Jump to: | Authorized Access | | | Attribution | | | Authorized Requests |
- Study Description
-
Important Links and Information
-
Request access via Authorized Access
- Instructions for requestors
- Data Use Certification (DUC) Agreement
- Talking Glossary of Genetic Terms
The Foundation Medicine adult cancer clinical dataset consists of 18,004 unique solid tumor samples that underwent genomic profiling on a single uniform platform as part of standard clinical care. The dataset is derived from the FoundationOne® genomic profiling assay version 2 that interrogates exonic regions of 287 cancer-related genes and selected introns from 19 genes known to undergo rearrangements in human cancer. Genomic DNA samples were sequenced to over 500x median coverage, and custom computational analyses identified all classes of genomic alterations (base substitutions, insertions and deletions, copy number alterations, and rearrangements). Since matched normal tissue was unavailable for analysis, these data underwent additional filtering to enrich for cancer-related events. The reported data includes genomic alterations that are known and suspected tumor drivers, as well as variants of unknown significance. To preserve patient anonymity, all known or suspected germline variants were removed from the data unless known to be associated with cancer development.
The dataset contains genomic alteration profiles generated by FoundationOne version 2 testing for adult cancer patients (over 18 y.o.), and represents a vast diversity of tumor subtypes, including many rare diseases not profiled as part of large-scale profiling efforts. Cases are grouped into 16 broad disease categories containing tumors from 162 unique disease subtypes. Since specimens were profiled as part of clinical care, limited clinical parameters were available, including age, gender, tissue of origin, % of tumor nuclei, and diagnosis. Publication of this dataset is intended to allow the broad scientific community access to this unique cohort for use in scientific research projects of common and rare types of cancer, both for generating leads regarding causal mechanisms as well as cross-testing and confirming existing hypotheses.
A pediatric cancer clinical dataset consisting of data from 1,215 patients under 18 y.o. is available separately at: FOUNDATION MEDICINE
- Study Weblinks:
- Study Design:
- Case Set
- Study Type:
- Case Set
- Total number of consented subjects: 18004
- Subject Sample Telemetry Report (SSTR)
-
Request access via Authorized Access
- Authorized Access
- Publicly Available Data (Public ftp)
- Study Inclusion/Exclusion Criteria
FoundationOne version 2 test results of confirmed solid epithelial tumors from patients over 18 y.o. are included. To protect patient privacy, cases within a disease category represented less than 5 times in the dataset were discarded or merged with other disease categories.
- Molecular Data
-
Type Source Platform Number of Oligos/SNPs SNP Batch Id Comment Targeted Genomic Sequencing Foundation Medicine FoundationOne v2 N/A N/A All exons of 287 genes and selected introns from 19 genes - Selected Publications
- Diseases/Traits Related to Study (MeSH terms)
- Links to Related Resources
- Authorized Data Access Requests
-
See research articles citing use of the data from this study
- Study Attribution
-
-
Principal Investigators
- Doron Lipson, PhD. Foundation Medicine Inc., Cambridge, MA, USA.
- Juliann Chmielecki, PhD. Foundation Medicine Inc., Cambridge, MA, USA.
-
Principal Investigators