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Phenotype-Driven Plasma Biobanking Strategies and Methods.

Bowton EA, Collier SP, Wang X, Sutcliffe CB, Van Driest SL, Couch LJ, Herrera M, Jerome RN, Slebos RJ, Alborn WE, Liebler DC, McNaughton CD, Mernaugh RL, Wells QS, Brown NJ, Roden DM, Pulley JM - J Pers Med (2015)

Bottom Line: BioVU, Vanderbilt's DNA biorepository linked to de-identified clinical EMRs, has proven fruitful in its capacity to extensively appeal to numerous areas of biomedical and clinical research, supporting the discovery of genotype-phenotype interactions.Expanding on experiences in BioVU creation and development, we have recently embarked on a parallel effort to collect plasma in addition to DNA from blood specimens leftover after routine clinical testing at Vanderbilt.This initiative offers expanded utility of BioVU by combining proteomic and metabolomic approaches with genomics and/or clinical outcomes, widening the breadth for potential research and subsequent future impact on clinical care.

View Article: PubMed Central - PubMed

Affiliation: Institute for Clinical and Translational Research, Vanderbilt University, Nashville, TN 37203, USA. erica.a.bowton@vanderbilt.edu.

ABSTRACT
Biobank development and integration with clinical data from electronic medical record (EMR) databases have enabled recent strides in genomic research and personalized medicine. BioVU, Vanderbilt's DNA biorepository linked to de-identified clinical EMRs, has proven fruitful in its capacity to extensively appeal to numerous areas of biomedical and clinical research, supporting the discovery of genotype-phenotype interactions. Expanding on experiences in BioVU creation and development, we have recently embarked on a parallel effort to collect plasma in addition to DNA from blood specimens leftover after routine clinical testing at Vanderbilt. This initiative offers expanded utility of BioVU by combining proteomic and metabolomic approaches with genomics and/or clinical outcomes, widening the breadth for potential research and subsequent future impact on clinical care. Here, we describe the considerations and components involved in implementing a plasma biobank program from a feasibility assessment through pilot sample collection.

No MeSH data available.


The sample plasma phenotype demonstrates clinical criteria used to define eligible samples in real time.
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jpm-05-00140-f004: The sample plasma phenotype demonstrates clinical criteria used to define eligible samples in real time.

Mentions: Algorithms for defining each phenotype are developed using a variety of potential strategies and data types, but are constrained by the requirement that the eligibility criteria be available in the EMR at the time of sample selection. For example, in our EMR system, all demographic, laboratory and vital sign data are available as formatted data elements immediately upon report and can be used to identify plasma samples for accrual. Previous diagnoses, defined based on ICD-9 codes, keywords in clinical documents or specific medication exposures, can also be used as inclusion or exclusion criteria. In contrast, discharge diagnoses for the current hospitalization are not typically entered until at or after discharge and would not be valid criteria. Each phenotype definition (potentially including both cases and controls or a spectrum of illness) must be developed and validated for each project; a well-established process in the context of BioVU research protocols and undertaken using an interactive, collaborative approach by the BioVU team and the investigator. A sample algorithm is shown in Figure A1.


Phenotype-Driven Plasma Biobanking Strategies and Methods.

Bowton EA, Collier SP, Wang X, Sutcliffe CB, Van Driest SL, Couch LJ, Herrera M, Jerome RN, Slebos RJ, Alborn WE, Liebler DC, McNaughton CD, Mernaugh RL, Wells QS, Brown NJ, Roden DM, Pulley JM - J Pers Med (2015)

The sample plasma phenotype demonstrates clinical criteria used to define eligible samples in real time.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4493492&req=5

jpm-05-00140-f004: The sample plasma phenotype demonstrates clinical criteria used to define eligible samples in real time.
Mentions: Algorithms for defining each phenotype are developed using a variety of potential strategies and data types, but are constrained by the requirement that the eligibility criteria be available in the EMR at the time of sample selection. For example, in our EMR system, all demographic, laboratory and vital sign data are available as formatted data elements immediately upon report and can be used to identify plasma samples for accrual. Previous diagnoses, defined based on ICD-9 codes, keywords in clinical documents or specific medication exposures, can also be used as inclusion or exclusion criteria. In contrast, discharge diagnoses for the current hospitalization are not typically entered until at or after discharge and would not be valid criteria. Each phenotype definition (potentially including both cases and controls or a spectrum of illness) must be developed and validated for each project; a well-established process in the context of BioVU research protocols and undertaken using an interactive, collaborative approach by the BioVU team and the investigator. A sample algorithm is shown in Figure A1.

Bottom Line: BioVU, Vanderbilt's DNA biorepository linked to de-identified clinical EMRs, has proven fruitful in its capacity to extensively appeal to numerous areas of biomedical and clinical research, supporting the discovery of genotype-phenotype interactions.Expanding on experiences in BioVU creation and development, we have recently embarked on a parallel effort to collect plasma in addition to DNA from blood specimens leftover after routine clinical testing at Vanderbilt.This initiative offers expanded utility of BioVU by combining proteomic and metabolomic approaches with genomics and/or clinical outcomes, widening the breadth for potential research and subsequent future impact on clinical care.

View Article: PubMed Central - PubMed

Affiliation: Institute for Clinical and Translational Research, Vanderbilt University, Nashville, TN 37203, USA. erica.a.bowton@vanderbilt.edu.

ABSTRACT
Biobank development and integration with clinical data from electronic medical record (EMR) databases have enabled recent strides in genomic research and personalized medicine. BioVU, Vanderbilt's DNA biorepository linked to de-identified clinical EMRs, has proven fruitful in its capacity to extensively appeal to numerous areas of biomedical and clinical research, supporting the discovery of genotype-phenotype interactions. Expanding on experiences in BioVU creation and development, we have recently embarked on a parallel effort to collect plasma in addition to DNA from blood specimens leftover after routine clinical testing at Vanderbilt. This initiative offers expanded utility of BioVU by combining proteomic and metabolomic approaches with genomics and/or clinical outcomes, widening the breadth for potential research and subsequent future impact on clinical care. Here, we describe the considerations and components involved in implementing a plasma biobank program from a feasibility assessment through pilot sample collection.

No MeSH data available.