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Biorepository

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https://www.readbyqxmd.com/read/29144792/effect-of-blood-collection-tube-type-and-time-to-processing-on-the-enumeration-and-high-content-characterization-of-circulating-tumor-cells-using-the-high-definition-single-cell-assay
#1
Mariam Rodríguez-Lee, Anand Kolatkar, Madelyn McCormick, Angel D Dago, Jude Kendall, Nils Anders Carlsson, Kelly Bethel, Emily J Greenspan, Shelley E Hwang, Kathryn R Waitman, Jorge J Nieva, James Hicks, Peter Kuhn
CONTEXT: - As circulating tumor cell (CTC) assays gain clinical relevance, it is essential to address preanalytic variability and to develop standard operating procedures for sample handling in order to successfully implement genomically informed, precision health care. OBJECTIVE: - To evaluate the effects of blood collection tube (BCT) type and time-to-assay (TTA) on the enumeration and high-content characterization of CTCs by using the high-definition single-cell assay (HD-SCA)...
November 16, 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/29118648/data-release-dna-barcodes-of-plant-species-collected-for-the-global-genome-initiative-for-gardens-program-national-museum-of-natural-history-smithsonian-institution
#2
Jose D Zúñiga, Morgan R Gostel, Daniel G Mulcahy, Katharine Barker, Asia Hill, Maryam Sedaghatpour, Samantha Q Vo, Vicki A Funk, Jonathan A Coddington
The Global Genome Initiative has sequenced and released 1961 DNA barcodes for genetic samples obtained as part of the Global Genome Initiative for Gardens Program. The dataset includes barcodes for 29 plant families and 309 genera that did not have sequences flagged as barcodes in GenBank and sequences from officially recognized barcoding genetic markers meet the data standard of the Consortium for the Barcode of Life. The genetic samples were deposited in the Smithsonian Institution's National Museum of Natural History Biorepository and their records were made public through the Global Genome Biodiversity Network's portal...
2017: PhytoKeys
https://www.readbyqxmd.com/read/29116062/-biobanks-as-the-basis-for-developing-biomedicine-problems-and-prospects
#3
O N Reznik, D O Kuzmin, A O Reznik
Biobanking is crucial for the development of life sciences in general and biomedical science in particular. A systematic study of stored biomaterials enables the discovery of new biomarkers for various physiological and pathophysiological states, identification of the drug targets, and validation of these findings in human population studies. During the last decades, the importance of biobanking has increased in parallel with the growth in their size from relatively small collections to very large national and international biorepositories...
September 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/29100308/integration-of-genomic-transcriptomic-and-functional-profiles-of-aggressive-osteosarcomas-across-multiple-species
#4
Lara E Davis, Sophia Jeng, Matthew N Svalina, Elaine Huang, Janét Pittsenbarger, Emma L Cantor, Noah Berlow, Bernard Seguin, Atiya Mansoor, Shannon K McWeeney, Charles Keller
In complex, highly unstable genomes such as in osteosarcoma, targeting aberrant checkpoint processes (metabolic, cell cycle or immune) may prove more successful than targeting specific kinase or growth factor signaling pathways. Here, we establish a comparative oncology approach characterizing the most lethal osteosarcomas identified in a biorepository of tumors from three different species: human, mouse and canine. We describe the development of a genetically-engineered mouse model of osteosarcoma, establishment of primary cell cultures from fatal human tumors, and a biorepository of osteosarcoma surgical specimens from pet dogs...
September 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28970045/absence-of-replication-competent-lentivirus-in-the-clinic-analysis-of-infused-t-cell-products
#5
Kenneth Cornetta, Lisa Duffy, Cameron J Turtle, Michael Jensen, Stephen Forman, Gwendolyn Binder-Scholl, Terry Fry, Anne Chew, David G Maloney, Carl H June
Exposure to replication-competent lentivirus (RCL) is a theoretical safety concern for individuals treated with lentiviral gene therapy. For certain ex vivo gene therapy applications, including cancer immunotherapy trials, RCL detection assays are used to screen the vector product as well as the vector-transduced cells. In this study, we reviewed T cell products screened for RCL using methodology developed in the National Gene Vector Biorepository. All trials utilized third-generation lentiviral vectors produced by transient transfection...
September 12, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28964418/serum-biomarkers-may-prognosticate-recurrence-in-node-negative-non-small-cell-lung-cancers-less-than-4-centimeters
#6
COMPARATIVE STUDY
Christopher W Seder, Andrew T Arndt, Lia Jordano, Sanjib Basu, Cristina L Fhied, Selina Sayidine, Gary W Chmielewski, Kelsey Gallo, Michael J Liptay, Jeffrey A Borgia
BACKGROUND: A significant proportion of patients who undergo lung resection for less than 4 cm non-small cell lung cancer (NSCLC) will die of disease recurrence within 5 years. The ability to identify patients at greatest risk for recurrence may help individualize treatment and surveillance regimens and improve outcomes. We hypothesized that a serum-based biomarker panel could help risk stratify patients with node-negative NSCLC less than 4 cm for recurrence after lung resection. METHODS: An institutional biorepository of more than 1,800 cases was used to identify patients with resected, node-negative NSCLC less than 4 cm in size...
November 2017: Annals of Thoracic Surgery
https://www.readbyqxmd.com/read/28938416/pancreatic-histopathology-of-human-monogenic-diabetes-due-to-causal-variants-in-kcnj11-hnf1a-gata6-and-lmna
#7
May Sanyoura, Laura Jacobsen, David Carmody, Daniela Del Gaudio, Gorka Alkorta-Aranburu, Kelly Arndt, Ying Ying Hu, Frances Kobiernicki, Irina Kusmartseva, Mark A Atkinson, Louis H Philipson, Desmond Schatz, Martha Campbell-Thompson, Siri Atma W Greeley
Context: Monogenic diabetes is thought to account for 2% of all diabetes cases but most patients are misdiagnosed as type 1 or type 2 diabetes. To date, little is known about the histopathological features of pancreases from patients with monogenic diabetes. Objective: Retrospective study of the JDRF Network for Pancreatic Organ donors with Diabetes biorepository was used to identify possible cases with monogenic diabetes and to compare effects of genetic variants on pancreas histology...
August 16, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28935999/integrating-a-biorepository-into-the-national-amyotrophic-lateral-sclerosis-registry
#8
D Kevin Horton, Wendy Kaye, Laurie Wagner
As part of our continuing effort to highlight innovative approaches to improving the health and environment of communities, the Journal is pleased to publish a bimonthly column from the Agency for Toxic Substances and Disease Registry (ATSDR). ATSDR is a federal public health agency of the U.S. Department of Health and Human Services (HHS) and shares a common office of the Director with the National Center for Environmental Health (NCEH) at the Centers for Disease Control and Prevention (CDC). ATSDR serves the public by using the best science, taking responsive public health actions, and providing trusted health information to prevent harmful exposures and diseases related to toxic substances...
November 2016: Journal of Environmental Health
https://www.readbyqxmd.com/read/28906323/novel-method-enabling-the-use-of-cryopreserved-primary-acute-myeloid-leukemia-cells-in-functional-drug-screens
#9
Michelle Degnin, Anupriya Agarwal, Katherine Tarlock, Soheil Meshinchi, Brian J Druker, Cristina E Tognon
The ability to assess antileukemic drug activity on primary patient samples is a powerful tool in determining potential drug targets and selection of therapeutic agents with biological and functional rationale. We previously established small molecule inhibitor screens for use on freshly isolated leukemia cells for this purpose. Here we describe a method that produces functional small molecule inhibitor screening results using cryopreserved primary acute myeloid leukemia cells. This method was established to take advantage of biorepositories containing archival material, such as those established by the Children's Oncology Group, and to enable validation of potential pathway dependencies uncovered by genomic analysis...
October 2017: Journal of Pediatric Hematology/oncology
https://www.readbyqxmd.com/read/28857146/recessive-mutations-in-ndufa2-cause-mitochondrial-leukoencephalopathy
#10
S Perrier, L Gauquelin, M Tétreault, L Tran, N Webb, M Srour, J J Mitchell, C Brunel-Guitton, J Majewski, V Long, S Keller, M J Gambello, C Simons, A Vanderver, G Bernard
Deficiencies of mitochondrial respiratory chain complex I frequently result in leukoencephalopathy in young patients, and different mutations in the genes encoding its subunits are still being uncovered. We report two patients with cystic leukoencephalopathy and complex I deficiency with recessive mutations in NDUFA2, an accessory subunit of complex I. The first patient was initially diagnosed with a primary systemic carnitine deficiency associated with a homozygous variant in SLC22A5, but also exhibited developmental regression and cystic leukoencephalopathy, and an additional diagnosis of complex I deficiency was suspected...
August 30, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28851791/organ-damage-in-sickle-cell-disease-study-ordiss-protocol-for-a-longitudinal-cohort-study-based-in-ghana
#11
Kofi A Anie, Vivian Paintsil, Ellis Owusu-Dabo, Daniel Ansong, Alex Osei-Akoto, Kwaku Ohene-Frempong, Kofi Aikins Amissah, Nicholas Addofoh, Ezekiel Bonwin Ackah, Amma Twumwa Owusu-Ansah, Solomon Fiifi Ofori-Acquah
INTRODUCTION: Sickle cell disease is highly prevalent in Africa with a significant public health burden. Nonetheless, morbidity and mortality in sickle cell disease that result from the progression of organ damage is not well understood. The Organ Damage in Sickle Cell Disease Study (ORDISS) is designed as a longitudinal cohort study to provide critical insight into cellular and molecular pathogenesis of chronic organ damage for the development of future innovative treatment. METHODS AND ANALYSIS: ORDISS aims to recruit children aged 0-15 years who attend the Kumasi Centre for Sickle Cell Disease based at the Komfo Anokye Teaching Hospital in Kumasi, Ghana...
August 28, 2017: BMJ Open
https://www.readbyqxmd.com/read/28840457/va-s-national-ptsd-brain-bank-a-national-resource-for-research
#12
REVIEW
Matthew J Friedman, Bertrand R Huber, Christopher B Brady, Robert J Ursano, David M Benedek, Neil W Kowall, Ann C McKee
The National PTSD Brain Bank (NPBB) is a brain tissue biorepository established to support research on the causes, progression, and treatment of PTSD. It is a six-part consortium led by VA's National Center for PTSD with participating sites at VA medical centers in Boston, MA; Durham, NC; Miami, FL; West Haven, CT; and White River Junction, VT along with the Uniformed Services University of Health Sciences. It is also well integrated with VA's Boston-based brain banks that focus on Alzheimer's disease, ALS, chronic traumatic encephalopathy, and other neurological disorders...
August 25, 2017: Current Psychiatry Reports
https://www.readbyqxmd.com/read/28834558/abstracts
#13
E Cotzomi, K D Petschke, K C O'Connor, A D Paltiel
INTRODUCTION: The Inclusion Body Myositis (IBM) Registry at Yale is the largest systematic categorization of IBM, consolidating demographic, natural history, and clinical management data collected from 916 patients via a self-reporting questionnaire. OBJECTIVE/METHODS: To expand and improve registry resources. The registry aims to inform patients about IBM using online tools and information disseminated via social media. For clinicians and researchers, this project aims to establish a platform for longitudinal data collection and a patient biorepository to support laboratory research...
August 23, 2017: Muscle & Nerve
https://www.readbyqxmd.com/read/28818355/ar-v7-in-peripheral-whole-blood-of-patients-with-castration-resistant-prostate-cancer-association-with-treatment-specific-outcome-under-abiraterone-and-enzalutamide
#14
Anna Katharina Seitz, Silvia Thoene, Andreas Bietenbeck, Roman Nawroth, Robert Tauber, Mark Thalgott, Sebastian Schmid, Ramona Secci, Margitta Retz, Jürgen E Gschwend, Jürgen Ruland, Christof Winter, Matthias M Heck
BACKGROUND: It has been demonstrated that androgen receptor splice variant 7 (AR-V7) expression in circulating tumor cells (CTCs) predicts poor treatment response in metastatic castration-resistant prostate cancer (mCRPC) patients treated with abiraterone or enzalutamide. OBJECTIVE: To develop a practical and robust liquid profiling approach for direct quantification of AR-V7 in peripheral whole blood without the need for CTC capture and to determine its potential for predicting treatment response in mCRPC patients...
November 2017: European Urology
https://www.readbyqxmd.com/read/28815116/reducing-clinical-noise-for-body-mass-index-measures-due-to-unit-and-transcription-errors-in-the-electronic-health-record
#15
Robert Goodloe, Eric Farber-Eger, Jonathan Boston, Dana C Crawford, William S Bush
Body mass index (BMI) is an important outcome and covariate adjustment for many clinical association studies. Accurate assessment of BMI, therefore, is a critical part of many study designs. Electronic health records (EHRs) are a growing source of clinical data for research purposes, and have proven useful for identifying and replicating genetic associations. EHR-based data collected for clinical and billing purposes have several unique properties, including a high degree of heterogeneity or "clinical noise...
2017: AMIA Summits on Translational Science Proceedings
https://www.readbyqxmd.com/read/28815105/extracting-country-of-origin-from-electronic-health-records-for-gene-environment-studies-as-part-of-the-epidemiologic-architecture-for-genes-linked-to-environment-eagle-study
#16
Eric Farber-Eger, Robert Goodloe, Jonathan Boston, William S Bush, Dana C Crawford
We describe here the extraction of country-of-origin, an acculturation variable relevant for gene-environment studies, in a biorepository linked to de-identified electronic health records (EHRs) assessed by the Epidemiologic Architecture for Genes Linked to Environment (EAGLE), a study site of the Population Architecture using Genomics and Epidemiology (PAGE) I study. We extracted country-of-origin from the unstructured clinical free text using regular expressions within the MySQL relational database system in a cohort of 15,863 subjects of mostly non-European descent (including 11,519 African Americans, 1,702 Hispanics, and 1,118 Asians)...
2017: AMIA Summits on Translational Science Proceedings
https://www.readbyqxmd.com/read/28814312/rationale-and-design-of-the-brigham-cohort-for-psoriasis-and-psoriatic-arthritis-registry-coppar
#17
Maria Schneeweiss, Joseph F Merola, Elizabeth W Karlson, Daniel H Solomon
BACKGROUND: Psoriasis (PsO) and psoriatic arthritis (PsA) are related conditions with poorly defined transition among them, risk factors for progression, complex treatment algorithms, and biomarkers for treatment response and long-term outcomes. We describe the development of a PsO/PsA registry at an academic medical center. METHODS: We developed a single-center PsO/PsA longitudinal disease registry including biorepository that captures relevant disease markers and treatment choices in a circumscribed population with a defined catchment area...
August 16, 2017: BMC Dermatology
https://www.readbyqxmd.com/read/28767408/integration-of-genomic-transcriptomic-and-functional-profiles-of-aggressive-osteosarcomas-across-multiple-species
#18
Lara E Davis, Sophia Jeng, Matthew N Svalina, Elaine Huang, Janét Pittsenbarger, Emma L Cantor, Noah Berlow, Bernard Seguin, Atiya Mansoor, Shannon K McWeeney, Charles Keller
In complex, highly unstable genomes such as in osteosarcoma, targeting aberrant checkpoint processes (metabolic, cell cycle or immune) may prove more successful than targeting specific kinase or growth factor signaling pathways. Here, we establish a comparative oncology approach characterizing the most lethal osteosarcomas identified in a biorepository of tumors from three different species: human, mouse and canine. We describe the development of a genetically-engineered mouse model of osteosarcoma, establishment of primary cell cultures from fatal human tumors, and a biorepository of osteosarcoma surgical specimens from pet dogs...
July 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/28750641/metabolome-alterations-in-severe-critical-illness-and-vitamin-d-status
#19
Jessica Lasky-Su, Amber Dahlin, Augusto A Litonjua, Angela J Rogers, Michael J McGeachie, Rebecca M Baron, Lee Gazourian, Diana Barragan-Bradford, Laura E Fredenburgh, Augustine M K Choi, Kris M Mogensen, Sadeq A Quraishi, Karin Amrein, Kenneth B Christopher
BACKGROUND: Metabolic homeostasis is substantially disrupted in critical illness. Given the pleiotropic effects of vitamin D, we hypothesized that metabolic profiles differ between critically ill patients relative to their vitamin D status. METHODS: We performed a metabolomics study on biorepository samples collected from a single academic medical center on 65 adults with systemic inflammatory response syndrome or sepsis treated in a 20-bed medical ICU between 2008 and 2010...
July 28, 2017: Critical Care: the Official Journal of the Critical Care Forum
https://www.readbyqxmd.com/read/28720207/thrombotic-microangiopathy-a-multidisciplinary-team%C3%A2-approach
#20
Craig E Gordon, Vipul C Chitalia, J Mark Sloan, David J Salant, David L Coleman, Karen Quillen, Katya Ravid, Jean M Francis
Thrombotic microangiopathy (TMA) is characterized by the presence of microangiopathic hemolytic anemia and thrombocytopenia along with organ dysfunction, and pathologically, by the presence of microthrombi in multiple microvascular beds. Delays in diagnosis and initiation of therapy are common due to the low incidence, variable presentation, and poor awareness of these diseases, underscoring the need for interdisciplinary approaches to clinical care for TMA. We describe a new approach to improve clinical management via a TMA team that originally stemmed from an Affinity Research Collaborative team focused on thrombosis and hemostasis...
November 2017: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
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