Browsing by Subject "Standardization"

Now showing 1 - 4 of 4
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    A protocol to evaluate RNA sequencing normalization methods
    (BMC, 2019-12-20) Abrams, Zachary B.; Johnson, Travis S.; Huang, Kun; Payne, Philip R. O.; Coombes, Kevin; Medicine, School of Medicine
    Background RNA sequencing technologies have allowed researchers to gain a better understanding of how the transcriptome affects disease. However, sequencing technologies often unintentionally introduce experimental error into RNA sequencing data. To counteract this, normalization methods are standardly applied with the intent of reducing the non-biologically derived variability inherent in transcriptomic measurements. However, the comparative efficacy of the various normalization techniques has not been tested in a standardized manner. Here we propose tests that evaluate numerous normalization techniques and applied them to a large-scale standard data set. These tests comprise a protocol that allows researchers to measure the amount of non-biological variability which is present in any data set after normalization has been performed, a crucial step to assessing the biological validity of data following normalization. Results In this study we present two tests to assess the validity of normalization methods applied to a large-scale data set collected for systematic evaluation purposes. We tested various RNASeq normalization procedures and concluded that transcripts per million (TPM) was the best performing normalization method based on its preservation of biological signal as compared to the other methods tested. Conclusion Normalization is of vital importance to accurately interpret the results of genomic and transcriptomic experiments. More work, however, needs to be performed to optimize normalization methods for RNASeq data. The present effort helps pave the way for more systematic evaluations of normalization methods across different platforms. With our proposed schema researchers can evaluate their own or future normalization methods to further improve the field of RNASeq normalization.
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    Revitalizing Hypothesis
    (Research Caucus of the Medical Library Association, 2021) Foster, Erin D.; Perryman, Carol L.; Ruth Lilly Medical Library, School of Medicine
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    Standardization can accelerate the adoption of pharmacogenomics: current status and the path forward
    (Future Medicine, 2018-07-01) Caudle, Kelly E.; Keeling, Nicholas J.; Klein, Teri E.; Whirl-Carrillo, Michelle; Pratt, Victoria M.; Hoffman, James M.; Medical & Molecular Genetics, IU School of Medicine
    Successfully implementing pharmacogenomics into routine clinical practice requires an efficient process to order genetic tests and report the results to clinicians and patients. Lack of standardized approaches and terminology in clinical laboratory processes, ordering of the test and reporting of test results all impede this workflow. Expert groups such as the Association for Molecular Pathology and the Clinical Pharmacogenetics Implementation Consortium have published recommendations for standardizing laboratory genetic testing, reporting and terminology. Other resources such as PharmGKB, ClinVar, ClinGen and PharmVar have established databases of nomenclature for pharmacogenetic alleles and variants. Opportunities remain to develop new standards and further disseminate existing standards which will accelerate the implementation of pharmacogenomics.
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    Utilizing a reviewer database to facilitate integration of an investigator-focused translational research and career development program across the state of Indiana
    (Cambridge University Press, 2018-06) Coffee, R. L., Jr.; Driscol, Julie; Saydyk, Tammy J.; Shekhar, Anantha; Denne, Scott C.; Hunt, Joe D.; Medicine, School of Medicine
    OBJECTIVES/SPECIFIC AIMS: The Indiana CTSI is investigating innovative approaches to integrate resources that will enrich scientific investigators. Our goals are to enhance the availability and communication among CTSI resources, for example internal funding, and to expand existing mentorship. METHODS/STUDY POPULATION: Developed a reviewer database that serves to streamline reviewer identification, decrease reviewer fatigue, and promote collaboration among disciplines. We started with a pool of NIH-funded investigators from across the Indiana CTSI core institutions and merged this list with previous CTSI reviewers and internal funding awardees. To expand this list, names and expertise from new faculty hires were added. RESULTS/ANTICIPATED RESULTS: Though this tool is relatively new, we have already observed an increase in junior faculty awareness and engagement with the CTSI. This database allows for increased opportunities of junior faculty to serve as reviewers and to refine grant writing skills and provides a platform for networking and collaborating across disciplines. It also allows for increased integration of programs with a shared reviewer database and promotes grant review standardization. DISCUSSION/SIGNIFICANCE OF IMPACT: Our database utilization seeks to decrease the time for junior faculty to obtain their first extramural grant, to enhance promotion and tenure packages, strengthen integration among CTSI programs, increase interactions between clinical and basic science investigators, and promote team science.