scholarly journals Quality Considerations When Using Tissue Samples for Biomarker Studies in Cancer Research

2021 ◽  
Vol 16 ◽  
pp. 117727192110095
Author(s):  
Valerie Speirs
Keyword(s):  
Cancer Research ◽  
Clinical Outcome ◽  
Clinical Data ◽  
Biological Samples ◽  
Tissue Samples ◽  
Biomarker Research

Tissue obtained from biobanks is frequently employed in biomarker studies. Biomarkers define objective, measurable characteristics of biological and biomedical procedures and have been used as indicators of clinical outcome. This article outlines some of the steps scientists should consider when embarking on biomarker research in cancer research using samples from biobanks and the importance and challenges of linking clinical data to biological samples.

Laboratory Specimens and Genetic Privacy: Evolution of Legal Theory

2013 ◽  
Vol 41 (S1) ◽  
pp. 65-68 ◽  
Author(s):  
Michelle Huckaby Lewis
Keyword(s):  
Biomedical Research ◽  
Biological Samples ◽  
Biological Tissue ◽  
Genetic Information ◽  
Legal Theory ◽  
Genetic Privacy ◽  
Tissue Samples

Human biological tissue samples are an invaluable resource for biomedical research designed to find causes of diseases and their treatments. Controversy has arisen, however, when research has been conducted with laboratory specimens either without the consent of the source of the specimen or when the research conducted with the specimen has expanded beyond the scope of the original consent agreement. Moreover, disputes have arisen regarding which party, the researcher or the source of the specimen, has control over who may use the specimens and for what purposes. The purposes of this article are: (1) to summarize the most important litigation regarding the use of laboratory specimens, and (2) to demonstrate how legal theory regarding control of laboratory specimens has evolved from arguments based upon property interests in biological samples to claims that the origins of laboratory specimens have privacy interests in their genetic information that should be protected.

Enabling Precision Medicine in Cancer Care Through a Molecular Data Warehouse: The Moffitt Experience

2021 ◽  
pp. 561-569
Author(s):  
Steven A. Eschrich ◽  
Jamie K. Teer ◽  
Phillip Reisman ◽  
Erin Siegel ◽  
Chandan Challa ◽  
...  
Keyword(s):  
Cancer Research ◽  
Precision Medicine ◽  
Data Warehouse ◽  
Clinical Data ◽  
Molecular Data ◽  
Project Planning ◽  
Cancer Genome ◽  
Open Communication ◽  
Clinical Data Warehouse ◽  
Research Studies

PURPOSE The use of genomics within cancer research and clinical oncology practice has become commonplace. Efforts such as The Cancer Genome Atlas have characterized the cancer genome and suggested a wealth of targets for implementing precision medicine strategies for patients with cancer. The data produced from research studies and clinical care have many potential secondary uses beyond their originally intended purpose. Effective storage, query, retrieval, and visualization of these data are essential to create an infrastructure to enable new discoveries in cancer research. METHODS Moffitt Cancer Center implemented a molecular data warehouse to complement the extensive enterprise clinical data warehouse (Health and Research Informatics). Seven different sequencing experiment types were included in the warehouse, with data from institutional research studies and clinical sequencing. RESULTS The implementation of the molecular warehouse involved the close collaboration of many teams with different expertise and a use case–focused approach. Cornerstones of project success included project planning, open communication, institutional buy-in, piloting the implementation, implementing custom solutions to address specific problems, data quality improvement, and data governance, unique aspects of which are featured here. We describe our experience in selecting, configuring, and loading molecular data into the molecular data warehouse. Specifically, we developed solutions for heterogeneous genomic sequencing cohorts (many different platforms) and integration with our existing clinical data warehouse. CONCLUSION The implementation was ultimately successful despite challenges encountered, many of which can be generalized to other research cancer centers.

scholarly journals Biomarkers in COPD – Challenging, Real or Illusive

Folia Medica ◽  
2018 ◽  
Vol 60 (3) ◽  
pp. 351-363
Author(s):  
Radostina V. Cherneva ◽  
Dimitar T. Kostadinov
Keyword(s):  
Respiratory Tract ◽  
Disease Severity ◽  
Biological Samples ◽  
Biological Sample ◽  
Respiratory Medicine ◽  
European Medicines Agency ◽  
Tissue Sampling ◽  
Huge Amount ◽  
Biomarker Research

Abstract Biomarker research in COPD is becoming the most rapidly progressing sphere in respiratory medicine. Although “omics” generate a huge amount of biomarkers, fibrinogen is the only one validated by the European Medicines Agency. Thousands of studies analyzing different biological samples from the respiratory tract, collected in different ways, using various kits and techniques are generating more and more data, rendering biomarkers very confusing rather than having practical value. It seems that in order to be applicable and validated, biomarkers should be analysed in an accurately described cohort of patients, homogeneous in disease severity and activity. As COPD has multiple mechanisms of pathobiology it raises the issue of which is the most appropriate biological sample reflecting each of them. Unified criteria for tissue sampling, validated kits for respiratory tract probes and standardized technologies should be announced. The review presents the biomarkers that are currently validated and raises the problem of standardization.

scholarly journals A Federated Network for Translational Cancer Research Using Clinical Data and Biospecimens

2015 ◽  
Vol 75 (24) ◽  
pp. 5194-5201 ◽  
Author(s):  
Rebecca S. Jacobson ◽  
Michael J. Becich ◽  
Roni J. Bollag ◽  
Girish Chavan ◽  
Julia Corrigan ◽  
...  
Keyword(s):  
Cancer Research ◽  
Clinical Data ◽  
Translational Cancer Research

scholarly journals CD56‐expression in bone marrow or other relevant tissue samples related to histopathological diagnosis and clinical outcome in children

2006 ◽  
Vol 20 (4) ◽  
Author(s):  
Birgitte Groenkaer Toft ◽  
Lars Peter Ryder ◽  
Mette Klarskov Andersen ◽  
Birgitte Frederiksen Lausen ◽  
Bodil Laub Petersen
Keyword(s):  
Bone Marrow ◽  
Clinical Outcome ◽  
Histopathological Diagnosis ◽  
Tissue Samples ◽  
Cd56 Expression

Integrating Biomolecular and Clinical Data for Cancer Research: Concepts and Challenges

2012 ◽  
pp. 159-172
Author(s):  
Pornpimol Charoentong ◽  
Hubert Hackl ◽  
Bernhard Mlecnik ◽  
Gabriela Bindea ◽  
Jerome Galon ◽  
...  
Keyword(s):  
Cancer Research ◽  
Clinical Data

scholarly journals A 3D Scanning System for Inverse Analysis of Moist Biological Samples: Design and Validation Using Tendon Fascicle Bundles

Sensors ◽  
2020 ◽  
Vol 20 (14) ◽  
pp. 3847 ◽  
Author(s):  
Sylwia Dabrowska ◽  
Martyna Ekiert ◽  
Kaja Wojcik ◽  
Marek Kalemba ◽  
Andrzej Mlyniec
Keyword(s):  
Biological Samples ◽  
Inverse Analysis ◽  
3D Model ◽  
Model Development ◽  
3D Scanning ◽  
Mechanical Tests ◽  
Scanning System ◽  
Cross Sectional ◽  
Tissue Samples ◽  
Accuracy And Repeatability

In this article, we present the design and validation of a non-contact scanning system for the development of a three-dimensional (3D) model of moist biological samples. Due to the irregular shapes and low stiffness of soft tissue samples, the use of a non-contact, reliable geometry scanning system with good accuracy and repeatability is required. We propose a reliable 3D scanning system consisting of a blue light profile sensor, stationary and rotating frames with stepper motors, gears and a five-phase stepping motor unit, single-axis robot, control system, and replaceable sample grips, which once mounted onto the sample, are used for both scanning and mechanical tests. The proposed system was validated by comparison of the cross-sectional areas calculated based on 3D models, digital caliper, and vision-based methods. Validation was done on regularly-shaped samples, a wooden twig, as well as tendon fascicle bundles. The 3D profiles were used for the development of the 3D computational model of the sample, including surface concavities. Our system allowed for 3D model development of samples with a relative error of less than 1.2% and high repeatability in approximately three minutes. This was crucial for the extraction of the mechanical properties and subsequent inverse analysis, enabling the calibration of complex material models.

PROCEEDINGS OF THE CANADIAN FRAILTY NETWORK WORKSHOP: IDENTIFYING BIOMARKERS OF FRAILTY TO SUPPORT FRAILTY RISK ASSESSMENT, DIAGNOSIS AND PROGNOSIS. TORONTO, JANUARY 15, 2018

2019 ◽  
pp. 1-11
Author(s):  
J. Muscedere ◽  
P.M. Kim ◽  
J. Afilalo ◽  
C. Balion ◽  
V.E. Baracos5 ◽  
...  
Keyword(s):  
Biological Samples ◽  
Data Access ◽  
The United States ◽  
Background Information ◽  
Afternoon Session ◽  
For Profit ◽  
Diagnosis And Prognosis ◽  
The Government ◽  
Government Of Canada ◽  
Biomarker Research

The Canadian Frailty Network (CFN), a pan-Canadian not-for-profit organization funded by the Government of Canada through the Networks of Centres of Excellence Program, is dedicated to improving the care of older Canadians living with frailty. The CFN has partnered with the Canadian Longitudinal Study on Aging (CLSA) to measure potential frailty biomarkers in biological samples (whole blood, plasma, urine) collected in over 30,000 CLSA participants. CFN hosted a workshop in Toronto on January 15 2018, bringing together experts in the field of biomarkers, aging and frailty. The overall objectives of the workshop were to start building a consensus on potential frailty biomarker domains and identify specific frailty biomarkers to be measured in the CLSA biological samples. The workshop was structured with presentations in the morning to frame the discussions for the afternoon session, which was organized as a free-flowing discussion to benefit from the expertise of the participants. Participants and speakers were from Canada, Italy, Spain, United Kingdom and the United States. Herein we provide pertinent background information, a summary of all the presentations with key figures and tables, and the distillation of the discussions. In addition, moving forward, the principles CFN will use to approach frailty biomarker research and development are outlined. Findings from the workshop are helping CFN and CLSA plan and conduct the analysis of biomarkers in the CLSA samples and which will inform a follow-up data access competition.

scholarly journals Selecting precise reference normal tissue samples for cancer research using a deep learning approach

2019 ◽  
Vol 12 (S1) ◽  
Author(s):  
William Z. D. Zeng ◽  
Benjamin S. Glicksberg ◽  
Yangyan Li ◽  
Bin Chen
Keyword(s):  
Cancer Research ◽  
Deep Learning ◽  
Normal Tissue ◽  
Learning Approach ◽  
Tissue Samples

scholarly journals Expression Of Intracellular Components of the NF-κB Alternative Pathway (NF-κB2, RelB, NIK and Bcl3) is Associated With Clinical Outcome of NSCLC Patients

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Foteinos-Ioannis D. Dimitrakopoulos ◽  
Anna G. Antonacopoulou ◽  
Anastasia E. Kottorou ◽  
Nikolaos Panagopoulos ◽  
Fotini Kalofonou ◽  
...  
Keyword(s):  
Multivariate Analysis ◽  
Clinical Outcome ◽  
Alternative Pathway ◽  
Mrna Levels ◽  
Regional Lymph Nodes ◽  
Tissue Samples ◽  
Nsclc Patients ◽  
Relapse Rates

Abstract A growing number of studies has shed light on the role of the NF-κΒ in non-small-cell lung cancer (NSCLC). To address the significance of major effectors of the NF-κΒ alternative pathway, we investigated the relationship between NF-κΒ2, RelB, NIK and Bcl3 expression (mRNA and protein) and the clinical outcome of NSCLC patients. NF-κΒ2, RelB, NIK and Bcl3 protein expression levels were assessed by immunohistochemistry in tissue samples from 151 NSCLC patients who had curative resection. mRNA levels were also evaluated in 69 patients using quantitative real-time PCR. Although all studied proteins were overexpressed in NSCLC (P < 0.001 for all), only RelB mRNA levels were strongly increased in cancerous specimens compared to tumor-adjacent non-neoplastic tissues (P = 0.009). Moreover, NF-κB2, RelB and Bcl3 expression was associated with overall survival (OS). In particular, cytoplasmic and mRNA expression of RelB was related to 5-year OS (P = 0.014 and P = 0.006, respectively). Multivariate analysis also showed that Bcl3 expression (nuclear and cytoplasmic) was associated with increased 5-year OS (P = 0.002 and P = 0.036, respectively). In addition, higher Bcl3 mRNA levels were associated with inferior OS in stages I & II and improved OS in stages III and IV after 5-year follow-up (P = 0.004 and P = 0.001, respectively). Furthermore, stage I patients with lower NF-κB2 mRNA levels had better 5-year survival in univariate and multivariate analysis (P = 0.031 and P = 0.028, respectively). Interestingly, RelB expression (cytoplasmic and mRNA) was inversely associated with relapse rates (P = 0.027 and P = 0.015, respectively), while low NIK cytoplasmic expression was associated with lower relapse rates (P = 0.019). Cytoplasmic NIK expression as well as NF-κB2/ Bcl3 detection was associated with lymph node infiltration (P = 0.039 and P = 0.014, respectively). The present study confirms the deregulation of the NF-κB alternative pathway in NSCLC and also demonstrates the importance of this pathway in prognosis, recurrence and infiltration of regional lymph nodes.

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