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Daniel G Mulcahy, Kenneth S Macdonald, Seán G Brady, Christopher Meyer, Katharine B Barker, Jonathan Coddington
Advances in biodiversity genomic sequencing will increasingly depend on the availability of DNA samples-and their quantifiable metadata-preserved in large institutional biorepositories that are discoverable to the scientific community. Improvements in sequencing technology constantly provide longer reads, such that longer fragment length, higher molecular weight, and overall "genome-quality" DNA (gDNA) will be desirable. Ideally, biorepositories should publish numerical scale measurements of DNA quality useful to the user community...
2016: PeerJ
Sarah A Weiss, Joseph Han, Farbod Darvishian, Jeremy Tchack, Sung Won Han, Karolina Malecek, Michelle Krogsgaard, Iman Osman, Judy Zhong
BACKGROUND: Age has been reported as an independent prognostic factor for melanoma-specific survival (MSS). We tested the hypothesis that age impacts the host anti-tumor immune response, accounting for age-specific survival outcomes in three unique melanoma patient cohorts. METHODS: We queried the U.S. population-based Surveillance, Epidemiology, and End Results Program (SEER), the prospective tertiary care hospital-based Interdisciplinary Melanoma Cooperative Group (IMCG) biorepository, and the Cancer Genome Atlas (TCGA) biospecimen database to test the association of patient age at time of melanoma diagnosis with clinicopathologic features and survival outcomes...
October 19, 2016: Journal of Translational Medicine
Rikki A Cannioto, Lara E Sucheston-Campbell, Shalaka Hampras, Ellen L Goode, Keith Knutson, Roberta Ness, Francesmary Modugno, Paul K Wallace, J Brian Szender, Paul Mayor, Chi-Chen Hong, Janine M Joseph, Grace Friel, Warren Davis, Mary Nesline, Kevin H Eng, Robert P Edwards, Bridget Kruszka, Kristina Schmitt, Kunle Odunsi, Kirsten B Moysich
OBJECTIVE: There is a mounting body of evidence demonstrating higher percentages of regulatory T (Treg) cells in the peripheral blood of patients with cancer in comparison to healthy controls, but there is a paucity of epidemiological literature characterizing circulating Treg cells among patients with epithelial ovarian cancer (EOC). To investigate the role of peripheral Treg cells in ovarian neoplasms, we conducted a case-control study to characterize circulating concentrations of Treg cells among patients with EOC, women with benign ovarian conditions, and healthy controls without a history of cancer...
October 18, 2016: International Journal of Gynecological Cancer
Rebecca O Barnes, Katheryn E Shea, Peter H Watson
As health research increasingly relies on biospecimens and associated data, new demands have emerged for biorepositories to provide assurances of the quality of their overall operations, not just assurances of the quality of the biospecimens and data that they hold. The biobanking community has responded in various ways, including the creation of two different programs to disseminate biobanking best practices. This article describes in detail the Canadian Tissue Repository Network (CTRNet) Biobank Certification Program and the College of American Pathologists (CAP) Biorepository Accreditation Program...
October 14, 2016: Biopreservation and Biobanking
Robert F Tamburro, Tammara L Jenkins, Patrick M Kochanek
OBJECTIVE: To summarize the scientific priorities and potential future research directions for pediatric critical care research discussed by a panel of experts at the inaugural Strategic Planning Conference of the Pediatric Trauma and Critical Illness Branch of the Eunice Kennedy Shriver National Institute of Child Health and Human Development. DATA SOURCES: Expert opinion expressed during the Strategic Planning Conference. STUDY SELECTION: Not applicable...
September 27, 2016: Pediatric Critical Care Medicine
Jelena-R Ghadri, Victoria L Cammann, Christian Templin
Takotsubo syndrome (TTS) was first described in Japan in 1990. The clinical presentation is similar to that of acute coronary syndrome (ACS). Cardiac enzymes are commonly elevated. A global initiative was launched and the InterTAK Registry was established to provide a systematic database. The major goals of the International Takotsubo Registry (InterTAK Registry) are to provide a comprehensive clinical characterization on natural history, treatment, and outcomes. We linked a biorepository to identify biomarkers for the diagnosis and prognosis and to investigate the genetic basis as well as disease-related factors...
October 2016: Heart Failure Clinics
Johann Wilhelm Schneider, Micheline Sanderson, Dieter Geiger, Mostafa Nokta, Sylvia Silver
Sub-Saharan Africa has one of the highest incidences of infection with HIV globally, but more people in this region are living longer owing to increased access to antiretroviral therapy. However, along with increased care and treatment, this population is expected to have an increase in HIV-associated cancers, as is being seen in the USA and other developed countries. To support translational research in HIV-associated cancers, Stellenbosch University in Cape Town, South Africa, was funded to house the state-of-the-art AIDS and Cancer Specimen Resource Sub-Saharan Africa Regional Biorepository (SSA RBR) to proactively obtain, manage and process biospecimens and associated clinical data representing both AIDS-defining and non-AIDS-defining cancers for research...
September 2016: South African Medical Journal, Suid-Afrikaanse Tydskrif Vir Geneeskunde
Elizabeth Stulberg, Deborah Fravel, Lita M Proctor, David M Murray, Jonathan LoTempio, Linda Chrisey, Jay Garland, Kelly Goodwin, Joseph Graber, M Camille Harris, Scott Jackson, Michael Mishkind, D Marshall Porterfield, Angela Records
Genome-enabled technologies have supported a dramatic increase in our ability to study microbial communities in environments and hosts. Taking stock of previously funded microbiome research can help to identify common themes, under-represented areas and research priorities to consider moving forward. To assess the status of US microbiome research, a team of government scientists conducted an analysis of federally funded microbiome research. Microbiomes were defined as host-, ecosystem- or habitat-associated communities of microorganisms, and microbiome research was defined as those studies that emphasize community-level analyses using 'omics technologies...
2016: Nature Microbiology
Travis Hyams, Deborah J Bowen, Celeste Condit, Jeremy Grossman, Megan Fitzmaurice, Deborah Goodman, Lari Wenzel, Karen L Edwards
BACKGROUND: The practice of biorepository-based genetics research raises questions related to what ethical obligations researchers have to their participants. It is important to explore and include the thoughts of current biorepository participants as we move forward with this type of research. METHODS: Thirty participants (17 cancer patients, 7 cancer-free controls, and 6 relatives) were drawn from the Northwest Cancer Genetics Registry and participated in qualitative interviews lasting between 45 and 90 min...
2016: Public Health Genomics
William E Grizzle, Dennis Otali, Katherine C Sexton, Daniel S Atherton
Frequently investigators request that tissues be collected and processed in less than one hour following removal from a patient. Some biorepositories expend significant personnel time and other resources in trying to meet such goals; however, it is unclear whether the perceived benefits of relatively short cold ischemia times warrant these added costs. The literature of human surgical tissues prospectively exposed to cold ischemia at several time points was reviewed to compare the changes in transcripts/genes and microRNA with time of cold ischemia...
August 23, 2016: Biopreservation and Biobanking
Kristjan Eerik Kaseniit, Mark R Theilmann, Alexander Robertson, Eric A Evans, Imran S Haque
BACKGROUND: Fragile X syndrome (FXS, OMIM #300624) is an X-linked condition caused by trinucleotide repeat expansions in the 5' UTR (untranslated region) of the fragile X mental retardation 1 (FMR1) gene. FXS testing is commonly performed in expanded carrier screening and has been proposed for inclusion in newborn screening. However, because pathogenic alleles are long and have low complexity (>200 CGG repeats), FXS is currently tested by a single-plex electrophoresis-resolved PCR assay rather than multiplexed approaches like next-generation sequencing or mass spectrometry...
October 2016: Clinical Chemistry
Alex S Felmeister, Aaron J Masino, Tyler J Rivera, Adam C Resnick, Jeffrey W Pennington
BACKGROUND: High throughput molecular sequencing and increased biospecimen variety have introduced significant informatics challenges for research biorepository infrastructures. We applied a modular system integration approach to develop an operational biorepository management system. This method enables aggregation of the clinical, specimen and genomic data collected for biorepository resources. METHODS: We introduce an electronic Honest Broker (eHB) and Biorepository Portal (BRP) open source project that, in tandem, allow for data integration while protecting patient privacy...
2016: BMC Genomics
Anurag Verma, Anna O Basile, Yuki Bradford, Helena Kuivaniemi, Gerard Tromp, David Carey, Glenn S Gerhard, James E Crowe, Marylyn D Ritchie, Sarah A Pendergrass
We performed a Phenome-Wide Association Study (PheWAS) to identify interrelationships between the immune system genetic architecture and a wide array of phenotypes from two de-identified electronic health record (EHR) biorepositories. We selected variants within genes encoding critical factors in the immune system and variants with known associations with autoimmunity. To define case/control status for EHR diagnoses, we used International Classification of Diseases, Ninth Revision (ICD-9) diagnosis codes from 3,024 Geisinger Clinic MyCode® subjects (470 diagnoses) and 2,899 Vanderbilt University Medical Center BioVU biorepository subjects (380 diagnoses)...
2016: PloS One
Damien C Croteau-Chonka, Weiliang Qiu, Fernando D Martinez, Robert C Strunk, Robert F Lemanske, Andrew H Liu, Frank D Gilliland, Joshua Millstein, W James Gauderman, Carole Ober, Jerry A Krishnan, Steven R White, Edward T Naureckas, Dan L Nicolae, Kathleen C Barnes, Stephanie J London, Albino Barraza-Villarreal, Vincent J Carey, Scott T Weiss, Benjamin A Raby
Maintaining optimal symptom control remains the primary objective of asthma treatment. Better understanding of the biological underpinnings of asthma control may lead to the development of improved clinical and pharmaceutical approaches.<br><br> Objective: We aimed to identify molecular pathways and interrelated genes whose differential expression were associated with asthma control.<br><br> Methods: We performed gene set enrichment analyses (GSEA) of asthma control in 1,170 adult asthmatic individuals, each with gene expression data derived from either whole blood (WB) or unstimulated CD4+ T-lymphocytes (CD4), and a self-reported asthma control score representing either the preceding six months (chronic) or seven days (acute)...
August 5, 2016: American Journal of Respiratory and Critical Care Medicine
Paul Mehta, Wendy Kaye, Leah Bryan, Theodore Larson, Timothy Copeland, Jennifer Wu, Oleg Muravov, Kevin Horton
PROBLEM/CONDITION: Amyotrophic lateral sclerosis (ALS), commonly known as Lou Gehrig's disease, is a progressive and fatal neuromuscular disease for which no cure or viable treatment has been identified. ALS, like most noncommunicable diseases, is not a nationally notifiable disease in the United States. The prevalence of ALS in the United States during 2010-2011 was estimated to be 3.9 cases per 100,000 persons in the general population. Updated prevalence estimates are needed to help monitor disease status, better understand etiology, and identify risk factors for ALS...
2016: MMWR. Surveillance Summaries: Morbidity and Mortality Weekly Report. Surveillance Summaries
Elisa M Rodriguez, Frances G Saad-Harfouche, Austin Miller, Martin C Mahoney, Christine B Ambrosone, Carl D Morrison, Willie Underwood, Deborah O Erwin
The disproportionately lower number of certain subpopulations participating in clinical and prevention research has a significant impact on the representativeness of scientific outcomes. The Hoy y Mañana program (Today and Tomorrow) was developed as a culturally and linguistically appropriate education program to engage diverse medically underserved populations without a cancer diagnosis in biospecimen donation for cancer genomic research. Participants were recruited to in-depth community-based educational programs (∼45-60-min duration) or during open events in the community based on a convenience sampling...
August 3, 2016: Journal of Community Genetics
Csaba Galambos, Angela D Minic, Douglas Bush, Dominique Nguyen, Blair Dodson, Gregory Seedorf, Steven H Abman
BACKGROUND AND AIMS: Infants with Down syndrome (DS) or Trisomy 21, are at high risk for developing pulmonary arterial hypertension (PAH), but mechanisms that increase susceptibility are poorly understood. Laboratory studies have shown that early disruption of angiogenesis during development impairs vascular and alveolar growth and causes PAH. Human chromosome 21 encodes known anti-angiogenic factors, including collagen18a1 (endostatin, ES), ß-amyloid peptide (BAP) and Down Syndrome Critical Region 1 (DSCR-1)...
2016: PloS One
Marisa S Klein-Gitelman
Neonatal lupus results from the passive transfer of autoantibodies; however, this transfer is not sufficient to cause disease. This article reviews clinical presentation with a focus on autoimmune-mediated congenital heart disease. Recent data looking for additional disease mechanisms and biomarkers as well as latest information on interventions will be reviewed. Our understanding of this rare disease is often dependent on patient participation in disease registries and biorepositories. Future participation in registries including descriptive as well as biophysical data is critical to our knowledge...
September 2016: Current Rheumatology Reports
Heather J Chalfin, Elizabeth Fabian, Leslie Mangold, David B Yeater, Kenneth J Pienta, Alan W Partin
In the current era of individualized medicine, a biorepository of human samples is essential to support clinical and translational research. There have been limited efforts in this arena within the field of urology, as costs, logistical, and ethical issues represent significant deterrents to biobanking. The Johns Hopkins Brady Urological Institute (JHBUI) Biorepository was founded in 1994 as a resource to facilitate discovery. Since its inception, the biorepository has enabled numerous research endeavors including pivotal trials leading to the regulatory approval of four diagnostic tests for prostate cancer...
July 28, 2016: BJU International
Ying Bao, Monica L Bertoia, Elizabeth B Lenart, Meir J Stampfer, Walter C Willett, Frank E Speizer, Jorge E Chavarro
We have summarized the evolution of the Nurses' Health Study (NHS), a prospective cohort study of 121 700 married registered nurses launched in 1976; NHS II, which began in 1989 and enrolled 116 430 nurses; and NHS3, which began in 2010 and has ongoing enrollment. Over 40 years, these studies have generated long-term, multidimensional data, including lifestyle- and health-related information across the life course and an extensive repository of various biological specimens. We have described the questionnaire data collection, disease follow-up methods, biorepository resources, and data management and statistical procedures...
September 2016: American Journal of Public Health
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