Oncotarget

Research Papers:

Blood-based next-generation sequencing analysis of neuroendocrine neoplasms

Katerina Zakka, Rebecca Nagy, Leylah Drusbosky, Mehmet Akce, Christina Wu, Olatunji B. Alese, Bassel F. El-Rayes, Pashtoon Murtaza Kasi, Kabir Mody, Jason Starr and Walid L. Shaib _

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Oncotarget. 2020; 11:1749-1757. https://doi.org/10.18632/oncotarget.27588

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Abstract

Katerina Zakka1, Rebecca Nagy2, Leylah Drusbosky2, Mehmet Akce1, Christina Wu1, Olatunji B. Alese1, Bassel F. El-Rayes1, Pashtoon Murtaza Kasi3, Kabir Mody4, Jason Starr4 and Walid L. Shaib1

1 Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA, USA

2 Guardant Health, Redwood City, CA, USA

3 Department of Hematology and Medical Oncology, University of Iowa, Iowa City, IA, USA

4 Department of Hematology and Medical Oncology, Mayo Clinic, Jacksonville, FL, USA

Correspondence to:

Walid L. Shaib,email: wshaib@emory.edu

Keywords: neuroendocrine neoplasm; neuroendocrine tumor; neuroendocrine carcinoma; next-generation sequencing; circulating tumor DNA

Received: February 21, 2020     Accepted: April 10, 2020     Published: May 12, 2020

ABSTRACT

Background: Neuroendocrine neoplasms (NENs) are a heterogeneous group of neoplasms that span from well-differentiated neuroendocrine tumors (NETs) to highly aggressive neoplasms classified as neuroendocrine carcinomas (NECs). The genomic landscape of NENs has not been well studied. The aim of this study is to confirm the feasibility of next generation sequencing (NGS) testing circulating tumor DNA (ctDNA) in patients with NENs and characterize common alterations in the genomic landscape.

Results: Of the 320 NEN patients, 182 (57%) were male with a median age of 63 years (range: 8-93) years. Tumor type included pancreatic NET (N = 165, 52%), gastrointestinal NEC (N = 52, 16%), large cell lung NEC (N = 21, 7%), nasopharyngeal NEC (N = 16, 5%) and NEC/NET not otherwise specified (N = 64, 20%). ctDNA NGS testing was performed on 338 plasma samples; 14 patients had testing performed twice and 2 patients had testing performed three times. Genomic alterations were defined in 280 (87.5%) samples with a total of 1,012 alterations identified after excluding variants of uncertain significance (VUSs) and synonymous mutations. Of the 280 samples with alterations, TP53 associated genes were most commonly altered (N = 145, 52%), followed by KRAS (N = 61, 22%), EGFR (N = 33, 12%), PIK3CA (N = 30, 11%), BRAF (N = 28, 10%), MYC (N = 28, 10%), CCNE1 (N = 28, 10%), CDK6 (N = 22, 8%), RB1 (N = 19, 7%), NF1 (N = 19, 7%), MET (N = 19, 7%), FGFR1 (N = 19, 7%), APC (N = 19, 7%), ERBB2 (N = 16, 6%) and PTEN (N = 14, 5%).

Conclusions: Evaluation of ctDNA was feasible among individuals with NEN. Liquid biopsies are non-invasive methods that can provide personalized options for targeted therapies in NEN patients.

Patients and Methods: Molecular alterations in 338 plasma samples from 320 patients with NEN were evaluated using clinical-grade NGS of ctDNA (Guardant360®) across multiple institutions. The test detects single nucleotide variants in 54-73 genes, copy number amplifications, fusions, and indels in selected genes.


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