Somatic Copy Number Alterations in Human Cancers: An Analysis of Publicly Available Data From The Cancer Genome Atlas

Luuk Harbers; Federico Agostini; Marcin Nicos; Dimitri Poddighe; Magda Bienko; Nicola Crosetto

doi:10.3389/fonc.2021.700568

Somatic Copy Number Alterations in Human Cancers: An Analysis of Publicly Available Data From The Cancer Genome Atlas

Front Oncol. 2021 Jul 28:11:700568. doi: 10.3389/fonc.2021.700568. eCollection 2021.

Authors

Luuk Harbers^{1

2}, Federico Agostini^{1

2}, Marcin Nicos³, Dimitri Poddighe^{4

5}, Magda Bienko^{1

2}, Nicola Crosetto^{1

2}

Affiliations

¹ Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
² Bienko-Crosetto Lab, Science for Life Laboratory, Stockholm, Sweden.
³ Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, Lublin, Poland.
⁴ Department of Medicine, Nazarbayev University School of Medicine, Nur-Sultan, Kazakhstan.
⁵ Clinical Academic Department of Pediatrics, National Research Center for Maternal and Child Health, University Medical Center, Nur-Sultan, Kazakhstan.

Abstract

Somatic copy number alterations (SCNAs) are a pervasive trait of human cancers that contributes to tumorigenesis by affecting the dosage of multiple genes at the same time. In the past decade, The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) initiatives have generated and made publicly available SCNA genomic profiles from thousands of tumor samples across multiple cancer types. Here, we present a comprehensive analysis of 853,218 SCNAs across 10,729 tumor samples belonging to 32 cancer types using TCGA data. We then discuss current models for how SCNAs likely arise during carcinogenesis and how genomic SCNA profiles can inform clinical practice. Lastly, we highlight open questions in the field of cancer-associated SCNAs.

Keywords: 3D genome; TCGA; cancer; copy number alterations; cosmic genes.