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https://www.readbyqxmd.com/read/28207879/comparison-of-hla-allelic-imputation-programs
#1
Jason H Karnes, Christian M Shaffer, Lisa Bastarache, Silvana Gaudieri, Andrew M Glazer, Heidi E Steiner, Jonathan D Mosley, Simon Mallal, Joshua C Denny, Elizabeth J Phillips, Dan M Roden
Imputation of human leukocyte antigen (HLA) alleles from SNP-level data is attractive due to importance of HLA alleles in human disease, widespread availability of genome-wide association study (GWAS) data, and expertise required for HLA sequencing. However, comprehensive evaluations of HLA imputations programs are limited. We compared HLA imputation results of HIBAG, SNP2HLA, and HLA*IMP:02 to sequenced HLA alleles in 3,265 samples from BioVU, a de-identified electronic health record database coupled to a DNA biorepository...
2017: PloS One
https://www.readbyqxmd.com/read/28186851/efficiently-maintaining-a-national-resource-of-historical-and-contemporary-biological-collections-the-nhlbi-biorepository-model
#2
Katheryn E Shea, Elizabeth L Wagner, Leah Marchesani, Kevin Meagher, Carol Giffen
INTRODUCTION: Reducing costs by improving storage efficiency has been a focus of the National Heart, Lung, and Blood Institute (NHLBI) Biologic Specimen Repository (Biorepository) and Biologic Specimen and Data Repositories Information Coordinating Center (BioLINCC) programs for several years. METHODS: Study specimen profiles were compiled using the BioLINCC collection catalog. Cost assessments and calculations on the return on investments to consolidate or reduce a collection, were developed and implemented...
February 2017: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/28157384/evaluation-of-the-analytical-and-clinical-concordance-of-25-hydroxyvitamin-d-levels-in-dried-blood-spots-dried-serum-spots-and-serum-as-potential-biorepository-specimens
#3
Gellert Karvaly, Györgyi Molnár-Világos, Krisztián Kovács, Katalin Mészáros, Attila Patócs, Barna Vásárhelyi
CONTEXT: The promising perspective of storing dried blood spot (DBS) for evaluating 25-hydroxyvitamin D (25OHD) levels is increasingly being realized. While strong correlations have been demonstrated between 25OHD levels measured in DBS and in systemic serum samples in earlier works, the clinical concordance of the assay results has not been evaluated. Moreover, the utility of dried serum spot (DSS), a highly suitable matrix for sample archiving, has not been investigated in this respect...
February 3, 2017: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/28152281/glutathione-s-transferase-p1-may-predispose-children-to-a-decline-in-pulmonary-function-after-stem-cell-transplant
#4
Julie Stark, Jamie Renbarger, James Slaven, Zhangsheng Yu, Jenny Then, Jodi Skiles, Stephanie Davis
RATIONALE: Pulmonary complications after hematopoietic stem cell transplant (SCT) are associated with increased mortality. Genetic markers for those at risk for pulmonary impairment post-SCT have not been widely investigated. METHODS: Forty-nine patients were retrospectively selected from a single institution's biorepository with linked clinical data. All subjects performed pre-SCT PFTs. Genotyping was conducted using the Infinium Exome-24 BeadChip. Four single nucleotide polymorphisms (SNPs) were selected (rs1800871, rs1695, rs1800629, rs12477314) and evaluated for association with PFT parameters as change over time from baseline...
February 2, 2017: Pediatric Pulmonology
https://www.readbyqxmd.com/read/28140617/progressive-consent-and-specimen-accrual-models-to-address-sustainability-a-decade-s-experience-at-an-oregon-biorepository
#5
John A Ost, Paul W Newton, Duncan R Neilson, Joseph A Cioffi, P Ashley Wackym, R Serene Perkins
BACKGROUND: The Legacy Biorepository is a College of American Pathologists-accredited biorepository operating within a seven-hospital healthcare system, with a decade's experience in specimen accrual, storage, and distribution. While standardization of our practices through accreditation remains a priority, we along with others face challenges with regard to sustainability. Purposeful changes in our consent process, which we term "progressive consent," are expected to improve sustainability and operational flexibility while increasing our scientific impact...
February 2017: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/28115308/a-supporting-role-of-chinese-national-immortalized-cell-bank-in-life-science-research
#6
Xu Chongfeng, Duan Ziyuan
A biorepository of human samples is essential to support the research of life science. Lymphoblastoid B cell line (LCL), which is easy to be prepared and can reproduce indefinitely, is a convenient form of sample preservation. LCLs are established from human B cells transformed by Epstein-Barr virus (EBV). Chinese National Immortalized Cell Bank has preserved human LCLs from different ethnic groups in China. As there are many studies on the nature of LCLs and public available resources with genome-wide data for LCLs, they have been widely applied in genetics, immunology, pharmacogenetics/genomics, regenerative medicine, cancer pathogenesis and immunotherapy, screening and generation of fully human neutralizing monoclonal antibodies and study on EBV pathogenesis...
January 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28104821/the-urine-preservative-acetic-acid-degrades-urine-protein-implications-for-urine-biorepositories-and-the-aask-cohort-study
#7
Salem Almaani, Lee A Hebert, Brad H Rovin, Daniel J Birmingham
Patients enrolled in the African American Study of Kidney Disease and Hypertension (AASK) Cohort Study who exhibited overt proteinuria have been reported to show high nonalbumin proteinuria (NAP), which is characteristic of a tubulopathy. To determine whether African American Study of Kidney Disease and Hypertension nephropathy (AASK-N) is a tubulopathy, we obtained urine samples of 37 patients with AASK-N, with 24-hour protein-to-creatinine ratios (milligrams per milligram) ranging from 0.2 to 1.0, from the National Institute of Diabetes and Digestive Kidney Diseases repository and tested for seven markers of tubular proteinuria...
January 19, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/28103080/organization-of-bbmri-pl-the-polish-biobanking-network
#8
Małgorzata Witoń, Dominik Strapagiel, Joanna Gleńska-Olender, Anna Chróścicka, Katarzyna Ferdyn, Jarosław Skokowski, Leszek Kalinowski, Jakub Pawlikowski, Błażej Marciniak, Markus Pasterk, Agnieszka Matera-Witkiewicz, Łukasz Kozera
In Poland storage of human biological samples takes place at most universities and scientific institutions conducting research projects in the field of biomedicine. The First International Biobanking Conference organized by the Ministry of Science and Higher Education in 2014 shed a light on the situation of Polish biobanking infrastructures. The country has around 40 large biorepositories, which store unique biological material such as whole brains, muscle fibers from patients with rare diseases, as well as thousands of samples from patients with lifestyle diseases...
January 19, 2017: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/28077492/dystonia-treatment-patterns-of-medication-use-in-an-international-cohort
#9
Sarah Pirio Richardson, Ashley R Wegele, Betty Skipper, Amanda Deligtisch, H A Jinnah
OBJECTIVE: To determine the frequency of medication use in patients with dystonia enrolled in an international biorepository study. METHODS: In a cross-sectional analysis, we included 2,026 participants enrolled at 37 sites in the United States, Canada, Europe, and Australia through Project 1 of the Dystonia Coalition, an international biorepository study. The primary aim was to assess the frequency of medication classes recommended for treating patients with dystonia, and the secondary aim was to compare characteristics (disease type, age, sex, duration of disease, comorbid conditions, severity)...
January 11, 2017: Neurology
https://www.readbyqxmd.com/read/28073890/pancreatic-cancer-cell-lines-as-patient-derived-avatars-genetic-characterisation-and-functional-utility
#10
Erik S Knudsen, Uthra Balaji, Brian Mannakee, Paris Vail, Cody Eslinger, Christopher Moxom, John Mansour, Agnieszka K Witkiewicz
OBJECTIVE: Pancreatic ductal adenocarcinoma (PDAC) is a therapy recalcitrant disease with the worst survival rate of common solid tumours. Preclinical models that accurately reflect the genetic and biological diversity of PDAC will be important for delineating features of tumour biology and therapeutic vulnerabilities. DESIGN: 27 primary PDAC tumours were employed for genetic analysis and development of tumour models. Tumour tissue was used for derivation of xenografts and cell lines...
January 10, 2017: Gut
https://www.readbyqxmd.com/read/27996341/platelet-extracellular-vesicles-as-biomarkers-for-arterial-thrombosis
#11
Aleksandra Gasecka, Anita N Böing, Krzysztof J Filipiak, Rienk Nieuwland
Arterial thrombosis is a major and global cause of human death and disability. Considering the socioeconomic costs of arterial thrombosis, identification of biomarkers to predict and detect arterial thrombosis at an early stage is an important public health goal. Platelet extracellular vesicles (PEV) are a new candidate biomarker of arterial thrombosis. PEV can be measured in biorepositories, thereby offering the possibility to validate PEV in multicenter clinical trials. PEV analysis has been hitherto hampered by lack of standardized methodology, but substantial technological improvements of PEV detection techniques have been achieved recently...
December 20, 2016: Platelets
https://www.readbyqxmd.com/read/27977307/crisis-management-for-biobanks
#12
Alison Parry-Jones, Jarle Hansen, Daniel Simeon-Dubach, Roger Bjugn
All organizations are subject to risk and uncertainty. Adverse events may disrupt normal organizational activity and may even cause complete failure of business operations. Biorepositories are also at risk and there have been instances where multiple samples or entire collections have been destroyed. Biobank guidelines accordingly recommend the establishment of contingency plans to reduce risk to an acceptable level. In this review article, we will use general theory on risk management and illustrate how such principles can be used to establish a practical crisis management plan for any biobank organization...
December 15, 2016: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/27931609/clinical-and-biological-insights-into-combined-post-and-pre-capillary-pulmonary-hypertension
#13
Tufik R Assad, Anna R Hemnes, Emma K Larkin, Andrew M Glazer, Meng Xu, Quinn S Wells, Eric H Farber-Eger, Quanhu Sheng, Yu Shyr, Frank E Harrell, John H Newman, Evan L Brittain
BACKGROUND: Pulmonary hypertension (PH) is a common and morbid complication of left heart disease with 2 subtypes: isolated post-capillary pulmonary hypertension (Ipc-PH) and combined post-capillary and pre-capillary pulmonary hypertension (Cpc-PH). Little is known about the clinical or physiological characteristics that distinguish these 2 subphenotypes or if Cpc-PH shares molecular similarities to pulmonary arterial hypertension (PAH). OBJECTIVES: The goal of this study was to test the hypothesis that the hemodynamic and genetic profile of Cpc-PH would more closely resemble PAH than Ipc-PH...
December 13, 2016: Journal of the American College of Cardiology
https://www.readbyqxmd.com/read/27929677/assessing-researcher-needs-for-a-virtual-biobank
#14
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/27927582/clonal-haemopoiesis-and-therapy-related-myeloid-malignancies-in-elderly-patients-a-proof-of-concept-case-control-study
#15
Nancy K Gillis, Markus Ball, Qing Zhang, Zhenjun Ma, YuLong Zhao, Sean J Yoder, Maria E Balasis, Tania E Mesa, David A Sallman, Jeffrey E Lancet, Rami S Komrokji, Alan F List, Howard L McLeod, Melissa Alsina, Rachid Baz, Kenneth H Shain, Dana E Rollison, Eric Padron
BACKGROUND: Clonal haemopoiesis of indeterminate potential (CHIP) is an age-associated genetic event linked to increased risk of primary haematological malignancies and increased all-cause mortality, but the prevalence of CHIP in patients who develop therapy-related myeloid neoplasms is unknown. We did this study to investigate whether chemotherapy-treated patients with cancer who have CHIP are at increased risk of developing therapy-related myeloid neoplasms. METHODS: We did a nested, case-control, proof-of-concept study to compare the prevalence of CHIP between patients with cancer who later developed therapy-related myeloid neoplasms (cases) and patients who did not develop these neoplasms (controls)...
December 2, 2016: Lancet Oncology
https://www.readbyqxmd.com/read/27896978/development-and-performance-of-text-mining-algorithms-to-extract-socioeconomic-status-from-de-identified-electronic-health-records
#16
Brittany M Hollister, Nicole A Restrepo, Eric Farber-Eger, Dana C Crawford, Melinda C Aldrich, Amy Non
Socioeconomic status (SES) is a fundamental contributor to health, and a key factor underlying racial disparities in disease. However, SES data are rarely included in genetic studies due in part to the difficultly of collecting these data when studies were not originally designed for that purpose. The emergence of large clinic-based biobanks linked to electronic health records (EHRs) provides research access to large patient populations with longitudinal phenotype data captured in structured fields as billing codes, procedure codes, and prescriptions...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27885077/highlights-of-the-russian-health-studies-program-and-updated-research-findings
#17
Barrett N Fountos
Recognized for conducting cutting-edge science in the field of radiation health effects research, the Department of Energy's (DOE) Russian Health Studies Program has continued to generate excitement and enthusiasm throughout its 23-year mission to assess worker and public health risks from radiation exposure resulting from nuclear weapons production activities in the former Soviet Union. The three goals of the Program are to: (1) clarify the relationship between health effects and chronic, low-to-medium dose radiation exposure; (2) estimate the cancer risks from exposure to gamma, neutron, and alpha radiation; and (3) provide information to the national and international organizations that determine radiation protection standards and practices...
November 24, 2016: Radiation Protection Dosimetry
https://www.readbyqxmd.com/read/27882430/identification-of-cardiovascular-risk-factors-associated-with-bone-marrow-cell-subsets-in-patients-with-stemi-a-biorepository-evaluation-from-the-cctrn-time-and-latetime-clinical-trials
#18
Ariadna Contreras, Aaron F Orozco, Micheline Resende, Robert C Schutt, Jay H Traverse, Timothy D Henry, Dejian Lai, John P Cooke, Roberto Bolli, Michelle L Cohen, Lem Moyé, Carl J Pepine, Phillip C Yang, Emerson C Perin, James T Willerson, Doris A Taylor
Autologous bone marrow mononuclear cell (BM-MNC) therapy for patients with ST-segment elevation myocardial infarction (STEMI) has produced inconsistent results, possibly due to BM-MNC product heterogeneity. Patient-specific cardiovascular risk factors (CRFs) may contribute to variations in BM-MNC composition. We sought to identify associations between BM-MNC subset frequencies and specific CRFs in STEMI patients. Bone marrow was collected from 191 STEMI patients enrolled in the CCTRN TIME and LateTIME trials...
January 2017: Basic Research in Cardiology
https://www.readbyqxmd.com/read/27881526/towards-the-genetic-basis-of-cerebral-venous-thrombosis-the-beast-consortium-a-study-protocol
#19
Ioana Cotlarciuc, Thomas Marjot, Muhammad S Khan, Sini Hiltunen, Elena Haapaniemi, Tiina M Metso, Jukka Putaala, Susanna M Zuurbier, Matthijs C Brouwer, Serena M Passamonti, Paolo Bucciarelli, Emanuela Pappalardo, Tasmin Patel, Paolo Costa, Marina Colombi, Patrícia Canhão, Aleksander Tkach, Rosa Santacroce, Maurizio Margaglione, Giovanni Favuzzi, Elvira Grandone, Donatella Colaizzo, Kostas Spengos, Antonio Arauz, Amanda Hodge, Reina Ditta, Stephanie Debette, Marialuisa Zedde, Guillaume Pare, José M Ferro, Vincent Thijs, Alessandro Pezzini, Jennifer J Majersik, Ida Martinelli, Jonathan M Coutinho, Turgut Tatlisumak, Pankaj Sharma
INTRODUCTION: Cerebral venous thrombosis (CVT) is a rare cerebrovascular condition accounting for <1% of all stroke cases and mainly affects young adults. Its genetic aetiology is not clearly elucidated. METHODS AND ANALYSIS: To better understand the genetic basis of CVT, we have established an international biobank of CVT cases, Biorepository to Establish the Aetiology of Sinovenous Thrombosis (BEAST) which aims to recruit highly phenotyped cases initially of European descent and later from other populations...
November 22, 2016: BMJ Open
https://www.readbyqxmd.com/read/27881091/conducting-a-large-multi-site-survey-about-patients-views-on-broad-consent-challenges-and-solutions
#20
Maureen E Smith, Saskia C Sanderson, Kyle B Brothers, Melanie F Myers, Jennifer McCormick, Sharon Aufox, Martha J Shrubsole, Nanibaá A Garrison, Nathaniel D Mercaldo, Jonathan S Schildcrout, Ellen Wright Clayton, Armand H Matheny Antommaria, Melissa Basford, Murray Brilliant, John J Connolly, Stephanie M Fullerton, Carol R Horowitz, Gail P Jarvik, Dave Kaufman, Terri Kitchner, Rongling Li, Evette J Ludman, Catherine McCarty, Valerie McManus, Sarah Stallings, Janet L Williams, Ingrid A Holm
BACKGROUND: As biobanks play an increasing role in the genomic research that will lead to precision medicine, input from diverse and large populations of patients in a variety of health care settings will be important in order to successfully carry out such studies. One important topic is participants' views towards consent and data sharing, especially since the 2011 Advanced Notice of Proposed Rulemaking (ANPRM), and subsequently the 2015 Notice of Proposed Rulemaking (NPRM) were issued by the Department of Health and Human Services (HHS) and Office of Science and Technology Policy (OSTP)...
November 24, 2016: BMC Medical Research Methodology
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