Genotyping data of routinely processed matched primary/metastatic tumor samples

Vassiliki Kotoula; Kyriakos Chatzopoulos; Kyriaki Papadopoulou; Eleni Giannoulatou; Georgia-Angeliki Koliou; Vasilios Karavasilis; Elissavet Pazarli; Stavroula Pervana; Georgia Kafiri; Georgios Tsoulfas; Sofia Chrisafi; Helen Sgouramali; Pavlos Papakostas; Dimitrios Pectasides; Prodromos Hytiroglou; George Pentheroudakis; George Fountzilas

doi:10.1016/j.dib.2020.106646

Genotyping data of routinely processed matched primary/metastatic tumor samples

Data Brief. 2020 Dec 11:34:106646. doi: 10.1016/j.dib.2020.106646. eCollection 2021 Feb.

Authors

Vassiliki Kotoula^{1

2}, Kyriakos Chatzopoulos^{1

2}, Kyriaki Papadopoulou¹, Eleni Giannoulatou^{3

4}, Georgia-Angeliki Koliou⁵, Vasilios Karavasilis⁶, Elissavet Pazarli⁷, Stavroula Pervana⁷, Georgia Kafiri⁸, Georgios Tsoulfas⁹, Sofia Chrisafi¹, Helen Sgouramali¹, Pavlos Papakostas¹⁰, Dimitrios Pectasides¹⁰, Prodromos Hytiroglou², George Pentheroudakis^{11

12}, George Fountzilas^{1

13

14}

Affiliations

¹ Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.
² Department of Pathology, School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece.
³ Bioinformatics and Systems Medicine Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.
⁴ The University of New South Wales, Kensington, NSW, Australia.
⁵ Section of Biostatistics, Hellenic Cooperative Oncology Group, Data Office, Athens, Greece.
⁶ Department of Medical Oncology, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece.
⁷ Department of Pathology, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece.
⁸ Department of Pathology, Hippokration Hospital, Athens, Greece.
⁹ Department of Surgery, Aristotle University of Thessaloniki, Thessaloniki, Greece.
¹⁰ Oncology Section, Second Department of Internal Medicine, Hippokration Hospital, Athens, Greece.
¹¹ Department of Medical Oncology, Medical School, University of Ioannina, Ioannina, Greece.
¹² Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), Ioannina, Greece.
¹³ Aristotle University of Thessaloniki, Thessaloniki, Greece.
¹⁴ German Oncology Center, Limassol, Cyprus.

Abstract

Genotypic and phenotypic comparisons of tumors in multiple tissue samples from the same patient are important for understanding disease evolution and treatment possibilities. Panel NGS genotyping is currently widely used in this context, whereby NGS variant filtering and final evaluation constitute the basis for meaningful comparisons. Here, we present the genotype data used for genotype / phenotype comparisons between matched primary / metastatic colorectal tumors in the work by Chatzopoulos et al (doi: 10.1016/j.humpath.2020.10.009), as well as the process followed for obtaining these data. We describe key issues while processing routinely formalin-fixed paraffin-embedded (FFPE) tumors for genotyping, NGS application (Ion Torrent), a stringent variant filtering algorithm for genotype analyses in FFPE tissues and particularly in matched tumor samples, and provide the respective datasets. Apart from research, tumor NGS genotyping is currently applied for clinical diagnostic purposes in Oncology. The datasets and method description provided herein (a) are important for comprehending the peculiarities of FFPE tumor genotyping, which is still mostly based on principles of germline DNA genotyping; (b) can be used in pooled analyses, e.g., of primary / metastatic tumors for the investigation of tumor evolution.

Keywords: Ampliseq panel; Colorectal cancer; Formalin fixed paraffin embedded tissue; Matched sample genotypes; Next generation sequencing; Targeted NGS; Tumor cell content.