Single Molecule Sequencing: Multi-Omics Integration

Instructors: Karolina Sienkiewicz
Lecture Summary: In this lecture, Karolina Sienkiewicz reviews the challenges inherent to the integration of multi-omics data across platforms, studies, and research groups. After reviewing more major statistical approaches for batch correction in biomarker prediction, she presents work based on her own implementation: SUMO (github.com/rat....
Course Summary: Sequencing-based research has become the dominant investigative practice within the biological sciences. Single-molecule sequencing: training, methods, and applications, responds to this development by providing a hands-on and in-depth introduction to sequencing for students, from Sanger to third-generation technologies. Utilizing an alternating lecture-lab schedule, students are introduced to fundamental basic principles of DNA & RNA science, progressing to cutting-edge library preparation and sequencing analysis techniques with Illumina and Nanopore technologies. Students will have the opportunity to perform direct-RNA sequencing samples on research samples, and experience first-hand the ethical implications of this data. Relevant concepts in biology and computer science will be addressed.
Relevant Papers:
Sienkiewicz et al., 2022, Cell Reports Methods 2, 100152
January 24, 2022 ª 2021 The Author(s).
doi.org/10.101...
Karolina Sienkiewicz, Aakrosh Ratan,
Protocol for integrative subtyping of lower-grade gliomas using the SUMO pipeline,
STAR Protocols,
Volume 3, Issue 1,
2022,
101110,
ISSN 2666-1667,
doi.org/10.101....
(www.sciencedir...)
Abstract: Summary
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; Health Sciences; Genomics; Gene Expression
Course website: physiology.med...
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