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Anonymized germline variants of prospectively characterized clinical cancer specimens

UID: 11300

Author(s): Berger, Michael Forman* * MSK affiliated

Description
Description from dbGaP:

"These clinical specimens represent solid tumors and matched blood controls that were collected as part of patients' routine care at Memorial Sloan Kettering Cancer Center. They were sequenced on the targeted platform MSK-IMPACT. Here, we performed germline variant calling on the normal blood specimens and assessed their zygosity in the concomitant tumor specimens for comprehensive exploration of the landscape of pathogenic germline variants in patients with advanced cancer."
Subject of Study
Homo sapiens
Subject(s)
Genetic Risk Score
Germ-Line Mutation
Neoplasms/genetics
Access via dbGaP


Accession #: phs001858.v1.p1

Access Restrictions
Application Required
Access Instructions
Full access to this dataset in dbGaP requires authorization through an Authorized Access Portal which can be requested for either 'data download' or 'view only'. Individual level data download requires a project request. With dbGaP DataBrowser approval, users may view the compilation of individual-level data of general research use. Upon approval, data can be downloaded. To view the data available with Authorized Access, click the link 'list of components' in the Authorized Access section. Upon approval, data can be downloaded.

Publicly available data such as data dictionaries, variable summaries, documents and truncated analysis are available the public download site FTP link.
Associated Publications
Srinivasan P, Bandlamudi C, Jonsson P, Kemel Y, Chavan S, Richards A, Penson A, Bielski C, Fong C, Syed A, Jayakumaran G, Prasad M, Hwee J, Sumer S, de Bruijn I, Li X, Gao J, Schultz N, Cambria R, Galle J, Mukherjee S, Vijai J, Cadoo K, Carlo M, Walsh M, Mandelker D, Ceyhan-Birsoy O, Shia J, Zehir A, Ladanyi M, Hyman D, Zhang L, Offit K, Robson M, Solit D, Stadler Z, Berger M, Taylor B. The context-specific role of germline pathogenicity in tumorigenesis. Nature Genetics. 2021; 53(11):1577-1585.
Jonsson P, Bandlamudi C, Cheng M, Srinivasan P, Chavan S, Friedman N, Rosen E, Richards A, Bouvier N, Selcuklu S, Bielski C, Abida W, Mandelker D, Birsoy O, Zhang L, Zehir A, Donoghue M, Baselga J, Offit K, Scher H, O’Reilly E, Stadler Z, Schultz N, Socci N, Viale A, Ladanyi M, Robson M, Hyman D, Berger M, Solit D, Taylor B. Tumour lineage shapes BRCA-mediated phenotypes. Nature. 2019; 571(7766):576-579.
Equipment Used
Illumina HiSeq 2500

High throughput sequencing system

Roche NimbleGen Custom

Targeted capture

Dataset Format(s)
PDF, XML, TAR, gzip, TXT
Dataset Size
2.39 MB
Data Catalog Record Updated
2024-07-11