Introduction to the analysis of next generation sequencing data and its application to venous thromboembolism

Marisa L. R. Cunha; Joost C. M. Meijers; Saskia Middeldorp

doi:10.1160/TH15-05-0411

Thrombosis and Haemostasis, Table of Contents

Thromb Haemost 2015; 114(05): 920-932
DOI: 10.1160/TH15-05-0411

Theme Issue Article

Schattauer GmbH

Introduction to the analysis of next generation sequencing data and its application to venous thromboembolism

Marisa L. R. Cunha

¹Department of Experimental Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands

²Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands

,

Joost C. M. Meijers

¹Department of Experimental Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands

³Department of Plasma Proteins, Sanquin Research, Amsterdam, the Netherlands

,

Saskia Middeldorp

²Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands

› Author Affiliations

Abstract

Summary

Despite knowledge of various inherited risk factors associated with venous thromboembolism (VTE), no definite cause can be found in about 50% of patients. The application of data-driven searches such as GWAS has not been able to identify genetic variants with implications for clinical care, and unexplained heritability remains. In the past years, the development of several so-called next generation sequencing (NGS) platforms is offering the possibility of generating fast, inexpensive and accurate genomic information. However, so far their application to VTE has been very limited. Here we review basic concepts of NGS data analysis and explore the application of NGS technology to VTE. We provide both computational and biological viewpoints to discuss potentials and challenges of NGS-based studies.

Keywords

Gene mutations - inherited coagulation disorders - venous thrombosis - polymorphisms - bioinformatics pipeline

Full Text

References

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