Human research tissue banks: the ATRA Project for establishing a human research tissue bank in switzerland

A large number of experiments in biomedical research are carried out on tissues, but, even though the results should be applicable to humans, these tissues are mainly of animal origin. The difficulty encountered in obtaining human organs and tissues is an acknowledged problem: not enough human tissues are available to meet research needs. We are introducing the ATRA Project, with the purpose of supporting progress in biomedical research in Switzerland through the establishment of one or more human tissue banks, which will be able to find, treat, preserve and supply human material. Where similar projects have already been launched, concerns have been expressed that donation for research purposes might compete with donation for transplantation, but most organs and tissues are in any case non-transplantable. Surplus surgical tissue is considered "sanitary waste", and must be treated according to specific regulations for collection, packaging, transport, treatment and disposal. A human tissue bank would not only abate the costs of treating sanitary waste, but would actually turn what is now considered waste into a resource which could be used to save human and animal lives.     

Assessing accuracy and precision for field and laboratory data: a perspective in ecosystem restoration

Unlike most laboratory studies, rigorous quality assurance/quality control (QA/QC) procedures may be lacking in ecosystem restoration (“ecorestoration”) projects, despite legislative mandates in the United States. This is due, in part, to ecorestoration specialists making the false assumption that some types of data (e.g. discrete variables such as species identification and abundance classes) are not subject to evaluations of data quality. Moreover, emergent behavior manifested by complex, adapting, and nonlinear organizations responsible for monitoring the success of ecorestoration projects tend to unconsciously minimize disorder, QA/QC being an activity perceived as creating disorder. We discuss similarities and differences in assessing precision and accuracy for field and laboratory data. Although the concepts for assessing precision and accuracy of ecorestoration field data are conceptually the same as laboratory data, the manner in which these data quality attributes are assessed is different. From a sample analysis perspective, a field crew is comparable to a laboratory instrument that requires regular “recalibration,” with results obtained by experts at the same plot treated as laboratory calibration standards. Unlike laboratory standards and reference materials, the “true” value for many field variables is commonly unknown. In the laboratory, specific QA/QC samples assess error for each aspect of the measurement process, whereas field revisits assess precision and accuracy of the entire data collection process following initial calibration. Rigorous QA/QC data in an ecorestoration project are essential for evaluating the success of a project, and they provide the only objective “legacy” of the dataset for potential legal challenges and future uses.     

A 3-year experience of quality control and quality assurance in the multisite delivery of a lymphocyte-based cellular therapy for renal cell carcinoma

Autolymphocyte therapy (ALT) is outpatient-based adoptive immunotherapy using ex vivo-activated memory T-cells. To support the safe and reproducible delivery of ALT at three cell processing facilities (Boston, MA; Atlanta, GA; Orange, CA) we created a comprehensive quality assurance/quality control program compliant with recent FDA guidance relevant to activated lymphocytes and somatic cell therapies. Each facility performed extensive QC testing to ensure sterility, viability, and proper cell yield. Additonally, several QC tests were performed at Cellocr's centralized reference laboratory to monitor cell potency and identity of the ex vivo-processed lymphocytes. We report here the successful implementation of this QA/QC program for ALT which has resulted in the safe preparation and delivery of cell infusion products amounting to over 3600 treatments at seven clinical sites nationwide. We believe this program will serve as a model for other cellular therapies.     

Announcement—guidance document for acquiring reliable data in ecological restoration projects

The Laurentian Great Lakes are undergoing intensive ecological restoration in Canada and the United States. In the United States, an interagency committee was formed to facilitate implementation of quality practices for federally funded restoration projects in the Great Lakes basin. The Committee's responsibilities include developing a guidance document that will provide a common approach to the application of quality assurance and quality control (QA/QC) practices for restoration projects. The document will serve as a “how‐to” guide for ensuring data quality during each aspect of ecological restoration projects. In addition, the document will provide suggestions on linking QA/QC data with the routine project data and hints on creating detailed supporting documentation. Finally, the document will advocate integrating all components of the project, including QA/QC applications, into an overarching decision‐support framework. The guidance document is expected to be released by the U.S. EPA Great Lakes National Program Office in 2017.     

DoRGaN: Development of Quality Assurance and Quality Control Systems for High Dose Rate Brachytherapy Based on GaN Dosimetry Probes

Background

Safe High Dose Rate Brachytherapy (HDR-BT) requires quality assurance/quality control (QA/QC) according to IPEM and ESTRO recommendations. Recent advances in real-time dosimetry and related developments of QA, QC and in vivo dosimetry (IVD) systems have offered new possibilities for effective independent treatment verification, and thus for improving the patient safety.

Quality control of human tissues-experience from the Indiana University Cancer Center-Lilly Research Labs human tissue bank

The success of molecular research and its applications in both the clinical and basic research arenas is strongly dependent on the collection, handling, storage, and quality control of fresh human tissue samples. This tissue bank was set up to bank fresh surgically obtained human tissue using a Clinical Annotated Tissue Database (CATD) in order to capture the associated patient clinical data and demographics using a one way patient encryption scheme to protect patient identification. In this study, we determined that high quality of tissue samples is imperative for both genomic and proteomic molecular research. This paper also contains a brief compilation of the literature involved in the patient ethics, patient informed consent, patient de-identification, tissue collection, processing, and storage as well as basic molecular research generated from the tissue bank using good clinical practices. The current applicable rules, regulations, and guidelines for handling human tissues are briefly discussed. More than 6,610 cancer patients have been consented (97% of those that were contacted by the consenter) and 16,800 tissue specimens have been banked from these patients in 9 years. All samples collected in the bank were QC’d by a pathologist. Approximately 1,550 tissue samples have been requested for use in basic, clinical, and/or biomarker cancer research studies. Each tissue aliquot removed from the bank for a research study were evaluated by a second H&E, if the samples passed the QC, they were submitted for genomic and proteomic molecular analysis/study. Approximately 75% of samples evaluated were of high histologic quality and used for research studies. Since 2003, we changed the patient informed consent to allow the tissue bank to gather more patient clinical follow-up information. Ninety two percent of the patients (1,865 patients) signed the new informed consent form and agreed to be re-contacted for follow-up information on their disease state. In addition, eighty five percent of patients (1,584) agreed to be re-contacted to provide a biological fluid sample to be used for biomarker research.     

Quality assurance and quality control processes: summary of a metabolomics community questionnaire

Introduction

The Metabolomics Society Data Quality Task Group (DQTG) developed a questionnaire regarding quality assurance (QA) and quality control (QC) to provide baseline information about current QA and QC practices applied in the international metabolomics community.

Objectives

The DQTG has a long-term goal of promoting robust QA and QC in the metabolomics community through increased awareness via communication, outreach and education, and through the promotion of best working practices. An assessment of current QA and QC practices will serve as a foundation for future activities and development of appropriate guidelines.

Method

QA was defined as the set of procedures that are performed in advance of analysis of samples and that are used to improve data quality. QC was defined as the set of activities that a laboratory does during or immediately after analysis that are applied to demonstrate the quality of project data. A questionnaire was developed that included 70 questions covering demographic information, QA approaches and QC approaches and allowed all respondents to answer a subset or all of the questions.

Result

The DQTG questionnaire received 97 individual responses from 84 institutions in all fields of metabolomics covering NMR, LC-MS, GC-MS, and other analytical technologies.

Conclusion

There was a vast range of responses concerning the use of QA and QC approaches that indicated the limited availability of suitable training, lack of Standard Operating Procedures (SOPs) to review and make decisions on quality, and limited use of standard reference materials (SRMs) as QC materials. The DQTG QA/QC questionnaire has for the first time demonstrated that QA and QC usage is not uniform across metabolomics laboratories. Here we present recommendations on how to address the issues concerning QA and QC measurements and reporting in metabolomics.

     

Pollen monitoring: minimum requirements and reproducibility of analysis

Training, quality assurance (QA) and quality control (QC) play an important role in building competence in monitoring and research in aerobiology. The main goals of this paper were to: (a) formulate an updated Minimum Requirements Report for pollen monitoring; (b) carry out a pilot QC exercise of staff involved in pollen counting from various national networks in order to examine between analysts reproducibility and develop a methodology that can be used in future QC exercises. A questionnaire survey was sent to coordinators of participating pollen monitoring networks. In addition, a total of 45 technicians from 15 European countries participated in the pilot QC exercise. All technicians were instructed to analyse two slides containing the following pollen types: (a) Poaceae and Betula pollen grains in the north of Europe; (b) Poaceae and Olea pollen grains in the south of Europe. Minimum Recommendations were produced based on the results of the questionnaire survey, published literature, and the outcomes of a workshop. In the QC exercise, it was noticed that technicians who followed the Minimum Recommendations and examined at least 10 % of the slide tended to have better indicators of precision and accuracy than those technicians who did not follow the Minimum Recommendations. The proposed Minimum Recommendations will help to improve the quality of scientific work, particularly for those who are considering the setting up of new monitoring sites. The results of the pilot QC exercise will help to develop a methodology that can be used again in the future, thereby ensuring data quality.     

National interests and international collaboration: tensions and ambiguity among Finns towards usages of tissue samples

Recent trends in biobanking indicate that the practices associated with the collection and use of human tissue samples and related health information are increasingly becoming premised on networks of biobanks. These networks and partnerships often involve international collaborations, as well as public–private partnerships. This article reports on the results of a study of people's attitudes towards biobanking and the biomedical use of tissue samples in Finland. Three approaches were used to study these attitudes: a population-based survey, focus group interviews among members of patient organizations and short interviews with research participants. In particular, we look at the attitudes of respondents in these three studies towards the use of tissue samples and use them as a catalyst to discuss two dimensions of biomedical research: public/private and domestic/international. Our discussion highlights how notions of value related to the use of tissue samples vary and provide contrasting perspectives and ambiguity that people may have towards various types of research partnerships and the benefits that may arise from them.     

Improving a consensus approach for protein structure selection by removing redundancy

In protein tertiary structure prediction, a crucial step is to select near-native structures from a large number of predicted structural models. Over the years, extensive research has been conducted for the protein structure selection problem with most approaches focusing on developing more accurate energy or scoring functions. Despite significant advances in this area, the discerning power of current approaches is still unsatisfactory. In this paper, we propose a novel consensus-based algorithm for the selection of predicted protein structures. Given a set of predicted models, our method first removes redundant structures to derive a subset of reference models. Then, a structure is ranked based on its average pairwise similarity to the reference models. Using the CASP8 data set containing a large collection of predicted models for 122 targets, we compared our method with the best CASP8 quality assessment (QA) servers, which are all consensus based, and showed that our QA scores correlate better with the GDT-TSs than those of the CASP8 QA servers. We also compared our method with the state-of-the-art scoring functions and showed its improved performance for near-native model selection. The GDT-TSs of the top models picked by our method are on average more than 8 percent better than the ones selected by the best performing scoring function.     

Convergence of human pluripotent stem cell,organoid, and genome editing technologies

The last decade has seen many exciting technological breakthroughs that greatly expanded the toolboxes for biological and biomedical research, yet few have had more impact than induced pluripotent stem cells and modern-day genome editing. These technologies are providing unprecedented opportunities to improve physiological relevance of experimental models, further our understanding of developmental processes, and develop novel therapies. One of the research areas that benefit greatly from these technological advances is the three-dimensional human organoid culture systems that resemble human tissues morphologically and physiologically. Here we summarize the development of human pluripotent stem cells and their differentiation through organoid formation. We further discuss how genetic modifications, genome editing in particular, were applied to answer basic biological and biomedical questions using organoid cultures of both somatic and pluripotent stem cell origins. Finally, we discuss the potential challenges of applying human pluripotent stem cell and organoid technologies for safety and efficiency evaluation of emerging genome editing tools.     

Supply and use of human tissue for research purposes: survey of BATB affiliated tissue banks

This paper describes a survey undertaken to identify the extent of supply and use of human tissue in research by BATB affiliated tissue banks. Approximately one third of tissue banks registered with the BATB are currently supplying samples that are found to be unsuitable for clinical use, for research. These banks all obtain consent for research and all supply tissue for in-house research. Some tissue is transferred to other public and commercial institutions. A harmonised network approach is proposed as the way forward to meet the increasing demand for human tissue in research.     

Tissue-growth-based synthetic tree generation and perfusion simulation

Biological tissues receive oxygen and nutrients from blood vessels by developing an indispensable supply and demand relationship with the blood vessels. We implemented a synthetic tree generation algorithm by considering the interactions between the tissues and blood vessels. We first segment major arteries using medical image data and synthetic trees are generated originating from these segmented arteries. They grow into extensive networks of small vessels to fill the supplied tissues and satisfy the metabolic demand of them. Further, the algorithm is optimized to be executed in parallel without affecting the generated tree volumes. The generated vascular trees are used to simulate blood perfusion in the tissues by performing multiscale blood flow simulations. One-dimensional blood flow equations were used to solve for blood flow and pressure in the generated vascular trees and Darcy flow equations were solved for blood perfusion in the tissues using a porous model assumption. Both equations are coupled at terminal segments explicitly. The proposed methods were applied to idealized models with different tree resolutions and metabolic demands for validation. The methods demonstrated that realistic synthetic trees were generated with significantly less computational expense compared to that of a constrained constructive optimization method. The methods were then applied to cerebrovascular arteries supplying a human brain and coronary arteries supplying the left and right ventricles to demonstrate the capabilities of the proposed methods. The proposed methods can be utilized to quantify tissue perfusion and predict areas prone to ischemia in patient-specific geometries.

     

Dynamic features of sensory and motor maps.

Recent data support the idea that the functional organizations of sensory and motor maps in the mature brain are dynamically maintained. Experiments employing peripheral injuries or other manipulations indicate that these maps are capable of extensive reorganization. A number of candidate mechanisms for these changes have been suggested, providing avenues for further research.     

Battelle Primate Facility

The Battelle Primate Facility houses one of the largest collections of neotropical primates in the United States. The facility is a research resource for undergraduate and graduate students. Battelle staff, as well as staff and faculty from U.S. and international institutions. Researchers have access to the animals for a variety of studies encompassing several disciplines, a large collection of preserved tissues, and an extensive biomedical database. The facility is a World Health Organization Collaborative Center for Clinical Pathology of Neotropical Primates and is involved with the Peruvian Primatological Project in Iquitos, Peru, which provides opportunities for research in primatology and conservation.     

Guidelines and considerations for the use of system suitability and quality control samples in mass spectrometry assays applied in untargeted clinical metabolomic studies

Background

Quality assurance (QA) and quality control (QC) are two quality management processes that are integral to the success of metabolomics including their application for the acquisition of high quality data in any high-throughput analytical chemistry laboratory. QA defines all the planned and systematic activities implemented before samples are collected, to provide confidence that a subsequent analytical process will fulfil predetermined requirements for quality. QC can be defined as the operational techniques and activities used to measure and report these quality requirements after data acquisition.

Aim of review

This tutorial review will guide the reader through the use of system suitability and QC samples, why these samples should be applied and how the quality of data can be reported.

Key scientific concepts of review

System suitability samples are applied to assess the operation and lack of contamination of the analytical platform prior to sample analysis. Isotopically-labelled internal standards are applied to assess system stability for each sample analysed. Pooled QC samples are applied to condition the analytical platform, perform intra-study reproducibility measurements (QC) and to correct mathematically for systematic errors. Standard reference materials and long-term reference QC samples are applied for inter-study and inter-laboratory assessment of data.

     

Efficacy and safety of new medicines: a human focus

The introduction of safe and effective new medicines is proving ever more difficult, a problem arguably due at least in part to over-reliance on experimental animal-based test systems. In light of the increasing awareness of the lack of predictiveness of such non-human approaches, the necessity to focus on human-based test methods is clear. There has been considerable progress in human in vivo (microdosing) and in silico approaches, primarily to identify ADMET issues, however, in vitro functional studies using human tissues are receiving inadequate attention. The potential scope of human tissue-based research is considerable, but much methodological development is required, which necessitates an increased willingness on the part of the Pharma industry to support it. This approach also requires considerably improved access to the cells and tissues themselves. While current acquisition is almost exclusively from surgery and post mortem, the range of tissue types, the quantity, quality and frequency of supply will remain inadequate to support human tissue as a key component of pre-clinical efficacy and safety testing. Additional routine access to non-transplantable tissues from organ donors for research purposes would be of inestimable value, but in order to realise this, true collaboration will be required between NHS, the Pharma and biotech industries, and the general public.     

A convenient method for distinguishing human and mouse cells in situ

Animal models play critical roles in the field of biomedical research.Mouse models with transplanted human cells or tissues,such as cell line-derived xenografts(CDX)and patient-derived xenografts(PDX),have been widely used[1].Tracking transplanted cells and understanding the spatial relationship between donor and host are extremely important for the study of these models.To distinguish cell sources in mouse xenograft models at the morphological level,antibody recognition methods(immunohistochemistry and immunofluorescence),transgenic reporter methods,and chromosome-specific probe labeling methods are widely used[2–5].However,these methods all need to consider the issues of label specificity,signal intensity,in situ applicability,and complexity of experimental operations,which increase the difficulty in use.In this report,we described a simple method for accurately distinguishing human and mouse nuclei based on 4′,6-diamidino-2-phenylindole(DAPI)staining.This method can accurately identify species not only in cultured cells,but also in mouse xenograft models.Using short-wavelength excitation and high brightness of DAPI stains,this easy-to-use method is expected to be widely used in the field of biomedical research.