The increasing uptake of multigene sequencing of germline DNA from children with cancer has led to an increase in the discovery of high- and moderate-penetrance germline pathogenic or likely pathogenic (P/LP) variants (here, combined as high/moderate-penetrance germline pathogenic variants, or hmGPVs) in persons with cancer.1 Some of these hmGPVs are truly associated with the cancer, whereas others are not. We set out to quantify the etiological association between hmGPVs in associated and nonassociated pediatric and adult-onset cancers.
This case-control study used publicly available deidentified human data and does not require institutional review board approval per the Tri-Council Policy Statement “Ethical Conduct for Research Involving Humans” Article 2.2b (TCPS2, 2018) and the Icahn School of Medicine at Mount Sinai (ISMMS) Human Subjects Research (HSR) Determination Guidance. We used tumor zygosity of hmGPVs in tumor suppressor genes (TSG) to ascertain whether hmGPVs are associated with tumorigenesis. We used germline and zygosity data from 2 recent prospectively matched tumor-normal panel-based germline testing studies: IMPACT in 751 pediatric patients with solid tumors (n = 99 hmGPVs)2 and Mi-ONCOSEQ in 1015 adult metastatic tumors (n = 129 hmGPVs).3 Zygosity of hmGPVs was determined using loss of heterozygosity (LOH) or a second coding sequence somatic hit. We determined if tumors were associated or nonassociated (eMethods in the Supplement). For the analysis of the pediatric data set, there were 45 eligible hmGPVs in associated tumors and 18 in nonassociated tumors. Among adult cancers, 59 and 55 hmGPVs were in associated and nonassociated tumors, respectively. The primary outcome was percentage of patients with GPVs with second hits in associated and nonassociated tumors. Two-sided χ2 test was used to determine proportion differences. The threshold for statistical significance was set at P < .05. We used R statistical software, version 4.0.5 (R Project for Statistical Computing).
A total of 99 pediatric patients (49 [49%] female; median age, 5 years [range, 0-19 years]), and 129 adult patients (65 [50%] female; median age, 56 years [range, 18-81 years]) with hmGPVs were included the analysis. Demographic data are shown in the Table. Forty-one of 45 pediatric tumors (91%) with an hmGPV in a TSG with zygosity information had LOH or a second somatic hit within the coding region of the gene (Figure). In contrast, only 1 of 18 (5.5%) hmGPVs in nonassociated tumors had a second hit in the tumor (difference, 85.6%; 95% CI, 62.1%-92.6%; P < .001) (Figure).2
Of 22 RB1-associated tumors with an RB1 GPV that had available zygosity information, 20 had second hit. In contrast, none of 3 cases in non–RB1-associated tumor types had second hits (although the RB1 GPVs likely played a role in the preceding bilateral retinoblastomas that were not tested). In contrast, 5 patients with BRCA1, BRCA2, and PALB2—all found in patients with tumor types not known to be associated with GPVs in these genes—did not have second hit and are unlikely to respond to PARP inhibitors.4
From the adult study, 16 of 59 (27%) nonassociated tumors with an hmGPV harbored second hits compared with 40 of 55 (73%) in patients with associated tumors (difference of 45.6%; 95% CI, 27.6%-59.5%; P < .001) (Figure).3
The high frequency of biallelic hits observed for TSGs that are known to be associated with the cancer in which the hmGPVs occurred indicate that in pediatric patients with cancer, when hmGPVs are detected in associated tumors, these variants are almost always associated with tumor development. In contrast, when the association between hmGPV and the cancer is not established, a hmGPV in a child with this class of cancer is rarely associated with the tested tumor. In adult carriers of hmGPVs, cancers can arise from multiple mechanisms, whereas in children, exposures are limited.5 These results demonstrate how companion tumor sequencing can be informative in determining the etiologic role of germline variants,6 especially during broad germline testing beyond associated cancer types for both adult and pediatric cases. This study has several limitations, such as a small sample size, especially regarding specific pairs of tumors and genes. In addition, functional assays to determine the role of hmGPVs are needed in addition to information on zygosity.
Accepted for Publication: September 24, 2021.
Published: November 18, 2021. doi:10.1001/jamanetworkopen.2021.35135
Open Access: This is an open access article distributed under the terms of the CC-BY License. © 2021 Mutetwa T et al. JAMA Network Open.
Corresponding Author: William D. Foulkes, MBBS, PhD, Research Institute, McGill University Health Centre, 1001 Décarie Blvd, Room EM0-3248, Montreal, QC H4A 3J1, Canada (email@example.com).
Author Contributions: Drs Polak and Foulkes had full access to all of the data in the study and take responsibility for the integrity of the data and the accuracy of the data analysis.
Concept and design: Foulkes, Polak.
Acquisition, analysis, or interpretation of data: All authors.
Drafting of the manuscript: Mutetwa, Foulkes, Polak.
Critical revision of the manuscript for important intellectual content: All authors.
Statistical analysis: Mutetwa, Polak.
Administrative, technical, or material support: Goudie.
Supervision: Foulkes, Polak.
Conflict of Interest Disclosures: Dr Foulkes reported grants from AstraZeneca in the form of funding to clinical lab outside the submitted work. No other disclosures were reported.
Funding/Support: This work was supported in part by the Canadian Institutes of Health Research (CIHR) Foundation grant (FDN. 148390).
Role of the Funder/Sponsor: The funder had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; and decision to submit the manuscript for publication.
Additional Contributions: We would like to acknowledge Maja Kuzman, PhD, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia, for her role in data analysis. Dr Kuzman was not compensated and approved her inclusion in the Acknowledgment section of the manuscript.
Additional Information: Data on the process for determining the association status of each gene/tumor pair are available from Dr Foulkes.
et al. Nationwide germline whole genome sequencing of 198 consecutive pediatric cancer patients reveals a high incidence of cancer prone syndromes. PLoS Genet
. 2020;16(12):e1009231. doi:10.1371/journal.pgen.1009231PubMedGoogle Scholar
et al. Prospective pan-cancer germline testing using MSK-IMPACT informs clinical translation in 751 patients with pediatric solid tumors. Nat Can
. 2021;2:357-365. doi:10.1038/s43018-021-00172-1Google ScholarCrossref