[go: up one dir, main page]
More Web Proxy on the site http://driver.im/ skip to main content
10.1145/2649387.2666618acmconferencesArticle/Chapter ViewAbstractPublication PagesbcbConference Proceedingsconference-collections
research-article

Towards the characterization of normal peripheral immune cells with data from ImmPort

Published: 20 September 2014 Publication History

Abstract

To date, our understanding of a normal immune system is far behind that of other healthy organ systems. One reason for this is the lack of standardization in the lab techniques, especially flow cytometry.
To take a step towards the characterization of a normal immune system, we re-analyzed and combined data that was made publicly available through the Immunology Database and Analysis Portal (ImmPort, immport.niaid.nih.gov) [1]. ImmPort is a public warehouse for the management and analysis of clinical and mechanistic data from NIAID/DAIT-funded research studies. Currently, 108 studies are made publicly available in ImmPort of which 27 contain raw FCS files from flow cytometry experiments run on samples of adults.
Here we use ImmPort as a source of publicly available raw flow cytometry files from hundreds of participants in several trials, to study immune cells from the blood of healthy individuals. To characterize well-defined cells in a normal immune system, we used an unbiased method to compare data from different cytometers and antibody staining panels.
As an initial step, we obtained the marker information from each raw FCS file in an automated fashion and made their nomenclature consistent.
We applied and evaluated various transformation strategies and normalized the data on a per-channel basis using the R function warpSet [2] from the flowStats package of Bioconductor to make the flow cytometry data more comparable across studies. Initial promising results were observed for the cell-surface markers used to define T and B cells in general in automatically gated lymphocyte populations. Using our pipeline, the distribution of percentages of B cells as well as CD4+ and CD8+ T cells of subjects is in the range as immunologically expected and mostly comparable across the different studies originating from different laboratories.
We plan to extend this approach to more cell types and eventually to studies of healthy individuals separated by gender, age group or ethnicity. Our approach promises to give further insights into the normal immune system.

References

[1]
Bhattacharya, S., Andorf, S., Gomes, L., Dunn, P., Schaefer, H., Pontius, J., Berger, P., Desborough, V., Smith, T., Campbell, J., Thomson, E., Monteiro, R., Guimaraes, P., Walters, B., Wiser, J. and Butte, A. J. 2014. ImmPort: disseminating data to the public for the future of immunology. Immunol Res. 58 (May 2014), 234--239.
[2]
Hahne, F., Khodabakhshi, A. H., Bashashati, A., Wong, C., Gascoyne, R. D., Weng, A. P., Seyfert-Margolis, V., Bourcier, K., Asare, A., Lumley, T., Gentleman, R. and Brinkman, R. R. 2010. Per-channel basis normalization methods for flow cytometry data. Cytom Part A. 77 (Feb 2010), 121--131.

Cited By

View all
  • (2017)Evidence for benefit of statins to modify cognitive decline and risk in Alzheimer’s diseaseAlzheimer's Research & Therapy10.1186/s13195-017-0237-y9:1Online publication date: 17-Feb-2017

Recommendations

Comments

Please enable JavaScript to view thecomments powered by Disqus.

Information & Contributors

Information

Published In

cover image ACM Conferences
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics
September 2014
851 pages
ISBN:9781450328944
DOI:10.1145/2649387
  • General Chairs:
  • Pierre Baldi,
  • Wei Wang
Permission to make digital or hard copies of part or all of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for third-party components of this work must be honored. For all other uses, contact the Owner/Author.

Sponsors

Publisher

Association for Computing Machinery

New York, NY, United States

Publication History

Published: 20 September 2014

Check for updates

Author Tags

  1. ImmPort
  2. flow cytometry
  3. immune system
  4. publicly available data

Qualifiers

  • Research-article

Conference

BCB '14
Sponsor:
BCB '14: ACM-BCB '14
September 20 - 23, 2014
California, Newport Beach

Acceptance Rates

Overall Acceptance Rate 254 of 885 submissions, 29%

Contributors

Other Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

  • Downloads (Last 12 months)0
  • Downloads (Last 6 weeks)0
Reflects downloads up to 31 Dec 2024

Other Metrics

Citations

Cited By

View all
  • (2017)Evidence for benefit of statins to modify cognitive decline and risk in Alzheimer’s diseaseAlzheimer's Research & Therapy10.1186/s13195-017-0237-y9:1Online publication date: 17-Feb-2017

View Options

Login options

View options

PDF

View or Download as a PDF file.

PDF

eReader

View online with eReader.

eReader

Media

Figures

Other

Tables

Share

Share

Share this Publication link

Share on social media