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Neuroinformatics

, Volume 16, Issue 3–4, pp 393–402 | Cite as

GPU Accelerated Browser for Neuroimaging Genomics

  • Bob Zigon
  • Huang Li
  • Xiaohui Yao
  • Shiaofen Fang
  • Mohammad Al Hasan
  • Jingwen Yan
  • Jason H. Moore
  • Andrew J. Saykin
  • Li Shen
  • Alzheimer’s Disease Neuroimaging Initiative
Original Article
  • 86 Downloads

Abstract

Neuroimaging genomics is an emerging field that provides exciting opportunities to understand the genetic basis of brain structure and function. The unprecedented scale and complexity of the imaging and genomics data, however, have presented critical computational bottlenecks. In this work we present our initial efforts towards building an interactive visual exploratory system for mining big data in neuroimaging genomics. A GPU accelerated browsing tool for neuroimaging genomics is created that implements the ANOVA algorithm for single nucleotide polymorphism (SNP) based analysis and the VEGAS algorithm for gene-based analysis, and executes them at interactive rates. The ANOVA algorithm is 110 times faster than the 4-core OpenMP version, while the VEGAS algorithm is 375 times faster than its 4-core OpenMP counter part. This approach lays a solid foundation for researchers to address the challenges of mining large-scale imaging genomics datasets via interactive visual exploration.

Keywords

GPU Genomics MRI Alzheimer’s disease Data mining Versatile gene based association study 

Notes

Acknowledgements

Data collection and sharing for this project was funded by the Alzheimer’s Disease Neuroimaging Initiative (ADNI) (National Institutes of Health Grant U01 AG024904) and DOD ADNI (Department of Defense award number W81XWH-12-2-0012). ADNI is funded by the National Institute on Aging, the National Institute of Biomedical Imaging and Bioengineering, and through generous contributions from the following: AbbVie, Alzheimer’s Association; Alzheimer’s Drug Discovery Foundation; Araclon Biotech; BioClinica, Inc.; Biogen; Bristol-Myers Squibb Company; CereSpir, Inc.; Eisai Inc.; Elan Pharmaceuticals, Inc.; Eli Lilly and Company; EuroImmun; F. Hoffmann-La Roche Ltd and its affiliated company Genentech, Inc.; Fujirebio; GE Healthcare; IXICO Ltd.; Janssen Alzheimer Immunotherapy Research & Development, LLC.; Johnson & Johnson Pharmaceutical Research & Development LLC.; Lumosity; Lundbeck; Merck & Co., Inc.; Meso Scale Diagnostics, LLC.; NeuroRx Research; Neurotrack Technologies; Novartis Pharmaceuticals Corporation; Pfizer Inc.; Piramal Imaging; Servier; Takeda Pharmaceutical Company; and Transition Therapeutics. The Canadian Institutes of Health Research is providing funds to support ADNI clinical sites in Canada. Private sector contributions are facilitated by the Foundation for the National Institutes of Health (www.fnih.org). The grantee organization is the Northern California Institute for Research and Education, and the study is coordinated by the Alzheimer’s Disease Cooperative Study at the University of California, San Diego. ADNI data are disseminated by the Laboratory for Neuro Imaging at the University of Southern California.

Funding Information

This work was funded in part by the National Institutes of Health (NIH) grants R01 EB022574, R01 LM011360, U01 AG024904, P30 AG10133, R01 AG019771 and IUPUI ITDP Program.

Compliance with Ethical Standards

Conflict of interests

The authors declare that they have no conflict of interest.

Supplementary material

(MP4 68.2 MB)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Bob Zigon
    • 1
  • Huang Li
    • 2
  • Xiaohui Yao
    • 3
  • Shiaofen Fang
    • 2
  • Mohammad Al Hasan
    • 2
  • Jingwen Yan
    • 3
  • Jason H. Moore
    • 4
  • Andrew J. Saykin
    • 5
  • Li Shen
    • 4
  • Alzheimer’s Disease Neuroimaging Initiative
  1. 1.Beckman CoulterIndianapolisUSA
  2. 2.Department of Computer ScienceIndiana University-Purdue University IndianapolisIndianapolisUSA
  3. 3.Department of BioHealth InformaticsIndiana University-Purdue University IndianapolisIndianapolisUSA
  4. 4.Department of Biostatistics, Epidemiology, Informatics, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaUSA
  5. 5.Department of Radiology and Imaging SciencesIU School of MedicineIndianapolisUSA

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