Practical aspects of NGS-based pathways analysis for personalized cancer science and medicine

Ekaterina A. Kotelnikova _, Mikhail Pyatnitskiy, Anna Paleeva, Olga Kremenetskaya and Dmitriy Vinogradov

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Oncotarget. 2016; 7:52493-52516. https://doi.org/10.18632/oncotarget.9370

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Ekaterina A. Kotelnikova1,2,3,*, Mikhail Pyatnitskiy1,6,7,*, Anna Paleeva1, Olga Kremenetskaya1,5 and Dmitriy Vinogradov1,2,4

1 Personal Biomedicine, Moscow, Russia

2 A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia

3 Institute Biomedical Research August Pi Sunyer (IDIBAPS), Hospital Clinic of Barcelona, Barcelona, Spain

4 Lomonosov Moscow State University, Moscow, Russia

5 Center for Theoretical Problems of Physicochemical Pharmacology RAS, Moscow, Russia

6 Orekhovich Institute of Biomedical Chemistry, Moscow, Russia

7 Pirogov Russian National Research Medical University, Moscow, Russia

* These authors have contributed equally to this work

Correspondence to:

Ekaterina A. Kotelnikova, email:

Keywords: next generation sequencing (NGS), systems biology, precision oncology, personalized medicine, pathways

Received: October 02, 2015 Accepted: April 18, 2016 Published: May 14, 2016


Nowadays, the personalized approach to health care and cancer care in particular is becoming more and more popular and is taking an important place in the translational medicine paradigm. In some cases, detection of the patient-specific individual mutations that point to a targeted therapy has already become a routine practice for clinical oncologists. Wider panels of genetic markers are also on the market which cover a greater number of possible oncogenes including those with lower reliability of resulting medical conclusions. In light of the large availability of high-throughput technologies, it is very tempting to use complete patient-specific New Generation Sequencing (NGS) or other “omics” data for cancer treatment guidance. However, there are still no gold standard methods and protocols to evaluate them. Here we will discuss the clinical utility of each of the data types and describe a systems biology approach adapted for single patient measurements. We will try to summarize the current state of the field focusing on the clinically relevant case-studies and practical aspects of data processing.

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