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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 16, 2024 |
| Title |
Nanopore Sequencing as a Cutting-Edge Technology for Medulloblastoma Classification |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
Background: Medulloblastoma (MB) is one of the most prevalent embryonal malignant brain tumors. Current classification organizes these tumors into four molecular groups (WNT-activated, SHH-activated and TP53-wild type, SHH-activated and TP53-mutant, and non-WNT/non-SHH). Recently, a comprehensive classification has been established, identifying numerous subgroups, some of which exhibit a poor prognosis. It is critical to establish effective subgrouping methods for accurate diagnosis and patient’s management that strikes a delicate balance between improving outcomes and minimizing the risk of comorbidities.
Methods: We evaluated the ability of Nanopore sequencing to provide clinically relevant methylation and copy number profiles of MB. Nanopore sequencing was applied to an EPIC discovery cohort of frozen MB, benchmarked against the gold standard EPIC array, and validated further evaluated on an integrated diagnosis cohort of MB.
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| Overall design |
For whole-genome Nanopore sequencing, DNA libraries were prepared using the SQK-RBK004 rapid barcoding kit from Oxford Nanopore Technologies. Two types of flow cells were used: MinION R9.4.1 (FLO-MIN106D) and Flongle R9.4.1 (FLO-FLG001). For MinION flow cells, 400 ng of DNA were tagmented, barcoded, repaired, and pooled in batches of six samples before adaptor ligation. Sequencing involved multiplexing six libraries, with each batch taking 48 to 72 hours per MinION R9.4.1 flow cell. For Flongle flow cells, the same SQK-RBK004 kit (Oxford Nanopore Technologies) was used, but 200 ng of DNA per tumor sample was sequenced individually on a Flongle flow cell for 24 hours. All sequencing was performed on MinION Mk1B or Mk1C devices, and sequencing runs were initiated and monitored using MinKnow software from Oxford Nanopore Technologies.
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| Contributor(s) |
Filser M, Masliah-Planchon J, Torrejon J, Ayrault O |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Oct 22, 2024 |
| Last update date |
Nov 16, 2024 |
| Contact name |
Mathilde Filser |
| E-mail(s) |
[email protected]
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| Organization name |
Institut Curie
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| Department |
Genetics Department
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| Street address |
26 rue d'Ulm
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| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
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| Platforms (1) |
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| Samples (158)
|
| GSM8586049 |
Medulloblastoma frozen tumor, SHH, M001RB10 |
| GSM8586050 |
Medulloblastoma frozen tumor, SHH, M005RB01 |
| GSM8586051 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M005RB02 |
| GSM8586052 |
Medulloblastoma frozen tumor, Group 3, M005RB03 |
| GSM8586053 |
Medulloblastoma frozen tumor, Group 4, M005RB04 |
| GSM8586054 |
Medulloblastoma frozen tumor, SHH, M006RB10 |
| GSM8586055 |
Medulloblastoma frozen tumor, WNT, M006RB12 |
| GSM8586056 |
Medulloblastoma frozen tumor, WNT, M007RB01 |
| GSM8586057 |
Medulloblastoma frozen tumor, SHH, M007RB02 |
| GSM8586058 |
Medulloblastoma frozen tumor, Group 3, M007RB03 |
| GSM8586059 |
Medulloblastoma frozen tumor, Group 4, M007RB04 |
| GSM8586060 |
Medulloblastoma frozen tumor, SHH, M007RB05 |
| GSM8586061 |
Medulloblastoma frozen tumor, SHH, M007RB06 |
| GSM8586062 |
Medulloblastoma frozen tumor, WNT, M008RB07 |
| GSM8586063 |
Medulloblastoma frozen tumor, WNT, M008RB08 |
| GSM8586064 |
Medulloblastoma frozen tumor, SHH, M008RB09 |
| GSM8586065 |
Medulloblastoma frozen tumor, SHH, M008RB10 |
| GSM8586066 |
Medulloblastoma frozen tumor, Group 3, M008RB11 |
| GSM8586067 |
Medulloblastoma frozen tumor, Group 4, M008RB12 |
| GSM8586068 |
Medulloblastoma frozen tumor, Group 3, M009RB01 |
| GSM8586069 |
Medulloblastoma frozen tumor, Group 4, M009RB02 |
| GSM8586070 |
Medulloblastoma frozen tumor, WNT, M009RB05 |
| GSM8586071 |
Medulloblastoma frozen tumor, Group 4, M009RB06 |
| GSM8586072 |
Medulloblastoma frozen tumor, WNT, M010RB07 |
| GSM8586073 |
Medulloblastoma frozen tumor, WNT, M010RB08 |
| GSM8586074 |
Medulloblastoma frozen tumor, SHH, M010RB09 |
| GSM8586075 |
Medulloblastoma frozen tumor, SHH, M010RB10 |
| GSM8586076 |
Medulloblastoma frozen tumor, Group 4, M010RB11 |
| GSM8586077 |
Medulloblastoma frozen tumor, WNT, M011RB01 |
| GSM8586078 |
Medulloblastoma frozen tumor, SHH, M011RB02 |
| GSM8586079 |
Medulloblastoma frozen tumor, Group 4, M011RB04 |
| GSM8586080 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M011RB05 |
| GSM8586081 |
Medulloblastoma frozen tumor, SHH, M011RB06 |
| GSM8586082 |
Medulloblastoma frozen tumor, WNT, M012RB07 |
| GSM8586083 |
Medulloblastoma frozen tumor, Group 3, M012RB08 |
| GSM8586084 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M012RB09 |
| GSM8586085 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M012RB10 |
| GSM8586086 |
Medulloblastoma frozen tumor, SHH,M012RB11 |
| GSM8586087 |
Medulloblastoma frozen tumor, Group 3, M012RB12 |
| GSM8586088 |
Medulloblastoma frozen tumor, SHH, M013RB05 |
| GSM8586089 |
Medulloblastoma frozen tumor, WNT, M013RB06 |
| GSM8586090 |
Medulloblastoma frozen tumor, Group 4, M014RB10 |
| GSM8586091 |
Medulloblastoma frozen tumor, SHH, M015RB01 |
| GSM8586092 |
Medulloblastoma frozen tumor, Group 4, M015RB03 |
| GSM8586093 |
Medulloblastoma frozen tumor, Group 4, M015RB05 |
| GSM8586094 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M015RB06 |
| GSM8586095 |
Medulloblastoma frozen tumor, Group 4, M016RB09 |
| GSM8586096 |
Medulloblastoma frozen tumor, WNT, M016RB10 |
| GSM8586097 |
Medulloblastoma frozen tumor, Group 4, M016RB11 |
| GSM8586098 |
Medulloblastoma frozen tumor, SHH, M016RB12 |
| GSM8586099 |
Medulloblastoma frozen tumor, SHH, M017RB03 |
| GSM8586100 |
Medulloblastoma frozen tumor, SHH, M018RB07 |
| GSM8586101 |
Medulloblastoma frozen tumor, SHH, M018RB09 |
| GSM8586102 |
Medulloblastoma frozen tumor, SHH, M018RB10 |
| GSM8586103 |
Medulloblastoma frozen tumor, SHH, M018RB11 |
| GSM8586104 |
Medulloblastoma frozen tumor, SHH, M018RB12 |
| GSM8586105 |
Medulloblastoma frozen tumor, SHH, M019RB01 |
| GSM8586106 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M019RB03 |
| GSM8586107 |
Medulloblastoma frozen tumor, Group 3, M022RB07 |
| GSM8586108 |
Medulloblastoma frozen tumor, SHH, M027RB07 |
| GSM8586109 |
Medulloblastoma frozen tumor, SHH, M027RB08 |
| GSM8586110 |
Medulloblastoma frozen tumor, SHH, M033RB07 |
| GSM8586111 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M035RB01 |
| GSM8586112 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M039RB09 |
| GSM8586113 |
Medulloblastoma frozen tumor, SHH, M039RB11 |
| GSM8586114 |
Medulloblastoma frozen tumor, SHH, M043RB02 |
| GSM8586115 |
Medulloblastoma frozen tumor, SHH, M043RB04 |
| GSM8586116 |
Medulloblastoma frozen tumor, Group 3, M045RB01 |
| GSM8586117 |
Medulloblastoma frozen tumor, Group 4, M045RB02 |
| GSM8586118 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M045RB03 |
| GSM8586119 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M046RB07 |
| GSM8586120 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M046RB10 |
| GSM8586121 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M046RB12 |
| GSM8586122 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M047RB01 |
| GSM8586123 |
Medulloblastoma frozen tumor, Group 4, M047RB05 |
| GSM8586124 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M047RB06 |
| GSM8586125 |
Medulloblastoma frozen tumor, SHH, M048RB12 |
| GSM8586126 |
Medulloblastoma frozen tumor, Group 4, M050RB09 |
| GSM8586127 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M052RB02 |
| GSM8586128 |
Medulloblastoma frozen tumor, Group 3, M054RB01 |
| GSM8586129 |
Medulloblastoma frozen tumor, Group 3, M055RB02 |
| GSM8586130 |
Medulloblastoma frozen tumor, Group 4, M056RB03 |
| GSM8586131 |
Medulloblastoma frozen tumor, WNT, M057RB04 |
| GSM8586132 |
Medulloblastoma frozen tumor, SHH, M058RB05 |
| GSM8586133 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M060RB07 |
| GSM8586134 |
Medulloblastoma frozen tumor, SHH, M067RB03 |
| GSM8586135 |
Medulloblastoma frozen tumor, SHH, M068RB04 |
| GSM8586136 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M071RB01 |
| GSM8586137 |
Medulloblastoma frozen tumor, WNT, M071RB02 |
| GSM8586138 |
Medulloblastoma frozen tumor, WNT, M073RB11 |
| GSM8586139 |
Medulloblastoma frozen tumor, WNT, M074RB01 |
| GSM8586140 |
Medulloblastoma frozen tumor, Group 3, M074RB02 |
| GSM8586141 |
Medulloblastoma frozen tumor, WNT, M074RB03 |
| GSM8586142 |
Medulloblastoma frozen tumor, WNT, M074RB04 |
| GSM8586143 |
Medulloblastoma frozen tumor, Group 3, M074RB05 |
| GSM8586144 |
Medulloblastoma frozen tumor, Group 3, M074RB06 |
| GSM8586145 |
Medulloblastoma frozen tumor, Group 3, M075RB07 |
| GSM8586146 |
Medulloblastoma frozen tumor, Group 3, M075RB08 |
| GSM8586147 |
Medulloblastoma frozen tumor, SHH, M075RB09 |
| GSM8586148 |
Medulloblastoma frozen tumor, Group 3, M075RB10 |
| GSM8586149 |
Medulloblastoma frozen tumor, WNT, M075RB11 |
| GSM8586150 |
Medulloblastoma frozen tumor, SHH, M075RB12 |
| GSM8586151 |
Medulloblastoma frozen tumor, Group 4, M076RB01 |
| GSM8586152 |
Medulloblastoma frozen tumor, Group 3, M076RB02 |
| GSM8586153 |
Medulloblastoma frozen tumor, Group 4, M076RB03 |
| GSM8586154 |
Medulloblastoma frozen tumor, SHH, M076RB04 |
| GSM8586155 |
Medulloblastoma frozen tumor, SHH, M076RB05 |
| GSM8586156 |
Medulloblastoma frozen tumor, SHH, M076RB06 |
| GSM8586157 |
Medulloblastoma frozen tumor, Group 4, M077RB07 |
| GSM8586158 |
Medulloblastoma frozen tumor, Group 3, M077RB08 |
| GSM8586159 |
Medulloblastoma frozen tumor, Group 4, M077RB09 |
| GSM8586160 |
Medulloblastoma frozen tumor, SHH, M077RB10 |
| GSM8586161 |
Medulloblastoma frozen tumor, Group 4, M077RB11 |
| GSM8586162 |
Medulloblastoma frozen tumor, SHH, M077RB12 |
| GSM8586163 |
Medulloblastoma frozen tumor, Group 4, M078RB01 |
| GSM8586164 |
Medulloblastoma frozen tumor, WNT, M078RB02 |
| GSM8586165 |
Medulloblastoma frozen tumor, Group 4, M078RB03 |
| GSM8586166 |
Medulloblastoma frozen tumor, Group 4, M078RB04 |
| GSM8586167 |
Medulloblastoma frozen tumor, WNT, M078RB05 |
| GSM8586168 |
Medulloblastoma frozen tumor, Group 4, M078RB06 |
| GSM8586169 |
Medulloblastoma frozen tumor, SHH, M079RB07 |
| GSM8586170 |
Medulloblastoma frozen tumor, WNT, M079RB08 |
| GSM8586171 |
Medulloblastoma frozen tumor, Group 4, M079RB09 |
| GSM8586172 |
Medulloblastoma frozen tumor, WNT, M079RB10 |
| GSM8586173 |
Medulloblastoma frozen tumor, SHH, M079RB11 |
| GSM8586174 |
Medulloblastoma frozen tumor, Group 3, M079RB12 |
| GSM8586175 |
Medulloblastoma frozen tumor, WNT, M080RB01 |
| GSM8586176 |
Medulloblastoma frozen tumor, WNT, M080RB02 |
| GSM8586177 |
Medulloblastoma frozen tumor, SHH, M080RB03 |
| GSM8586178 |
Medulloblastoma frozen tumor, Group 3, M080RB04 |
| GSM8586179 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M080RB05 |
| GSM8586180 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M080RB06 |
| GSM8586181 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M081RB07 |
| GSM8586182 |
Medulloblastoma frozen tumor, WNT, M081RB09 |
| GSM8586183 |
Medulloblastoma frozen tumor, Group 3, M082RB01 |
| GSM8586184 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M083RB08 |
| GSM8586185 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M085RB02 |
| GSM8586186 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M085RB04 |
| GSM8586187 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M085RB05 |
| GSM8586188 |
Medulloblastoma frozen tumor, SHH, M087RB10 |
| GSM8586189 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M087RB11 |
| GSM8586190 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M088RB09 |
| GSM8586191 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M089RB10 |
| GSM8586192 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M090RB11 |
| GSM8586193 |
Medulloblastoma frozen tumor, Group 3, M091RB12 |
| GSM8586194 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M092RB03 |
| GSM8586195 |
Medulloblastoma frozen tumor, SHH, M095RB02 |
| GSM8586196 |
Medulloblastoma frozen tumor, SHH, M095RB03 |
| GSM8586197 |
Medulloblastoma frozen tumor, SHH, M095RB04 |
| GSM8586198 |
Medulloblastoma frozen tumor, SHH, M095RB05 |
| GSM8586199 |
Medulloblastoma frozen tumor, SHH, M095RB06 |
| GSM8586200 |
Medulloblastoma frozen tumor, SHH, M096RB01 |
| GSM8586201 |
Medulloblastoma frozen tumor, WNT, M098RB01 |
| GSM8586202 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M098RB02 |
| GSM8586203 |
Medulloblastoma frozen tumor, SHH, M098RB03 |
| GSM8586204 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M100RB07 |
| GSM8586205 |
Medulloblastoma frozen tumor, Non-WNT/Non-SHH, M102RB08 |
| GSM8586206 |
Medulloblastoma frozen tumor, Group 3, M112RB05 |
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| Relations |
| BioProject |
PRJNA1176014 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE280038_RAW.tar |
4.2 Gb |
(http)(custom) |
TAR (of TSV) |
SRA Run Selector |
| Raw data are available in SRA |
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