Affiliation:
1. Convergent Science Institute in Cancer, Michelson Center for Convergent Bioscience, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA
2. The Vision Center, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA
3. USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
4. The Center for Personalized Medicine, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA
Abstract
Retinoblastoma (RB) is a childhood cancer that forms in the developing retina of young children; this tumor cannot be biopsied due to the risk of provoking extraocular tumor spread, which dramatically alters the treatment and survival of the patient. Recently, aqueous humor (AH), the clear fluid in the anterior chamber of the eye, has been developed as an organ-specific liquid biopsy for investigation of in vivo tumor-derived information found in the cell-free DNA (cfDNA) of the biofluid. However, identifying somatic genomic alterations, including both somatic copy number alterations (SCNAs) and single nucleotide variations (SNVs) of the RB1 gene, typically requires either: (1) two distinct experimental protocols—low-pass whole genome sequencing for SCNAs and targeted sequencing for SNVs—or (2) expensive deep whole genome or exome sequencing. To save time and cost, we applied a one-step targeted sequencing method to identify both SCNAs and RB1 SNVs in children with RB. High concordance (median = 96.2%) was observed in comparing SCNA calls derived from targeted sequencing to the traditional low-pass whole genome sequencing method. We further applied this method to investigate the degree of concordance of genomic alterations between paired tumor and AH samples from 11 RB eyes. We found 11/11 AH samples (100%) had SCNAs, and 10 of them (90.1%) with recurrent RB-SCNAs, while only nine out of 11 tumor samples (81.8%) had positive RB-SCNA signatures in both low-pass and targeted methods. Eight out of the nine (88.9%) detected SNVs were shared between AH and tumor samples. Ultimately, 11/11 cases have somatic alterations identified, including nine RB1 SNVs and 10 recurrent RB-SCNAs with four focal RB1 deletions and one MYCN gain. The results presented show the feasibility of utilizing one sequencing approach to obtain SCNA and targeted SNV data to capture a broad genomic scope of RB disease, which may ultimately expedite clinical intervention and be less expensive than other methods.
Funder
National Cancer Institute of the National Institute of Health
Miriam and Sheldon G. Adelson Medical Research Foundation
The Wright Foundation
Children’s Oncology Group/St. Baldrick’s Foundation
The Knights Templar Eye Foundation
Hyundai Hope on Wheels, Danhaki Family Foundation
Childhood Eye Cancer Trust, and Children’s Cancer Research Fund
The Berle & Lucy Adams Chair in Cancer Research
The Larry and Celia Moh Foundation
Children’s Hospital Los Angeles
Research to Prevent Blindness
A. Linn Murphree, MD, Chair in Ocular Oncology
The Institute for Families, Inc.
Subject
Inorganic Chemistry,Organic Chemistry,Physical and Theoretical Chemistry,Computer Science Applications,Spectroscopy,Molecular Biology,General Medicine,Catalysis
Cited by
4 articles.
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