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hemaClass.org: Online One-By-One Microarray Normalization and Classification of Hematological Cancers for Precision Medicine.

Publication ,  Journal Article
Falgreen, S; Ellern Bilgrau, A; Brøndum, RF; Hjort Jakobsen, L; Have, J; Lindblad Nielsen, K; El-Galaly, TC; Bødker, JS; Schmitz, A; H Young, K ...
Published in: PLoS One
2016

BACKGROUND: Dozens of omics based cancer classification systems have been introduced with prognostic, diagnostic, and predictive capabilities. However, they often employ complex algorithms and are only applicable on whole cohorts of patients, making them difficult to apply in a personalized clinical setting. RESULTS: This prompted us to create hemaClass.org, an online web application providing an easy interface to one-by-one RMA normalization of microarrays and subsequent risk classifications of diffuse large B-cell lymphoma (DLBCL) into cell-of-origin and chemotherapeutic sensitivity classes. Classification results for one-by-one array pre-processing with and without a laboratory specific RMA reference dataset were compared to cohort based classifiers in 4 publicly available datasets. Classifications showed high agreement between one-by-one and whole cohort pre-processsed data when a laboratory specific reference set was supplied. The website is essentially the R-package hemaClass accompanied by a Shiny web application. The well-documented package can be used to run the website locally or to use the developed methods programmatically. CONCLUSIONS: The website and R-package is relevant for biological and clinical lymphoma researchers using affymetrix U-133 Plus 2 arrays, as it provides reliable and swift methods for calculation of disease subclasses. The proposed one-by-one pre-processing method is relevant for all researchers using microarrays.

Duke Scholars

Published In

PLoS One

DOI

EISSN

1932-6203

Publication Date

2016

Volume

11

Issue

10

Start / End Page

e0163711

Location

United States

Related Subject Headings

  • Workflow
  • Web Browser
  • Software
  • Reproducibility of Results
  • Precision Medicine
  • Patient Portals
  • Middle Aged
  • Male
  • Humans
  • Hematologic Neoplasms
 

Citation

APA
Chicago
ICMJE
MLA
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Falgreen, S., Ellern Bilgrau, A., Brøndum, R. F., Hjort Jakobsen, L., Have, J., Lindblad Nielsen, K., … Bøgsted, M. (2016). hemaClass.org: Online One-By-One Microarray Normalization and Classification of Hematological Cancers for Precision Medicine. PLoS One, 11(10), e0163711. https://doi.org/10.1371/journal.pone.0163711
Falgreen, Steffen, Anders Ellern Bilgrau, Rasmus Froberg Brøndum, Lasse Hjort Jakobsen, Jonas Have, Kasper Lindblad Nielsen, Tarec Christoffer El-Galaly, et al. “hemaClass.org: Online One-By-One Microarray Normalization and Classification of Hematological Cancers for Precision Medicine.PLoS One 11, no. 10 (2016): e0163711. https://doi.org/10.1371/journal.pone.0163711.
Falgreen S, Ellern Bilgrau A, Brøndum RF, Hjort Jakobsen L, Have J, Lindblad Nielsen K, et al. hemaClass.org: Online One-By-One Microarray Normalization and Classification of Hematological Cancers for Precision Medicine. PLoS One. 2016;11(10):e0163711.
Falgreen, Steffen, et al. “hemaClass.org: Online One-By-One Microarray Normalization and Classification of Hematological Cancers for Precision Medicine.PLoS One, vol. 11, no. 10, 2016, p. e0163711. Pubmed, doi:10.1371/journal.pone.0163711.
Falgreen S, Ellern Bilgrau A, Brøndum RF, Hjort Jakobsen L, Have J, Lindblad Nielsen K, El-Galaly TC, Bødker JS, Schmitz A, H Young K, Johnsen HE, Dybkær K, Bøgsted M. hemaClass.org: Online One-By-One Microarray Normalization and Classification of Hematological Cancers for Precision Medicine. PLoS One. 2016;11(10):e0163711.

Published In

PLoS One

DOI

EISSN

1932-6203

Publication Date

2016

Volume

11

Issue

10

Start / End Page

e0163711

Location

United States

Related Subject Headings

  • Workflow
  • Web Browser
  • Software
  • Reproducibility of Results
  • Precision Medicine
  • Patient Portals
  • Middle Aged
  • Male
  • Humans
  • Hematologic Neoplasms