Dataset Information

Harmonizing Cell-Free DNA Collection and Processing Practices through Evidence-Based Guidance.

ABSTRACT: Circulating cell-free DNA (cfDNA) is rapidly transitioning from discovery research to an important tool in clinical decision making. However, the lack of harmonization of preanalytic practices across institutions may compromise the reproducibility of cfDNA-derived data and hamper advancements in cfDNA testing in the clinic. Differences in cellular genomic contamination, cfDNA yield, integrity, and fragment length have been attributed to different collection tube types and anticoagulants, processing delays and temperatures, tube agitation, centrifugation protocols and speeds, plasma storage duration and temperature, the number of freeze-thaw events, and cfDNA extraction and quantification methods, all of which can also ultimately impact subsequent downstream analysis. Thus, there is a pressing need for widely applicable standards tailored for cfDNA analysis that include all preanalytic steps from blood draw to analysis. The NCI's Biorepositories and Biospecimen Research Branch has developed cfDNA-specific guidelines that are based upon published evidence and have been vetted by a panel of internationally recognized experts in the field. The guidelines include optimal procedures as well as acceptable alternatives to facilitate the generation of evidence-based protocols by individual laboratories and institutions. The aim of the document, which is entitled "Biospecimen Evidence-based Best Practices for Cell-free DNA: Biospecimen Collection and Processing," is to improve the accuracy of cfDNA analysis in both basic research and the clinic by improving and harmonizing practices across institutions.

SUBMITTER: Greytak SR

PROVIDER: S-EPMC7334102 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Harmonizing Cell-Free DNA Collection and Processing Practices through Evidence-Based Guidance.

Greytak Sarah R SR Engel Kelly B KB Parpart-Li Sonya S Murtaza Muhammed M Bronkhorst Abel J AJ Pertile Mark D MD Moore Helen M HM

Clinical cancer research : an official journal of the American Association for Cancer Research 20200302 13

Circulating cell-free DNA (cfDNA) is rapidly transitioning from discovery research to an important tool in clinical decision making. However, the lack of harmonization of preanalytic practices across institutions may compromise the reproducibility of cfDNA-derived data and hamper advancements in cfDNA testing in the clinic. Differences in cellular genomic contamination, cfDNA yield, integrity, and fragment length have been attributed to different collection tube types and anticoagulants, process ...[more]

PMID: 32122922

Similar Datasets

Project description:BackgroundThe coronavirus disease (COVID-19) presents unique challenges in health care, including mental health care provision. Telepsychiatry can provide an alternative to face-to-face assessment and can also be used creatively with other technologies to enhance care, but clinicians and patients may feel underconfident about embracing this new way of working.ObjectiveThe aim of this paper is to produce an open-access, easy-to-consult, and reliable source of information and guidance about telepsychiatry and COVID-19 using an evidence-based approach.MethodsWe systematically searched existing English language guidelines and websites for information on telepsychiatry in the context of COVID-19 up to and including May 2020. We used broad search criteria and included pre-COVID-19 guidelines and other digital mental health topics where relevant. We summarized the data we extracted as answers to specific clinical questions.ResultsFindings from this study are presented as both a short practical checklist for clinicians and detailed textboxes with a full summary of all the guidelines. The summary textboxes are also available on an open-access webpage, which is regularly updated. These findings reflected the strong evidence base for the use of telepsychiatry and included guidelines for many of the common concerns expressed by clinicians about practical implementation, technology, information governance, and safety. Guidelines across countries differ significantly, with UK guidelines more conservative and focused on practical implementation and US guidelines more expansive and detailed. Guidelines on possible combinations with other digital technologies such as apps (eg, from the US Food and Drug Administration, the National Health Service Apps Library, and the National Institute for Health and Care Excellence) are less detailed. Several key areas were not represented. Although some special populations such as child and adolescent, and older adult, and cultural issues are specifically included, important populations such as learning disabilities, psychosis, personality disorder, and eating disorders, which may present particular challenges for telepsychiatry, are not. In addition, the initial consultation and follow-up sessions are not clearly distinguished. Finally, a hybrid model of care (combining telepsychiatry with other technologies and in-person care) is not explicitly covered by the existing guidelines.ConclusionsWe produced a comprehensive synthesis of guidance answering a wide range of clinical questions in telepsychiatry. This meets the urgent need for practical information for both clinicians and health care organizations who are rapidly adapting to the pandemic and implementing remote consultation. It reflects variations across countries and can be used as a basis for organizational change in the short- and long-term. Providing easily accessible guidance is a first step but will need cultural change to implement as clinicians start to view telepsychiatry not just as a replacement but as a parallel and complementary form of delivering therapy with its own advantages and benefits as well as restrictions. A combination or hybrid approach can be the most successful approach in the new world of mental health post-COVID-19, and guidance will need to expand to encompass the use of telepsychiatry in conjunction with other in-person and digital technologies, and its use across all psychiatric disorders, not just those who are the first to access and engage with remote treatment.

Project description:Fermented cereal-based foods play a crucial role in attaining food and nutrition security for resource-poor populations in sub-Saharan Africa. These products are widely produced by spontaneous fermentation using of cereal grains as raw material. They have a unique taste and flavour, are rich sources of energy and their non-alcoholic nature makes them ideal for consumption by the entire population, including children. Lactic acid bacteria dominate the fermentation process and lead to a low pH of around 4, which suppresses the growth of pathogenic bacteria, thereby increasing the shelf-life and safety of the food. Knowledge about processing practices, consumption patterns and bacterial communities is essential to regulate processing and design appropriate mixes of micro-organisms to produce starter cultures for commercial production of standard-quality fermented foods that meet desired quality characteristics. In four regions of Zambia, we surveyed processing practices and consumption patterns of a spontaneously fermented cereal-based beverage called Munkoyo, commonly produced in Zambia and the Democratic Republic of Congo. Variations in processing practices exist in cooking time of the unfermented maize porridge and time allowed for fermentation. Consumption is mainly at household level and the product is considered as an energy drink. Characterisation of the bacterial communities of over 90 samples with 16S amplicon sequencing on DNA extracted from the entire bacterial community revealed six dominant families, namely Streptococcaceae, Leuconostocaceae, Enterobacteriaceae, Lactabacillales, Bacillaceae and Aeromonadaceae, and a Shannon index of up to 1.18 with an effective number of 3.44 bacterial species. Bacterial communities that underlie the fermentation in Munkoyo differ in their composition for the different regions using common processing steps, suggesting that different combinations of bacteria can be used to achieve successful Munkoyo fermentation. Analysis of aroma profiles in 15 different samples from two different Provinces showed that aldehydes, esters, organic acids, alkanes, alkenes and alcohols dominated.

Dataset Information

Harmonizing Cell-Free DNA Collection and Processing Practices through Evidence-Based Guidance.

Publications

Harmonizing Cell-Free DNA Collection and Processing Practices through Evidence-Based Guidance.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure