CCDC - Childhood Cancer Data Catalog

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

dbGaP

Data Resource: dbGaP

Point of Contact:

David A. Wheeler, PhD,

wheeler@bcm.edu

Project

About This Dataset

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.

Core Data Elements

Number of Cases

28

Case Sex

Female (4); Male (24)

Case Age At Diagnosis

0 to 4 years (6); 5 to 9 years (6); 10 to 14 years (8); 15 to 19 years (4); 20 to 24 years (3); 30 to 34 years (1)

Case Race

Not Reported (28)

Case Ethnicity

Not Reported (28)

Case Disease Diagnosis

Intracranial Germcell Tumor (28)

Number of Samples

56

Sample Anatomic Site

Blood (28); Brain (28)

Additional Data Elements

DBGAP STUDY IDENTIFIER

Grant Information

5U54HG003273

The Human Genome Sequencing Center

Published In

https://doi.org/10.1038/nature13296

https://doi.org/10.1038/nature13296

Charts

Male (24); Female (4)