Visual integration of results from a large DNA biobank (BIOVU) using synthesis-view

Sarah Pendergrass, Scott M. Dudek, Dan M. Roden, Dana C. Crawford, Marylyn Deriggi Ritchie

Research output: Chapter in Book/Report/Conference proceedingConference contribution

12 Citations (Scopus)

Abstract

In this paper, we describe using Synthesis-View, a new method of presenting complex genetic data, to revisit results of a study from the BioVU Vanderbilt DNA databank. BioVU is a biorepository of DNA samples coupled with de-identified electronic medical records (EMR). In the Ritchie et al. study 1 ∼10,000 BioVU samples were genotyped for 21 SNPs that were previously associated with 5 diseases: atrial fibrillation, Crohn Disease, multiple sclerosis, rheumatoid arthritis, and type 2 diabetes. In the proof-of-concept study, the 21 tests of association replicated previous findings where sample size provided adequate power. The majority of the BioVU results were originally presented in tabular form. Herein we have revisited the results of this study using Synthesis-View. The Synthesis-View software tool visually synthesizes the results of complex, multi-layered studies that aim to characterize associations between small numbers of single-nucleotide polymorphisms (SNPs) and diseases and/or phenotypes, such as the results of replication and meta-analysis studies. Using Synthesis-View with the data of the Ritchie et al. study and presenting these data in this integrated visual format demonstrates new ways to investigate and interpret these kinds of data. Synthesis-View is freely available for non-commercial research institutions, for full details see .

Original languageEnglish (US)
Title of host publicationPacific Symposium on Biocomputing 2011, PSB 2011
Pages265-275
Number of pages11
StatePublished - Dec 1 2011
Event16th Pacific Symposium on Biocomputing, PSB 2011 - Kohala Coast, HI, United States
Duration: Jan 3 2011Jan 7 2011

Other

Other16th Pacific Symposium on Biocomputing, PSB 2011
CountryUnited States
CityKohala Coast, HI
Period1/3/111/7/11

Fingerprint

Single Nucleotide Polymorphism
DNA
Electronic Health Records
Nucleic Acid Databases
Crohn Disease
Sample Size
Atrial Fibrillation
Type 2 Diabetes Mellitus
Multiple Sclerosis
Meta-Analysis
Rheumatoid Arthritis
Nucleotides
Polymorphism
Software
Phenotype
Electronic medical equipment
Research
Medical problems
Association reactions

All Science Journal Classification (ASJC) codes

  • Computational Theory and Mathematics
  • Biomedical Engineering
  • Medicine(all)

Cite this

Pendergrass, S., Dudek, S. M., Roden, D. M., Crawford, D. C., & Ritchie, M. D. (2011). Visual integration of results from a large DNA biobank (BIOVU) using synthesis-view. In Pacific Symposium on Biocomputing 2011, PSB 2011 (pp. 265-275)
Pendergrass, Sarah ; Dudek, Scott M. ; Roden, Dan M. ; Crawford, Dana C. ; Ritchie, Marylyn Deriggi. / Visual integration of results from a large DNA biobank (BIOVU) using synthesis-view. Pacific Symposium on Biocomputing 2011, PSB 2011. 2011. pp. 265-275
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Pendergrass, S, Dudek, SM, Roden, DM, Crawford, DC & Ritchie, MD 2011, Visual integration of results from a large DNA biobank (BIOVU) using synthesis-view. in Pacific Symposium on Biocomputing 2011, PSB 2011. pp. 265-275, 16th Pacific Symposium on Biocomputing, PSB 2011, Kohala Coast, HI, United States, 1/3/11.

Visual integration of results from a large DNA biobank (BIOVU) using synthesis-view. / Pendergrass, Sarah; Dudek, Scott M.; Roden, Dan M.; Crawford, Dana C.; Ritchie, Marylyn Deriggi.

Pacific Symposium on Biocomputing 2011, PSB 2011. 2011. p. 265-275.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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Pendergrass S, Dudek SM, Roden DM, Crawford DC, Ritchie MD. Visual integration of results from a large DNA biobank (BIOVU) using synthesis-view. In Pacific Symposium on Biocomputing 2011, PSB 2011. 2011. p. 265-275