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Genentech Small Cell Lung Cancer (SCLC) Screen

Exome capture, RNA-Seq, whole genome sequencing of set of Small Cell Lung Cancer samples.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

5 Datasets 16 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001000221	Whole genome sequencing of SCLC tumor/normal samples	Illumina HiSeq 2000	4
EGAD00001000222	Exome capture sequencing of SCLC tumor/normal pairs and cell lines	Illumina HiSeq 2000	103
EGAD00001000223	RNA sequencing of SCLC tumor/normal sample pairs and cell lines	Illumina HiSeq 2000	79
EGAD00010000276	SCLC tumor genotypes	Illumina_2.5M	56
EGAD00010000278	SCLC matched normal genotypes	Illumina_2.5M	51

Publications	Citations
Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer. Rudin CM, Durinck S, Stawiski EW, Poirier JT, Modrusan Z, Shames DS, Bergbower EA, Guan Y, Shin J, Guillory J, Rivers CS, Foo CK, Bhatt D, Stinson J, Gnad F, Haverty PM, Gentleman R, Chaudhuri S, Janakiraman V, Jaiswal BS, Parikh C, Yuan W, Zhang Z, Koeppen H, Wu TD, Stern HM, Yauch RL, Huffman KE, Paskulin DD, Illei PB, Varella-Garcia M, Gazdar AF, de Sauvage FJ, Bourgon R, Minna JD, Brock MV, Seshagiri S. Nat Genet 44: 2012 1111-1116	632
DNA methylation in small cell lung cancer defines distinct disease subtypes and correlates with high expression of EZH2. Poirier JT, Gardner EE, Connis N, Moreira AL, de Stanchina E, Hann CL, Rudin CM. Oncogene 34: 2015 5869-5878	132
Automated identification of reference genes based on RNA-seq data. Carmona R, Arroyo M, Jiménez-Quesada MJ, Seoane P, Zafra A, Larrosa R, Alché JD, Claros MG. Biomed Eng Online 16: 2017 65	17
Significantly mutated genes and regulatory pathways in SCLC-a meta-analysis. Sundaresan V, Lin VT, Liang F, Kaye FJ, Kawabata-Iwakawa R, Shiraishi K, Kohno T, Yokota J, Zhou L. Cancer Genet 216-217: 2017 20-28	10
Targeting CREB Pathway Suppresses Small Cell Lung Cancer. Xia Y, Zhan C, Feng M, Leblanc M, Ke E, Yeddula N, Verma IM. Mol Cancer Res 16: 2018 825-832	24
MYC paralog-dependent apoptotic priming orchestrates a spectrum of vulnerabilities in small cell lung cancer. Dammert MA, Brägelmann J, Olsen RR, Böhm S, Monhasery N, Whitney CP, Chalishazar MD, Tumbrink HL, Guthrie MR, Klein S, Ireland AS, Ryan J, Schmitt A, Marx A, Ozretić L, Castiglione R, Lorenz C, Jachimowicz RD, Wolf E, Thomas RK, Poirier JT, Büttner R, Sen T, Byers LA, Reinhardt HC, Letai A, Oliver TG, Sos ML. Nat Commun 10: 2019 3485	34
Transposable element expression in tumors is associated with immune infiltration and increased antigenicity. Kong Y, Rose CM, Cass AA, Williams AG, Darwish M, Lianoglou S, Haverty PM, Tong AJ, Blanchette C, Albert ML, Mellman I, Bourgon R, Greally J, Jhunjhunwala S, Chen-Harris H. Nat Commun 10: 2019 5228	103
Biomarker potential of repetitive-element transcriptome in lung cancer. Arroyo M, Bautista R, Larrosa R, Cobo MÁ, Claros MG. PeerJ 7: 2019 e8277	5
ASCL1-regulated DARPP-32 and t-DARPP stimulate small cell lung cancer growth and neuroendocrine tumour cell proliferation. Alam SK, Wang L, Ren Y, Hernandez CE, Kosari F, Roden AC, Yang R, Hoeppner LH. Br J Cancer 123: 2020 819-832	16
Ferroptosis response segregates small cell lung cancer (SCLC) neuroendocrine subtypes. Bebber CM, Thomas ES, Stroh J, Chen Z, Androulidaki A, Schmitt A, Höhne MN, Stüker L, de Pádua Alves C, Khonsari A, Dammert MA, Parmaksiz F, Tumbrink HL, Beleggia F, Sos ML, Riemer J, George J, Brodesser S, Thomas RK, Reinhardt HC, von Karstedt S. Nat Commun 12: 2021 2048	48
Therapeutic targeting of ATR yields durable regressions in small cell lung cancers with high replication stress. Thomas A, Takahashi N, Rajapakse VN, Zhang X, Sun Y, Ceribelli M, Wilson KM, Zhang Y, Beck E, Sciuto L, Nichols S, Elenbaas B, Puc J, Dahmen H, Zimmermann A, Varonin J, Schultz CW, Kim S, Shimellis H, Desai P, Klumpp-Thomas C, Chen L, Travers J, McKnight C, Michael S, Itkin Z, Lee S, Yuno A, Lee MJ, Redon CE, Kindrick JD, Peer CJ, Wei JS, Aladjem MI, Figg WD, Steinberg SM, Trepel JB, Zenke FT, Pommier Y, Khan J, Thomas CJ. Cancer Cell 39: 2021 566-579.e7	72
A GPC2 antibody-drug conjugate is efficacious against neuroblastoma and small-cell lung cancer via binding a conformational epitope. Raman S, Buongervino SN, Lane MV, Zhelev DV, Zhu Z, Cui H, Martinez B, Martinez D, Wang Y, Upton K, Patel K, Rathi KS, Navia CT, Harmon DB, Li Y, Pawel B, Dimitrov DS, Maris JM, Julien JP, Bosse KR. Cell Rep Med 2: 2021 100344	12
ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer. Trincado JL, Reixachs-Solé M, Pérez-Granado J, Fugmann T, Sanz F, Yokota J, Eyras E. PLoS Comput Biol 17: 2021 e1009411	2
Identification of TAZ as the essential molecular switch in orchestrating SCLC phenotypic transition and metastasis. Jin Y, Zhao Q, Zhu W, Feng Y, Xiao T, Zhang P, Jiang L, Hou Y, Guo C, Huang H, Chen Y, Tong X, Cao J, Li F, Zhu X, Qin J, Gao D, Liu XY, Zhang H, Chen L, Thomas RK, Wong KK, Zhang L, Wang Y, Hu L, Ji H. Natl Sci Rev 9: 2022 nwab232	4
Expression of down-regulated ERV LTR elements associates with immune activation in human small-cell lung cancers. Russo M, Morelli S, Capranico G. Mob DNA 14: 2023 2	0
Immunogenomic Landscape of Neuroendocrine Prostate Cancer. Bhinder B, Ferguson A, Sigouros M, Uppal M, Elsaeed AG, Bareja R, Alnajar H, Eng KW, Conteduca V, Sboner A, Mosquera JM, Elemento O, Beltran H. Clin Cancer Res 29: 2023 2933-2943	1