Protocol for integrative subtyping of lower-grade gliomas using the SUMO pipeline

Karolina Sienkiewicz; Aakrosh Ratan

doi:10.1016/j.xpro.2021.101110

Protocol for integrative subtyping of lower-grade gliomas using the SUMO pipeline

STAR Protoc. 2022 Jan 19;3(1):101110. doi: 10.1016/j.xpro.2021.101110. eCollection 2022 Mar 18.

Authors

Karolina Sienkiewicz¹, Aakrosh Ratan^{1

2

3}

Affiliations

¹ Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA.
² Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA.
³ University of Virginia Cancer Center, Charlottesville, VA 22908, USA.

Abstract

Grouping patients into subtypes with homogeneous molecular features can guide diagnosis and therapeutic interventions. SUMO is a computational pipeline that uses nonnegative matrix factorization of patient-similarity networks to integrate continuous multi-omic datasets for molecular subtyping of a disease. Here, we present a detailed protocol to demonstrate its use in determining subtypes of lower-grade gliomas by integrating gene expression, DNA methylation, and miRNA expression data from the TCGA-LGG cohort. For complete details on the use and execution of this profile, please refer to Sienkiewicz et al. (2022).

Keywords: Bioinformatics; Cancer; Gene Expression; Genomics; Health Sciences.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Algorithms
DNA Methylation / genetics
Glioma* / diagnosis
Humans
MicroRNAs* / genetics

Substances

MicroRNAs

Grants and funding

P30 CA044579/CA/NCI NIH HHS/United States