Table 1.
Diagnostic molecular genetic alterations in 25 patients with embryonal brain tumors. Genetic alterations (SNVs and copy number alterations) detected in clinical molecular analysis are listed according to their detection in the primary tumor and in CSF cfDNA. Only SNVs of diagnostic impact are reported.
| Patient Number | Primary Tumor Molecular Diagnosis: SNV | SNV in CSF cfDNA | Primary Tumor Molecular Diagnosis: CNA | CNA in CSF cfDNA |
|---|---|---|---|---|
| 1 | SMARCB1: c.851C>G/(p.Ser284*) | SMARCB1: c.851C>G/(p.Ser284*) | SMARCB1 loss | SMARCB1 loss |
| 2 | SMARCB1 loss | SMARCB1 loss | ||
| 3 | SMARCB1: c.601C>T/p.(Arg201*) | not found/CSF cfDNA non-contributive | ||
| 4 | Gains: 2pter-p22.3 (subclone), 7, 17q12.2-qter Losses: 11pter-p11.12, 17q12.2-qter |
not found/CSF cfDNA non-contributive | ||
| 5 | CTNNB1: Gly34Arg (c. 100G>A) | CTNNB1: Gly34Arg (c. 100G>A) | chr6 loss chr2pter-p13.2 gain |
chr2pter-p13.2 gain |
| 6 | 17q gain, 17p loss | not found/CSF cfDNA non-contributive | ||
| 7 | Losses: chr10, 2, 11, 13, 16, et 20 | not found/CSF cfDNA non-contributive | ||
| 8 | Gains: 1q, 2, 10, 20 Losses: 1p, 3, 9, 12, 14, 15, 19, X |
Gains: 1q, 2, 10, 20 Losses: 3, 9, 12, 14, 15, 19 |
||
| 9 | 17p loss, 17q gain | not found/CSF cfDNA non-contributive | ||
| 10 | Amplicon 2p24.3-2 containing MYCN. Losses: 5q31.2-ter 8q12.3-ter, 10q, 16q, 17pter-p11.2 Gains: 10p, 17p11.2-qter |
Amplicon 2p24.3-2 containing MYCN. Losses: 5q31,2-ter, 8q12.3-ter, 17pter-p11.2 Gains: 17p11.2-qter |
||
| 11 | PTCH1: c.1359_1360insG (p.cys454valfs*43) | not found/CSF cfDNA non-contributive | 9q loss 3q gain |
not found/CSF cfDNA non-contributive |
| 12 | APC: c.3183_3187del/p.Gln1062* germline APC: c.3758del/p.Ser1253Leufs*12 |
APC: c.3183_3187del/p.Gln1062* germline APC: c.3758del/p.Ser1253Leufs*12 |
chr6 monosomy | chr6 monosomy |
| 13 | 17p loss 17pq gain |
17p loss 17pq gain |
||
| 14 | ||||
| 15 | CCND3 c.774_775delCTinsTG p.(Ser259Ala) COL3A1 c.946G>A p.(Ala316Thr) FANCD2 (c.1588C>T p.(Arg530*) NCKIPSD c.1650_1651delGCinsTT p.(Pro551Ser) PTPRC c.3452A>G p.(Lys1151Arg) |
altered genes not included in targeted sequencing CSF cfDNA panel | ||
| 16 | Gains: 1q(210.34 Mb-tel), 3p(tel-5.17 Mb) | not found/CSF cfDNA non-contributive | ||
| 17 | Losses: 17p(tel-18.91 Mb) harboring TP53 Gains: 17pq(19.14 Mb-tel) |
Losses: 17p(tel-18.91 Mb) harboring TP53 Gains: 17pq(19.14 Mb-tel) |
||
| 18 | Losses: 11p-, 17p(tel-22.22 Mb) Gains: 4q(142.07 Mb-tel), 13q(90.81–96.80 Mb), 15q(54.53 Mb-tel), 17pq(25.28 Mb-tel) Amplicons: 7q(92.20–96.80 Mb) harboring CDK6 |
not found/CSF cfDNA non-contributive | ||
| 19 | Losses: 2q(213.21 Mb-tel), 8p(tel-10,18 Mb), 16q(57.83 Mb-tel), 17p(tel-18.15 Mb), X(78.64-Tel), X(16.68–17.87 Mb) Subclonal segmental losses: 4q(170.70 Mb-tel), 5q(170.87 Mb-tel), 8q(55.00–70.23 Mb), 9p(tel-11.78 Mb), 10q(107.71 Mb-tel), 12q(40.77–57.69 Mb) |
No CN analysis for target seq data | ||
| 20 | CTNNB1: c.98C>G/p.(Ser33Cys) PIK3CA: c.311C>G/p.(Pro104Arg) (50, 3%; 193X) |
CTNNB1: c.98C>G/p.(Ser33Cys) | chr6 monosomy | No CN analysis for target seq data |
| 21 | Losses: 17p(tel-18.91 Mb) Gains: 17pq(19.14 Mb-tel) |
No CN analysis for target seq data | ||
| 22 | Losses: 16q(66.57 Mb-tel) Subclonal segmental losses: 8q(52.57 Mb-tel), 11q(75.97 Mb-tel), 13q(25.30–31.39 Mb), 13q(50.05–81.10 Mb) Gains: 7p(tel-4,88 Mb), 13q(20,28–25,27 Mb), 13q(31.45–49.99 Mb), 13q(81.14 Mb-tel), 17q(46.78 Mb-tel) |
No CN analysis for target seq data | ||
| 23 | Amplification 19q13.41 | Amplification 19q13.41 | ||
| 24 | PTPRK p.(Thr395AspfsTer6) | not found/CSF cfDNA non-contributive | Gains: 1q, 7, 8q | Gains: 1q |
| 25 | KDR: Hist1144Asp TP53: Arg175His KRAS: Gly12Asp |
not found/CSF cfDNA non-contributive | Gains: 2, 7, 12, 19. Amplification chr 20(30.5–30.8 Mb) |
Gains: 2, 7, 12, 19. Amplification chr 20(30.5–30.8 Mb) |