Literature DB >> 33434514

Exploration of Coding and Non-coding Variants in Cancer Using GenomePaint.

Xin Zhou1, Jian Wang2, Jaimin Patel2, Marc Valentine3, Ying Shao2, Scott Newman2, Edgar Sioson2, Liqing Tian2, Yu Liu2, Samuel W Brady2, Diane Flasch2, Xiaotu Ma2, Yanling Liu2, Robin Paul2, Michael N Edmonson2, Michael C Rusch2, Chunliang Li4, Suzanne J Baker5, John Easton2, Jinghui Zhang6.   

Abstract

GenomePaint (https://genomepaint.stjude.cloud/) is an interactive visualization platform for whole-genome, whole-exome, transcriptome, and epigenomic data of tumor samples. Its design captures the inter-relatedness between DNA variations and RNA expression, supporting in-depth exploration of both individual cancer genomes and full cohorts. Regulatory non-coding variants can be inspected and analyzed along with coding variants, and their functional impact further explored by examining 3D genome data from cancer cell lines. Further, GenomePaint correlates mutation and expression patterns with patient outcomes, and supports custom data upload. We used GenomePaint to unveil aberrant splicing that disrupts the RING domain of CREBBP, discover cis activation of the MYC oncogene by duplication of the NOTCH1-MYC enhancer in B-lineage acute lymphoblastic leukemia, and explore the inter- and intra-tumor heterogeneity at EGFR in adult glioblastomas. These examples demonstrate that deep multi-omics exploration of individual cancer genomes enabled by GenomePaint can lead to biological insights for follow-up validation.
Copyright © 2020 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  cancer; gene expression; genome browser; mutation

Mesh：

Year:  2021        PMID： 33434514      PMCID： PMC7884056          DOI： 10.1016/j.ccell.2020.12.011

Source DB:  PubMed          Journal:  Cancer Cell        ISSN： 1535-6108            Impact factor:   31.743


  38 in total

1.  MDM2 antagonists induce p53-dependent apoptosis in AML: implications for leukemia therapy.

Authors:  Kensuke Kojima; Marina Konopleva; Ismael J Samudio; Masato Shikami; Maria Cabreira-Hansen; Teresa McQueen; Vivian Ruvolo; Twee Tsao; Zhihong Zeng; Lyubomir T Vassilev; Michael Andreeff
Journal:  Blood       Date:  2005-07-12       Impact factor: 22.113

2.  13q12.2 deletions in acute lymphoblastic leukemia lead to upregulation of FLT3 through enhancer hijacking.

Authors:  Minjun Yang; Setareh Safavi; Eleanor L Woodward; Nicolas Duployez; Linda Olsson-Arvidsson; Jonas Ungerbäck; Mikael Sigvardsson; Marketa Zaliova; Jan Zuna; Thoas Fioretos; Bertil Johansson; Karolin H Nord; Kajsa Paulsson
Journal:  Blood       Date:  2020-08-20       Impact factor: 22.113

3.  Exploring genomic alteration in pediatric cancer using ProteinPaint.

Authors:  Xin Zhou; Michael N Edmonson; Mark R Wilkinson; Aman Patel; Gang Wu; Yu Liu; Yongjin Li; Zhaojie Zhang; Michael C Rusch; Matthew Parker; Jared Becksfort; James R Downing; Jinghui Zhang
Journal:  Nat Genet       Date:  2016-01       Impact factor: 38.330

4.  Genetic heterogeneity in Rubinstein-Taybi syndrome: mutations in both the CBP and EP300 genes cause disease.

Authors:  Jeroen H Roelfsema; Stefan J White; Yavuz Ariyürek; Deborah Bartholdi; Dunja Niedrist; Francesco Papadia; Carlos A Bacino; Johan T den Dunnen; Gert-Jan B van Ommen; Martijn H Breuning; Raoul C Hennekam; Dorien J M Peters
Journal:  Am J Hum Genet       Date:  2005-02-10       Impact factor: 11.025

5.  CREBBP mutations in relapsed acute lymphoblastic leukaemia.

Authors:  Charles G Mullighan; Jinghui Zhang; Lawryn H Kasper; Stephanie Lerach; Debbie Payne-Turner; Letha A Phillips; Sue L Heatley; Linda Holmfeldt; J Racquel Collins-Underwood; Jing Ma; Kenneth H Buetow; Ching-Hon Pui; Sharyn D Baker; Paul K Brindle; James R Downing
Journal:  Nature       Date:  2011-03-10       Impact factor: 49.962

6.  Synthetic lethality in ATM-deficient RAD50-mutant tumors underlies outlier response to cancer therapy.

Authors:  Hikmat Al-Ahmadie; Gopa Iyer; Marcel Hohl; Saurabh Asthana; Akiko Inagaki; Nikolaus Schultz; Aphrothiti J Hanrahan; Sasinya N Scott; A Rose Brannon; Gregory C McDermott; Mono Pirun; Irina Ostrovnaya; Philip Kim; Nicholas D Socci; Agnes Viale; Gary K Schwartz; Victor Reuter; Bernard H Bochner; Jonathan E Rosenberg; Dean F Bajorin; Michael F Berger; John H J Petrini; David B Solit; Barry S Taylor
Journal:  Cancer Discov       Date:  2014-06-16       Impact factor: 39.397

7.  The landscape of genomic alterations across childhood cancers.

Authors:  Susanne N Gröbner; Barbara C Worst; Joachim Weischenfeldt; Ivo Buchhalter; Kortine Kleinheinz; Vasilisa A Rudneva; Pascal D Johann; Gnana Prakash Balasubramanian; Maia Segura-Wang; Sebastian Brabetz; Sebastian Bender; Barbara Hutter; Dominik Sturm; Elke Pfaff; Daniel Hübschmann; Gideon Zipprich; Michael Heinold; Jürgen Eils; Christian Lawerenz; Serap Erkek; Sander Lambo; Sebastian Waszak; Claudia Blattmann; Arndt Borkhardt; Michaela Kuhlen; Angelika Eggert; Simone Fulda; Manfred Gessler; Jenny Wegert; Roland Kappler; Daniel Baumhoer; Stefan Burdach; Renate Kirschner-Schwabe; Udo Kontny; Andreas E Kulozik; Dietmar Lohmann; Simone Hettmer; Cornelia Eckert; Stefan Bielack; Michaela Nathrath; Charlotte Niemeyer; Günther H Richter; Johannes Schulte; Reiner Siebert; Frank Westermann; Jan J Molenaar; Gilles Vassal; Hendrik Witt; Birgit Burkhardt; Christian P Kratz; Olaf Witt; Cornelis M van Tilburg; Christof M Kramm; Gudrun Fleischhack; Uta Dirksen; Stefan Rutkowski; Michael Frühwald; Katja von Hoff; Stephan Wolf; Thomas Klingebiel; Ewa Koscielniak; Pablo Landgraf; Jan Koster; Adam C Resnick; Jinghui Zhang; Yanling Liu; Xin Zhou; Angela J Waanders; Danny A Zwijnenburg; Pichai Raman; Benedikt Brors; Ursula D Weber; Paul A Northcott; Kristian W Pajtler; Marcel Kool; Rosario M Piro; Jan O Korbel; Matthias Schlesner; Roland Eils; David T W Jones; Peter Lichter; Lukas Chavez; Marc Zapatka; Stefan M Pfister
Journal:  Nature       Date:  2018-02-28       Impact factor: 49.962

8.  Multiplexed analysis of chromosome conformation at vastly improved sensitivity.

Authors:  James O J Davies; Jelena M Telenius; Simon J McGowan; Nigel A Roberts; Stephen Taylor; Douglas R Higgs; Jim R Hughes
Journal:  Nat Methods       Date:  2015-11-23       Impact factor: 28.547

9.  The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia.

Authors:  Yu Liu; John Easton; Ying Shao; Jamie Maciaszek; Zhaoming Wang; Mark R Wilkinson; Kelly McCastlain; Michael Edmonson; Stanley B Pounds; Lei Shi; Xin Zhou; Xiaotu Ma; Edgar Sioson; Yongjin Li; Michael Rusch; Pankaj Gupta; Deqing Pei; Cheng Cheng; Malcolm A Smith; Jaime Guidry Auvil; Daniela S Gerhard; Mary V Relling; Naomi J Winick; Andrew J Carroll; Nyla A Heerema; Elizabeth Raetz; Meenakshi Devidas; Cheryl L Willman; Richard C Harvey; William L Carroll; Kimberly P Dunsmore; Stuart S Winter; Brent L Wood; Brian P Sorrentino; James R Downing; Mignon L Loh; Stephen P Hunger; Jinghui Zhang; Charles G Mullighan
Journal:  Nat Genet       Date:  2017-07-03       Impact factor: 38.330

10.  The whole-genome landscape of medulloblastoma subtypes.

Authors:  Paul A Northcott; Ivo Buchhalter; A Sorana Morrissy; Volker Hovestadt; Joachim Weischenfeldt; Tobias Ehrenberger; Susanne Gröbner; Maia Segura-Wang; Thomas Zichner; Vasilisa A Rudneva; Hans-Jörg Warnatz; Nikos Sidiropoulos; Aaron H Phillips; Steven Schumacher; Kortine Kleinheinz; Sebastian M Waszak; Serap Erkek; David T W Jones; Barbara C Worst; Marcel Kool; Marc Zapatka; Natalie Jäger; Lukas Chavez; Barbara Hutter; Matthias Bieg; Nagarajan Paramasivam; Michael Heinold; Zuguang Gu; Naveed Ishaque; Christina Jäger-Schmidt; Charles D Imbusch; Alke Jugold; Daniel Hübschmann; Thomas Risch; Vyacheslav Amstislavskiy; Francisco German Rodriguez Gonzalez; Ursula D Weber; Stephan Wolf; Giles W Robinson; Xin Zhou; Gang Wu; David Finkelstein; Yanling Liu; Florence M G Cavalli; Betty Luu; Vijay Ramaswamy; Xiaochong Wu; Jan Koster; Marina Ryzhova; Yoon-Jae Cho; Scott L Pomeroy; Christel Herold-Mende; Martin Schuhmann; Martin Ebinger; Linda M Liau; Jaume Mora; Roger E McLendon; Nada Jabado; Toshihiro Kumabe; Eric Chuah; Yussanne Ma; Richard A Moore; Andrew J Mungall; Karen L Mungall; Nina Thiessen; Kane Tse; Tina Wong; Steven J M Jones; Olaf Witt; Till Milde; Andreas Von Deimling; David Capper; Andrey Korshunov; Marie-Laure Yaspo; Richard Kriwacki; Amar Gajjar; Jinghui Zhang; Rameen Beroukhim; Ernest Fraenkel; Jan O Korbel; Benedikt Brors; Matthias Schlesner; Roland Eils; Marco A Marra; Stefan M Pfister; Michael D Taylor; Peter Lichter
Journal:  Nature       Date:  2017-07-19       Impact factor: 49.962
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  7 in total

Review 1.  Computational analysis of cancer genome sequencing data.

Authors:  Isidro Cortés-Ciriano; Doga C Gulhan; Jake June-Koo Lee; Giorgio E M Melloni; Peter J Park
Journal:  Nat Rev Genet       Date:  2021-12-08       Impact factor: 53.242

2.  The genomic landscape of pediatric acute lymphoblastic leukemia.

Authors:  Samuel W Brady; Kathryn G Roberts; Zhaohui Gu; Lei Shi; Stanley Pounds; Deqing Pei; Cheng Cheng; Yunfeng Dai; Meenakshi Devidas; Chunxu Qu; Ashley N Hill; Debbie Payne-Turner; Xiaotu Ma; Ilaria Iacobucci; Pradyuamna Baviskar; Lei Wei; Sasi Arunachalam; Kohei Hagiwara; Yanling Liu; Diane A Flasch; Yu Liu; Matthew Parker; Xiaolong Chen; Abdelrahman H Elsayed; Omkar Pathak; Yongjin Li; Yiping Fan; J Robert Michael; Michael Rusch; Mark R Wilkinson; Scott Foy; Dale J Hedges; Scott Newman; Xin Zhou; Jian Wang; Colleen Reilly; Edgar Sioson; Stephen V Rice; Victor Pastor Loyola; Gang Wu; Evadnie Rampersaud; Shalini C Reshmi; Julie Gastier-Foster; Jaime M Guidry Auvil; Patee Gesuwan; Malcolm A Smith; Naomi Winick; Andrew J Carroll; Nyla A Heerema; Richard C Harvey; Cheryl L Willman; Eric Larsen; Elizabeth A Raetz; Michael J Borowitz; Brent L Wood; William L Carroll; Patrick A Zweidler-McKay; Karen R Rabin; Leonard A Mattano; Kelly W Maloney; Stuart S Winter; Michael J Burke; Wanda Salzer; Kimberly P Dunsmore; Anne L Angiolillo; Kristine R Crews; James R Downing; Sima Jeha; Ching-Hon Pui; William E Evans; Jun J Yang; Mary V Relling; Daniela S Gerhard; Mignon L Loh; Stephen P Hunger; Jinghui Zhang; Charles G Mullighan
Journal:  Nat Genet       Date:  2022-09-01       Impact factor: 41.307

3.  Clinical and Functional Significance of TP53 Exon 4-Intron 4 Splice Junction Variants.

Authors:  Emilia M Pinto; Kara N Maxwell; Hadeel Halalsheh; Aaron Phillips; Jacquelyn Powers; Suzanne MacFarland; Michael F Walsh; Kelsey Breen; Maria N Formiga; Richard Kriwacki; Kim E Nichols; Roya Mostafavi; Jinling Wang; Michael R Clay; Carlos Rodriguez-Galindo; Raul C Ribeiro; Gerard P Zambetti
Journal:  Mol Cancer Res       Date:  2021-10-21       Impact factor: 6.333

4.  CCL22 mutations drive natural killer cell lymphoproliferative disease by deregulating microenvironmental crosstalk.

Authors:  Constance Baer; Shunsuke Kimura; Mitra S Rana; Andrew B Kleist; Tim Flerlage; David J Feith; Peter Chockley; Wencke Walter; Manja Meggendorfer; Thomas L Olson; HeeJin Cheon; Kristine C Olson; Aakrosh Ratan; Martha-Lena Mueller; James M Foran; Laura J Janke; Chunxu Qu; Shaina N Porter; Shondra M Pruett-Miller; Ravi C Kalathur; Claudia Haferlach; Wolfgang Kern; Elisabeth Paietta; Paul G Thomas; M Madan Babu; Thomas P Loughran; Ilaria Iacobucci; Torsten Haferlach; Charles G Mullighan
Journal:  Nat Genet       Date:  2022-05-05       Impact factor: 41.307

5.  Aberrant GATA2 Activation in Pediatric B-Cell Acute Lymphoblastic Leukemia.

Authors:  Han Wang; Bowen Cui; Huiying Sun; Fang Zhang; Jianan Rao; Ronghua Wang; Shuang Zhao; Shuhong Shen; Yu Liu
Journal:  Front Pediatr       Date:  2022-01-11       Impact factor: 3.418

6.  A platform for oncogenomic reporting and interpretation.

Authors:  Caralyn Reisle; Laura M Williamson; Erin Pleasance; Anna Davies; Brayden Pellegrini; Dustin W Bleile; Karen L Mungall; Eric Chuah; Martin R Jones; Yussanne Ma; Eleanor Lewis; Isaac Beckie; David Pham; Raphael Matiello Pletz; Amir Muhammadzadeh; Brandon M Pierce; Jacky Li; Ross Stevenson; Hansen Wong; Lance Bailey; Abbey Reisle; Matthew Douglas; Melika Bonakdar; Jessica M T Nelson; Cameron J Grisdale; Martin Krzywinski; Ana Fisic; Teresa Mitchell; Daniel J Renouf; Stephen Yip; Janessa Laskin; Marco A Marra; Steven J M Jones
Journal:  Nat Commun       Date:  2022-02-09       Impact factor: 14.919

7.  Epigenetic activation of the FLT3 gene by ZNF384 fusion confers a therapeutic susceptibility in acute lymphoblastic leukemia.

Authors:  Xujie Zhao; Ping Wang; Jonathan D Diedrich; Brandon Smart; Noemi Reyes; Satoshi Yoshimura; Jingliao Zhang; Wentao Yang; Kelly Barnett; Beisi Xu; Zhenhua Li; Xin Huang; Jiyang Yu; Kristine Crews; Allen Eng Juh Yeoh; Marina Konopleva; Chia-Lin Wei; Ching-Hon Pui; Daniel Savic; Jun J Yang
Journal:  Nat Commun       Date:  2022-09-14       Impact factor: 17.694
  7 in total

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