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Andrea R Mazzocchi, Shiny A P Rajan, Konstantinos I Votanopoulos, Adam R Hall, Aleksander Skardal
Variability in patient response to anti-cancer drugs is currently addressed by relating genetic mutations to chemotherapy through precision medicine. However, practical benefits of precision medicine to therapy design are less clear. Even after identification of mutations, oncologists are often left with several drug options, and for some patients there is no definitive treatment solution. There is a need for model systems to help predict personalized responses to chemotherapeutics. We have microengineered 3D tumor organoids directly from fresh tumor biopsies to provide patient-specific models with which treatment optimization can be performed before initiation of therapy...
February 13, 2018: Scientific Reports
Peggy Manders, Tessa M A Peters, Ariaan E Siezen, Iris A L M van Rooij, Roger Snijder, Dorine W Swinkels, Gerhard A Zielhuis
INTRODUCTION: Current guidelines for clinical biobanking have a strong focus on obtaining, handling, and storage of biospecimens. However, to allow for research tying biomarker analysis to clinical decision making, there should be more focus on collection of data on donor characteristics. Therefore, our aim was to develop a stepwise procedure to define a framework as a tool to help start the data collection process in clinical biobanking. MATERIALS AND METHODS: The Radboud Biobank (RB) is a central clinical biobanking facility designed in accordance with the standards set by the Parelsnoer Institute, a Dutch national biobank originally initiated with eight different disease cohorts...
February 13, 2018: Biopreservation and Biobanking
David G Huntsman, Marc Ladanyi
As the cancer genomics of most major cancer types have been comprehensively catalogued over the past decade through a variety of national and international efforts, the delineation of cancer subtypes has been refined, and our understanding of critical cancer drivers and of the potentially targetable vulnerabilities they create has grown tremendously. The 2018 Annual Review Issue of The Journal of Pathology provides in-depth assessments of how these pan-genomic approaches have enabled advances in cancer classification, targeted therapy selection, and assessment of cancer progression, all of which are now genomically informed, using several cancer types as examples...
February 13, 2018: Journal of Pathology
Samuel O Antwi, Gloria M Petersen
Many risk factors have been firmly established for pancreatic cancer (PC), but the molecular processes by which known risk factors influence susceptibility to PC are not clear. There has been a recent upsurge of interest in the role of telomere length (TL), the protective DNA sequence repeats at chromosome ends, in pancreatic carcinogenesis. Given this heightened interest, we performed an in-depth, focused, and up-to-date review of the epidemiological evidence linking leukocyte TL (LTL) with PC risk. We searched MEDLINE, Embase, and the Cochrane Library databases for all published studies on LTL and PC risk, up to May 2017...
March 2018: Pancreas
Giulio Ferrero, Francesca Cordero, Sonia Tarallo, Maddalena Arigoni, Federica Riccardo, Gaetano Gallo, Guglielmo Ronco, Marco Allasia, Neha Kulkarni, Giuseppe Matullo, Paolo Vineis, Raffaele A Calogero, Barbara Pardini, Alessio Naccarati
The role of non-coding RNAs in different biological processes and diseases is continuously expanding. Next-generation sequencing together with the parallel improvement of bioinformatics analyses allows the accurate detection and quantification of an increasing number of RNA species. With the aim of exploring new potential biomarkers for disease classification, a clear overview of the expression levels of common/unique small RNA species among different biospecimens is necessary. However, except for miRNAs in plasma, there are no substantial indications about the pattern of expression of various small RNAs in multiple specimens among healthy humans...
January 9, 2018: Oncotarget
Maimuna Mendy, Rita T Lawlor, Anne Linda van Kappel, Peter H J Riegman, Fay Betsou, Oliver D Cohen, Marianne K Henderson
Biobanks provide a critical infrastructure to support research in human health. Biospecimens and their accompanying data are increasingly needed to support biomedical research and clinical care. The original text was initially published in the Handbook for Cancer Research in Africa. The value of this publication is great as it underlines the importance of biobanks in Africa as a key resource to increase quality scientific research and participate in global health research. Therefore, a revision to extend these principles to other low resource contexts, to include updated material and references and add the topic of biobank sustainability were relevant...
March 2018: Clinics in Laboratory Medicine
Oh Yoen Kim, Jiyoung Moon, Garam Jo, So-Young Kwak, Ji Young Kim, Min-Jeong Shin
BACKGROUND/OBJECTIVES: This study aimed to test the association between APOA5 3'-UTR variants (rs662799) and cardiometabolic traits in Koreans. SUBJECTS/METHODS: For this study, epidemiological data, Apolipoprotein A5 (APOA5) genotype information, and lymphoblastoid cell line (LCL) biospecimens from a subset of the Ansung-Ansan cohort within the Korean Genome and Epidemiology study (KoGES-ASAS; n = 7,704) as well as epidemiological data along with genomic DNA biospecimens of participants from a subset of the Korea National Health and Nutrition Examination Survey (KNHANES 2011-12; n = 2,235) were obtained...
February 2018: Nutrition Research and Practice
Kristopher J Bough, Jonathan D Pollock
Addiction is a brain disease, and current diagnostic criteria for substance use disorders (SUDs) are qualitative. Nevertheless, scientific advances are beginning to characterize neurobiological domains. Combining multiple units of measure may provide an opportunity to deconstruct the heterogeneities of a SUD and define endophenotypes by using peripheral biospecimens. There are several recent examples of potential biomarker types that can be examined, together with their categorical applications for SUDs. We propose that, in conjunction with rapidly advancing statistical and mathematical modeling techniques, there is now a unique opportunity for the discovery of composite biomarkers within specific domains of addiction; these may lay the foundation for future biomarker qualification, with important implications for drug development and medical care...
January 15, 2018: Trends in Molecular Medicine
Teddy D Warner, Carol J Weil, Christopher Andry, Howard B Degenholtz, Lisa Parker, Latarsha J Carithers, Michelle Feige, David Wendler, Rebecca D Pentz
Commentators are concerned that broad consent may not provide biospecimen donors with sufficient information regarding possible future research uses of their tissue. We surveyed with interviews 302 cancer patients who had recently provided broad consent at four diverse academic medical centers. The majority of donors believed that the consent form provided them with sufficient information regarding future possible uses of their biospecimens. Donors expressed very positive views regarding tissue donation in general and endorsed the use of their biospecimens in future research across a wide range of contexts...
January 1, 2018: Journal of Empirical Research on Human Research Ethics: JERHRE
D R S Middleton, M J Watts, E M Hamilton, J D Coe, T Fletcher, H Crabbe, R Close, G S Leonardi, D A Polya
Dust elemental levels can be expressed as concentrations (bulk samples) or surface loadings (wipe samples). Wipe sampling has not been widely adopted for elements other than lead (Pb). In this study, 433 wipe samples from 130 households in south west England - a region of widespread, natural and anthropogenic arsenic contamination linked with previous mining activities-were analysed to (i) quantify loadings of arsenic (As); (ii) assess the quality of wipe data using QA/QC criteria; (iii) estimate, using published ingestion rates, human exposure to As in dust using loadings and concentrations from 97 bulk samples and (iv) comparatively assess the performance of wipe and bulk sampling using associations with As biomonitoring data (urine, toenails and hair)...
February 1, 2018: Environmental Science. Processes & Impacts
Cynthia Kleeberger, David Shore, Elaine Gunter, Dale P Sandler, Clarice R Weinberg
BACKGROUND: Cohort studies typically bank biospecimens for many years prior to assay and investigators do not know whether levels of analytes have degraded. METHODS: We collected control samples from 22 non-study participants using the same enrollment criteria and specimen collection, processing, and storage protocols as The Sister Study. Serum samples were assayed for 21 analytes at collection and 6 years later. For each sample, the difference between the result at baseline and at 6 years was calculated for each analyte...
January 30, 2018: Epidemiology
Zurab Bzhalava, Emilie Hultin, Joakim Dillner
When human samples are sequenced, many assembled contigs are "unknown", as conventional alignments find no similarity to known sequences. Hidden Markov models (HMM) exploit the positions of specific nucleotides in protein-encoding codons in various microbes. The algorithm HMMER3 implements HMM using a reference set of sequences encoding viral proteins, "vFam". We used HMMER3 analysis of "unknown" human sample-derived sequences and identified 510 contigs distantly related to viruses (Anelloviridae (n = 1), Baculoviridae (n = 34), Circoviridae (n = 35), Caulimoviridae (n = 3), Closteroviridae (n = 5), Geminiviridae (n = 21), Herpesviridae (n = 10), Iridoviridae (n = 12), Marseillevirus (n = 26), Mimiviridae (n = 80), Phycodnaviridae (n = 165), Poxviridae (n = 23), Retroviridae (n = 6) and 89 contigs related to described viruses not yet assigned to any taxonomic family)...
2018: PloS One
Sa Liu, Hasmik Grigoryan, William Matthew Bell Edmands, Sonia Dagnino, Rudy Sinharay, Paul Cullinan, Peter Collins, Kian Fan Chung, Benjamin M Barratt, Frank J Kelly, Paolo Vineis, Stephen M Rappaport
Oxidative stress generates reactive species that modify proteins, deplete antioxidant defenses and contribute to chronic obstructive pulmonary disease (COPD) and ischemic heart disease (IHD). To determine whether protein modifications differ between COPD or IHD patients and healthy subjects, we performed untargeted analysis of adducts at the Cys34 locus of human serum albumin (HSA). Biospecimens were obtained from nonsmoking participants from London, U.K., including healthy subjects (n=20) and patients with COPD (n=20) or IHD (n=10)...
January 19, 2018: Environmental Science & Technology
Sarah Ringold, Peter A Nigrovic, Brian M Feldman, George A Tomlinson, Emily von Scheven, Carol A Wallace, Adam M Huber, Laura E Schanberg, Suzanne C Li, Pamela F Weiss, Robert C Fuhlbrigge, Esi M Morgan, Yukiko Kimura
The pediatric rheumatic diseases are a heterogeneous group of rare diseases, posing a number of challenges for the use of traditional clinical and translational research approaches. Innovative comparative effectiveness approaches are needed to efficiently study treatment approaches and disease outcomes. The Childhood Arthritis and Rheumatology Research Alliance (CARRA) developed the consensus treatment plan (CTP) approach as a comparative effectiveness tool for research in pediatric rheumatology. CTPs are treatment strategies, developed by consensus methods among CARRA members, intended to reduce variation in treatment approaches, standardize outcome measurements, and allow for comparison of the effectiveness of different approaches with the goal of improving disease outcomes...
January 15, 2018: Arthritis & Rheumatology
Ann M Gronowski, Melanie L Yarbrough
Pregnancy remains a significant health risk to women in both developed and underdeveloped countries. Worldwide, 10 to 20 million women have pregnancy complications including ectopic pregnancy, preterm birth, gestational diabetes mellitus, and hypertensive states, including preeclampsia. Despite advancements in women's health research, there is a large gap in the diagnostic tools available to screen, diagnose, and monitor these conditions. Herein, we examine existing diagnostic tools, such as the human chorionic gonadotropin discriminatory zone, cervicovaginal fetal fibronectin, sFlt-1:PlGF ratio, and glucose tolerance testing...
February 1, 2018: Endocrinology
Jessica M Page, Vanessa Thorsten, Uma M Reddy, Donald J Dudley, Carol J Rowland Hogue, George R Saade, Halit Pinar, Corette B Parker, Deborah Conway, Barbara J Stoll, Donald Coustan, Radek Bukowski, Michael W Varner, Robert L Goldenberg, Karen Gibbins, Robert M Silver
OBJECTIVE: To estimate the proportion of potentially preventable stillbirths in the United States. METHODS: We conducted a secondary analysis of 512 stillbirths with complete evaluation enrolled in the Stillbirth Collaborative Research Network from 2006 to 2008. The Stillbirth Collaborative Research Network was a multisite, geographically, racially, and ethnically diverse, population-based case-control study of stillbirth in the United States. Cases of stillbirth underwent standard evaluation that included maternal interview, medical record abstraction, biospecimen collection, postmortem examination, placental pathology, and clinically recommended evaluation...
February 2018: Obstetrics and Gynecology
Collin Dickerson, Yanshen Hsu, Sandra Mendoza, Iman Osman, Jennifer Ogilvie, Kepal Patel, Andre L Moreira
Biospecimen quality can vary depending on many pre- and post-collection variables. In this study, we consider a natural disaster as a post-collection variable that may have compromised the quality of frozen tissue specimens. To investigate this possible link, we compared the quality of nucleic acids, the level of antigenicity, and the preservation of histology from frozen specimens collected before and after the power outage caused by Hurricane Sandy. To analyze nucleic acid quality, we extracted both DNA and RNA and performed capillary electrophoresis to compare the quality and concentrations of the nucleic acids...
January 3, 2018: Biopreservation and Biobanking
Tye E Arbuckle, Chun Lei Liang, Mandy Fisher, Nicolas J Caron, William D Fraser
Given that prenatal exposure to tobacco smoke can lead to increased risks of adverse health effects, having valid measures of exposure is important. In a Canadian cohort (nā€‰=ā€‰2000), maternal and infant biospecimens were analysed for cotinine. Sensitivity and specificity of self-reported active smoking status were estimated. Regression modelling was used to identify potential predictors of maternal and infant plasma cotinine in non-smoking women. During the first trimester, 60.6% of the women reported never smoking, 27...
January 3, 2018: Journal of Exposure Science & Environmental Epidemiology
Lokesh Agrawal, Kelly B Engel, Sarah R Greytak, Helen M Moore
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...
December 16, 2017: Seminars in Cancer Biology
Maria De Matteis, Giovanni Cecchetto, Giada Munari, Laura Balsamo, Marina Paola Gardiman, Renzo Giordano, Guido Viel, Matteo Fassan
Sudden and unexpected death in epilepsy (SUDEP) represents one of the most challenging fields for clinical, forensic and preventative pathology. Several authors have emphasized the search of innovative biomarkers related to drug-resistance for an appropriate risk stratification in these patients. However, no reliable biomarker has been implemented into clinical practice, so far. Herein, we present a case of SUDEP due to drug-resistant mesial temporal lobe epilepsy (MTLE) in which we performed miRNA expression profiling (miR-301a-3p, miR-194-5p, miR-30b-5p, mIR-342-5p, and miR-4446-3p) from both the plasma and the temporal lobe in comparison to ten autopsies for traumatic or asphyxia deaths...
December 4, 2017: Legal Medicine
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