Emerging Approaches for Tumor Analyses in Epidemiological Studies

Welcome to the GitHub pages for the Emerging Approaches for Tumor Analyses in Epidemiological Studies course. This course is provided by NCI-ITEB, and taught by bioinformaticians from the Division of Cancer Epidemiology and Genetics (DCEG), NCI; the University of Chicago; and the University of California San Diego, many of whom are involved in the Sherlock-Lung study of lung cancer in never smokers.

Registration for the 2022-2023 workshop is currently closed.

2022-2023 Schedule

Module 1

  • Nov. 2, 2022: Introduction to Computing Clusters and Bioinformatics
  • Nov. 9, 2022: Public databases
  • Nov. 16, 2022: DNA sequencing strategies and quality control
  • Nov. 23, 2022: “Ask a Bioinformatician” I

Module 2

  • Jan. 11, 2023: Mutation calling and analysis
  • Jan. 18, 2023: Mutational signatures
    • Jan. 19, 2023 - Speaker: Ludmil Alexandrov - Anthology of unusual patterns of somatic mutations in cancer genomes
  • Jan. 25, 2023: Structural variant (SV) analysis
  • Feb. 1, 2023: “Ask a Bioinformatician” II
    • Feb. 16, 2023 - Speaker: Peter Park - Structural alterations in cancer genomes

Module 3

  • Mar. 8, 2023: Somatic copy number alterations (SCNAs)
  • Mar. 13*, 2023: Identifying cancer drivers
  • Mar. 20*, 2023: Tumor evolution
    • Mar. 23, 2023- Speaker: Núria López-Bigas - Somatic mutations in tumors and normal tissues
  • Mar. 29, 2023: “Ask a Bioinformatician” III
    • Apr. 20, 2023- Speaker: David Wedge - Tumour evolution in diverse human populations

Module 4

  • Apr. 26, 2023: Transcriptome-based study designs
  • May 3, 2023: RNA-seq data mining
    • May 11, 2023- Speaker: Marcin Imieliński - Origin and identity in lung adenocarcinoma evolution
  • May 15*, 2023: Data visualization approaches
  • May 17, 2023: “Ask a Bioinformatician” IV
    • May 25, 2023- Speaker: Charles Swanton - Title TBD
    • June 8, 2023- Speaker: David Adams - Cross-species oncogenomics of melanoma and other malignancies to define disease drivers

*Date changed

Course Description

This course aims to provide basic information on the types of analyses that can be conducted using tumor specimens to study the etiology and progression of cancer within epidemiological studies.

The course includes 12 sessions divided into 4 modules, taking place from November 2022 to May 2023. Participants are encouraged to attend all sessions but may choose specific sessions based on topics of interest. Participants who attend the entire course will receive a certificate of completion. Moreover, the skill sets acquired through the course could enable participants to test their own hypotheses and approaches using Sherlock-Lung data or other genomics data. The results of these analyses may serve as “preliminary data” to apply for NCI/DCEG awards. There will also be “Ask a Bioinformatician” sessions where course participants can join an open-door virtual meeting room to ask questions. These sessions will be held once at the end of each module and will cover the topics presented in the weeks before.

All sessions will consist of two 1-hour segments separated by a 15-minute break. The first “lecture” hour will include theoretical explanations of the topic and a 10-minute question and answer period. The second “practical” hour is aimed at investigators or fellows that want to learn how to conduct these types of analyses or interpret results. The practical hour will include hands-on practice for participants to conduct analyses with instructors’ help and will be conducted in-person at the NCI Shady Grove campus. Sessions will be led by two or three investigators, and occasionally with teachers invited from NIH or other institutions.

There will also be DCEG-wide seminars from senior leaders in the field who will cover specific session topics. Details on how to connect for the seminars will be announced in the future.

Learning objectives and materials (including codes, data, questions, instructions, and software checklist) will be uploaded to this website prior to each session. Course slides and links to recordings of the DCEG-wide seminars on related topics will also be posted on this page for future use. After each session and at the end of the course, participants will be invited to complete a brief evaluation form online to provide feedback to the course organizers and teachers.

We expect that changes to the workshop plan will be made along the way, based on feedback from participants.

Latest Posts

Modules 3+4 Dates Changed and New Schedule

Please be advised, due to conflicts in room availability we’ve shifted the dates for three sessions in Modules 3 and 4.

A successful first session, and details for Session 2

First of all, thank you to all of the participants yesterday! It was great to see so much interest both virtually and in person, and we hope you all learned a lot!

Emerging Approaches for Tumor Analyses in Epidemiological Studies begins next week!

As a reminder, the first session of the Emerging Approaches for Tumor Analyses in Epidemiological Studies course is this upcoming Wednesday, Nov. 2, at 9:30 AM. The lecture components will be held both virtually and in person at the NCI Shady Grove campus, auditorium TE 406/408/410.