Dataset Information


Expression profile of Gastro-Entero-Pancreatic Neuroendocrine Tumors (GEP-NET)

ABSTRACT: Expression profile of human GEP-NET tumors, including 113 fresh frozen biopsies of primary and metastatic tumours originating from pancreas (P-NET, 83 primary and 30 metastasis), 81 from small intestine (SI-NET, 44 primary and 37 metastasis), and 18 from rectum (RE-NET, 3 primary and 15 metastasis). Overall design: 212 GEP-NET samples with cellularity >70% were analyzed. Total RNA was isolated and RNA integrity assayed by a 2100 Bioanalyzer (Agilent Technologies). High-quality total RNA samples, with RIN (RNA integrity number) above 7, were processed by TruSeq library preparation for RNA-Seq profiling (Illumina). For each sample, a minimum of 30 million 100bp single-end reads or 90 million 100bp paired-end reads were sequenced on the Illumina HiSeq2500 platform. RNA-Seq reads were mapped to the Homo sapiens assembly 19 reference genome, using Bowtie. Reads mapping to known genes, based on Entrez Gene identifiers, were then counted using the GenomicFeatures R-system package (Bioconductor).

INSTRUMENT(S): Illumina HiSeq 2500 (Homo sapiens)

SUBMITTER: Mariano Javier Alvarez  

PROVIDER: GSE98894 | GEO | 2018-02-25


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A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors.

Alvarez Mariano J MJ   Subramaniam Prem S PS   Tang Laura H LH   Grunn Adina A   Aburi Mahalaxmi M   Rieckhof Gabrielle G   Komissarova Elena V EV   Hagan Elizabeth A EA   Bodei Lisa L   Clemons Paul A PA   Dela Cruz Filemon S FS   Dhall Deepti D   Diolaiti Daniel D   Fraker Douglas A DA   Ghavami Afshin A   Kaemmerer Daniel D   Karan Charles C   Kidd Mark M   Kim Kyoung M KM   Kim Hee C HC   Kunju Lakshmi P LP   Langel Ülo Ü   Li Zhong Z   Lee Jeeyun J   Li Hai H   LiVolsi Virginia V   Pfragner Roswitha R   Rainey Allison R AR   Realubit Ronald B RB   Remotti Helen H   Regberg Jakob J   Roses Robert R   Rustgi Anil A   Sepulveda Antonia R AR   Serra Stefano S   Shi Chanjuan C   Yuan Xiaopu X   Barberis Massimo M   Bergamaschi Roberto R   Chinnaiyan Arul M AM   Detre Tony T   Ezzat Shereen S   Frilling Andrea A   Hommann Merten M   Jaeger Dirk D   Kim Michelle K MK   Knudsen Beatrice S BS   Kung Andrew L AL   Leahy Emer E   Metz David C DC   Milsom Jeffrey W JW   Park Young S YS   Reidy-Lagunes Diane D   Schreiber Stuart S   Washington Kay K   Wiedenmann Bertram B   Modlin Irvin I   Califano Andrea A  

Nature genetics 20180618 7

We introduce and validate a new precision oncology framework for the systematic prioritization of drugs targeting mechanistic tumor dependencies in individual patients. Compounds are prioritized on the basis of their ability to invert the concerted activity of master regulator proteins that mechanistically regulate tumor cell state, as assessed from systematic drug perturbation assays. We validated the approach on a cohort of 212 gastroenteropancreatic neuroendocrine tumors (GEP-NETs), a rare ma  ...[more]

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