Dataset Information

Human sample authentication in biomedical research: comparison of two platforms.

ABSTRACT: Samples used in biomedical research are often collected over years, in some cases from subjects that may have died and thus cannot be retrieved in any way. The value of these samples is priceless. Sample misidentification or mix-up are unfortunately common problems in biomedical research and can eventually result in the publication of incorrect data. Here we have compared the Fluidigm SNPtrace and the Agena iPLEX Sample ID panels for the authentication of human genomic DNA samples. We have tested 14 pure samples and simulated their cross-contamination at different percentages (2%, 5%, 10%, 25% and 50%). For both panels, we report call rate, allele intensity/probability score, performance in distinguishing pure samples and contaminated samples at different percentages, and sex typing. We show that both panels are reliable and efficient methods for sample authentication and we highlight their advantages and disadvantages. We believe that the data provided here is useful for sample authentication especially in biorepositories and core facility settings.

SUBMITTER: Manjunath HS

PROVIDER: S-EPMC8263568 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

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Human sample authentication in biomedical research: comparison of two platforms.

Manjunath Harshitha Shobha HS James Nicola N Mathew Rebecca R Al Hashmi Muna M Silcock Lee L Biunno Ida I De Blasio Pasquale P Manickam Chidambaram C Tomei Sara S

Scientific reports 20210707 1

Samples used in biomedical research are often collected over years, in some cases from subjects that may have died and thus cannot be retrieved in any way. The value of these samples is priceless. Sample misidentification or mix-up are unfortunately common problems in biomedical research and can eventually result in the publication of incorrect data. Here we have compared the Fluidigm SNPtrace and the Agena iPLEX Sample ID panels for the authentication of human genomic DNA samples. We have teste ...[more]

PMID: 34234171

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Project description:BackgroundWorking together efficiently and effectively presents a significant challenge in large-scale, complex, interdisciplinary research projects. Collaboratories are a nascent method to help meet this challenge. However, formal collaboratories in biomedical research centers are the exception rather than the rule.ObjectiveThe main purpose of this paper is to compare and describe two collaboratories that used off-the-shelf tools and relatively modest resources to support the scientific activity of two biomedical research centers. The two centers were the Great Lakes Regional Center for AIDS Research (HIV/AIDS Center) and the New York University Oral Cancer Research for Adolescent and Adult Health Promotion Center (Oral Cancer Center).MethodsIn each collaboratory, we used semistructured interviews, surveys, and contextual inquiry to assess user needs and define the technology requirements. We evaluated and selected commercial software applications by comparing their feature sets with requirements and then pilot-testing the applications. Local and remote support staff cooperated in the implementation and end user training for the collaborative tools. Collaboratory staff evaluated each implementation by analyzing utilization data, administering user surveys, and functioning as participant observers.ResultsThe HIV/AIDS Center primarily required real-time interaction for developing projects and attracting new participants to the center; the Oral Cancer Center, on the other hand, mainly needed tools to support distributed and asynchronous work in small research groups. The HIV/AIDS Center's collaboratory included a center-wide website that also served as the launch point for collaboratory applications, such as NetMeeting, Timbuktu Conference, PlaceWare Auditorium, and iVisit. The collaboratory of the Oral Cancer Center used Groove and Genesys Web conferencing. The HIV/AIDS Center was successful in attracting new scientists to HIV/AIDS research, and members used the collaboratory for developing and implementing new research studies. The Oral Cancer Center successfully supported highly distributed and asynchronous research, and the collaboratory facilitated real-time interaction for analyzing data and preparing publications.ConclusionsThe two collaboratory implementations demonstrated the feasibility of supporting biomedical research centers using off-the-shelf commercial tools, but they also identified several barriers to successful collaboration. These barriers included computing platform incompatibilities, network infrastructure complexity, variable availability of local versus remote IT support, low computer and collaborative software literacy, and insufficient maturity of available collaborative software. Factors enabling collaboratory use included collaboration incentives through funding mechanism, a collaborative versus competitive relationship of researchers, leadership by example, and tools well matched to tasks and technical progress. Integrating electronic collaborative tools into routine scientific practice can be successful but requires further research on the technical, social, and behavioral factors influencing the adoption and use of collaboratories.

Dataset Information

Human sample authentication in biomedical research: comparison of two platforms.

Publications

Human sample authentication in biomedical research: comparison of two platforms.

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Dataset Information

Human sample﻿ authentication in biomedical research: comparison of two platforms.

Publications

Human sample﻿ authentication in biomedical research: comparison of two platforms.

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OmicsDI is part of the ELIXIR infrastructure

Tweets

Human sample authentication in biomedical research: comparison of two platforms.

Human sample authentication in biomedical research: comparison of two platforms.