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.