Comprehensive Genomic Analysis of Medulloblastoma

Tumor specimens were analyzed using Infinium Methylation EPIC or 450K BeadChip arrays (Illumina, San Diego, CA) from either freshly frozen or FFPE tissue (Data Supplement). Medulloblastoma subgroup and subtype predictions were determined using DNA methylation–based classification of CNS tumors (MolecularNeuropathology, Heidelberg, Germany, version 11b4) and trained random forest predictions.^{18 (link)} Genome-wide DNA copy number alterations were inferred from DNA methylation arrays using the Conumee R package.
Next-generation (whole-exome or targeted gene panel) sequencing was performed on tumor samples with sufficient material available. Additional details regarding bioinformatic processing are given in the Appendix Methods (Data Supplement). Genomic datasets included in this study can be freely explored using the online St Jude Cloud pediatric genomic data resource.²⁵

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Kumar R., Smith K.S., Deng M., Terhune C., Robinson G.W., Orr B.A., Liu A.P., Lin T., Billups C.A., Chintagumpala M., Bowers D.C., Hassall T.E., Hansford J.R., Khuong-Quang D.A., Crawford J.R., Bendel A.E., Gururangan S., Schroeder K., Bouffet E., Bartels U., Fisher M.J., Cohn R., Partap S., Kellie S.J., McCowage G., Paulino A.C., Rutkowski S., Fleischhack G., Dhall G., Klesse L.J., Leary S., Nazarian J., Kool M., Wesseling P., Ryzhova M., Zheludkova O., Golanov A.V., McLendon R.E., Packer R.J., Dunham C., Hukin J., Fouladi M., Faria C.C., Pimentel J., Walter A.W., Jabado N., Cho Y.J., Perreault S., Croul S.E., Zapotocky M., Hawkins C., Tabori U., Taylor M.D., Pfister S.M., Klimo P J.r., Boop F.A., Ellison D.W., Merchant T.E., Onar-Thomas A., Korshunov A., Jones D.T., Gajjar A., Ramaswamy V, & Northcott P.A. (2021). Clinical Outcomes and Patient-Matched Molecular Composition of Relapsed Medulloblastoma. Journal of Clinical Oncology, 39(7), 807-821.

Publication 2021

Infinium Methylation EPIC 450K BeadChip

Copy number alterations Dna methylation Exome Frozen Gene Genomic Medulloblastoma Methylation Supplement Tissue Tumor Tumors of cns

Corresponding Organization : St. Jude Children's Research Hospital

Other organizations : German Cancer Research Center, Heidelberg University, Baylor College of Medicine, Children's Cancer Center, The University of Texas Southwestern Medical Center, Queensland Children’s Hospital, Royal Children's Hospital, Rady Children's Hospital-San Diego, University of California, San Diego, Duke University, University of Toronto, Hospital for Sick Children, SickKids Foundation, Children's Hospital of Philadelphia, Sydney Children's Hospital, Stanford University, Children's Hospital at Westmead, The University of Texas MD Anderson Cancer Center, Universität Hamburg, University Medical Center Hamburg-Eppendorf, Essen University Hospital, Children's Hospital of Los Angeles, Seattle Children's Hospital, Children's National, Princess Máxima Center, Burdenko Neurosurgery Institute, Research Center of Neurology, Duke Medical Center, British Columbia Children's Hospital, Cincinnati Children's Hospital Medical Center, University of Lisbon, Hospital de Santa Maria, Alfred I. duPont Hospital for Children, McGill University Health Centre, Oregon Health & Science University, Centre Hospitalier Universitaire Sainte-Justine, Dalhousie University, Charles University, Hopp Children's Cancer Center Heidelberg

Top 5 similar protocols

Variable analysis

independent variables

Infinium Methylation EPIC or 450K BeadChip arrays (Illumina, San Diego, CA)
DNA methylation–based classification of CNS tumors (MolecularNeuropathology, Heidelberg, Germany, version 11b4) and trained random forest predictions
Next-generation (whole-exome or targeted gene panel) sequencing

dependent variables

Medulloblastoma subgroup and subtype predictions
Genome-wide DNA copy number alterations

control variables

Tumor specimens from either freshly frozen or FFPE tissue

controls

Positive controls: Not explicitly mentioned.
Negative controls: Not explicitly mentioned.

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