CS 598MEB: Computational Cancer Genomics

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Semester	Spring 2021
Instructor	Prof. Mohammed El-Kebir
Time	TR 2:00-3:15 PM
Location	Zoom: [link] (requires Illinois Zoom account)
Office hours	Tuesdays 3:15-4:15 PM in 3216 Siebel Center

Course description

This course introduces fundamental problems and algorithmic approaches in cancer genomics. Covered topics include:

1. tumor phylogeny inference,
2. cancer immunotherapy,
3. driver mutation identification,
4. somatic variant calling.

This course will not teach you how to run popular bioinformatics tools. Rather, we will focus on the underlying algorithmic ideas and the issues that arise when translating a biological problem into a computational problem and ultimately an accurate tool for biologists to use. In addition, this course will teach you how to read scientific papers and how to propose and conduct independent research.

Prerequisites

This course is appropriate for graduate students in computer science, bioengineering, mathematics and statistics. Familiarity with basic statistics, probability and algorithms is expected.

Grading

• Class participation: 20%
• Asking critical questions
• Peer review
• Paper presentation: 30%
• Project: 50%
• Proposal
• Report/paper
• Presentation

Course schedule

Date	Presenter	Slides	Reading
01/26/2021	Mohammed El-Kebir	Introduction [slides] [recording]	Biology for Computer Scientists -- Lawrence Hunter [link]
01/28/2021	Mohammed El-Kebir	Cancer Phylogenetics I [slides] [recording]	Lecture notes [link] M. El-Kebir, L. Oesper, H. Acheson-Field and B. J. Raphael. Reconstruction of clonal trees and tumor composition from multi-sample sequencing data. Bioinformatics (Special Issue: Proceedings of ISMB), 31(12):i62-i70, 2015
02/02/2021	Mohammed El-Kebir	Cancer Phylogenetics II [slides] [recording]	M. El-Kebir, L. Oesper, H. Acheson-Field and B. J. Raphael. Reconstruction of clonal trees and tumor composition from multi-sample sequencing data. Bioinformatics (Special Issue: Proceedings of ISMB), 31(12):i62-i70, 2015 Y. Qi, D. Pradhan and M. El-Kebir. Implications of non-uniqueness in phylogenetic deconvolution of bulk DNA samples of tumors. Algorithms for Molecular Biology, 14:19, 2019
02/04/2021	Mohammed El-Kebir	Cancer Phylogenetics III [slides] [recording]	Y. Qi, D. Pradhan and M. El-Kebir. Implications of non-uniqueness in phylogenetic deconvolution of bulk DNA samples of tumors. Algorithms for Molecular Biology, 14:19, 2019
02/09/2021	Mohammed El-Kebir	Consensus Trees [slides] [recording]	N. Aguse, Y. Qi and M. El-Kebir. Summarizing the Solution Space in Tumor Phylogeny Inference using Multiple Consensus Trees. Bioinformatics (ISMB/ECCB 2019), 35:i408-i146, 2019
02/11/2021	Mohammed El-Kebir	Single-cell Phylogenetics [slides] [recording]	M. El-Kebir. SPhyR: Tumor Phylogeny Estimation from Single-Cell Sequencing Data under Loss and Error. Bioinformatics (ECCB 2018), 34(17):i671-679, 2018
02/16/2021	Mohammed El-Kebir	Mutation Clusters I [slides] [recording]	G. Satas, S. Zaccaria, M. El-Kebir and B.J. Raphael. DeCiFering the Elusive Cancer Cell Fraction in Tumor Heterogeneity and Evolution. [see piazza]
02/18/2021	Mohammed El-Kebir	Mutation Clusters II [slides] [notes] [recording]	G. Satas, S. Zaccaria, M. El-Kebir and B.J. Raphael. DeCiFering the Elusive Cancer Cell Fraction in Tumor Heterogeneity and Evolution. [see piazza]
02/23/2021	Mohammed El-Kebir	Signatures [slides] [recording]	S. Christensen, M.D.M. Leiserson, M. El-Kebir. PhySigs: Phylogenetic Inference of Mutational Signature Dynamics. Pacific Symposium on Biocomputing, 25:226-237, 2021
02/25/2021	Mohammed El-Kebir	RECAP [slides] [recording]	S. Christensen, J. Kim, N. Chia, O. Koyejo and M. El-Kebir. Detecting Evolutionary Patterns of Cancers using Consensus Trees. Bioinformatics (ECCB 2020), 36:i362–i370, 2020
03/02/2021	Simone Zaccaria	CNA Calling I [recording]	S. Zaccaria S and B.J. Raphael. Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data. Nat Commun. 2020;11(1):4301
03/04/2021	Simone Zaccaria	CNA Calling II	Zaccaria S, Raphael BJ. Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL. Nat Biotechnol. 39:207-214, 2021
03/09/2021	Mohammed El-Kebir	Metastasis I [slides]	M. El-Kebir, G. Satas and B.J. Raphael. Inferring parsimonious migration histories for metastatic cancers. Nature Genetics, 50:718-726, 2018
03/11/2021	Mohammed El-Kebir	Metastasis II [slides]	M. El-Kebir, G. Satas and B.J. Raphael. Inferring parsimonious migration histories for metastatic cancers. Nature Genetics, 50:718-726, 2018

Deadlines

All deadlines are 11:59pm CST.

• TBD: Pick paper to present
• TBD: Project proposal
• TBD: Proposal peer reviews
• TBD: Initial project report submission
• TBD: Initial project report peer reviews
• TBD: Final project report submission

Further instructions are on piazza.

Papers

See schedule.

Project

Example projects:

• Analyze cancer progression using SEER data
• Non-uniqueness and consensus tree clustering of 1-Dollo phylogenies

Statement on Mental Health

Diminished mental health, including significant stress, mood changes, excessive worry, substance/alcohol abuse, or problems with eating and/or sleeping can interfere with optimal academic performance, social development, and emotional wellbeing. The University of Illinois offers a variety of confidential services including individual and group counseling, crisis intervention, psychiatric services, and specialized screenings at no additional cost. If you or someone you know experiences any of the above mental health concerns, it is strongly encouraged to contact or visit any of the University’s resources provided below. Getting help is a smart and courageous thing to do -- for yourself and for those who care about you.

Counseling Center	217-333-3704	610 East John Street Champaign, IL 61820
McKinley Health Center	217-333-2700	1109 South Lincoln Avenue, Urbana, Illinois 61801