Complex Patterns of Genomic Heterogeneity Identified in 42 Tumor Samples and ctDNA of a Pulmonary Atypical Carcinoid Patient

Abstract

Tumor evolution underlies many challenges facing precision oncology, and improving our understanding has the potential to improve clinical care. This study represents a rare opportunity to study tumor heterogeneity and evolution in a patient with an understudied cancer type. A patient with pulmonary atypical carcinoid, a neuroendocrine tumor, metastatic to 90 sites, requested and consented to donate tissues for research. 42 tumor samples collected at rapid autopsy from 14 anatomically distinct sites were analyzed through DNA whole-exome sequencing and RNA-Seq, and five analyzed through linked-read sequencing. Targeted DNA sequencing was completed on two clinical tissue biopsies and one blood plasma sample. Chromosomal alterations and gene variants accumulated over time, and specific chromosomal alterations preceded the single predicted gene driver variant (ARID1A). At the time of autopsy, all sites shared the gain of one copy of Chr 5, loss of one copy of Chr 6 and 21, chromothripsis of one copy of Chr 11, and 39 small variants. Two tumor clones (carrying additional variants) were detected at metastatic sites, and occasionally in different regions of the same organ (e.g., within the pancreas). Circulating tumor DNA (ctDNA) sequencing detected shared tumor variants in the blood plasma and captured marked genomic heterogeneity, including all metastatic clones but few private tumor variants. This study describes genomic tumor evolution and dissemination of a pulmonary atypical carcinoid donated by a single generous patient. It highlights the critical role of chromosomal alterations in tumor initiation and explores the potential of ctDNA analysis to represent genomically heterogeneous disease.

Dynamic ctDNA Mutational Complexity in Patients with Melanoma Receiving Immunotherapy

“…In this study, the ctDNA mutation with the highest concentration in plasma was used since: (i) for many of these patients multiple metastatic tumours may contribute to the measured ctDNA in plasma. As others have shown [ 66 ], and as we have recently found in a patient with over 30 metastatic tumours [ 67 ], ctDNA mutations with the highest concentrations in plasma commonly represent truncal mutations found in multiple metastases, which may potentially provide a more holistic survey of tumour burden than ctDNAs with lower plasma concentration (which may potentially represent new ‘private’ mutations evolving in single metastatic lesions), and (ii) conversely, when a single clinically important metastatic lesion is rapidly progressing, discordant to other more stable lesions, the measured ctDNA mutation with the highest concentration may be more representative of this rapidly growing lesion, since plasma ctDNA levels have been shown to correlate with metabolically active tumour burden measured by FDG positron emission tomography (PET)/CT [ 68 ], and (iii) ctDNA mutations with the highest concentrations in plasma in general are further above the noise threshold of the assay, and may therefore provide more reliable data.…”