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. 2020 Sep;9(17):6093-6101.
doi: 10.1002/cam4.3144. Epub 2020 Jul 7.

Cell-free DNA profiling in retinoblastoma patients with advanced intraocular disease: An MSKCC experience

Prachi Kothari  1 , Francesco Marass  2   3 , Julie L Yang  1 , Caitlin M Stewart  1 , Dennis Stephens  1 , Juber Patel  1 , Maysun Hasan  1 , Xiaohong Jing  1 , Fanli Meng  1 , Jeanette Enriquez  1 , Kety Huberman  1 , Agnes Viale  1 , Jasmine H Francis  1   4 , Michael F Berger  1   4 , Neerav Shukla  1 , David H Abramson  1   4 , Ira J Dunkel  1   4 , Dana W Y Tsui  1   4
Affiliations

Cell-free DNA profiling in retinoblastoma patients with advanced intraocular disease: An MSKCC experience

Prachi Kothari et al. Cancer Med. 2020 Sep.

Abstract

Purpose: The enucleation rate for retinoblastoma has dropped from over 95% to under 10% in the past 10 years as a result of improvements in therapy. This reduces access to tumor tissue for molecular profiling, especially in unilateral retinoblastoma, and hinders the confirmation of somatic RB1 mutations necessary for genetic counseling. Plasma cell-free DNA (cfDNA) has provided a platform for noninvasive molecular profiling in cancer, but its applicability in low tumor burden retinoblastoma has not been shown. We analyzed cfDNA collected from 10 patients with available tumor tissue to determine whether sufficient tumorderived cfDNA is shed in plasma from retinoblastoma tumors to enable noninvasive RB1 mutation detection.

Methods: Tumor tissue was collected from eye enucleations in 10 patients diagnosed with advanced intra-ocular unilateral retinoblastoma, three of which went on to develop metastatic disease. Tumor RB1 mutation status was determined using an FDA-cleared tumor sequencing assay, MSK-IMPACT. Plasma samples were collected before eye enucleation and analyzed with a customized panel targeting all exons of RB1.

Results: Tumor-guided genotyping detected 10 of the 13 expected somatic RB1 mutations in plasma cfDNA in 8 of 10 patients (average variant allele frequency 3.78%). Without referring to RB1 status in the tumor, de novo mutation calling identified 7 of the 13 expected RB1 mutations (in 6 of 10 patients) with high confidence.

Conclusion: Plasma cfDNA can detect somatic RB1 mutations in patients with unilateral retinoblastoma. Since intraocular biopsies are avoided in these patients because of concern about spreading tumor, cfDNA can potentially offer a noninvasive platform to guide clinical decisions about treatment, follow-up schemes, and risk of metastasis.

Keywords: RB1 mutation; liquid biopsy; molecular profiling in retinoblastoma; plasma cell-free DNA; retinoblastoma.

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Conflict of interest statement

PK, JY, CMS, DS, XJ, JE, KH, AV, JHF, NS, and DHA have nothing to disclose. MFB, DWYT, JP, MH, and FM are co‐inventors on a provisional patent application for systems and methods for detecting cancer via cfDNA screening (PCT/US2019/027487). DT and FM are co‐inventors on a provisional patent application for systems and methods for distinguishing pathological mutations from clonal hematopoietic mutations in plasma cell‐free DNA by fragment size analysis. MFB has received consulting fees from Roche and grant support from Illumina and Grail. DT has received research support from ThermoFisher Scientific, EPIC Sciences, speaking honoraria and travel support from Nanodigmbio, Cowen, BoA Merrill Lynch. IJD reports non‐financial support from Apexigen, personal fees from Bayer, grants from Bristol‐Myers Squibb, personal fees from Celgene, grants from Genentech, grants from Novartis, outside the submitted work.

Figures

Figure 1
Figure 1
Concept figure showing the application of plasma cfDNA to detect somatic mutations derived from retinoblastoma tumor cells for noninvasive genetic profiling. Reprinted with permission from Memorial Sloan Kettering Cancer Center
Figure 2
Figure 2
RB1 mutations detected by tumor directed genotyping. Figure 2A: Variant allele frequencies (VAF) of each RB1 mutation detected in the 10 plasma cfDNA samples obtained. The solid boxes below are plasma cfDNA samples in which the RB1 mutation was detected by genotyping. Figure 2B: VAFs compared from tumor, cfDNA, and buffy coats of all 10 patients. AF, allele frequency; T, tumor; cf, cfDNA; BC, Buffy Coat
Figure 3
Figure 3
De novo identification of somatic RB1 mutation. Results in both cfDNA and buffy coat are shown. BC, buffy coat; cf, cfDNA
See this image and copyright information in PMC

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