| Author (year) . | N . | Reservoir . | No. of samples . | Sequencing method . | Genomic studies . | Detection rate . | Other findings and potential applications . |
|---|---|---|---|---|---|---|---|
| Escudero et al. (2020) [11] | 13 | CSF and Plasma | Serial | Tumor: NGS CSF: NGS and ddPCR Plasma: ddPCR | WES | CSF: 10/13 (76.9%) (baseline) Plasma: 1/13 (7.7%) | CSF ctDNA reflects tumor genomic alterations and evolution, allows MB subgroup classification, and identifies MRD |
| Li et al. (2020) [12] | 3 | CSF | Serial | WGBS and CMS-IP-Seq | WGMeth (WGBS and CMS-IP-Seq) | ctDNA WGMeth precedes positive cytology and identifies markers with predictive and prognostic value | |
| Liu et al. (2021) [13] | 123 | CSF | Serial | NGS | WGS | MRD: 67/105 (64%) MRD SHH vs WNT vs G3 vs G4: 32% vs 63% vs 77% vs 75% Metastatic: 29/34 (85%) Non-metastatic: 38/71 (54%) | High concordance tumor-CSF MRD detection preceded relapse by ≥3 m |
| Sun et al. (2021) [14] | 58 | CSF: 58 Plasma: 6 | Single | NGS | WES | 15/58 (26%) | ctDNA-positive CSF associated with worse prognosis |
| Lee et al. (2022) [15] | 40 | CSF | Single | RNA-seq and HRMS | RNA-seq and HRMS | — | Different transcriptomic profile, cirRNA and metabolic profiles in CSF between pts with MB and pts without MB |
| Pagès et al. (2022) [16] | 258 | CSF Plasma | Single | ULP-WGS | ULP-WGS | CSF CNA: 9/46 (20%) CSF alterations: 3/10 (30%) Plasma CNA: 3/230 (1.3%) Plasma alterations: 2/74 (2.7%) | CSF is more reliable than plasma for genomic analyses in children with MB |
| Arthur et al. (2023) [17] | 12 | CSF and Plasma | Serial | Tumor: NGS CSF: ddPCR | SNCAIP, CTNNB1, PIK3CA, FOSL2, ZNF536, HEXB, MAX, PTCH1, B4GALT1, KDM5D, CDK6, SAMD8, PRMT7, KMT2D, OFD1, SMO, KDM6A | CSF: 7/12 Plasma: 4/9 | CSF ctDNA positive in tumors growing into a CSF reservoir |
| Current study | 1 | Plasma | Serial | dPCR | PTCH1 Y873* | 10/18 timepoints positive 8/8 false negative | ctDNA PTCH1 mutation dynamics mirrored accurately radiological response |
| Author (year) . | N . | Reservoir . | No. of samples . | Sequencing method . | Genomic studies . | Detection rate . | Other findings and potential applications . |
|---|---|---|---|---|---|---|---|
| Escudero et al. (2020) [11] | 13 | CSF and Plasma | Serial | Tumor: NGS CSF: NGS and ddPCR Plasma: ddPCR | WES | CSF: 10/13 (76.9%) (baseline) Plasma: 1/13 (7.7%) | CSF ctDNA reflects tumor genomic alterations and evolution, allows MB subgroup classification, and identifies MRD |
| Li et al. (2020) [12] | 3 | CSF | Serial | WGBS and CMS-IP-Seq | WGMeth (WGBS and CMS-IP-Seq) | ctDNA WGMeth precedes positive cytology and identifies markers with predictive and prognostic value | |
| Liu et al. (2021) [13] | 123 | CSF | Serial | NGS | WGS | MRD: 67/105 (64%) MRD SHH vs WNT vs G3 vs G4: 32% vs 63% vs 77% vs 75% Metastatic: 29/34 (85%) Non-metastatic: 38/71 (54%) | High concordance tumor-CSF MRD detection preceded relapse by ≥3 m |
| Sun et al. (2021) [14] | 58 | CSF: 58 Plasma: 6 | Single | NGS | WES | 15/58 (26%) | ctDNA-positive CSF associated with worse prognosis |
| Lee et al. (2022) [15] | 40 | CSF | Single | RNA-seq and HRMS | RNA-seq and HRMS | — | Different transcriptomic profile, cirRNA and metabolic profiles in CSF between pts with MB and pts without MB |
| Pagès et al. (2022) [16] | 258 | CSF Plasma | Single | ULP-WGS | ULP-WGS | CSF CNA: 9/46 (20%) CSF alterations: 3/10 (30%) Plasma CNA: 3/230 (1.3%) Plasma alterations: 2/74 (2.7%) | CSF is more reliable than plasma for genomic analyses in children with MB |
| Arthur et al. (2023) [17] | 12 | CSF and Plasma | Serial | Tumor: NGS CSF: ddPCR | SNCAIP, CTNNB1, PIK3CA, FOSL2, ZNF536, HEXB, MAX, PTCH1, B4GALT1, KDM5D, CDK6, SAMD8, PRMT7, KMT2D, OFD1, SMO, KDM6A | CSF: 7/12 Plasma: 4/9 | CSF ctDNA positive in tumors growing into a CSF reservoir |
| Current study | 1 | Plasma | Serial | dPCR | PTCH1 Y873* | 10/18 timepoints positive 8/8 false negative | ctDNA PTCH1 mutation dynamics mirrored accurately radiological response |
Abbreviations: CNA: copy number alterations, CMS-IP-Seq: anti-cytosine-5-methylenesulfonate immunoprecipitation sequencing, CSF: cerebrospinal fluid, ctDNA: circulating tumor DNA, dPCR: digital PCR, ddPCR: droplet digital PCR, G3: group 3 MB, G4: group 4 MB, HRMS: high-resolution mass spectrometry, MB: medulloblastoma, MRD: minimal residual disease, NGS: next-generation sequencing, SHH: sonic hedgehog activated MB, ULP-WGS: ultra-low pass whole-genome sequencing, WES: whole-exome sequencing, WGMeth: whole-genome methylation, WGBS: whole-genome bisulfite sequencing, WGS: whole-genome sequencing, WNT: WNT-altered MB.
| Author (year) . | N . | Reservoir . | No. of samples . | Sequencing method . | Genomic studies . | Detection rate . | Other findings and potential applications . |
|---|---|---|---|---|---|---|---|
| Escudero et al. (2020) [11] | 13 | CSF and Plasma | Serial | Tumor: NGS CSF: NGS and ddPCR Plasma: ddPCR | WES | CSF: 10/13 (76.9%) (baseline) Plasma: 1/13 (7.7%) | CSF ctDNA reflects tumor genomic alterations and evolution, allows MB subgroup classification, and identifies MRD |
| Li et al. (2020) [12] | 3 | CSF | Serial | WGBS and CMS-IP-Seq | WGMeth (WGBS and CMS-IP-Seq) | ctDNA WGMeth precedes positive cytology and identifies markers with predictive and prognostic value | |
| Liu et al. (2021) [13] | 123 | CSF | Serial | NGS | WGS | MRD: 67/105 (64%) MRD SHH vs WNT vs G3 vs G4: 32% vs 63% vs 77% vs 75% Metastatic: 29/34 (85%) Non-metastatic: 38/71 (54%) | High concordance tumor-CSF MRD detection preceded relapse by ≥3 m |
| Sun et al. (2021) [14] | 58 | CSF: 58 Plasma: 6 | Single | NGS | WES | 15/58 (26%) | ctDNA-positive CSF associated with worse prognosis |
| Lee et al. (2022) [15] | 40 | CSF | Single | RNA-seq and HRMS | RNA-seq and HRMS | — | Different transcriptomic profile, cirRNA and metabolic profiles in CSF between pts with MB and pts without MB |
| Pagès et al. (2022) [16] | 258 | CSF Plasma | Single | ULP-WGS | ULP-WGS | CSF CNA: 9/46 (20%) CSF alterations: 3/10 (30%) Plasma CNA: 3/230 (1.3%) Plasma alterations: 2/74 (2.7%) | CSF is more reliable than plasma for genomic analyses in children with MB |
| Arthur et al. (2023) [17] | 12 | CSF and Plasma | Serial | Tumor: NGS CSF: ddPCR | SNCAIP, CTNNB1, PIK3CA, FOSL2, ZNF536, HEXB, MAX, PTCH1, B4GALT1, KDM5D, CDK6, SAMD8, PRMT7, KMT2D, OFD1, SMO, KDM6A | CSF: 7/12 Plasma: 4/9 | CSF ctDNA positive in tumors growing into a CSF reservoir |
| Current study | 1 | Plasma | Serial | dPCR | PTCH1 Y873* | 10/18 timepoints positive 8/8 false negative | ctDNA PTCH1 mutation dynamics mirrored accurately radiological response |
| Author (year) . | N . | Reservoir . | No. of samples . | Sequencing method . | Genomic studies . | Detection rate . | Other findings and potential applications . |
|---|---|---|---|---|---|---|---|
| Escudero et al. (2020) [11] | 13 | CSF and Plasma | Serial | Tumor: NGS CSF: NGS and ddPCR Plasma: ddPCR | WES | CSF: 10/13 (76.9%) (baseline) Plasma: 1/13 (7.7%) | CSF ctDNA reflects tumor genomic alterations and evolution, allows MB subgroup classification, and identifies MRD |
| Li et al. (2020) [12] | 3 | CSF | Serial | WGBS and CMS-IP-Seq | WGMeth (WGBS and CMS-IP-Seq) | ctDNA WGMeth precedes positive cytology and identifies markers with predictive and prognostic value | |
| Liu et al. (2021) [13] | 123 | CSF | Serial | NGS | WGS | MRD: 67/105 (64%) MRD SHH vs WNT vs G3 vs G4: 32% vs 63% vs 77% vs 75% Metastatic: 29/34 (85%) Non-metastatic: 38/71 (54%) | High concordance tumor-CSF MRD detection preceded relapse by ≥3 m |
| Sun et al. (2021) [14] | 58 | CSF: 58 Plasma: 6 | Single | NGS | WES | 15/58 (26%) | ctDNA-positive CSF associated with worse prognosis |
| Lee et al. (2022) [15] | 40 | CSF | Single | RNA-seq and HRMS | RNA-seq and HRMS | — | Different transcriptomic profile, cirRNA and metabolic profiles in CSF between pts with MB and pts without MB |
| Pagès et al. (2022) [16] | 258 | CSF Plasma | Single | ULP-WGS | ULP-WGS | CSF CNA: 9/46 (20%) CSF alterations: 3/10 (30%) Plasma CNA: 3/230 (1.3%) Plasma alterations: 2/74 (2.7%) | CSF is more reliable than plasma for genomic analyses in children with MB |
| Arthur et al. (2023) [17] | 12 | CSF and Plasma | Serial | Tumor: NGS CSF: ddPCR | SNCAIP, CTNNB1, PIK3CA, FOSL2, ZNF536, HEXB, MAX, PTCH1, B4GALT1, KDM5D, CDK6, SAMD8, PRMT7, KMT2D, OFD1, SMO, KDM6A | CSF: 7/12 Plasma: 4/9 | CSF ctDNA positive in tumors growing into a CSF reservoir |
| Current study | 1 | Plasma | Serial | dPCR | PTCH1 Y873* | 10/18 timepoints positive 8/8 false negative | ctDNA PTCH1 mutation dynamics mirrored accurately radiological response |
Abbreviations: CNA: copy number alterations, CMS-IP-Seq: anti-cytosine-5-methylenesulfonate immunoprecipitation sequencing, CSF: cerebrospinal fluid, ctDNA: circulating tumor DNA, dPCR: digital PCR, ddPCR: droplet digital PCR, G3: group 3 MB, G4: group 4 MB, HRMS: high-resolution mass spectrometry, MB: medulloblastoma, MRD: minimal residual disease, NGS: next-generation sequencing, SHH: sonic hedgehog activated MB, ULP-WGS: ultra-low pass whole-genome sequencing, WES: whole-exome sequencing, WGMeth: whole-genome methylation, WGBS: whole-genome bisulfite sequencing, WGS: whole-genome sequencing, WNT: WNT-altered MB.
This PDF is available to Subscribers Only
View Article Abstract & Purchase OptionsFor full access to this pdf, sign in to an existing account, or purchase an annual subscription.
