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Study Description

The earliest genetic abnormalities in cancer represent a unique opportunity for timely clinical diagnosis. Classic deep sequencing of tumors identifies many aberrations acquired later in cancer progression. In this study, data regarding simple mutation and chromosomal aberration were integrated to trace the evolution of cutaneous squamous cell carcinomas and ovarian adenocarcinomas. Only after the second allele of TP53 was lost did the genome enter a window of extreme genomic vulnerability, in both cancer types, eventually acquiring more than 100,000 mutations in skin cancers. Inactivating Notch mutations were also identified as prevalent secondary changes. These results add context to the idea of TP53 mutation as dominant negative and occurring later in tumorigenesis.

  • Study Type: Tumor vs. Matched-Normal
  • Number of study subjects that have individual level data available through Authorized Access: 8

Authorized Access
Publicly Available Data (Public ftp)

Connect to the public download site. The site contains release notes and manifests. If available, the site also contains data dictionaries, variable summaries, documents, and truncated analyses.

Study Inclusion/Exclusion Criteria

Between the years of 2006 and 2010, one woman and seven men were enrolled in the study of skin cancer. Their ages ranged from 61 to 87 years. Informed consent was provided according to UCSF Committee on Human Research guidelines for large-scale genetic analysis. Data sharing is allowed so long as identity is not revealed. Board certified dermatopathologists confirmed the diagnosis of squamous cell carcinoma of the skin, from biopsies, for all study samples. Tissue was isolated using curettage before Mohs micrographic surgery. Control samples were obtained from adjacent normal skin.

Molecular Data
TypeSourcePlatformNumber of Oligos/SNPsSNP Batch IdComment
Exome Sequencing Illumina Genome Analyzer II N/A N/A
Selected publications
Diseases/Traits Related to Study (MESH terms)
Authorized Data Access Requests
Study Attribution

  • Principal Investigator
    • Raymond Cho, MD, PhD. University of California San Francisco School of Medicine, San Francisco, CA, USA

Acknowledgement Statement: Please cite/reference the use of dbGaP data by including the dbGaP accession phs000418.v1.p1. Additionally, use the following statement to acknowledge the submitter(s) of this study:

This research was supported under J.W. Gray [by the Director, Office of Science, Office of Biological and Environmental Research, U.S. Department of Energy, under Contract DE-AC02-05CH11231; by NIH, National Cancer Institute (NCI) Grants P50 CA 58207, U54 CA 112970, and NHGRI U24 CA 126551; by the Department of the Army, Award W81XWH-07-1-0663 (The U.S. Army Medical Research Acquisition Activity, Fort Detrick, Maryland, is the awarding and administering acquisition office); and by the Stand Up To Cancer–American Association for Cancer Research Dream Team Translational Cancer Research Grant SU2C-AACR-DT0409. The content of this information does not necessarily reflect the position or the policy of the federal government, and no official endorsement should be inferred]; P.T. Spellman (by NIH/NCI U24 CA1437991); R.J. Cho (by an unrestricted gift grant from the Samsung Advanced Institute of Technology); T.M. Mauro (by NIH Grants AR051930 and R01AG028492, and the Medical Research Service, Department of Veterans Affairs); and A. Balmain (by NIH/National Institute of Arthritis and Musculoskeletal and Skin.