRC), Belgium (formerly IRMM); the Korea Research Institute of Standards and Science (KRISS), South Korea; LGC, United Kingdom, the National Institute for Standards and Technology (NIST), USA; the National Measurement Institute of Australia (NMIA), Australia; the National Metrology Institute of South Africa (NMISA), South Africa; and the National Research Council Canada (NRCC), Canada. Attendees participated physically or via videoconference. In preparation for the meeting, each participating organisation provided a list of current and planned projects. During the meeting itself, each institution presented its main fields of activity and offered additional information on its RM programme as required. Discussions not only addressed detailed technical questions but also dealt with questions on policy and legal status. Additional meetings like this can help to assist in the overall prioritisation of RM production internationally. This meeting report discusses the drivers and approaches taken by publicly funded RM-producers, and analyses the areas of RM development currently being covered. A view of current areas of activity of the publicly funded RM-producers is provided and a summary of some future trends is given.JRC.F.6-Reference Material

Risk of COVID-19 after natural infection or vaccinationResearch in context

Summary: Background: While vaccines have established utility against COVID-19, phase 3 efficacy studies have generally not comprehensively evaluated protection provided by previous infection or hybrid immunity (previous infection plus vaccination). Individual patient data from US government-supported harmonized vaccine trials provide an unprecedented sample population to address this issue. We characterized the protective efficacy of previous SARS-CoV-2 infection and hybrid immunity against COVID-19 early in the pandemic over three-to six-month follow-up and compared with vaccine-associated protection. Methods: In this post-hoc cross-protocol analysis of the Moderna, AstraZeneca, Janssen, and Novavax COVID-19 vaccine clinical trials, we allocated participants into four groups based on previous-infection status at enrolment and treatment: no previous infection/placebo; previous infection/placebo; no previous infection/vaccine; and previous infection/vaccine. The main outcome was RT-PCR-confirmed COVID-19 >7–15 days (per original protocols) after final study injection. We calculated crude and adjusted efficacy measures. Findings: Previous infection/placebo participants had a 92% decreased risk of future COVID-19 compared to no previous infection/placebo participants (overall hazard ratio [HR] ratio: 0.08; 95% CI: 0.05–0.13). Among single-dose Janssen participants, hybrid immunity conferred greater protection than vaccine alone (HR: 0.03; 95% CI: 0.01–0.10). Too few infections were observed to draw statistical inferences comparing hybrid immunity to vaccine alone for other trials. Vaccination, previous infection, and hybrid immunity all provided near-complete protection against severe disease. Interpretation: Previous infection, any hybrid immunity, and two-dose vaccination all provided substantial protection against symptomatic and severe COVID-19 through the early Delta period. Thus, as a surrogate for natural infection, vaccination remains the safest approach to protection. Funding: National Institutes of Health

Risk of COVID-19 after natural infection or vaccinationResearch in context

Background: While vaccines have established utility against COVID-19, phase 3 efficacy studies have generally not comprehensively evaluated protection provided by previous infection or hybrid immunity (previous infection plus vaccination). Individual patient data from US government-supported harmonized vaccine trials provide an unprecedented sample population to address this issue. We characterized the protective efficacy of previous SARS-CoV-2 infection and hybrid immunity against COVID-19 early in the pandemic over three-to six-month follow-up and compared with vaccine-associated protection. Methods: In this post-hoc cross-protocol analysis of the Moderna, AstraZeneca, Janssen, and Novavax COVID-19 vaccine clinical trials, we allocated participants into four groups based on previous-infection status at enrolment and treatment: no previous infection/placebo; previous infection/placebo; no previous infection/vaccine; and previous infection/vaccine. The main outcome was RT-PCR-confirmed COVID-19 >7–15 days (per original protocols) after final study injection. We calculated crude and adjusted efficacy measures. Findings: Previous infection/placebo participants had a 92% decreased risk of future COVID-19 compared to no previous infection/placebo participants (overall hazard ratio [HR] ratio: 0.08; 95% CI: 0.05–0.13). Among single-dose Janssen participants, hybrid immunity conferred greater protection than vaccine alone (HR: 0.03; 95% CI: 0.01–0.10). Too few infections were observed to draw statistical inferences comparing hybrid immunity to vaccine alone for other trials. Vaccination, previous infection, and hybrid immunity all provided near-complete protection against severe disease. Interpretation: Previous infection, any hybrid immunity, and two-dose vaccination all provided substantial protection against symptomatic and severe COVID-19 through the early Delta period. Thus, as a surrogate for natural infection, vaccination remains the safest approach to protection. Funding: National Institutes of Health