Redefining germline predisposition in children with molecularly characterized ependymoma: a population-based 20-year cohort

Abstract

Ependymoma is the second most common malignant brain tumor in children. The etiology is largely unknown and germline DNA sequencing studies focusing on childhood ependymoma are limited. We therefore performed germline whole-genome sequencing on a population-based cohort of children diagnosed with ependymoma in Denmark over the past 20 years (n = 43). Single nucleotide and structural germline variants in 457 cancer related genes and 2986 highly evolutionarily constrained genes were assessed in 37 children with normal tissue available for sequencing. Molecular ependymoma classification was performed using DNA methylation profiling for 39 children with available tumor tissue. Pathogenic germline variants in known cancer predisposition genes were detected in 11% (4/37; NF2, LZTR1, NF1 & TP53). However, DNA methylation profiling resulted in revision of the histopathological ependymoma diagnosis to non-ependymoma tumor types in 8% (3/39). This included the two children with pathogenic germline variants in TP53 and NF1 whose tumors were reclassified to a diffuse midline glioma and a rosette-forming glioneuronal tumor, respectively. Consequently, 50% (2/4) of children with pathogenic germline variants in fact had other tumor types. A meta-analysis combining our findings with pediatric pan-cancer germline sequencing studies showed an overall frequency of pathogenic germline variants of 3.4% (7/207) in children with ependymoma. In summary, less than 4% of childhood ependymoma is explained by genetic predisposition, virtually restricted to pathogenic variants in NF2 and NF1. For children with other cancer predisposition syndromes, diagnostic reconsideration is recommended for ependymomas without molecular classification. Additionally, LZTR1 is suggested as a novel putative ependymoma predisposition gene.

Germline (epi)genetics reveals high predisposition in females: a 5-year, nationwide, prospective Wilms tumour cohort

“…We show that pLoF variants in evolutionarily constrained genes were significantly more likely to play a role in kidney development; including CTNND1 , not previously linked with WT predisposition. Today, the long-term survival of children with WT in high-income nations is high (~90%) 26 34. Yet, throughout human35 and prehuman36 evolution, the cancer, typically presenting in the first 5 years of life, presumably meant that affected individuals did not survive into adulthood.…”

“…23 Next, full genome predicted loss-of-function (pLoF) variants were filtered and subjected to constraint gene analysis, as previously presented. [24][25][26] Additionally, pyrosequencing of IC1 was performed on peripheral blood and, when available, tumour DNA from individuals with WT and relevant controls, using methods described previously. 27 Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA, ME030-C3, MRC Holland, Amsterdam, The Netherlands) was conducted according to the manufacturer's instructions.…”

“…Whole-genome sequencing (WGS) was performed and rare variants in a panel of 390 selected genes20–22 were reviewed by a multidisciplinary team 23. Next, full genome predicted loss-of-function (pLoF) variants were filtered and subjected to constraint gene analysis, as previously presented 24–26…”

The Evolutionary Impact of Childhood Cancer on the Human Gene Pool

“…Furthermore, it seems logical that analyses focused on constrained genes have the potential to accelerate discovery of genes speci cally associated with pediatric-onset, as opposed to adult-onset, cancer. We have recently applied this approach in childhood cancer cohorts with germline whole genome sequencing available, and identi ed novel candidate pCPS genes 86,102 .…”

Splicing-Disrupting Mutations in Inherited Predisposition to Solid Pediatric Cancer

“…The etiology is largely unknown, and germline DNA sequencing studies on pediatric EP are scarce. Pathogenic germline variants in known cancer predisposition genes have been detected in genes such as NF2 , LZTR1 , NF1 , and TP53 [ 76 ]. EP can be associated with type 2 neurofibromatosis with a high proportion of pathogenic mutations in NF2 .…”