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https://www.readbyqxmd.com/read/27929677/assessing-researcher-needs-for-a-virtual-biobank
#1
Jenna van Draanen, Pamela Davidson, Helene Bour-Jordan, LeeAnna Bowman-Carpio, David Boyle, Steve Dubinett, Brian Gardner, Jachael Gardner, Courtney McFall, Dan Mercola, Terry Nakazono, Stephanie Soares, Hubert Stoppler, Margaret Tempero, Scott Vandenberg, Yu-Jui Yvonne Wan, Sarah Dry
INTRODUCTION: Biosamples and associated clinical data accelerate translational and clinical research discoveries. A lack of high quality biosamples both stalls projects and limits research advances. In this study, we targeted a wide audience of University of California (UC) biobanking stakeholders who were either involved with the collection or the utilization of biosamples to assess the scope of their biobanking activities and their interest in virtual biobanking or cooperating in the formation of the UC-wide biorepository...
December 8, 2016: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/27929525/the-precision-medicine-initiative-s-all-of-us-research-program-an-agenda-for-research-on-its-ethical-legal-and-social-issues
#2
REVIEW
Pamela L Sankar, Lisa S Parker
The Precision Medicine Initiative (PMI) is an innovative approach to developing a new model of health care that takes into account individual differences in people's genes, environments, and lifestyles. A cornerstone of the initiative is the PMI All of Us Research Program (formerly known as PMI-Cohort Program) which will create a cohort of 1 million volunteers who will contribute their health data and biospecimens to a centralized national database to support precision medicine research. The PMI All of US Research Program is the largest longitudinal study in the history of the United States...
December 8, 2016: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/27926908/community-perceptions-of-biobanking-participation-a-qualitative-study-among-mexican-americans-in-three-texas-cities
#3
Natalia I Heredia, Sarah Krasny, Larkin L Strong, Laura Von Hatten, Lynne Nguyen, Belinda M Reininger, Lorna H McNeill, María E Fernández
BACKGROUND: Most biospecimens in the US are collected from non-Hispanic Whites, limiting the generalizability of findings. There is a need to increase participation in biobanking among ethnic and racial minorities. The purpose of this study was to use qualitative methods to identify factors that may influence Mexican-American individuals' willingness to participate in biobanking. METHODS: We conducted 15 focus groups in three Texas cities with Mexican-American individuals, in both Spanish and English...
December 8, 2016: Public Health Genomics
https://www.readbyqxmd.com/read/27925796/a-severe-asthma-disease-signature-from-gene-expression-profiling-of-peripheral-blood-from-u-biopred-cohorts
#4
Jeannette Bigler, Michael Boedigheimer, James P R Schofield, Paul J Skipp, Julie Corfield, Anthony Rowe, Ana R Sousa, Martin Timour, Lori Twehues, Xuguang Hu, Graham Roberts, Andrew A Welcher, Wen Yu, Kian F Chung, Ian M Adcock, Peter J Sterk, Ratko Djukanović
RATIONALE: Stratification of asthma at the molecular level, especially using accessible biospecimens, could greatly enable patient selection for targeted therapy. OBJECTIVES: To determine the value of blood to identify transcriptional differences between clinically defined asthmatic and non-asthmatic groups, identify potential patient subgroups based on gene expression, and explore biological pathways associated with identified differences. METHODS: Transcriptomics profiles were generated by microarray analysis of blood from 610 asthmatic and control participants in U-BIOPRED...
December 7, 2016: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/27924041/exposome-explorer-a-manually-curated-database-on-biomarkers-of-exposure-to-dietary-and-environmental-factors
#5
Vanessa Neveu, Alice Moussy, Héloïse Rouaix, Roland Wedekind, Allison Pon, Craig Knox, David S Wishart, Augustin Scalbert
Exposome-Explorer (http://exposome-explorer.iarc.fr) is the first database dedicated to biomarkers of exposure to environmental risk factors. It contains detailed information on the nature of biomarkers, their concentrations in various human biospecimens, the study population where measured and the analytical techniques used for measurement. It also contains correlations with external exposure measurements and data on biological reproducibility over time. The data in Exposome-Explorer was manually collected from peer-reviewed publications and organized to make it easily accessible through a web interface for in-depth analyses...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27914218/disruptive-influences-on-research-in-academic-pathology-departments-proposed-changes-to-the-common-rule-governing-informed-consent-for-research-use-of-biospecimens-and-to-rules-governing-return-of-research-results
#6
REVIEW
Mark E Sobel, Jennifer C Dreyfus
Academic pathology departments will be dramatically affected by proposed United States federal government regulatory initiatives. Pathology research will be substantially altered if proposed changes to the Common Rule (Code of Federal Regulations: Protection of Human Subjects title 45 CFR 46) and regulations governing the return of individual research results are approved and finalized, even more so now that the Precision Medicine initiative has been launched. Together, these changes are disruptive influences on academic pathology research as we know it, straining limited resources and compromising advances in diagnostic and academic pathology...
November 30, 2016: American Journal of Pathology
https://www.readbyqxmd.com/read/27899076/the-kaiser-permanente-northern-california-research-program-on-genes-environment-and-health-rpgeh-pregnancy-cohort-study-design-methodology-and-baseline-characteristics
#7
M M Hedderson, A Ferrara, L A Avalos, S K Van den Eeden, E P Gunderson, D K Li, A Altschuler, S Woo, S Rowell, V Choudhary, F Xu, T Flanagan, C Schaefer, L A Croen
BACKGROUND: Exposures during the prenatal period may have lasting effects on maternal and child health outcomes. To better understand the effects of the in utero environment on children's short- and long-term health, large representative pregnancy cohorts with comprehensive information on a broad range of environmental influences (including biological and behavioral) and the ability to link to prenatal, child and maternal health outcomes are needed. The Research Program on Genes, Environment and Health (RPGEH) pregnancy cohort at Kaiser Permanente Northern California (KPNC) was established to create a resource for conducting research to better understand factors influencing women's and children's health...
November 29, 2016: BMC Pregnancy and Childbirth
https://www.readbyqxmd.com/read/27884938/the-russian-human-radiobiological-tissue-repository-a-unique-resource-for-studies-of-plutonium-exposed-workers
#8
Christopher Loffredo, David Goerlitz, Svetlana Sokolova, Leonidas Leondaridis, Mariya Zakharova, Valentina Revina, Evgeniya Kirillova
The Russian Radiobiological Human Tissue Repository (RHTR) at the Southern Urals Biophysics Institute in Ozyorsk, Russia, was established to collect and store biospecimens supporting research on health consequences of chronic, low-dose radiation exposures. The purpose of this paper is to describe the RHTR resources and the availability of high-quality biological specimens. RHTR has enrolled two groups of subjects from 1951 to the present time: exposed workers at the Mayak Production Association facilities and residents of Ozyorsk who were never occupationally exposed to ionizing radiation (controls)...
November 24, 2016: Radiation Protection Dosimetry
https://www.readbyqxmd.com/read/27864463/increased-brain-hemopexin-levels-improve-outcomes-after-intracerebral-hemorrhage
#9
Jenna L Leclerc, Juan Santiago-Moreno, Alex Dang, Andrew S Lampert, Pedro E Cruz, Awilda M Rosario, Todd E Golde, Sylvain Doré
Following intracerebral hemorrhage (ICH), extracellular heme precipitates secondary brain injury, which results in irreversible brain damage and enduring neurological deficits. Hemopexin (Hpx) is an endogenous protein responsible for scavenging heme, thereby modulating its intrinsic proxidant/proinflammatory properties. Although Hpx is present in the brain, the endogenous levels are insufficient to combat the massive heme overload following ICH. We hypothesized that increasing brain Hpx levels would improve ICH outcomes...
November 18, 2016: Journal of Cerebral Blood Flow and Metabolism
https://www.readbyqxmd.com/read/27861202/novel-approaches-to-early-detection-of-endometrial-cancer
#10
Madhu Bagaria, Emily Shields, Jamie N Bakkum-Gamez
PURPOSE OF REVIEW: Detection of endometrial cancer at an early stage leads to better oncologic outcomes. To date, a screening test for endometrial cancer does not exist. RECENT FINDINGS: Evolving knowledge of molecular changes involved in endometrial cancer carcinogenesis paired with sensitive and high-throughput technological advancements are a promising combination that can be leveraged to detect tumor DNA and proteins. These molecular biomarkers can be identified in biospecimens collected via minimally invasive and noninvasive approaches...
November 17, 2016: Current Opinion in Obstetrics & Gynecology
https://www.readbyqxmd.com/read/27834768/design-and-implementation-of-a-prospective-adult-congenital-heart-disease-biobank
#11
Alexander R Opotowsky, Brittani Loukas, Christina Ellervik, Lilamarie E Moko, Michael N Singh, Elizabeth I Landzberg, Eric B Rimm, Michael J Landzberg
BACKGROUND: Adults with congenital heart disease (ACHD) comprise a growing, increasingly complex population. The Boston Adult Congenital Heart Disease Biobank is a program for the collection and storage of biospecimens to provide a sustainable resource for scientific biomarker investigation in ACHD. METHODS: We describe a protocol to collect, process, and store biospecimens for ACHD or associated diagnoses developed based on existing literature and consultation with cardiovascular biomarker epidemiologists...
November 2016: World Journal for Pediatric & Congenital Heart Surgery
https://www.readbyqxmd.com/read/27820856/piphillin-improved-prediction-of-metagenomic-content-by-direct-inference-from-human-microbiomes
#12
Shoko Iwai, Thomas Weinmaier, Brian L Schmidt, Donna G Albertson, Neil J Poloso, Karim Dabbagh, Todd Z DeSantis
Functional analysis of a clinical microbiome facilitates the elucidation of mechanisms by which microbiome perturbation can cause a phenotypic change in the patient. The direct approach for the analysis of the functional capacity of the microbiome is via shotgun metagenomics. An inexpensive method to estimate the functional capacity of a microbial community is through collecting 16S rRNA gene profiles then indirectly inferring the abundance of functional genes. This inference approach has been implemented in the PICRUSt and Tax4Fun software tools...
2016: PloS One
https://www.readbyqxmd.com/read/27807829/experimental-and-study-design-considerations-for-uncovering-oncometabolites
#13
Majda Haznadar, Ewy A Mathé
Metabolomics as a field has gained attention due to its potential for biomarker discovery, namely because it directly reflects disease phenotype and is the downstream effect of posttranslational modifications. The field provides a "top-down," integrated view of biochemistry in complex organisms, as opposed to the traditional "bottom-up" approach that aims to analyze networks of interactions between genes, proteins and metabolites. It also allows for the detection of thousands of endogenous metabolites in various clinical biospecimens in a high-throughput manner, including tissue and biofluids such as blood and urine...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27788264/draq5-and-eosin-d-e-as-an-analog-to-hematoxylin-and-eosin-for-rapid-fluorescence-histology-of-fresh-tissues
#14
Katherine N Elfer, Andrew B Sholl, Mei Wang, David B Tulman, Sree H Mandava, Benjamin R Lee, J Quincy Brown
Real-time on-site histopathology review of biopsy tissues at the point-of-procedure has great potential for significant clinical value and improved patient care. For instance, on-site review can aid in rapid screening of diagnostic biopsies to reduce false-negative results, or in quantitative assessment of biospecimen quality to increase the efficacy of downstream laboratory and histopathology analysis. However, the only currently available rapid pathology method, frozen section analysis (FSA), is too time- and labor-intensive for use in screening large quantities of biopsy tissues and is too destructive for maximum tissue conservation in multiple small needle core biopsies...
2016: PloS One
https://www.readbyqxmd.com/read/27785453/distributed-cognition-and-process-management-enabling-individualized-translational-research-the-nih-undiagnosed-diseases-program-experience
#15
Amanda E Links, David Draper, Elizabeth Lee, Jessica Guzman, Zaheer Valivullah, Valerie Maduro, Vlad Lebedev, Maxim Didenko, Garrick Tomlin, Michael Brudno, Marta Girdea, Sergiu Dumitriu, Melissa A Haendel, Christopher J Mungall, Damian Smedley, Harry Hochheiser, Andrew M Arnold, Bert Coessens, Steven Verhoeven, William Bone, David Adams, Cornelius F Boerkoel, William A Gahl, Murat Sincan
The National Institutes of Health Undiagnosed Diseases Program (NIH UDP) applies translational research systematically to diagnose patients with undiagnosed diseases. The challenge is to implement an information system enabling scalable translational research. The authors hypothesized that similar complex problems are resolvable through process management and the distributed cognition of communities. The team, therefore, built the NIH UDP integrated collaboration system (UDPICS) to form virtual collaborative multidisciplinary research networks or communities...
2016: Frontiers in Medicine
https://www.readbyqxmd.com/read/27776981/asthma-metabolomics-and-the-potential-for-integrative-omics-in-research-and-the-clinic
#16
Rachel S Kelly, Amber Dahlin, Michael J McGeachie, Weiliang Qiu, Joanne Sordillo, Emily S Wan, Ann Chen Wu, Jessica Lasky-Su
Asthma is a complex disease well suited to metabolomic profiling, both for the development of novel biomarkers and for the improved understanding of pathophysiology. In this review, we summarize the 21 existing metabolomic studies of asthma in humans, all of which reported significant findings and concluded that individual metabolites and metabolomic profiles measured in exhaled breath condensate, urine, plasma and serum could identify asthmatics and asthma phenotypes with high discriminatory ability. There was considerable consistency across the studies in terms of the reported biomarkers, regardless of biospecimen, profiling technology and population age...
October 21, 2016: Chest
https://www.readbyqxmd.com/read/27776540/the-alliance-between-genetic-biobanks-and-patient-organisations-the-experience-of-the-telethon-network-of-genetic-biobanks
#17
Chiara Baldo, Lorena Casareto, Alessandra Renieri, Giuseppe Merla, Barbara Garavaglia, Stefano Goldwurm, Elena Pegoraro, Maurizio Moggio, Marina Mora, Luisa Politano, Luca Sangiorgi, Raffaella Mazzotti, Valeria Viotti, Ilaria Meloni, Maria Teresa Pellico, Chiara Barzaghi, Chiuhui Mary Wang, Lucia Monaco, Mirella Filocamo
BACKGROUND: Rare diseases (RDs) are often neglected because they affect a small percentage of the population (6-8 %), which makes research and development of new therapies challenging processes. Easy access to high-quality samples and associated clinical data is therefore a key prerequisite for biomedical research. In this context, Genetic Biobanks are critical to developing basic, translational and clinical research on RDs. The Telethon Network of Genetic Biobanks (TNGB) is aware of the importance of biobanking as a service for patients and has started a dialogue with RD-Patient Organisations via promotion of dedicated meetings and round-tables, as well as by including their representatives on the TNGB Advisory Board...
October 24, 2016: Orphanet Journal of Rare Diseases
https://www.readbyqxmd.com/read/27775701/gpr133-adgrd1-an-adhesion-g-protein-coupled-receptor-is-necessary-for-glioblastoma-growth
#18
N S Bayin, J D Frenster, J R Kane, J Rubenstein, A S Modrek, R Baitalmal, I Dolgalev, K Rudzenski, L Scarabottolo, D Crespi, L Redaelli, M Snuderl, J G Golfinos, W Doyle, D Pacione, E C Parker, A S Chi, A Heguy, D J MacNeil, N Shohdy, D Zagzag, D G Placantonakis
Glioblastoma (GBM) is a deadly primary brain malignancy with extensive intratumoral hypoxia. Hypoxic regions of GBM contain stem-like cells and are associated with tumor growth and angiogenesis. The molecular mechanisms that regulate tumor growth in hypoxic conditions are incompletely understood. Here, we use primary human tumor biospecimens and cultures to identify GPR133 (ADGRD1), an orphan member of the adhesion family of G-protein-coupled receptors, as a critical regulator of the response to hypoxia and tumor growth in GBM...
October 24, 2016: Oncogenesis
https://www.readbyqxmd.com/read/27770794/national-ethics-guidance-in-sub-saharan-africa-on-the-collection-and-use-of-human-biological-specimens-a-systematic-review
#19
Francis Barchi, Madison T Little
BACKGROUND: Ethical and regulatory guidance on the collection and use of human biospecimens (HBS) for research forms an essential component of national health systems in Sub-Saharan Africa (SSA), where rapid advances in genetic- and genomic-based technologies are fueling clinical trials involving HBS and the establishment of large-scale biobanks. METHODS: An extensive multi-level search for publicly available ethics regulatory guidance was conducted for each SSA country...
October 22, 2016: BMC Medical Ethics
https://www.readbyqxmd.com/read/27768182/association-of-distinct-mutational-signatures-with-correlates-of-increased-immune-activity-in-pancreatic-ductal-adenocarcinoma
#20
Ashton A Connor, Robert E Denroche, Gun Ho Jang, Lee Timms, Sangeetha N Kalimuthu, Iris Selander, Treasa McPherson, Gavin W Wilson, Michelle A Chan-Seng-Yue, Ivan Borozan, Vincent Ferretti, Robert C Grant, Ilinca M Lungu, Eithne Costello, William Greenhalf, Daniel Palmer, Paula Ghaneh, John P Neoptolemos, Markus Buchler, Gloria Petersen, Sarah Thayer, Michael A Hollingsworth, Alana Sherker, Daniel Durocher, Neesha Dhani, David Hedley, Stefano Serra, Aaron Pollett, Michael H A Roehrl, Prashant Bavi, John M S Bartlett, Sean Cleary, Julie M Wilson, Ludmil B Alexandrov, Malcolm Moore, Bradly G Wouters, John D McPherson, Faiyaz Notta, Lincoln D Stein, Steven Gallinger
Importance: Outcomes for patients with pancreatic ductal adenocarcinoma (PDAC) remain poor. Advances in next-generation sequencing provide a route to therapeutic approaches, and integrating DNA and RNA analysis with clinicopathologic data may be a crucial step toward personalized treatment strategies for this disease. Objective: To classify PDAC according to distinct mutational processes, and explore their clinical significance. Design, Setting, and Participants: We performed a retrospective cohort study of resected PDAC, using cases collected between 2008 and 2015 as part of the International Cancer Genome Consortium...
October 20, 2016: JAMA Oncology
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