Targeted next-generation sequencing of 13 chordoid gliomas of the third ventricle

Type: Cancer Genomics
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

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Dataset ID	Description	Technology	Samples
EGAD00001003818	BAM files of targeted next-generation DNA sequencing data of 13 chordoid gliomas of the third ventricle (2 paired tumor-normal samples and 11 tumor-only samples). Genomic DNA was extracted from formalin-fixed, paraffin-embedded blocks of tumor tissue from 13 patients with chordoid glioma of the third ventricle using the QIAamp DNA FFPE Tissue Kit (Qiagen). Genomic DNA was also extracted from leukocytes in a peripheral blood sample from one of the patients and a non-neoplastic gastric biopsy specimen from one of the patients. Capture-based next-generation DNA sequencing was performed at the University of California, San Francisco Clinical Cancer Genomics Laboratory, using an assay that targets all coding exons of approximately 500 cancer-related genes, select introns of 47 genes, and TERT promoter with a total sequencing footprint of 2.8 Mb (UCSF500 Cancer Panel). Sequencing libraries were prepared from genomic DNA, and target enrichment was performed by hybrid capture using a custom oligonucleotide library (Nimblegen SeqCap EZ Choice). Captured libraries were sequenced as paired-end 100 bp reads on an Illumina HiSeq 2500 instrument. Duplicate sequencing reads were removed computationally to allow for accurate allele frequency determination and copy number calling.	Illumina HiSeq 2500	15

Publications	Citations
A recurrent kinase domain mutation in PRKCA defines chordoid glioma of the third ventricle. Goode B, Mondal G, Hyun M, Ruiz DG, Lin YH, Van Ziffle J, Joseph NM, Onodera C, Talevich E, Grenert JP, Hewedi IH, Snuderl M, Brat DJ, Kleinschmidt-DeMasters BK, Rodriguez FJ, Louis DN, Yong WH, Lopes MB, Rosenblum MK, Butowski N, Tihan T, Bollen AW, Phillips JJ, Wiita AP, Yeh I, Jacobson MP, Bastian BC, Perry A, Solomon DA. Nat Commun 9: 2018 810	31

Publications

Citations

A recurrent kinase domain mutation in PRKCA defines chordoid glioma of the third ventricle.
Goode B, Mondal G, Hyun M, Ruiz DG, Lin YH, Van Ziffle J, Joseph NM, Onodera C, Talevich E, Grenert JP, Hewedi IH, Snuderl M, Brat DJ, Kleinschmidt-DeMasters BK, Rodriguez FJ, Louis DN, Yong WH, Lopes MB, Rosenblum MK, Butowski N, Tihan T, Bollen AW, Phillips JJ, Wiita AP, Yeh I, Jacobson MP, Bastian BC, Perry A, Solomon DA. Nat Commun 9: 2018 810