Methods and results
The index patient III.1 (Figure 1A) was diagnosed with a non-metastatic posterior fossa brain tumor at the age of 6 years. Histology was consistent with an ATRT. After gross total tumor resection and treatment with radio-chemotherapy according to the EURHAB recommendations, the patient has remained in complete remission for 15 years after diagnosis. His father II.2 was diagnosed with aBRAF V600 wild-type hairy cell leukemia variant (HCL-v, with co-expression of CD19, CD103, CD11c, CD25) at the age of 47 years. He achieved a complete remission after 5 cycles of cladribin, but suffered from a relapse 9 years later, with a very good partial response to additional cycles of cladribin. With 54 years he underwent surgery for an L2-3 spinal ependymoma. At age 57 a hemi-colectomy for steroid-resistant ulcerative colitis was performed, apparently unrelated to his other malignoma.
Sanger sequencing of SMARCB1 did not detect any mutations in peripheral blood lymphocytes (PBL) of the index patient III.1(Figure 1B). However, a pattern suggesting gain of one copy of exon 6 of SMARCB1 was found by multiplex ligation-dependent probe amplification (MLPA). MLPA detected an apparently identicalSMARCB1 exon 6 gain in PBL of his father II.2 and two of his sisters III.2 , III.4. Targeted next generation sequencing (NGS) confirmed the absence of a single nucleotide variant or small indel but could not identify the genomic integration site of the gained exon 6 sequences. SMARCB1 mutations were absent in PBL of the index patient’s grandmother I.1 , mother II.1 , and of another sister III.3 . No material was available from a cousin IV.1 , who had died from surgical complications of a malignant brain tumor at the age of 8 months. The index patient’s grandfather I.2 had died from non-malignant disease and could not be tested. In the ten children of the grandfather I.2, a diagnosis of a malignancy was only known in II.2 . No detected carrier had any overt intellectual impairment, except for a learning disability in III.1 attributed to leukencephalopathy after intensive multi-modal treatment at young age. High resolution spinal and lower extremity MRI in III.1 and III.2 did not detect dorsal nerve root or peripheral nerve schwannoma.
BAF47 staining was negative in the ATRT of III.1 and in the myxopapillary ependymoma of II.1 (Figure 2A-F). Results from the Infinium Methylation EPIC BeadChip DNA methylation analysis for the ATRT and the ependymoma did not assign a molecular diagnosis in the online Heidelberg classifier tool2. However,t -SNE plotting associated the ATRT with the clinically favorable subclass of ATRT-TYR (Figure 2G) and the ependymoma with the myxopapillary subclass (Figure 2I). Copy number profiles confirmed a heterozygous loss of Chr 22 in both tumors (Figure 2H, J). In line MLPA detected large deletions of SMARCB1 in both tumors and indicated, that the allele containing the exon 6 gain was retained in the tumors whereas the wild-type allele was deleted. No additional SMARCB1mutation was found in the HCL-v of II.2 .