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Bioinformatics Tools and Resources for Cancer Immunotherapy Study

  • Alida Palmisano
  • Julia Krushkal
  • Ming-Chung Li
  • Jianwen Fang
  • Dmitriy Sonkin
  • George Wright
  • Laura Yee
  • Yingdong ZhaoEmail author
  • Lisa McShaneEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2055)

Abstract

In recent years, cancer immunotherapy has emerged as a highly promising approach to treat patients with cancer, as the patient’s own immune system is harnessed to attack cancer cells. However, the application of these approaches is still limited to a minority of patients with cancer and it is difficult to predict which patients will derive the greatest clinical benefit.

One of the challenges faced by the biomedical community in the search of more effective biomarkers is the fact that translational research efforts involve collecting and accessing data at many different levels: from the type of material examined (e.g., cell line, animal models, clinical samples) to multiple data type (e.g., pharmacodynamic markers, genetic sequencing data) to the scale of a study (e.g., small preclinical study, moderate retrospective study on stored specimen sets, clinical trials with large cohorts).

This chapter reviews several publicly available bioinformatics tools and data resources for high throughput molecular analyses applied to a range of data types, including those generated from microarray, whole-exome sequencing (WES), RNA-seq, DNA copy number, and DNA methylation assays, that are extensively used for integrative multidimensional data analysis and visualization.

Key words

Bioinformatics tools Whole-exome sequencing (WES) RNA-seq DNA copy number DNA methylation 

Notes

Acknowledgments

We thank Ms. Alicia Livinski of NIH Library for her diligent editorial assistance.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • Alida Palmisano
    • 1
  • Julia Krushkal
    • 1
  • Ming-Chung Li
    • 1
  • Jianwen Fang
    • 1
  • Dmitriy Sonkin
    • 1
  • George Wright
    • 1
  • Laura Yee
    • 1
  • Yingdong Zhao
    • 1
    Email author
  • Lisa McShane
    • 1
    Email author
  1. 1.Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer InstituteNational Institutes of HealthBethesdaUSA

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