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"Vaught, Jim"
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Preanalytical Variables Affecting the Integrity of Human Biospecimens in Biobanking
by
Vaught, Jim
,
Ellervik, Christina
in
Bias
,
Biological Specimen Banks - economics
,
Biomedical Research - methods
2015
Most errors in a clinical chemistry laboratory are due to preanalytical errors. Preanalytical variability of biospecimens can have significant effects on downstream analyses, and controlling such variables is therefore fundamental for the future use of biospecimens in personalized medicine for diagnostic or prognostic purposes.
The focus of this review is to examine the preanalytical variables that affect human biospecimen integrity in biobanking, with a special focus on blood, saliva, and urine. Cost efficiency is discussed in relation to these issues.
The quality of a study will depend on the integrity of the biospecimens. Preanalytical preparations should be planned with consideration of the effect on downstream analyses. Currently such preanalytical variables are not routinely documented in the biospecimen research literature. Future studies using biobanked biospecimens should describe in detail the preanalytical handling of biospecimens and analyze and interpret the results with regard to the effects of these variables.
Journal Article
Assessment of knowledge about biobanking among healthcare students and their willingness to donate biospecimens
by
Al-Qahtani, Mohammed H.
,
Gadi, Rawan
,
Saddick, Salina Y.
in
Attitudes
,
Biobank
,
Biological Specimen Banks
2017
Background
Biobanks and biospecimen collections are becoming a primary means of delivering personalized diagnostics and tailoring individualized therapeutics. This shift towards precision medicine (PM) requires interactions among a variety of stakeholders, including the public, patients, healthcare providers, government, and donors. Very few studies have investigated the role of healthcare students in biobanking and biospecimen donations. The main aims of this study were (1) to evaluate the knowledge of senior healthcare students about biobanks and (2) to assess the students’ willingness to donate biospecimens and the factors influencing their attitudes.
Methods
A cross-sectional study was conducted among senior healthcare students at King Abdulaziz University (KAU), Saudi Arabia. The data were obtained using a self-administered questionnaire in English. In addition to the respondents’ biographical data section, the questionnaire assessed the respondents’ general knowledge about biobanking, the factors influencing their willingness to donate biospecimens to biobanks and their general attitudes towards biomedical research.
Results
A total of 597 senior healthcare students were included in the study. The general knowledge score was 3.2 (±1.6) out of 7. Only approximately 44% and 27% of students were aware of the terms “Human Genome Project” (HGP) and “biobank,” respectively. The majority of the students (89%) were willing to donate biospecimens to biobanks. Multiple factors were significantly associated with their willingness to donate, including their perceived general health (
p
< 0.001), past experience with both tissue testing (
p
< 0.04) and tissue donation (
p
< 0.001), biobanking knowledge score (
p
< 0.001) and biomedical research attitude score (
p
< 0.001). The main reasons for students’ willingness to donate were advancement of medical research and societal benefits, whereas misuse of biospecimens and confidentiality breaches were the main reasons for a reluctance to donate.
Conclusion
Despite their strong willingness to donate biospecimens, students exhibited a notable lack of knowledge about biobanking and the HGP. To expedite the transition towards PM, it is highly recommended to enhance healthcare curricula by including more educational and awareness programmes to familiarize students with OMICs technologies in addition to the scope of research and clinical applications.
Journal Article
Notable Histologie Findings in a \Normal\ Cohort The National Institutes of Health Genotype-Tissue Expression (GTEx) Project
2025
(Arch Pathol Lab Med. 2025;149:233-241; doi: 10.5858/ arpa.2023-0468-OA) The Genotype-Tissue Expression (GTEx) project, a National Institutes of Health (NIH) Common Fund study, was designed to evaluate how genetic variation and epigenetic effects influence gene expression in normal tissue and to gain insight into tissue-specific gene expression and regulation.1'2 GTEx tissue collection was coordinated by the National Cancer Institute (NCI) Biorepositories and Biospecimen Research Branch using a specialized infra-structure developed in accordance with the NCI Best Practices for Biospecimen Resources.3,4 Tissue collection, when completed, resulted in more than 25 000 tissue samples from up to 40 grossly nondiseased tissues from nearly 1000 postmortem or organ donors. The GTEx project has (1) established a molecular resource database with aggregated genotypic and gene expression data (www.gtexportal.org), (2) shared the full data set, including raw DNA/RNA sequences and the available clinical data for each donor, to the database of genotypes and phenotypes (dbGaP; dbGaP accession No. phs000424; https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/ study.cgi?study_id=phs000424), (3) created a view-only tissue image library of micrographs (biospecimens.cancer.gov/gtex-biobank/histology_viewer.asp) as well as micrographs compatible with image analysis that are available upon request (email: ncibbrb@nih.gov), and (4) established an associated tissue bank (biospecimens.cancer.gov/gtexbiobank and gtex-portal.org/home/biobank) for the scientific community to pur-sue additional studies. Uninten-tional inclusion of missampled or diseased tissue could increase variability and potentially confound genetic analysis. [...]a multiphase approach was applied: tissue that appeared grossly normal upon collection was preferentially sampled; each tissue sample collected underwent histologie review by a project pathologist to confirm the sample was rep-resentative of the target tissue, was of suitable quality and was absent of disease; and sequencing data were used to ver-ify recorded donor sex and the absence of chromosomal anomalies and genetic conditions. Briefly, research authorization was obtained from a member of each donor's family.3'6'7 In the present study, any of the following resulted in donor exclusion: an antemortem transfusion within 48 hours of death, a history of metastatic malignancy, expo-sure to HrV/AIDS or the hepatitis C virus within the 5 years pre-ceding death, repeated positive reactive screening tests for HIV-1 or HIV-2 antibodies, active sepsis, or multiple documented or con-firmed pathologie conditions.
Journal Article
Histologic and Quality Assessment of Genotype-Tissue Expression (GTEx) Research Samples: A Large Postmortem Tissue Collection
2025
The National Institutes of Health Genotype-Tissue Expression (GTEx) project was developed to elucidate how genetic variation influences gene expression in multiple normal tissues procured from postmortem donors.
To provide critical insight into a biospecimen's suitability for subsequent analysis, each biospecimen underwent quality assessment measures that included evaluation for underlying disease and potential effects introduced by preanalytic factors.
Electronic images of each tissue collected from nearly 1000 postmortem donors were evaluated by board-certified pathologists for the extent of autolysis, tissue purity, and the type and abundance of any extraneous tissue. Tissue-specific differences in the severity of autolysis and RNA integrity were evaluated, as were potential relationships between these markers and the duration of postmortem interval and rapidity of death.
Tissue-specific challenges in the procurement and preservation of the nearly 30 000 tissue specimens collected during the GTEx project are summarized. Differences in the degree of autolysis and RNA integrity number were observed among the 40 tissue types evaluated, and tissue-specific susceptibilities to the duration of postmortem interval and rapidity of death were observed.
Ninety-five percent of tissues were of sufficient quality to support RNA sequencing analysis. Biospecimens, annotated whole slide images, de-identified clinical data, and genomic data generated for GTEx represent a high-quality and comprehensive resource for the scientific community that has contributed to its use in approximately 1695 articles. Biospecimens and data collected under the GTEx project are available via the GTEx portal and authorized access to the Database of Genotypes and Phenotypes; procedures and whole slide images are available from the National Cancer Institute.
Journal Article
Two Accreditation Options for Biorepositories: College of American Pathologists Biorepository Accreditation Program and International Standards Organization 20387 General Requirements for Biobanking
by
Davis, Richard C.
,
Summers, Thomas
,
McCall, Shannon J.
in
Accreditation
,
Accreditation - standards
,
Biobanks
2025
Biomedical research relies on available biomaterials and associated data, and the quality of this starting material can have a significant impact on the quality of the experimental results. In the 2000s, best-practice documents and guidelines for biorepositories were published, followed in the 2010s by standards documents used to support accreditation. The College of American Pathologists Biorepository Accreditation Program and the International Standards Organization's standard 20387 were launched in 2012 and 2018, respectively.
To identify quantitative and qualitative differences between the 2 aforementioned biorepository accreditation standards for use by the larger biomedical research community; the results will empower biorepositories to select an accreditation program that best fits their goals.
Individual requirements of both accreditation standards were identified and a bidirectional crosswalk was performed to identify gaps. Requirements were assigned to one of several standardized categories to enable comparison of the relative emphasis of different categories between the standards.
Quantitatively, the College of American Pathologists program is comprehensive and stands alone, with 523 requirements, whereas the International Standards Organization program contains 167 requirements and is comprehensive through its incorporation and reference to numerous related standards documents. Qualitatively, both programs rely heavily on the implementation of an overarching quality management system and both programs can accommodate different types of biobanks (eg, human and animal).
The standards differ in number of requirements, distribution of requirements across categories, and amount of reliance on separate standard documents. This information may aid in selection of an appropriate accreditation standard.
Journal Article
Notable Histologic Findings in a “Normal” Cohort: The National Institutes of Health Genotype-Tissue Expression (GTEx) Project
2025
The National Institutes of Health (NIH) Genotype-Tissue Expression (GTEx) project was designed to evaluate how genetic variation and epigenetic effects influence gene expression in normal tissue.
To ensure that the grossly normal-appearing tissues collected were free from disease, each specimen underwent histologic evaluation.
In total, nearly 30 000 tissue aliquots collected from almost 1000 postmortem donors underwent histologic review by project pathologists, and detailed observations of any abnormalities or lesions present were recorded.
Despite sampling of normal-appearing tissue, in-depth review revealed incidental findings among GTEx samples that included neoplastic, autoimmune, and genetic conditions; the incidence of some of these conditions among GTEx donors differed from those previously reported for other populations. A number of age-related abnormalities observed during histologic review of tissue specimens are also described.
Histologic findings from the GTEx project may serve to improve populational awareness of several conditions and present a unique opportunity for others to explore age- and sex-influenced conditions. Resources from the study, including histologic image and sequencing data, are publicly available for research.
Journal Article
Histologie and Quality Assessment of Genotype-Tissue Expression (GTEx) Research Samples: A Large Postmortem Tissue Collection
2025
(Arch Pathol Lab Med. 2025;149:217-232; doi: 10.5858/ arpa.2023-0467-OA) The Genotype-Tissue Expression (GTEx) project launched in 2010 as a National Institutes of Health (NIH) Common Fund study that aimed to (1) create a reference of gene expression across \"normal\" human tissues and (2) elucidate how genetic variation influences gene expression. Since the initial RNA sequencing of more than 1000 samples from the GTEx pilot phase,2 2057 data access requests to dbGap from established researchers have been authorized, and 1695 manuscripts utilizing GTEx data have been published and indexed in PubMed. Available evi-dence suggests that postmortem interval (PMI), the duration of time between death and tissue preservation, may adversely affect DNA integrity,7 RNA integrity7-9 mRNA levels,8 micro RNA levels,10 pH in brain tissue,11 and ultrastructural morpho-logic details that are indicative of autolysis severity (cellular destruction by intracellular enzymes).12,13 However, the timing and magnitude of PMI-associated effects remain unclear given that other studies have reported an absence of effect14-17 or tis-sue-specific effects.18-20 A comprehensive picture of PMI effects has proved elusive as individual studies differ from one another in the tissues examined, sample sizes, and PMI ranges investi-gated. Any of the following resulted in exclusion from the study: a diagnosis of metastatic cancer; treatment with che-motherapy or radiation for cancer or any other condition within 2 years of death; a blood transfusion within 48 hours of death; active sepsis; exposure to human immunodeficiency virus/acquired immunodefi-ciency syndrome (HTV7AIDS), hepatitis C virus, or hepatitis B virus within the 5 years preceding death, including intravenous drug use, or repeated positive reactive screening tests for HV-l or HV-2 antibod-ies; an inconsistency between documented and geneticaUy confirmed sex; and a documented or geneticaUy confirmed severe congenital pathologie disorder or condition.
Journal Article
Critical Issues in International Biobanking
by
Peakman, Tim
,
Abayomi, Akin
,
Vaught, Jim
in
Biological Specimen Banks - economics
,
Biological Specimen Banks - standards
,
Deoxyribonucleic acid
2014
[...]patients who donate biospecimens are becoming more interested in learning more about their own sample's use and in see- ing the actual results of the research. Implementation of QM activities requires dedicated time and a re- sourcing strategy which can be very costly. [...]the scope and scale of the program should be dictated by the scope and scale of the biobank and the nature of the research it is intended to support.\\n These data sets are very large and heterogeneous and present challenges of storage, accessibility, and use.
Journal Article
Two Accreditation Options for Biorepositories
2024
Biomedical research relies on available biomaterials and associated data, and the quality of this starting material can have a significant impact on the quality of the experimental results. In the 2000s, best-practice documents and guidelines for biorepositories were published, followed in the 2010s by standards documents used to support accreditation. The College of American Pathologists Biorepository Accreditation Program and the International Standards Organization's standard 20387 were launched in 2012 and 2018, respectively.CONTEXT.—Biomedical research relies on available biomaterials and associated data, and the quality of this starting material can have a significant impact on the quality of the experimental results. In the 2000s, best-practice documents and guidelines for biorepositories were published, followed in the 2010s by standards documents used to support accreditation. The College of American Pathologists Biorepository Accreditation Program and the International Standards Organization's standard 20387 were launched in 2012 and 2018, respectively.To identify quantitative and qualitative differences between the two aforementioned biorepository accreditation standards for use by the larger biomedical research community; the results will empower biorepositories to select an accreditation program that best fits their goals.OBJECTIVE.—To identify quantitative and qualitative differences between the two aforementioned biorepository accreditation standards for use by the larger biomedical research community; the results will empower biorepositories to select an accreditation program that best fits their goals.Individual requirements of both accreditation standards were identified and a bidirectional crosswalk was performed to identify gaps. Requirements were assigned to one of several standardized categories to enable comparison of the relative emphasis of different categories between the standards.DESIGN.—Individual requirements of both accreditation standards were identified and a bidirectional crosswalk was performed to identify gaps. Requirements were assigned to one of several standardized categories to enable comparison of the relative emphasis of different categories between the standards.Quantitatively, the College of American Pathologists program is comprehensive and stands alone, with 523 requirements, whereas the International Standards Organization program contains 167 requirements and is comprehensive through its incorporation and reference to numerous related standards documents. Qualitatively, both programs rely heavily on the implementation of an overarching quality management system and both programs can accommodate different types of biobanks (eg, human and animal).RESULTS.—Quantitatively, the College of American Pathologists program is comprehensive and stands alone, with 523 requirements, whereas the International Standards Organization program contains 167 requirements and is comprehensive through its incorporation and reference to numerous related standards documents. Qualitatively, both programs rely heavily on the implementation of an overarching quality management system and both programs can accommodate different types of biobanks (eg, human and animal).The standards differ in number of requirements, distribution of requirements across categories, and amount of reliance on separate standard documents. This information may aid in selection of an appropriate accreditation standard.CONCLUSIONS.—The standards differ in number of requirements, distribution of requirements across categories, and amount of reliance on separate standard documents. This information may aid in selection of an appropriate accreditation standard.
Journal Article
Histologic and Quality Assessment of Genotype-Tissue Expression
2025
* Context.--The National Institutes of Health Genotype-Tissue Expression (GTEx) project was developed to elucidate how genetic variation influences gene expression in multiple normal tissues procured from postmortem donors. Objective.--To provide critical insight into a biospecimen's suitability for subsequent analysis, each biospecimen underwent quality assessment measures that included evaluation for underlying disease and potential effects introduced by preanalytic factors. Design.--Electronic images of each tissue collected from nearly 1000 postmortem donors were evaluated by board-certified pathologists for the extent of autolysis, tissue purity, and the type and abundance of any extraneous tissue. Tissue-specific differences in the severity of autolysis and RNA integrity were evaluated, as were potential relationships between these markers and the duration of postmortem interval and rapidity of death. Results.--Tissue-specific challenges in the procurement and preservation of the nearly 30 000 tissue specimens collected during the GTEx project are summarized. Differences in the degree of autolysis and RNA integrity number were observed among the 40 tissue types evaluated, and tissue-specific susceptibilities to the duration of postmortem interval and rapidity of death were observed. Conclusions.--Ninety-five percent of tissues were of sufficient quality to support RNA sequencing analysis. Biospecimens, annotated whole slide images, de-identified clinical data, and genomic data generated for GTEx represent a high-quality and comprehensive resource for the scientific community that has contributed to its use in approximately 1695 articles. Biospecimens and data collected under the GTEx project are available via the GTEx portal and authorized access to the Database of Genotypes and Phenotypes; procedures and whole slide images are available from the National Cancer Institute. (Arch Pathol Lab Med. 2025;149:217-232; doi: 10.5858/arpa.2023-0467-OA)
Journal Article