Frequency of pathogenic germline variants in pediatric medulloblastoma survivors

Abstract

Background: Medulloblastoma is the most common malignant brain tumor in children. Most cases are sporadic, but well characterized germline alterations in APC, ELP1, GPR161, PTCH1, SUFU, and TP53 predispose to medulloblastoma. However, knowledge about pathogenic/likely pathogenic (P/LP) variants that predispose to medulloblastoma vary based on genes evaluated, patient demographics, and pathogenicity definitions.

Methods: Germline exome sequencing was conducted on 160 childhood survivors of medulloblastoma. Analyses focused on rare variants in 239 known cancer susceptibility genes (CSGs). P/LP variants were identified using ClinVar and InterVar. Variants of unknown significance in known medulloblastoma predisposing genes (APC, ELP1, GPR161, PTCH1, SUFU, TP53) were further classified for loss of function variants. We compared the frequency of P/LP variants in cases to that in 1,259 cancer-free adult controls.

Results: Twenty cases (12.5%) had a P/LP variant in an autosomal dominant CSG versus 5% in controls (p=1.0 x10^-3), and 10 (6.3%) of these were P/LP variants in a known medulloblastoma gene, significantly greater than 0.2% observed in controls (p=1.4x10^-8). The CSGs with the most P/LP variants in cases, and significantly higher than controls, were ELP1 (p=3.0x10^-4) and SUFU (p=1.4x10^-3).

Conclusion: Approximately one in eight pediatric medulloblastoma survivors had an autosomal dominant P/LP CSG variant. We confirm several known associated genes and identify novel genes that may be important in medulloblastoma.

Keywords: germline; medulloblastoma; pathogenic; pediatric; survivor.

Figure 1

Frequency of rare pathogenic or likely pathogenic variants in cancer susceptibility genes in participants with medulloblastoma vs. controls. Includes all 160 medulloblastoma survivors and 1,259 cancer-free controls. Variants of unknown significance in known medulloblastoma CSGs predicted to be loss of function are included with P/LP variants for autosomal dominant and MBL genes. CSG, cancer susceptibility genes; P, pathogenic; LP, likely pathogenic; MBL genes, six genes known to predispose to medulloblastoma.

Figure 2

Frequency of pathogenic and likely pathogenic variants in cancer susceptibility genes with autosomal dominant inheritance in medulloblastoma cases vs. controls by gene of interest. Includes all 160 medulloblastoma survivors and 1,259 cancer-free controls. Predicted loss of function (pLoF) included two variants in known medulloblastoma CSGs. Only p-values <0.05 are noted in the figure.

Figure 3

Frequency of pathogenic and likely pathogenic variants in cancer susceptibility genes with autosomal recessive inheritance in medulloblastoma cases vs. controls by gene of interest. Includes all 160 medulloblastoma survivors and 1,259 cancer-free controls. Predicted loss of function (pLoF) included two variants in known medulloblastoma CSGs only. No participants were found with homozygous or compound heterozygous inheritance P/LP variants in these recessive cancer susceptibility genes or to have predicted loss of function. Only p-values <0.05 are noted in the figure.