Description: Summary from dbGap: "A subset of advanced prostate cancers can progress from an androgen receptor (AR)-driven state to AR independence, often associated with low or absent AR expression and extensive neuroendocrine differentiation. Once neuroendocrine prostate cancer (NEPC) develops, patients typically demonstrate an aggressive clinical course and poor overall survival. Early diagnosis is important but remains challenging as the clinical and pathologic features associate with AR independence and NEPC are poorly defined. We performed whole exome sequencing of 114 metastatic tumors from 81 patients (35 with morphologic features of NEPC). Serial or synchronous samples were included to characterize heterogeneity and the transition from adenocarcinoma to NEPC. Computational analysis of clonality and allele specific quantification were performed using CLONET. Quantitative mRNA assessment including AR signaling genes and DNA methylation were evaluated in the context of genomic changes."

Subject of Study

Homo sapiens

Subject(s)

Adenocarcinoma

Carcinoma, Neuroendocrine

Prostatic Neoplasms

Receptors, Androgen

OncoTree Cancer Type(s)

Prostate Neuroendocrine Carcinoma
Prostate

Access via dbGaP
Bisulfite Sequence reads , RNA Sequence reads, and WXS samples.
Accession #: phs000909.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.

A full list of and information about the SRA runs, BioSamples, and experiments is publicly viewable by going to the 'Molecular Datasets' tab and clicking on 'RunSelector' at the bottom of the page. This will take you to the NCBI SRA Run Selector platform. View and download of the datasets themselves, however, still requires authorization through dbGaP.

Publicly available data such as data dictionaries, variable summaries, documents and truncated analysis are available the public download site FTP link. A link for the list of components downloadable from Authorized Access is featured at the bottom of the Authorized Access Section.
Associated Publications: Prandi D, Baca SC, Romanel A, et al. Unraveling the clonal hierarchy of somatic genomic aberrations [published correction appears in Genome Biol. 2017 May 2;18(1):80]. Genome Biol. 2014;15(8):439. Published 2014 Aug 26.

Beltran H, Rickman DS, Park K, et al. Molecular characterization of neuroendocrine prostate cancer and identification of new drug targets. Cancer Discov. 2011;1(6):487-495.

Epstein J, Amin M, Beltran H, et al. Proposed morphologic classification of prostate cancer with neuroendocrine differentiation. American Journal of Surgical Pathology. 2014; 38(6):756-767.
Data Type: Genomic
Equipment Used: Illumina Genome Analyzer II
The Genome Analyzer supports a wide range of applications, including whole-genome and candidate region resequencing, transcriptome analysis, small RNA discovery, methylation profi ling, and protein-nucleic acid interaction analysis at a genome-wide scale.

Illumina HiSeq 2000
High throughput gene sequencing system

Illumina HiSeq 2500
High throughput sequencing system
Software Used: SRA Toolkit
The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.
Dataset Format(s): FASTQ, SRA
Data Tool(s): RNA Seq

WXS

Bisulfite-Seq
Dataset Size: 923 GB

Data Catalog Record Updated: 2021-08-05

Molecular Basis of Neuroendocrine Prostate Cancer (Trento/Cornell/Broad 2015)