Notable Histologic Findings in a "Normal" Cohort: The National Institutes of Health Genotype-Tissue Expression (GTEx) Project

CONTEXT.—

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.

OBJECTIVE.—

To ensure that the grossly normal-appearing tissues collected were free from disease, each specimen underwent histologic evaluation.

DESIGN.—

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.

RESULTS.—

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.

CONCLUSIONS.—

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 gender-influenced conditions. Resources from the study, including histologic image and sequencing data, are publicly available for research.

Evidence-based procedures to improve the reliability of circulating miRNA biomarker assays

Circulating cell-free microRNAs (cfmiRNA) are an emerging class of biomarkers that have shown great promise in the clinical diagnosis, treatment, and monitoring of several pathological conditions, including cancer. However, validation and clinical implementation of cfmiRNA biomarkers has been hindered by the variability introduced during different or suboptimal specimen collection and handling practices. To address the need for standardization and evidence-based guidance, the National Cancer Institute (NCI) developed a new Biospecimen Evidenced-Based Practices (BEBP) document, entitled "Cell-free miRNA (cfmiRNA): Blood Collection and Processing". The BEBP, the fourth in the document series, contains step-by-step procedural guidelines on blood collection, processing, storage, extraction, and quality assessment that are tailored specifically for cfmiRNA analysis of plasma and serum. The workflow outlined in the BEBP is based on the available literature and recommendations of an expert panel. The BEBP contains the level of detail required for development of evidence-based standard operating procedures (SOPs) as well as the flexibility needed to accomodate (i) discovery- and inquiry-based studies and (ii) the different constraints faced by research labs, industry, clinical and academic institutions to foster widespread implementation. Guidance from the expert panel also included recommendations on study design, validating changes in workflow, and suggested quality thresholds to delineate meaningful changes in cfmiRNA levels. The NCI cfmiRNA: Blood Collection and Processing BEBP is available here as supplementary information as well as through the NCI Biorepositories and Biospecimen Research Branch (BBRB) (https://biospecimens.cancer.gov/resources/bebp.asp).

Formalin Fixation, Delay to Fixation, and Time in Fixative Adversely Impact Copy Number Variation Analysis by aCGH

Although molecular profiling of DNA isolated from formalin-fixed, paraffin-embedded (FFPE) tumor specimens has become more common in recent years, it remains unclear how discrete FFPE processing variables may affect detection of copy number variation (CNV). To better understand such effects, array comparative genomic hybridization (aCGH) profiles of FFPE renal cell carcinoma specimens that experienced different delays to fixation (DTFs; 1, 2, 3, and 12 hours) and times in fixative (TIFs; 6, 12, 23, and 72 hours) were compared to snap-frozen tumor and blood specimens from the same patients. A greater number of regions containing CNVs relative to commercial reference DNA were detected in DNA from FFPE tumor specimens than snap-frozen tumor specimens even though they originated from the same tumor blocks. Extended DTF and TIF affected the number of DNA segments with a copy number status that differed between FFPE and frozen tumor specimens; a DTF ≥3 hours led to more segments, while a TIF of 72 hours led to fewer segments. Importantly, effects were not random as a higher guanine-cytosine (GC) content and/or a higher percentage of repeats were observed among stable regions. While limiting aCGH analysis to FFPE specimens with a DTF <3 hours and a TIF <72 hours may circumvent some effects, results from FFPE specimens should be validated against fresh or frozen specimens whenever possible.

Abstract 2632: Fostering engagement in biobanking and research through the NCI Cancer Moonshot Biobank patient and provider engagement website

The National Cancer Institute's (NCI) Cancer Moonshot Biobank (the Biobank) aims to accelerate cancer research on treatment resistance and sensitivity through collection of longitudinal biospecimens and health data donated by participants diagnosed with late-stage cancer and receiving standard of care therapy at participating NCI Community Oncology Research Program (NCORP) sites.

Participant and provider engagement are a central tenet of the Biobank. We therefore created an innovative website to interface directly with participants and providers and to meet our engagement goals of returning value to stakeholders, operating with transparency, maintaining bi-directional communication, and enrolling a diverse population that represents the U.S. including racial/ethnic minorities, rural populations and others that are historically underrepresented in clinical research. The Biobank engagement website has several features designed to provide return of value to stakeholders. This includes clear information about the program, transparency about how biospecimens and data will be used in research, and the ability to access and download documents such as clinical biomarker tests and signed consent forms. The website also includes project updates, participant and provider resources, and educational material.

The Cancer Moonshot Biobank Participant and Provider Engagement website serves as an important interface between the Biobank and its stakeholders. Its ultimate aim is to facilitate project engagement and return value to participants and providers.

Citation Format: Esmeralda Casas-Silva, Lokesh Agrawal, Helena J. Ellis, Veena Gopalakrishnan, Ping Guan, Mark Jensen, Natalie Madero, Sean McDermott, Jeffrey McLean, Abhi Rao, James Suh, Jane Wanyiri, Carol J. Weil, Mickey Williams, Helen M. Moore. Fostering engagement in biobanking and research through the NCI Cancer Moonshot Biobank patient and provider engagement website [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2632.

Impact of Preanalytical Factors on the Measurement of Tumor Tissue Biomarkers Using Immunohistochemistry

Analysis of formalin-fixed paraffin-embedded (FFPE) tissue by immunohistochemistry (IHC) is commonplace in clinical and research laboratories. However, reports suggest that IHC results can be compromised by biospecimen preanalytical factors. The National Cancer Institute's Biospecimen Preanalytical Variables Program conducted a systematic study to examine the potential effects of delay to fixation (DTF) and time in fixative (TIF) on IHC using 24 cancer biomarkers. Differences in IHC staining, relative to controls with a DTF of 1 hr, were observed in FFPE kidney tumor specimens after a DTF of ≥2 hr. Reductions in H-score and/or staining intensity were observed for c-MET, p53, PAX2, PAX8, pAKT, and survivin, whereas increases were observed for RCC1, EGFR, and CD10. Prolonged TIF of 72 hr resulted in significantly reduced H-scores of CD44 and c-Met in kidney tumor specimens, compared with controls with 12-hr TIF. An elevated probability of altered staining intensity due to DTF was observed for nine antigens, whereas for prolonged TIF an elevated probability was observed for one antigen. Results reported here and elsewhere across tumor types and antigens support limiting DTF to ≤1 hr when possible and fixing tissues in formalin for 12-24 hr to avoid confounding effects of these preanalytical factors on IHC.

Harmonizing Cell-Free DNA Collection and Processing Practices through Evidence-Based Guidance

Circulating cell-free DNA (cfDNA) is rapidly transitioning from discovery research to an important tool in clinical decision making. However, the lack of harmonization of preanalytic practices across institutions may compromise the reproducibility of cfDNA-derived data and hamper advancements in cfDNA testing in the clinic. Differences in cellular genomic contamination, cfDNA yield, integrity, and fragment length have been attributed to different collection tube types and anticoagulants, processing delays and temperatures, tube agitation, centrifugation protocols and speeds, plasma storage duration and temperature, the number of freeze-thaw events, and cfDNA extraction and quantification methods, all of which can also ultimately impact subsequent downstream analysis. Thus, there is a pressing need for widely applicable standards tailored for cfDNA analysis that include all preanalytic steps from blood draw to analysis. The NCI's Biorepositories and Biospecimen Research Branch has developed cfDNA-specific guidelines that are based upon published evidence and have been vetted by a panel of internationally recognized experts in the field. The guidelines include optimal procedures as well as acceptable alternatives to facilitate the generation of evidence-based protocols by individual laboratories and institutions. The aim of the document, which is entitled "Biospecimen Evidence-based Best Practices for Cell-free DNA: Biospecimen Collection and Processing," is to improve the accuracy of cfDNA analysis in both basic research and the clinic by improving and harmonizing practices across institutions.

Deleterious effects of formalin-fixation and delays to fixation on RNA and miRNA-Seq profiles

The National Cancer Institute conducted the Biospecimen Pre-analytical Variables (BPV) study to determine the effects of formalin fixation and delay to fixation (DTF) on the analysis of nucleic acids. By performing whole transcriptome sequencing and small RNA profiling on matched snap-frozen and FFPE specimens exposed to different delays to fixation, this study aimed to determine acceptable delays to fixation and proper workflow for accurate and reliable Next-Generation Sequencing (NGS) analysis of FFPE specimens. In comparison to snap-freezing, formalin fixation changed the relative proportions of intronic/exonic/untranslated RNA captured by RNA-seq for most genes. The effects of DTF on NGS analysis were negligible. In 80% of specimens, a subset of RNAs was found to differ between snap-frozen and FFPE specimens in a consistent manner across tissue groups; this subset was unaffected in the remaining 20% of specimens. In contrast, miRNA expression was generally stable across various formalin fixation protocols, but displayed increased variability following a 12 h delay to fixation.

The Biospecimen Preanalytical Variables Program: A Multiassay Comparison of Effects of Delay to Fixation and Fixation Duration on Nucleic Acid Quality

CONTEXT.—

Despite widespread use of formalin-fixed, paraffin-embedded (FFPE) tissue in clinical and research settings, potential effects of variable tissue processing remain largely unknown.

OBJECTIVE.—

To elucidate molecular effects associated with clinically relevant preanalytical variability, the National Cancer Institute initiated the Biospecimen Preanalytical Variables (BPV) program.

DESIGN.—

The BPV program, a well-controlled series of systematic, blind and randomized studies, investigated whether a delay to fixation (DTF) or time in fixative (TIF) affects the quantity and quality of DNA and RNA isolated from FFPE colon, kidney, and ovarian tumors in comparison to case-matched snap-frozen controls.

RESULTS.—

DNA and RNA yields were comparable among FFPE biospecimens subjected to different DTF and TIF time points. DNA and RNA quality metrics revealed assay- and time point-specific effects of DTF and TIF. A quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assay was superior when assessing RNA quality, consistently detecting differences between FFPE and snap-frozen biospecimens and among DTF and TIF time points. RNA Integrity Number and DV₂₀₀ (representing the percentage of RNA fragments longer than 200 nucleotides) displayed more limited sensitivity. Differences in DNA quality (Q-ratio) between FFPE and snap-frozen biospecimens and among DTF and TIF time points were detected with a qPCR-based assay.

CONCLUSIONS.—

DNA and RNA quality may be adversely affected in some tumor types by a 12-hour DTF or a TIF of 72 hours. Results presented here as well as those of additional BPV molecular analyses underway will aid in the identification of acceptable delays and optimal fixation times, and quality assays that are suitable predictors of an FFPE biospecimen's fit-for-purpose.

Critical Financial Challenges for Biobanking: Report of a National Cancer Institute Study

BACKGROUND

Researchers and other key stakeholders in biobanking often do not have a thorough understanding of the true costs and challenges associated with initiating, running, and maintaining a biobank. The National Cancer Institute's Biorepositories and Biospecimen Research Branch (BBRB) commissioned the Biobanking Financial Sustainability survey to better understand the challenges that biobanks face in supporting ongoing operations. A series of interviews with biobanking managers and an international focus group session informed the content of the survey.

METHODS

The design of the survey included five main sections, each containing questions related to primary topics as follows: general demographics, operations, funding sources, costs, and financial challenges. While the survey focused on financial issues and challenges, it also explored staffing and strategic planning as these issues relate to the sustainability of operations and financial support. U.S. and international biobanks were included in the survey.

RESULTS

Biobanks in general are dependent on public funding and most biobanks do not have formal plans for the long-term stewardship of their collections. Respondents are working at a critical level of personnel and are not in a position to further reduce staffing. Smaller biobanks in particular need assistance in defining reasonable cost recovery user fees for biospecimens and related services.

CONCLUSIONS

The survey results highlight several issues that are important for long-term biobank sustainability. It is critical to prepare for such issues as effective biobanking practices have increasingly been recognized as a key component for the advancement of precision medicine.

Cold Ischemia Score: An mRNA Assay for the Detection of Extended Cold Ischemia in Formalin-Fixed, Paraffin-Embedded Tissue

Although there are thousands of formalin-fixed paraffin-embedded (FFPE) tissue blocks potentially available for scientific research, many are of questionable quality, partly due to unknown preanalytical variables. We analyzed FFPE tissue biospecimens as part of the National Cancer Institute (NCI) Biospecimen Preanalytical Variables program to identify mRNA markers denoting cold ischemic time. The mRNA was extracted from colon, kidney, and ovary cancer FFPE blocks (40 patients, 10-12 hr fixation time) with 1, 2, 3, and 12 hr cold ischemic times, then analyzed using qRT-PCR for 23 genes selected following a literature search. No genes tested could determine short ischemic times (1-3 hr). However, a combination of three unstable genes normalized to a more stable gene could generate a "Cold Ischemia Score" that could distinguish 1 to 3 hr cold ischemia from 12 hr cold ischemia with 62% sensitivity and 84% specificity.

Development of a consensus approach for return of pathology incidental findings in the Genotype-Tissue Expression (GTEx) project

The active debate about the return of incidental or secondary findings in research has primarily focused on return to research participants, or in some cases, family members. Particular attention has been paid to return of genomic findings. Yet, research may generate other types of findings that warrant consideration for return, including findings related to the pathology of donated biospecimens. In the case of deceased biospecimen donors who are also organ and/or tissue transplant donors, pathology incidental findings may be relevant not to family members, but to potential organ or tissue transplant recipients. This paper will describe the ethical implications of pathology incidental findings in the Genotype-Tissue Expression (GTEx) project, the process for developing a consensus approach as to if/when such findings should be returned, possible implications for other research projects collecting postmortem tissues and how the scenario encountered in GTEx fits into the larger return of results/incidental findings debate.

Understanding preanalytical variables and their effects on clinical biomarkers of oncology and immunotherapy

Identifying a suitable course of immunotherapy treatment for a given patient as well as monitoring treatment response is heavily reliant on biomarkers detected and quantified in blood and tissue biospecimens. Suboptimal or variable biospecimen collection, processing, and storage practices have the potential to alter clinically relevant biomarkers, including those used in cancer immunotherapy. In the present review, we summarize effects reported for immunologically relevant biomarkers and highlight preanalytical factors associated with specific analytical platforms and assays used to predict and gauge immunotherapy response. Given that many of the effects introduced by preanalytical variability are gene-, transcript-, and protein-specific, biospecimen practices should be standardized and validated for each biomarker and assay to ensure accurate results and facilitate clinical implementation of newly identified immunotherapy approaches.

Abstract 5947: The NCI Best Practices for Biospecimen Resources: 2016 revised recommendations

Improved biospecimen handling practices are increasingly important for cancer research as advanced molecular analysis becomes routine in clinical trials and more frequently available in standard of care medicine. Biospecimens and associated clinical data collected in a consistent, established fashion can greatly facilitate cancer biomarker validation and development and validation of clinical diagnostic assays. In order to establish a set of guidelines to improve the quality of biospecimen-related research, the NCI’s Biorepositories and Biospecimen Research Branch developed the NCI Best Practices for Biospecimen Resources which includes technical recommendations on biospecimen handling as well as ethical and regulatory best practices. The 3rd, 2016 revised version of these Best Practices focused on updating technical and operational best practices with recommendations based on more recent research, guidance and standards for collecting, processing and storing biospecimens; revised informatics best practices; and updated ethical, legal and policy sections describing new developments on return of research results, informed consent for genomics research, data sharing, and community engagement. These Best Practices aim to help patients by improving the reproducibility of cancer research data. The NCI Best Practices are also foundational to the NIH Precision Medicine Initiative, part of which aims to establish the world’s largest research biobank that will support studies that utilize biospecimens from a cohort of one million individuals in the United States.

Citation Format: Abhi Rao, Jim Vaught, Ping Guan, Carol Weil, Helen M. Moore. The NCI Best Practices for Biospecimen Resources: 2016 revised recommendations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5947. doi:10.1158/1538-7445.AM2017-5947

Abstract 376: Biospecimen and data resources for cancer research from NCI’s BPV program

The Biospecimen Preanalytical Variables (BPV) Program was initiated by the National Cancer Institute’s Biorepositories and Biospecimen Research Branch to evaluate the impact of preanalytical factors on the molecular integrity of biospecimens. Selected preanalytical factors including cold ischemic time (delay to formalin fixation (DTF)), time in formalin (TIF), freezing methods, and storage temperatures and durations were examined for their potential effects on molecular profiles from surgical resection tissues and matched blood from four cancer types (kidney, ovary, colon and lung). The BPV program has collected tumor specimens from 364 cancer patients. Each specimen was annotated with 300+ data elements that cover steps in the collection, handling, and processing procedures, pathology review, and clinical information. NCI conducted multiple studies using these specimens to evaluate the preanalytical impacts on different analytical platforms including gene expression profiling, copy number variation, proteomics and metabolomics profiling. The program invites interested organizations to work with NCI through collaboration to further evaluate preanalytical effects on molecular analyses (https://techtransfer.cancer.gov/availabletechnologies/e-000-2013). The remaining specimens are available to support relevant research focusing on biospecimen science and/or clinical biomarker assay development (https://specimens.cancer.gov/search/). The IT infrastructure that was developed to support BPV biospecimen collection and management has been further developed into open source products (https://github.com/NCIP/CDR and https://github.com/NCIP/CDR-Lite). The controlled vocabulary that records the terms and definitions used in describing the overall biospecimen collection efforts has been refined and published at publicly accessible CDE repositories: NCI’s caDSR (https://cdebrowser.nci.nih.gov/CDEBrowser/ ) and NIH’s CDE portal (https://cde.nlm.nih.gov/cde/search ). An ongoing collaboration with an academic ontology consortium will map the CDEs to existing biobanking ontology frameworks and make them publicly available. The BPV program has generated a wide range of ~omics data. We are preparing a BPV data compendium to be submitted to dbGaP at NCBI. These data will be used as the experimental evidence to develop evidence-based best practices for fit-for-purpose collection, processing, and storage of biospecimens for cancer research.

Citation Format: Ping Guan, Helen M. Moore. Biospecimen and data resources for cancer research from NCI’s BPV program [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 376. doi:10.1158/1538-7445.AM2017-376

The Biobank Economic Modeling Tool (BEMT): Online Financial Planning to Facilitate Biobank Sustainability

BACKGROUND

Biospecimens are essential resources for advancing basic and translational research. However, there are little data available regarding the costs associated with operating a biobank, and few resources to enable their long-term sustainability. To support the research community in this effort, the National Institutes of Health, National Cancer Institute's Biorepositories and Biospecimen Research Branch has developed the Biobank Economic Modeling Tool (BEMT). The tool is accessible at http://biospecimens.cancer.gov/resources/bemt.asp.

METHODS

To obtain market-based cost information and to inform the development of the tool, a survey was designed and sent to 423 biobank managers and directors across the world. The survey contained questions regarding infrastructure investments, salary costs, funding options, types of biospecimen resources and services offered, as well as biospecimen pricing and service-related costs.

RESULTS

A total of 106 responses were received. The data were anonymized, aggregated, and used to create a comprehensive database of cost and pricing information that was integrated into the web-based tool, the BEMT. The BEMT was built to allow the user to input cost and pricing data through a seven-step process to build a cost profile for their biobank, define direct and indirect costs, determine cost recovery fees, perform financial forecasting, and query the anonymized survey data from comparable biobanks.

CONCLUSION

A survey was conducted to obtain a greater understanding of the costs involved in operating a biobank. The anonymized survey data was then used to develop the BEMT, a cost modeling tool for biobanks. Users of the tool will be able to create a cost profile for their biobanks' specimens, products and services, establish pricing, and allocate costs for biospecimens based on percent cost recovered, and perform project-specific cost analyses and financial forecasting.

Comparison of microbubble presence in the right heart during mechanochemical and radiofrequency ablation for varicose veins

Objective

Mechanochemical ablation is a novel technique for ablation of varicose veins utilising a rotating catheter and liquid sclerosant. Mechanochemical ablation and radiofrequency ablation have no reported neurological side-effect but the rotating mechanism of mechanochemical ablation may produce microbubbles. Air emboli have been implicated as a cause of cerebrovascular events during ultrasound-guided foam sclerotherapy and microbubbles in the heart during ultrasound-guided foam sclerotherapy have been demonstrated. This study investigated the presence of microbubbles in the right heart during varicose vein ablation by mechanochemical abaltion and radiofrequency abaltion.

Methods

Patients undergoing great saphenous vein ablation by mechanochemical abaltion or radiofrequency ablation were recruited. During the ablative procedure, the presence of microbubbles was assessed using transthoracic echocardiogram. Offline blinded image quantification was performed using International Consensus Criteria grading guidelines.

Results

From 32 recruited patients, 28 data sets were analysed. Eleven underwent mechanochemical abaltion and 17 underwent radiofrequency abaltion. There were no neurological complications. In total, 39% (11/28) of patients had grade 1 or 2 microbubbles detected. Thirty-six percent (4/11) of mechanochemical abaltion patients and 29% (5/17) of radiofrequency ablation patients had microbubbles with no significant difference between the groups ( p=0.8065).

Conclusion

A comparable prevalence of microbubbles between mechanochemical abaltion and radiofrequency ablation both of which are lower than that previously reported for ultrasound-guided foam sclerotherapy suggests that mechanochemical abaltion may not confer the same risk of neurological events as ultrasound-guided foam sclerotherapy for treatment of varicose veins.

A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project

The Genotype-Tissue Expression (GTEx) project, sponsored by the NIH Common Fund, was established to study the correlation between human genetic variation and tissue-specific gene expression in non-diseased individuals. A significant challenge was the collection of high-quality biospecimens for extensive genomic analyses. Here we describe how a successful infrastructure for biospecimen procurement was developed and implemented by multiple research partners to support the prospective collection, annotation, and distribution of blood, tissues, and cell lines for the GTEx project. Other research projects can follow this model and form beneficial partnerships with rapid autopsy and organ procurement organizations to collect high quality biospecimens and associated clinical data for genomic studies. Biospecimens, clinical and genomic data, and Standard Operating Procedures guiding biospecimen collection for the GTEx project are available to the research community.

Abstract 4500: Normal tissue and data resources for cancer research from the GTEx program

The NIH Common Fund's Genotype-Tissue Expression (GTEx) project aims to study gene expression and regulation across multiple human tissues from approximately 1000 healthy normal postmortem donors. GTEx will provide valuable insights into gene regulation and its tissue specificity, to identify correlations between genetic variations and variations in gene expression levels as expression quantitative trait loci (eQTLs), and to help understand inherited susceptibility to disease.

Initiated in 2010, the GTEx program has generated a large volume of data associated with each donor, including clinical and histopathological, as well as genotyping and gene expression data from whole genome sequencing, whole exome sequencing, expression array, and RNAseq data. The program has published research results in multiple scientific journals over the past year.

The following public resources are available from the GTEx program:

1. GTEx Portal: an open access database of GTEx expression data and analysis results: http://www.gtexportal.org

2. Database of Genotypes and Phenotypes (dbGaP): controlled access of comprehensive GTEx clinical data and raw sequencing data: http://www.ncbi.nlm.nih.gov/gap

3. Access to residual GTEx biospecimens for research: http://www.gtexportal.org/home/samplesPage

4. SOPs and best practices from GTEx biospecimen collections: http://biospecimens.cancer.gov/resources/sops/library.asp

5. GTEx histological image viewer: http://biospecimens.cancer.gov/resources/tissue_image_library.asp

6. GTEx donors’ families website: a lay description of the GTEx project tailored to the GTEx donors’ families: http://www.genome.gov/gtex

GTEx data can be used in combination with other data sets such as The Cancer Genome Atlas (TCGA) and genome-wide association studies (GWAS) to further explore the genetic causes and biology of cancer. The eQTL data from multiple tissues will help prioritize candidate genes within GWAS-associated loci; allow evaluation of tissue specificity of associated loci, and pinpoint target tissues for disease studies. Researchers are using GTEx resources to: study cancer heterogeneity by subtracting normal tissue expression; identify mutations in protein-truncating variants which may cause cancer; and explore gene activity from multiple donors across multiple tissue types to better understand the age/gender bias in cancer and other diseases.

Citation Format: Ping Guan, Abhi Rao, Simona Volpi, Susan Koester, Helen M. Moore, GTEx consortium. Normal tissue and data resources for cancer research from the GTEx program. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4500.

Factors impacting on patient perception of procedural success and satisfaction following treatment for varicose veins

Background

Patient-reported outcome measures (PROMs) have been collected from patients undergoing varicose vein treatments in the National Health Service since 2009. The aim of this retrospective cohort study was to examine PROMs for varicose vein interventions, characterizing factors that might predict patient-reported perception of procedural success and satisfaction.

Methods

Centrally compiled PROMs data for varicose vein procedures carried out from 2009 to 2011 were obtained from the Hospital Episode Statistics data warehouse for England. As data were not distributed normally, non-parametric statistical tests were employed.

Results

Data for 35 039 patient episodes (62·8 per cent women) were available for analysis. Some 23·4 per cent of patients reported a degree of anxiety or depression before treatment; a formal diagnosis of depression was present in 7·8 per cent. Quality of life, measured by generic EQ-5D-3L™ index and the Aberdeen Varicose Vein Questionnaire (AVVQ) improved after intervention by 11·7 per cent (0·77 to 0·86) and 40·1 per cent (18·95 to 11·36) respectively. No significant improvement was found in EQ-5D™ visual analogue scale scores. There was a significant improvement in self-perceived anxiety or depression after the intervention (P &lt; 0·001, McNemar–Bowker test). Both preoperative and postoperative depression or anxiety had a statistically significant relationship with self-reported success and satisfaction (both P &lt; 0·001, χ2 test).

Conclusion

This analysis of PROMs is evidence that treatment of varicose veins improves quality of life, and anxiety or depression. Preoperative and postoperative anxiety or depression scores impact on patient-perceived success and satisfaction rates.

Surgical procedures and postsurgical tissue processing significantly affect expression of genes and EGFR-pathway proteins in colorectal cancer tissue

An understanding of tissue data variability in relation to processing techniques during and postsurgery would be desirable when testing surgical specimens for clinical diagnostics, drug development, or identification of predictive biomarkers.

Specimens of normal and colorectal cancer (CRC) tissues removed during colon and liver resection surgery were obtained at the beginning of surgery and postsurgically, tissue was fixed at 10, 20, and 45 minutes. Specimens were analyzed from 50 patients with primary CRC and 43 with intrahepatic metastasis of CRC using a whole genome gene expression array. Additionally, we focused on the epidermal growth factor receptor pathway and quantified proteins and their phosphorylation status in relation to tissue processing timepoints.

Gene and protein expression data obtained from colorectal and liver specimens were influenced by tissue handling during surgery and by postsurgical processing time. To obtain reliable expression data, tissue processing for research and diagnostic purposes needs to be highly standardized.

Accuracy of Molecular Data Generated with FFPE Biospecimens: Lessons from the Literature

Formalin-fixed and paraffin-embedded (FFPE) tissue biospecimens are a valuable resource for molecular cancer research. Although much can be gained from their use, it remains unclear whether the genomic and expression profiles obtained from FFPE biospecimens accurately reflect the physiologic condition of the patient from which they were procured, or if such profiles are confounded by biologic effects from formalin fixation and processing. To assess the physiologic accuracy of genomic and expression data generated with FFPE specimens, we surveyed the literature for articles investigating genomic and expression endpoints in case-matched FFPE and fresh or frozen human biospecimens using the National Cancer Institute's Biospecimen Research Database (http://biospecimens.cancer.gov/brd). Results of the survey revealed that the level of concordance between differentially preserved biospecimens varied among analytical parameters and platforms but also among reports, genes/transcripts of interest, and tumor status. The identified analytical techniques and parameters that resulted in strong correlations between FFPE and frozen biospecimens may provide guidance when optimizing molecular protocols for FFPE use; however, discrepancies reported for similar assays also illustrate the importance of validating protocols optimized for use with FFPE specimens with a case-matched fresh or frozen cohort for each platform, gene or transcript, and FFPE processing regime. On the basis of evidence published to date, validation of analytical parameters with a properly handled frozen cohort is necessary to ensure a high degree of concordance and confidence in the results obtained with FFPE biospecimens.

Retrograde inversion stripping as a complication of the ClariVein mechanochemical venous ablation procedure

The endovenous revolution has accelerated the development of new techniques and devices for the treatment of varicose veins. The ClariVein mechanochemical ablation device offers tumescentless treatment with a rotating ablation tip that can theoretically become stuck in tissue. We present the first report of retrograde stripping of the small saphenous vein without anaesthesia following attempted use of the ClariVein device, without adverse sequelae.

A review of preanalytical factors affecting molecular, protein, and morphological analysis of formalin-fixed, paraffin-embedded (FFPE) tissue: how well do you know your FFPE specimen?

CONTEXT

Formalin fixation and paraffin embedding is a timeless, cost-efficient, and widely adopted method of preserving human tissue biospecimens that has resulted in a substantial reservoir of formalin-fixed, paraffin-embedded blocks that represent both the pathology and preanalytical handling of the biospecimen. This reservoir of specimens is increasingly being used for DNA, RNA, and proteomic analyses.

OBJECTIVE

To evaluate the impact of preanalytical factors associated with the formalin fixation and paraffin embedding process on downstream morphological and molecular endpoints.

DATA SOURCES

We surveyed the existing literature using the National Cancer Institute's Biospecimen Research Database for published reports investigating the potential influence of preanalytical factors associated with the formalin fixation and paraffin embedding process on DNA, RNA, protein, and morphological endpoints.

CONCLUSIONS

Based on the literature evidence, the molecular, proteomic, and morphological endpoints can be altered in formalin-fixed, paraffin-embedded specimens by suboptimal processing conditions. While the direction and magnitude of effects associated with a given preanalytical factor were dependent on the analyte (DNA, RNA, protein, and morphology) and analytical platform, acceptable conditions are highlighted, and a summary of conditions that could preclude analysis is provided.

The Genotype-Tissue Expression (GTEx) Project: Linking Clinical Data with Molecular Analysis to Advance Personalized Medicine

Evaluation of how genetic mutations or variability can directly affect phenotypic outcomes, the development of disease, or determination of a tailored treatment protocol is fundamental to advancing personalized medicine. To understand how a genotype affects gene expression and specific phenotypic traits, as well as the correlative and causative associations between such, the Genotype-Tissue Expression (GTEx) Project was initiated The GTEx collection of biospecimens and associated clinical data links extensive clinical data with genotype and gene expression data to provide a wealth of data and resources to study the underlying genetics of normal physiology. These data will help inform personalized medicine through the identification of normal variation that does not contribute to disease. Additionally, these data can lead to insights into how gene variation affects pharmacodynamics and individualized responses to therapy.

Meeting research needs with postmortem biospecimen donation: summary of recommendations for postmortem recovery of normal human biospecimens for research

Normal human tissues, bodily fluids, and other biospecimens of known quality are essential for research to understand the development of cancer and other diseases and to develop new diagnostics and therapies. However, obtaining normal biospecimens appropriate for contemporary large-scale molecular and genomic research is one of the most challenging biospecimen acquisition problems for scientists and biospecimen resources that support research. Recognizing this challenge, the U.S. National Cancer Institute recently convened a series of workshops and meetings focused on the acquisition of normal tissues for research and produced an extensive document, Recommendations for Postmortem Recovery of Normal Human Biospecimens for Research. This article summarizes these recommendations, addressing key ethical, operational, and scientific elements for collecting normal reference biospecimens from postmortem donors in the U.S. Awareness of these recommendations can foster more effective collaborations and mitigate potential logistical challenges, while promoting postmortem biospecimen donation options for families and increasing the availability of high quality normal biospecimens for research. The recommendations have been put into practice in the collection of normal human biospecimens for the NIH Genotype-Tissue Expression Program (GTEx), a pilot study of human gene expression and regulation in multiple tissues which will provide valuable insights into the mechanisms of gene regulation and, in the future, its disease-related perturbations (http://commonfund.nih.gov/GTEx/).

National Cancer Institute Biospecimen Evidence-Based Practices: a novel approach to pre-analytical standardization

Variable biospecimen collection, processing, and storage practices may introduce variability in biospecimen quality and analytical results. This risk can be minimized within a facility through the use of standardized procedures; however, analysis of biospecimens from different facilities may be confounded by differences in procedures and inferred biospecimen quality. Thus, a global approach to standardization of biospecimen handling procedures and their validation is needed. Here we present the first in a series of procedural guidelines that were developed and annotated with published findings in the field of human biospecimen science. The series of documents will be known as NCI Biospecimen Evidence-Based Practices, or BEBPs. Pertinent literature was identified via the National Cancer Institute (NCI) Biospecimen Research Database ( brd.nci.nih.gov ) and findings were organized by specific biospecimen pre-analytical factors and analytes of interest (DNA, RNA, protein, morphology). Meta-analysis results were presented as annotated summaries, which highlight concordant and discordant findings and the threshold and magnitude of effects when applicable. The detailed and adaptable format of the document is intended to support the development and execution of evidence-based standard operating procedures (SOPs) for human biospecimen collection, processing, and storage operations.

Acoustic reflectors are visible in the right heart during radiofrequency ablation of varicose veins

Objective

Cerebrovascular events have been noted after foam sclerotherapy for varicose veins. One hypothesis is migration of microemboli to the brain through a cardiac septal defect. The aim of this study was to identify whether acoustic reflectors are found in the right side of the heart during radiofrequency ablation of varicose veins, as neurological events are not reported during these procedures.

Methods

Transthoracic echocardiography was performed during local anaesthetic radiofrequency ablation (VNUS ClosureFast) of the great saphenous vein in 14 patients. An apical view was captured at the start of the procedure, during each cycle of heating and at 1 min post-treatment. Patients were monitored for 1 h. Video loops were read by an independent cardiologist. The presence of acoustic reflectors was classified as: 0 = absent, 1 = occasional, 2 = stream, 3 = complete opacification.

Results

Loops were of diagnostic quality in 11/14 (79%) patients. After the second cycle of heating, acoustic reflectors moving through the right heart were seen in 5/11 (45%) patients. These were classified as grade 1 in four patients and grade 2 in one patient. No acoustic reflectors were seen in the left heart. No neurological symptoms were reported.

Conclusion

Acoustic reflectors in the right heart are a common finding during radiofrequency ablation of varicose veins. Considering the prevalence of cardiac septal defects (17%), more neurological events would be expected if these particles were indeed responsible for these events. Further work is required to elicit the mechanisms underlying neurological complications following sclerotherapy.

Haemodynamic changes with the use of neuromuscular electrical stimulation compared to intermittent pneumatic compression

INTRODUCTION

Enhancement of peripheral circulation has been shown to be of benefit in many vascular disorders, and the clinical effectiveness of intermittent pneumatic compression is well established in peripheral vascular disease. This study compares the haemodynamic efficacy of a novel neuromuscular electrical stimulation device with intermittent pneumatic compression in healthy subjects.

METHODS

Ten healthy volunteers (mean age 27.1 ± 3.8 years, body mass index 24.8 ± 3.6 kg/m(2)) were randomised into two groups, in an interventional crossover trial. Devices used were the SCD Express™ Compression System, (Covidien, Ireland) and the geko™, (Firstkind Ltd, UK). Devices were applied bilaterally, and haemodynamic measurements taken from the left leg. Changes to haemodynamic parameters (superficial femory artery and femoral vein) and laser Doppler measurements from the hand and foot were compared.

RESULTS

Intermittent pneumatic compression caused 51% (p = 0.002), 5% (ns) and 3% (ns) median increases in venous peak velocity, time-averaged maximum velocity and volume flow, respectively; neuromuscular electrical stimulator stimulation caused a 103%, 101% and 101% median increases in the same parameters (all p = 0.002). The benefit was lost upon deactivation. Intermittent pneumatic compression did not improve arterial haemodynamics. Neuromuscular electrical stimulator caused 11%, 84% and 75% increase in arterial parameters (p < 0.01). Laser Doppler readings taken from the leg were increased by neuromuscular electrical stimulator (p < 0.001), dropping after deactivation. For intermittent pneumatic compression, the readings decreased during use but increased after cessation. Hand flux signal dropped during activation of both devices, rising after cessation.

DISCUSSION

The neuromuscular electrical stimulator device used in this study enhances venous flow and peak velocity in the legs of healthy subjects and is equal or superior to intermittent pneumatic compression. This warrants further clinical and economic evaluation for deep venous thrombosis prophylaxis and exploration of the haemodynamic effect in venous pathology. It also enhances arterial time-averaged maximum velocity and flow rate, which may prove to be of clinical use in the management of peripheral arterial disease. The effect on the microcirculation as evidenced by laser Doppler fluximetry may reflect a clinically beneficial target in microvascular disease, such as in the diabetic foot.

Percutaneous pharmacomechanical thrombectomy for acute iliofemoral deep vein thrombosis: A suitability study

Objectives

Percutaneous pharmacomechanical thrombectomy is an emerging therapy for acute deep vein thrombosis and may reduce long-term incidence of post-thrombotic syndrome. This study investigates the proportion of patients presenting with lower limb deep vein thrombosis who are potentially suitable for percutaneous pharmacomechanical thrombectomy.

Methods

A retrospective review of all duplex ultrasound scans for lower limb deep vein thrombosis over two-year period at a regional vascular unit was conducted. All acute occlusive iliofemoral deep vein thrombosis were screened for percutaneous pharmacomechanical thrombectomy suitability according to predefined criteria.

Results

There were 2513 duplex ultrasound scans for suspected lower limb deep vein thrombosis in the two-year period. There were 120 cases of acute occlusive iliofemoral deep vein thrombosis. After application of inclusion and exclusion criteria 48 out of 120 (40%) patients were identified as potential candidates for percutaneous pharmacomechanical thrombectomy.

Conclusions

This indicates that a large randomised trial of percutaneous pharmacomechanical thrombectomy is feasible given expected recruitment rates in a multicentre study.

The European burden of primary varicose veins

BACKGROUND

The treatment of varicose veins has been demonstrated to improve quality of life, alleviate symptoms of depression and treat the complications of venous disease. This study aims to show the studies which contain information regarding the prevalence and distribution of venous disease. Then using the population and prevalence data for venous disease, and considering the cost of treating varicose veins, this study aims to analyse the treatment of varicose veins and assess whether there is a disparity between European countries.

METHODS

Relevant papers regarding the prevalence or incidence of venous disease were identified through searches of PubMed (1966 to October 2010). The search terms 'prevalence OR incidence' AND 'varicose veins or venous disease' were used. Population data, prevalence data and the number of varicose vein procedures performed in each country was obtained for 2010.

RESULTS

Four studies were included. From calculated values comparing the predicted and actual number of patients requiring treatment for venous disease, the UK, Finland and Sweden are potentially not treating all patients with C2 disease. In contrast to this, all other European countries represented are treating more patients, suggesting that they may be treating additional patients. There was up to a four-fold difference in the numbers of procedures per million population that were performed for varicose veins in different European countries.

CONCLUSION

There is a marked disparity across Europe between the predicted number of patients with varicose veins requiring treatment and the actual care given. The factors influencing this need more detailed investigation.

Post-thrombotic syndrome: a clinical review

Up to half of patients with proximal deep vein thrombosis (DVT) will develop post-thrombotic syndrome (PTS) despite optimal anticoagulant therapy. PTS significantly impacts upon quality of life and has major health-economic implications. This narrative review describes the pathophysiology, risk factors, and diagnosis, prevention and treatment of PTS, to improve our understanding of the disease and guide treatment. Relevant articles were identified through systematic searches of the PubMed, EMBASE and Cochrane databases between 1966 and November 2011. Studies were included for detailed assessment if they met the following criteria: published in English, human study participants, study population aged > 18 years, and lower limb post-thrombotic syndrome. All non-systematic reviews and single patient case reports were excluded. Recurrent thrombosis, thrombus location and obesity are major risk factors, whereas the importance of gender and age remain uncertain. The diagnosis of PTS is based on clinical findings in patients with a known history of DVT. Several clinical scales have been described, with the Villalta Score gaining increasing popularity. Adequate anticoagulation and use of elastic compression stockings (ECS) following DVT can reduce the incidence of PTS. Catheter-directed thrombolysis and mechanical thrombectomy of acute DVT may preserve valvular function. Studies to date of these techniques are encouraging, and have reported improved hemodynamics and a reduced incidence of PTS. The management of established PTS is challenging. Compression therapy, aimed at reducing the underling venous hypertension, remains the mainstay of treatment. This is despite a paucity of high-quality evidence to support its use. Pharmacologic and surgical treatments have also been described, with a number of studies citing symptomatic improvement.

Abstract 5149: Translating biospecimen science research results to improved biospecimen practices

Cancer tissues and blood are collected, processed and stored in different ways, across the country and across the world. Biospecimen Science is the study of how different methods of biospecimen collection, processing, and storage affect downstream analysis. The NCI Biospecimen Research Network (BRN) program sponsors, conducts, and collaborates on Biospecimen Science research to better understand how biospecimen pre-analytical factors influence the molecular integrity of biospecimens, and in turn, how such variation affects the reproducibility of research results. New data on how pre-analytical variation affects molecular integrity will support best practice Standard Operating Procedures for research and clinical trials biospecimens.

This presentation will focus on results from the first phase of the BRN program and current efforts to translate research results to evidence-based biospecimen practices. A summary of research results will be presented from several research studies which have performed systematic perturbations of blood and tissue collection and processing procedures, with subsequent molecular analysis. We will also present an overview of the Biospecimen Research Database (BRD; https://brd.nci.nih.gov), developed to improve access to the literature in Biospecimen Science. The BRD is a free and publicly accessible web-based database that currently contains over 1500 review and research articles covering a broad range of topics spanning the biospecimen lifecycle. Articles are meticulously categorized and annotated by a team of Ph.D. level scientists according to the type of biospecimen and technology platform used, the experimental variables investigated, and many other parameters. Progress will be described on a new approach to perform meta-analyses of the literature evidence related to different tissue preservation methodologies, such as freezing and temperature storage methods and formalin fixation and paraffin embedding. In addition, we will describe current progress on the development of evidence-based biospecimen practices based on BRN research results, literature evidence, and expert input.

Citation Format: Helen M. Moore, Kelly Engel, Sarah Greytak, B. Paige Bass, Jim Vaught. Translating biospecimen science research results to improved biospecimen practices. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5149. doi:10.1158/1538-7445.AM2013-5149

Patterns of short saphenous vein incompetence

The significance of short saphenous vein (SSV) reflux is an under-explored territory in chronic venous disease (CVD). We have examined the origin and significance of SSV reflux in primary and secondary CVD. While the natural history of SSV incompetence remains uncertain, its prevalence has been shown to approximate 3.5%, rising with progressing clinical venous insufficiency, and bears an association with lateral malleolar venous ulceration. The most common pattern of reflux extends throughout the SSV Patterns of incompetence in recurrent disease are highly variable, but SSV reflux may itself pose a risk for recurrence, in part due to the complex anatomy of the saphenopopliteal system. Further studies are required to delineate the impact of SSV reflux in secondary venous disease and deep venous incompetence.

Number and location of venous valves within the popliteal and femoral veins: a review of the literature

Although deep venous insufficiency is common and important, the anatomy of deep vein valves is poorly understood. The aim of this study was to investigate the location, number and consistency of venous valves in the femoral and popliteal veins in normal subjects. A detailed literature search of PubMed was performed. Abstracts and selected full text articles were scrutinised and relevant studies published between 1949 and 2010 reporting anatomical details of deep vein valves were included. From 7470 articles identified by the initial search strategy, nine studies with a total of 476 legs were included in this review. All studies were cadaveric and subjects ranged from stillborn fetuses to 103 years of age. Studies suggested that femoral veins contain between one and six valves, and popliteal veins contain between zero and four valves. Deep vein valves were consistently located in the common femoral vein (within 5 cm of the inguinal ligament), the femoral vein (within 3 cm of the deep femoral vein tributary) and in the popliteal vein near the adductor hiatus. Valves are consistently located at specific locations in the deep veins of the leg, although there is often significant variability between subjects. Further anatomical and functional studies using new imaging modalities available should target these areas to identify whether certain valves play a more important role in venous disease. This may guide us in the development of new treatment options for patients with deep venous disease.

Biospecimen reporting for improved study quality (BRISQ)

Human biospecimens are subject to a number of different collection, processing, and storage factors that can significantly alter their molecular composition and consistency. These biospecimen preanalytical factors, in turn, influence experimental outcomes and the ability to reproduce scientific results. Currently, the extent and type of information specific to the biospecimen preanalytical conditions reported in scientific publications and regulatory submissions varies widely. To improve the quality of research utilizing human tissues, it is critical that information regarding the handling of biospecimens be reported in a thorough, accurate, and standardized manner. The Biospecimen Reporting for Improved Study Quality (BRISQ) recommendations outlined herein are intended to apply to any study in which human biospecimens are used. The purpose of reporting these details is to supply others, from researchers to regulators, with more consistent and standardized information to better evaluate, interpret, compare, and reproduce the experimental results. The BRISQ guidelines are proposed as an important and timely resource tool to strengthen communication and publications around biospecimen-related research and help reassure patient contributors and the advocacy community that the contributions are valued and respected.

Effects of preanalytical variables on the detection of proteins by immunohistochemistry in formalin-fixed, paraffin-embedded tissue

CONTEXT

While formalin fixation and paraffin embedding has become a universal mechanism of tissue preservation and a gold standard for immunohistochemistry, fixation and processing variables that may confound assay effectiveness have received little attention from the scientific community.

OBJECTIVE

To identify discrete steps in specimen fixation and processing that may impact immunostaining, assess the magnitude of reported effects in the literature, and highlight preanalytical variables that require further investigation.

DATA SOURCES

Thirty-nine primary research articles that investigated immunohistochemical effects of 1 or more preanalytical variables were identified by our literature survey. Thresholds identified in the literature were then compared with published immunohistochemistry guidelines for formalin-fixed, paraffin-embedded specimens.

CONCLUSIONS

Of the 62 preanalytical variables identified, 27 were examined in published research. Meta-analysis revealed 15 preanalytical variables that were capable of impacting immunohistochemistry (including fixation delay; fixative type; time in fixative; reagents and conditions of dehydration, clearing, and paraffin impregnation; and conditions of slide drying and storage) and 12 variables with no reported influence (including the type of processor used; the number and position of specimens during dehydration, clearing, and paraffin impregnation; and the duration of paraffin block storage). Variables with antigen-dependent or inconsistent effects were highlighted. Comparison of literature-supported thresholds with published recommendations revealed (1) strong agreement among preanalytical variables for optimal immunostaining, (2) discrepancies among thresholds for adequate immunostaining, and (3) the continued need for rigorous research and comprehensive guidelines on specimen fixation, processing, and storage.