Main description:

This book presents protocols for identification of genetic drivers of cancer. Chapters guide readers through a brief history of cancer gene discovery, in silico approaches, in vitro approaches, and in vivo approaches using forward genetic screens in mice. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Cancer Driver Genes: Methods and Protocols aims to provide protocols that will be used and adapted by cancer researchers to expand the knowledge base of molecular mechanisms contributing to initiation, progression, and metastasis of cancer.

Contents:

1. Cancer Gene Discovery: Past and Present

Christopher R. Clark, Wilaiwan DuRose, and Timothy K. Starr

Part I: Cancer Gene discovery In Silico based on Sequencing Data

2. Identification of Cancer Driver Genes from a Custom Set of Next Generation Sequencing Data

Shu-Hsuan Liu and Wei-Chung Cheng

3. Cancer Gene Discovery by Network Analysis of Somatic Mutations using the MUFFINN Server

Heonjong Han, Ben Lehner, and Insuk Lee

4. Identifying Driver Interfaces Enriched for Somatic Missense Mutations in Tumors

Kivilcim Ozturk and Hannah Carter

5. Identification of Cancer Genes Based on de novo Transposon Insertion Site Analysis using RNA and DNA Sequencing

Aaron Sarver

PartII: Cancer Gene Discovery using Cell and Organoid Systems

6. A Cell-based Method for Identification of Chemotherapy Resistance Cancer Genes

Raffaele Hellweg, Ashley Mooneyham, and Martina Bazzaro

7. Engineering a Bioartificial Human Colon Model through Decellularization and Recellularization

Huanhuan Joyce Chen and Michael L. Shuler

8. Mutagenesis Screens for Prostate Cancer using Replication-Incompetent Lentiviral Vectors

Grant D. Trobridge

9. Arrayed shRNA Screening to Identify Suppressors of Anchorage-independent Growth

Ugur Eskiocak

10. Genome-wide CRISPR/Cas9 Screening for Identification of Cancer Genes in Cell Lines

Charles H. Adelmann, Tim Wang, David M. Sabatini, and Eric S. Lander

11. CRISPR/Cas9 Based Positive Screens for Cancer Related Traits

Nicholas J. Slipek, Jyotika Varshney, and David A. Largaespada

12. Ex vivo Transposon-Mediated Genetic Screens for Cancer Gene Discovery

Kathryn A. O'Donnell, Yabin Guo, Shruthy Suresh, Barrett L. Updegraff, and Xiaorong Zhou

Part III: Cancer Gene Discovery using Animal Models

13. Cancer Gene Discovery Utilizing Sleeping Beauty Transposon Mutagenesis

Kelsie L. Becklin, Branden A. Smeester, and Branden S. Moriarity

14. PiggyBac Transposon-based Insertional Mutagenesis in Mice

Mathias J. Friedrich, Iraad F. Bronner, Pentao Liu, Allan Bradley, and Roland Rad

15. Liver-specific Delivery of Sleeping Beauty Transposon System by Hydrodynamic Injection for Cancer Gene Validation

Amy P. Chiu and Vincent W. Keng

16. Engineering Large Genomic Rearrangement in Mouse Embryonic Stem Cell for Cancer Gene Discovery

Yuen-Yi Tseng and Anindya Bagchi