Analysis of Somatic Alterations in Cancer Genome: From SNP Arrays to Next Generation Sequencing

Tatiana Popova (1) , Valentina Boeva (2, 3) , Elodie Manié (1) , Yves Rozenholc (4) , Emmanuel Barillot (3) , Marc-Henri Stern (5)

1 U830 - Unité de génétique et biologie des cancers
2 CBIO - Centre de Bioinformatique
3 Cancer et génome: Bioinformatique, biostatistiques et épidémiologie d'un système complexe
4 SELECT - Model selection in statistical learning
5 Institut Curie [Paris]

In this chapter we consider basic hypothesis, problem statements and technological and computa- tional solutions for analysis of copy number alterations in tumor genomes. We provide a data mining tech- nique (based on the GAP method described in (Popova et al., 2009)) which allows extraction of absolute copy numbers and allelic contents from the whole genome copy number variation and allelic imbalance profiles obtained by SNP arrays or NGS.

Domaines: Bio-Informatique, Biologie Systémique [q-bio.QM]; Cancer

Tatiana Popova, Valentina Boeva, Elodie Manié, Yves Rozenholc, Emmanuel Barillot, et al.. Analysis of Somatic Alterations in Cancer Genome: From SNP Arrays to Next Generation Sequencing. Genomics I Humans, Animals and Plants, 2013. ⟨hal-01108425⟩