Diagnostic value of next-generation sequencing in an unusual sphenoid tumor

Abstract

Extraordinary advancements in sequencing technology have made what was once a decade-long multi-institutional endeavor into a methodology with the potential for practical use in a clinical setting. We therefore set out to examine the clinical value of next-generation sequencing by enrolling patients with incurable or ambiguous tumors into the Personalized OncoGenomics initiative at the British Columbia Cancer Agency whereby whole genome and transcriptome analyses of tumor/normal tissue pairs are completed with the ultimate goal of directing therapeutics. First, we established that the sequencing, analysis, and communication with oncologists could be completed in less than 5 weeks. Second, we found that cancer diagnostics is an area that can greatly benefit from the comprehensiveness of a whole genome analysis. Here, we present a scenario in which a metastasized sphenoid mass, which was initially thought of as an undifferentiated squamous cell carcinoma, was rediagnosed as an SMARCB1-negative rhabdoid tumor based on the newly acquired finding of homozygous SMARCB1 deletion. The new diagnosis led to a change in chemotherapy and a complete nodal response in the patient. This study also provides additional insight into the mutational landscape of an adult SMARCB1-negative tumor that has not been explored at a whole genome and transcriptome level.

Keywords: Atypical teratoid/rhabdoid tumor; Next-generation sequencing; Rhabdoid; SMARCB1; Sphenoid.

Conflict of interest statement

Disclosures of potential conflicts of interest may be found at the end of this article.

©AlphaMed Press.

Figures

Figure 1.

Imaging. (A): From left to right, sagittal and coronal and sections from the patient’s magnetic resonance imaging at initial presentation. There is a destructive process (arrow) in the central base of the skull that is centered in the sphenoid and extends to the posterior ethmoid. There is extension in the posterior orbit (more prominent on the right) with destruction of the medial wall at the orbital apex. (B): Fat-saturated T1-weighted magnetic resonance imaging representations from postsurgery. (C): The recurrence with the white arrow pointing to the main tumor mass. The recurrent tumor extended into the ethmoid sinus. Abbreviations: A, anterior; L, left; P, posterior; R, right.

Figure 2.

Hematoxylin- and eosin-stained section from the 2010 primary tumor on the left and the 2012 recurrence on the right. Magnification, ×40.

Figure 3.

Circos plot showing the genomic landscape. From outer circle: chromosomes, somatic single nucleotide variations, CNV, LOH, and structural variations. Single nucleotide variations are indicated by blue dots. CNV gains are shown in red and losses in green. LOH is shown in blue bars. Structural variations, fusions, and inversions are shown as lines connecting breakpoints, with orange lines indicating transcriptome and blue lines indicating genome data. Abbreviations: CNV, copy number variations; LOH, loss of heterozygosity.

Figure 4.

Loss of SMARCB1. (A): Copy number status shown across chromosome 22 from the 2010 primary (bottom) and the 2012 recurrent (top) tumors. The single homozygously deleted region found in both samples includes 15 genes, of which the only established tumor suppressor was SMARCB1 (supplemental online Appendix 1). The focal amplifications seen in the 2010 specimen are artifact created because of poorer quality and presequencing amplification step of formalin-fixed paraffin embedded samples. (B): Immunohistochemistry done using BAF47 antibody targeting SMARCB1 protein. All tumor cells from both the 2010 primary (Bi) and 2012 recurrence (Bii) were negative. Endothelial cells staining served as an internal positive control. Fluorescent in situ hybridization confirmed homozygous deletion of SMARCB1(Biii). The red probe, RP11-71G19, hybridizes to a region spanning SMARBC1 and the green probe, RP11-262A13, hybridizes to the telomeric region as a marker for chromosome 22. A normal cell with intact copies of chromosome 22 can be seen in the top left. The surrounding tumor cells have lost both red signals corresponding to the homozygous SMARCB1 deletion, whereas they still maintain copies of chromosome 22 shown by the green fluorescent signals.

Figure 5.

Patient response. (A): Positron emission tomography (PET) showing recurrence of the tumor as well as nodal metastases to the right mediastinum, right hilum, and upper retroperitoneum (shown by white arrows). The hypodense lesion in the lateral right lobe of the liver had been stable in size since previous PET computerized tomography scans and likely represents a benign lesion. (B): Complete nodal response after next-generation sequencing-based diagnosis of rhabdoid tumor with SMARCB1 loss and change in treatment.

Figure 6.

An overview of the timeline from initial presentation to realignment of diagnosis after deep sequencing results. The sequencing and analysis were completed in only 5 weeks, which led to a new therapeutic approach. This is a relatively short period compared with the overall course of treatment.