BAM files of targeted next-generation DNA sequencing data of 13 chordoid gliomas of the third ventricle

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.

本数据集包含13例第三脑室脉络丛星形细胞瘤的靶向下一代DNA测序数据BAM文件（2对肿瘤-正常样本和11个肿瘤样本）。采用Qiagen公司的QIAamp DNA FFPE Tissue Kit从13例第三脑室脉络丛星形细胞瘤患者的石蜡包埋肿瘤组织块中提取基因组DNA。此外，还从其中一位患者的周围血白细胞样本以及另一位患者的非肿瘤性胃活检标本中提取了基因组DNA。在加州大学旧金山分校临床癌症基因组学实验室，利用针对约500个癌症相关基因的所有编码外显子、47个基因的选择性内含子和TERT启动子的捕获式下一代DNA测序技术（UCSF500癌症阵列）进行测序。从基因组DNA制备测序文库，并通过Nimblegen SeqCap EZ Choice定制寡核苷酸库进行杂交捕获富集。捕获的文库在Illumina HiSeq 2500仪器上以双端100碱基读长进行测序。通过计算方法移除重复的测序读数，以实现准确的等位基因频率测定和拷贝数调用。