OpenPBTA: The Open Pediatric Brain Tumor Atlas.
OpenPBTA: The Open Pediatric Brain Tumor Atlas.
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DOI：
10.1016/j.xgen.2023.100340
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发表时间：
2023-07-12
期刊：
影响因子：
--
通讯作者：
Taroni, Jaclyn N.
中科院分区：
文献类型：
--
作者：
Shapiro, Joshua A.;Gaonkar, Krutika S.;Spielman, Stephanie J.;Savonen, Candace L.;Bethell, Chante J.;Jin, Run;Rathi, Komal S.;Zhu, Yuankun;Egolf, Laura E.;Farrow, Bailey K.;Miller, Daniel P.;Yang, Yang;Koganti, Tejaswi;Noureen, Nighat;Koptyra, Mateusz P.;Duong, Nhat;Santi, Mariarita;Kim, Jung;Robins, Shannon;Storm, Phillip B.;Mack, Stephen C.;Lilly, Jena, V;Xie, Hongbo M.;Jain, Payal;Raman, Pichai;Rood, Brian R.;Lulla, Rishi R.;Nazarian, Javad;Kraya, Adam A.;Vaksman, Zalman;Heath, Allison P.;Kline, Cassie;Scolaro, Laura;Viaene, Angela N.;Huang, Xiaoyan;Way, Gregory P.;Foltz, Steven M.;Zhang, Bo;Poetsch, Anna R.;Mueller, Sabine;Ennis, Brian M.;Prados, Michael;Diskin, Sharon J.;Zheng, Siyuan;Guo, Yiran;Kannan, Shrivats;Waanders, Angela J.;Margol, Ashley S.;Kim, Meen Chul;Hanson, Derek;Van Kuren, Nicholas;Wong, Jessica;Kaufman, Rebecca S.;Coleman, Noel;Blackden, Christopher;Cole, Kristina A.;Mason, Jennifer L.;Madsen, Peter J.;Koschmann, Carl J.;Stewart, Douglas R.;Wafula, Eric;Brown, Miguel A.;Resnick, Adam C.;Greene, Casey S.;Rokita, Jo Lynne;Taroni, Jaclyn N.
儿童脑癌和脊髓癌是儿童死亡的主要疾病相关原因；因此，我们迫切需要针对这些肿瘤的治疗策略。为了加速这些发现，儿童脑肿瘤网络（CBTN）和太平洋儿童神经肿瘤联盟（PNOC）创建了一个系统的过程，用于肿瘤生物银行、模型生成和测序，可以立即访问统一的数据。我们利用这些数据建立了OpenPBTA，这是一个开放的合作项目，拥有超过40个可扩展的分析模块，可以对1,074个儿童脑肿瘤进行基因组表征。转录组学分类显示，在错配修复缺陷高突变的高级别胶质瘤中，TP53普遍失调，TP53缺失是室管膜瘤和H3 k28突变的弥散性中线胶质瘤总生存率差的重要标志。OpenPBTA已经被积极应用于其他儿科癌症和PNOC分子肿瘤董事会决策，是儿科肿瘤学社区的宝贵资源。OpenPBTA合作分析为1074例儿童脑肿瘤建立了基于ngs的与世卫组织一致的综合诊断，对1074例肿瘤中的644例进行了RNA-Seq分析，推断成神经管细胞瘤亚型、TP53状态和端粒酶活性。OpenPBTA将加速基因组见解的治疗转化。合作开放科学倡议，将研究人员和临床医生聚集在一起，对1,074个儿童脑肿瘤和22个患者来源的细胞系进行基因组表征。Shapiro等人创建了40多个开源、可扩展的模块来执行癌症基因组学分析，并提供了58种脑肿瘤组织学的丰富注释体细胞数据集。OpenPBTA框架可以作为大规模数据集成的模型，为基础研究、治疗靶点识别和临床翻译提供信息。
Pediatric brain and spinal cancers are collectively the leading disease-related cause of death in children; thus, we urgently need curative therapeutic strategies for these tumors. To accelerate such discoveries, the Children’s Brain Tumor Network (CBTN) and Pacific Pediatric Neuro-Oncology Consortium (PNOC) created a systematic process for tumor biobanking, model generation, and sequencing with immediate access to harmonized data. We leverage these data to establish OpenPBTA, an open collaborative project with over 40 scalable analysis modules that genomically characterize 1,074 pediatric brain tumors. Transcriptomic classification reveals universal TP53 dysregulation in mismatch repair-deficient hypermutant high-grade gliomas and TP53 loss as a significant marker for poor overall survival in ependymomas and H3 K28-mutant diffuse midline gliomas. Already being actively applied to other pediatric cancers and PNOC molecular tumor board decision-making, OpenPBTA is an invaluable resource to the pediatric oncology community. OpenPBTA collaborative analyses establish resource for 1,074 pediatric brain tumors NGS-based WHO-aligned integrated diagnoses generated for 644 of 1,074 tumors RNA-Seq analysis infers medulloblastoma subtypes, TP53 status, and telomerase activity OpenPBTA will accelerate therapeutic translation of genomic insights The OpenPBTA is a global, collaborative open-science initiative that brought together researchers and clinicians to genomically characterize 1,074 pediatric brain tumors and 22 patient-derived cell lines. Shapiro et al. create over 40 open-source, scalable modules to perform cancer genomics analyses and provide a richly annotated somatic dataset across 58 brain tumor histologies. The OpenPBTA framework can be used as a model for large-scale data integration to inform basic research, therapeutic target identification, and clinical translation.
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DOI：
10.1093/bioinformatics/btr670
发表时间：
2012-02-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Boeva V;Popova T;Bleakley K;Chiche P;Cappo J;Schleiermacher G;Janoueix-Lerosey I;Delattre O;Barillot E
通讯作者：
Barillot E
影响因子：
4
作者：
Aronson, Melyssa;Colas, Chrystelle;Tabori, Uri
通讯作者：
Tabori, Uri
MYB-QKI重排在血管中心神经胶质瘤中通过三方机制驱动肿瘤性。
影响因子：
30.8
作者：
Bandopadhayay P;Ramkissoon LA;Jain P;Bergthold G;Wala J;Zeid R;Schumacher SE;Urbanski L;O'Rourke R;Gibson WJ;Pelton K;Ramkissoon SH;Han HJ;Zhu Y;Choudhari N;Silva A;Boucher K;Henn RE;Kang YJ;Knoff D;Paolella BR;Gladden-Young A;Varlet P;Pages M;Horowitz PM;Federation A;Malkin H;Tracy AA;Seepo S;Ducar M;Van Hummelen P;Santi M;Buccoliero AM;Scagnet M;Bowers DC;Giannini C;Puget S;Hawkins C;Tabori U;Klekner A;Bognar L;Burger PC;Eberhart C;Rodriguez FJ;Hill DA;Mueller S;Haas-Kogan DA;Phillips JJ;Santagata S;Stiles CD;Bradner JE;Jabado N;Goren A;Grill J;Ligon AH;Goumnerova L;Waanders AJ;Storm PB;Kieran MW;Ligon KL;Beroukhim R;Resnick AC
通讯作者：
Resnick AC
影响因子：
28.2
作者：
Chang MT;Bhattarai TS;Schram AM;Bielski CM;Donoghue MTA;Jonsson P;Chakravarty D;Phillips S;Kandoth C;Penson A;Gorelick A;Shamu T;Patel S;Harris C;Gao J;Sumer SO;Kundra R;Razavi P;Li BT;Reales DN;Socci ND;Jayakumaran G;Zehir A;Benayed R;Arcila ME;Chandarlapaty S;Ladanyi M;Schultz N;Baselga J;Berger MF;Rosen N;Solit DB;Hyman DM;Taylor BS
通讯作者：
Taylor BS
影响因子：
4
作者：
de Blank, Peter M.;Ostrom, Quinn T.;Barnholtz-Sloan, Jill S.
通讯作者：
Barnholtz-Sloan, Jill S.