Whole-exome Sequencing of Intracranial Germ Cell Tumors performed at Human Genome Sequencing Center, Baylor College of Medicine

Intracranial germ cell tumors (IGCTs) are rare and biologically diverse tumors affecting mainly male adolescents with the highest incidence in Japan and other Asian countries. They are divided into two main groups, pure germinoma and nongerminomatous germ cell tumors (NGGCTs). Germinoma is the most common subtype. NGGCTs include teratoma, embryonal carcinoma, yolk sac tumor and choriocarcinoma. About 10% of germinomas and most NGGCTs remain refractory to multimodality therapy. Little is currently known about IGCTs except for KIT mutation or overexpression, observed in ~25% of pure germinomas and rarely seen in NGGCTs. As yet, there are no clues for the puzzle of onset during puberty, geographic and gender discrepancy in the incidence of IGCTs. With the collaboration of Texas Children's Hospital, Saitama Medical University Hospital, Kumamoto University Hospital, Nagoya University Hospital, Hokkaido University Hospital and Chinese University of Hong Kong, the Human Genome Sequencing Center at Baylor College of Medicine had access to 62 tumor specimens and 52 matched normal blood samples from 68 IGCT patients. We performed whole-exome sequencing, targeted deep sequencing and high-resolution SNP arrays to characterize the profile of somatic mutations, germline variants and DNA copy number alterations. The deposited BAM files record the sequence alignments used to generate the mutation data.