bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from Identification of IGF2 as Genomic Driver and Actionable Therapeutic Target in Hepatoblastoma
Authors: Abril-Fornaguera Jordi , Torrens Laura , Andreu-Oller Carmen , Carrillo-Reixach Juan , Rialdi Alex , Balaseviciute Ugne , Pinyol Roser , Montironi Carla , Haber Philipp K. , Del Río-Álvarez Álvaro , Domingo-Sàbat Montserrat , Royo Laura , Akers Nicholas K. , Willoughby Catherine E. , Peix Judit , Torres-Martin Miguel , Puigvehi Marc , Cairo Stefano , Childs Margaret , Maibach Rudolf , Alaggio Rita , Czauderna Piotr , Morland Bruce , Losic Bojan , Mazzaferro Vincenzo , Guccione Ernesto , Sia Daniela , Armengol Carolina , Llovet Josep M.
Published: April 2023

Abstract
Management of hepatoblastoma (HB), the most frequent pediatric liver cancer, is based on surgical resection and perioperative chemotherapy regimens. In this study, we aimed to identify actionable targets in HB and assess the efficacy of molecular therapies in preclinical models of HB. Paired tumor and adjacent tissues from 31 HBs and a validation set of 50 HBs were analyzed using RNA-seq, SNP, and methylation arrays. IGF2 overexpression was identified as the top targetable HB driver, present in 71% of HBs (22/31). IGF2high tumors displayed progenitor cell features and shorter recurrence-free survival. IGF2 overexpression was associated in 91% of cases with fetal promoter hypomethylation, ICR1 deregulation, 11p15.5 loss of heterozygosity or miR483-5p overexpression. The antitumor effect of xentuzumab (a monoclonal antibody targeting IGF1/2) alone or in combination with the conventional therapeutic agent cisplatin was assessed in HB cell lines, in PDX-derived HB organoids and in a xenograft HB murine model. The combination of xentuzumab with cisplatin showed strong synergistic antitumor effects in organoids and in IGF2high cell lines. In mice (n = 55), the combination induced a significant decrease in tumor volume and improved survival compared with cisplatin alone. These results suggest that IGF2 is an HB actionable driver and that, in preclinical models of HB, the combination of IGF1/2 inhibition with cisplatin induces superior antitumor effects than cisplatin monotherapy. Overall, our study provides a rationale for testing IGF2 inhibitors in combination with cisplatin in HB patients with IGF2 overexpression.
Abstract 561: Development of competing and non-competing fully human internalizing anti-Her2 monoclonal antibodies
Authors: Serrero Ginette , Yue Binbin , Dong Jianping , Dong Chun , Hayashi Jun
Published: April 2023

The human epidermal growth factor receptor (HER) family of receptors has been implicated in several human cancers. Among them, HER2 is overexpressed in several cancers with or without gene amplification with prognostic and predictive implications. In 15-30% of breast cancers, HER2 overexpression and amplification are associated with shorter disease-free and overall survivals along with resistance to hormonal agents as well as increased risk of brain metastasis. Two types of HER2 targeting have been developed: anti-HER2 monoclonal antibodies and small molecule tyrosine kinase inhibitors. Trastuzumab is a humanized anti-HER2 monoclonal antibody that binds to domain IV of HER2 extracellular segment and blocks its signaling. It is the first therapeutic antibody targeting Her2 overexpression approved by the FDA. More recently, two antibody drug conjugates using trastuzumab have been approved: Ado-Trastuzumab-Emtansine (Kadcyla) consisting of trastuzumab conjugated to the drug mertansine DM1 and fam-trastuzumab-deruxtecan-nhki (Enhertu to deliver the topoisomerase inhibitor deruxtecan. We are reporting here the development of fully human internalizing anti-Her2 antibodies that compete or not with trastuzumab for binding to Her2. These antibodies have been developed by immunizing fully human (TC-Mab mouse) mice with recombinant Her2 protein. After production of hybridoma secreting fully human immunoglobulins, the screening process included inhibition of binding of trastuzumab to Her2 by enzyme linked immunoassay and by Octet epitope binning as well as internalization assay. Several internalizing antibodies able to compete or not with trastuzumab and with high affinity (Kd ranging from 10−9 M to 10−12 M) were selected. They were next investigated for their ability to deliver a cytotoxic payload in HER2 overexpressing cells breast cancer cells such as SKBR3, BT474 and AU565. Two antibodies: one competing with trastuzumab and the other one non-competing were further characterized. Data related to these antibodies’ biochemical characteristics as well as their ability to inhibit proliferation in vitro and in vivo in mouse xenografts studies will be presented here. In conclusion, the use of fully human mice in our laboratory provides a powerful and attractive approach to develop fully human monoclonal antibodies against cancer targets allowing to by-pass the need for humanization and affinity maturation of antibodies.

Citation Format: Ginette Serrero, Binbin Yue, Jianping Dong, Chun Dong, Jun Hayashi. Development of competing and non-competing fully human internalizing anti-Her2 monoclonal antibodies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 561.
Supplementary Figure 1 from Nano-Architectural Alterations in Mucus Layer Fecal Colonocytes in Field Carcinogenesis: Potential for Screening
Authors: Roy Hemant K. , Damania Dhwanil P. , DelaCruz Mart , Kunte Dhananjay P. , Subramanian Hariharan , Crawford Susan E. , Tiwari Ashish K. , Wali Ramesh K. , Backman Vadim
Published: April 2023

PDF file - 94K, Fecal colonocytes disorder strength in the control (saline-injected) rats over time.
Supplementary Figure 2 from Curcumin Suppresses Proliferation of Colon Cancer Cells by Targeting CDK2
Authors: Lim Tae-Gyu , Lee Sung-Young , Huang Zunnan , Lim Do Young , Chen Hanyong , Jung Sung Keun , Bode Ann M. , Lee Ki Won , Dong Zigang
Published: April 2023

PDF file - 2098KB, In silico model of curcumin binding with CDKs at the ATP binding site. To better understand how curcumin interacts with CDK1/4, we performed a computational docking model using the Glide docking program from Schrodinger Suite 2013. The binding affinity between curcumin and CDK1 and 4 was predicted by a score of −8.94 and −7.63 kcal/mol, respectively. In the docked models, curcumin can bind at the ATP binding pocket of CDK1 or 4 and form some hydrogen bonds and other interactions. (Some images were generated with the UCSF Chimera program 3). A) Binding of curcumin at the ATP binding pocket of CDK1 or 4. B) Ligand Interaction Diagram (LID) for curcumin binding with CDKs. C) LID legend.
Supplementary Table S1 from Association of Prostate Cancer Risk Loci with Disease Aggressiveness and Prostate Cancer–Specific Mortality
Authors: Pomerantz Mark M. , Werner Lillian , Xie Wanling , Regan Meredith M. , Lee Gwo-Shu Mary , Sun Tong , Evan Carolyn , Petrozziello Gillian , Nakabayashi Mari , Oh William K. , Kantoff Philip W. , Freedman Matthew L.
Published: April 2023

Supplementary Table S1 from Association of Prostate Cancer Risk Loci with Disease Aggressiveness and Prostate Cancer–Specific Mortality
Supplementary Table 3 from Aberrant Methylation of RASGRF1 Is Associated with an Epigenetic Field Defect and Increased Risk of Gastric Cancer
Authors: Takamaru Hiroyuki , Yamamoto Eiichiro , Suzuki Hiromu , Nojima Masanori , Maruyama Reo , Yamano Hiro-o , Yoshikawa Kenjiro , Kimura Tomoaki , Harada Taku , Ashida Masami , Suzuki Ryo , Yamamoto Hiroyuki , Kai Masahiro , Tokino Takashi , Sugai Tamotsu , Imai Kohzoh , Toyota Minoru , Shinomura Yasuhisa
Published: April 2023

XLS file - 78K, Genes hypermethylated in background gastric mucosae from patients with diffuse type GC
Related Article from The Ultimate in Cancer Chemoprevention: Cancer Vaccines
Authors: Disis Mary L.
Published: April 2023

Related Article from The Ultimate in Cancer Chemoprevention: Cancer Vaccines
Perspective on This Article from Estrogen Stimulates the Expression of Mismatch Repair Gene hMLH1 in Colonic Epithelial Cells
Authors: Jin Peng , Lu Xiao-juan , Sheng Jian-qiu , Fu Lei , Meng Xiao-ming , Wang Xin , Shi Tai-ping , Li Shi-rong , Rao Jianyu
Published: April 2023

Perspective on This Article from Estrogen Stimulates the Expression of Mismatch Repair Gene hMLH1 in Colonic Epithelial Cells
Supplementary Material 8 from Gene Expression Profiling Predicts the Development of Oral Cancer
Authors: Saintigny Pierre , Zhang Li , Fan You-Hong , El-Naggar Adel K. , Papadimitrakopoulou Vassiliki A. , Feng Lei , Lee J. Jack , Kim Edward S. , Ki Hong Waun , Mao Li
Published: April 2023

Supplementary Material 8 from Gene Expression Profiling Predicts the Development of Oral Cancer
Supplementary Material 3 from Gene Expression Profiling Predicts the Development of Oral Cancer
Authors: Saintigny Pierre , Zhang Li , Fan You-Hong , El-Naggar Adel K. , Papadimitrakopoulou Vassiliki A. , Feng Lei , Lee J. Jack , Kim Edward S. , Ki Hong Waun , Mao Li
Published: April 2023

Supplementary Material 3 from Gene Expression Profiling Predicts the Development of Oral Cancer
Supplementary Material 2 from Gene Expression Profiling Predicts the Development of Oral Cancer
Authors: Saintigny Pierre , Zhang Li , Fan You-Hong , El-Naggar Adel K. , Papadimitrakopoulou Vassiliki A. , Feng Lei , Lee J. Jack , Kim Edward S. , Ki Hong Waun , Mao Li
Published: April 2023

Supplementary Material 2 from Gene Expression Profiling Predicts the Development of Oral Cancer
Perspective on this Article from Effects of Oral Contraceptives or a Gonadotropin-Releasing Hormone Agonist on Ovarian Carcinogenesis in Genetically Engineered Mice
Authors: Romero Iris L. , Gordon Ilyssa O. , Jagadeeswaran Sujatha , Mui Keeley L. , Lee Woo Seok , Dinulescu Daniela M. , Krausz Thomas N. , Kim Helen H. , Gilliam Melissa L. , Lengyel Ernst
Published: April 2023

Perspective on this Article from Effects of Oral Contraceptives or a Gonadotropin-Releasing Hormone Agonist on Ovarian Carcinogenesis in Genetically Engineered Mice
Supplementary Figure 1 from Chronic Social Isolation Is Associated with Metabolic Gene Expression Changes Specific to Mammary Adipose Tissue
Authors: Volden Paul A. , Wonder Erin L. , Skor Maxwell N. , Carmean Christopher M. , Patel Feenalie N. , Ye Honggang , Kocherginsky Masha , McClintock Martha K. , Brady Matthew J. , Conzen Suzanne D.
Published: April 2023

PDF file - 1999K, Tumor and behavior measurements from isolated and group housed mice between 11-17 weeks of age.
Supplementary Figure S2 from Oral Iloprost Improves Endobronchial Dysplasia in Former Smokers
Authors: Keith Robert L. , Blatchford Patrick J. , Kittelson John , Minna John D. , Kelly Karen , Massion Pierre P. , Franklin Wilbur A. , Mao Jenny , Wilson David O. , Merrick Daniel T. , Hirsch Fred R. , Kennedy Timothy C. , Bunn Paul A. , Geraci Mark W. , Miller York E.
Published: April 2023

Supplementary Figure S2 from Oral Iloprost Improves Endobronchial Dysplasia in Former Smokers
Supplementary Figure 2 from 6-Shogaol from Dried Ginger Inhibits Growth of Prostate Cancer Cells Both In Vitro and In Vivo through Inhibition of STAT3 and NF-κB Signaling
Authors: Saha Achinto , Blando Jorge , Silver Eric , Beltran Linda , Sessler Jonathan , DiGiovanni John
Published: April 2023

PDF - 119K, Supplemental Figure 2. G-SHO does not reduce survival of NMVP cells. Cells were treated with the indicated concentrations of G-SHO for 48 or 72 h and cell survival was measured by MTT assay. The data are presented as mean(plus/minus)SEM.
Perspective on This Article from A Pilot Study of Low-Cost, High-Resolution Microendoscopy as a Tool for Identifying Women with Cervical Precancer
Authors: Pierce Mark C. , Guan YaoYao , Quinn Mary Kate , Zhang Xun , Zhang Wen-Hua , Qiao You-Lin , Castle Philip , Richards-Kortum Rebecca
Published: April 2023

Perspective on This Article from A Pilot Study of Low-Cost, High-Resolution Microendoscopy as a Tool for Identifying Women with Cervical Precancer
Supplementary Figure 1 from Soy Isoflavone Supplementation for Breast Cancer Risk Reduction: A Randomized Phase II Trial
Authors: Khan Seema A. , Chatterton Robert T. , Michel Nancy , Bryk Michelle , Lee Oukseub , Ivancic David , Heinz Richard , Zalles Carola M. , Helenowski Irene B. , Jovanovic Borko D. , Franke Adrian A. , Bosland Maarten C. , Wang Jun , Hansen Nora M. , Bethke Kevin P. , Dew Alexander , Coomes Margerie , Bergan Raymond C.
Published: April 2023

PDF file - 65K, The correlation between Ct values of unamplified cDNA (assayed by qRT-PCR) and post-amplification samples (using TLDA) was examined in seven RNA samples with sufficient amount available for both methods.
Supplementary Figure 3 from 17β-Estradiol and Tamoxifen Prevent Gastric Cancer by Modulating Leukocyte Recruitment and Oncogenic Pathways in Helicobacter Pylori–Infected INS-GAS Male Mice
Authors: Sheh Alexander , Ge Zhongming , Parry Nicola M.A. , Muthupalani Sureshkumar , Rager Julia E. , Raczynski Arkadiusz R. , Mobley Melissa W. , McCabe Amanda F. , Fry Rebecca C. , Wang Timothy C. , Fox James G.
Published: April 2023

PDF file - 529K, Significant molecular networks affected by the common genes between E2 and TAM treatments (P=10-45). P-values represent the probability of these interactions occurring by chance.
Supplementary Table 3 from Aberrant DNA Methylation at Genes Associated with a Stem Cell-like Phenotype in Cholangiocarcinoma Tumors
Authors: Sriraksa Ruethairat , Zeller Constanze , Dai Wei , Siddiq Afshan , Walley Andrew J. , Limpaiboon Temduang , Brown Robert
Published: April 2023

PDF file - 337K, List of genes associated with hypermethylated CpG sites in CCA compared to adjacent normal samples.
Supplementary Table 1 from Aberrant DNA Methylation at Genes Associated with a Stem Cell-like Phenotype in Cholangiocarcinoma Tumors
Authors: Sriraksa Ruethairat , Zeller Constanze , Dai Wei , Siddiq Afshan , Walley Andrew J. , Limpaiboon Temduang , Brown Robert
Published: April 2023

PDF file - 57K, Histopathological features of CCA and matched adjacent normal samples.
Supplementary Figure S3 from Chemoprevention with Cyclooxygenase and Epidermal Growth Factor Receptor Inhibitors in Familial Adenomatous Polyposis Patients: mRNA Signatures of Duodenal Neoplasia
Authors: Delker Don A. , Wood Austin C. , Snow Angela K. , Samadder N. Jewel , Samowitz Wade S. , Affolter Kajsa E. , Boucher Kenneth M. , Pappas Lisa M. , Stijleman Inge J. , Kanth Priyanka , Byrne Kathryn R. , Burt Randall W. , Bernard Philip S. , Neklason Deborah W.
Published: April 2023

CD56 stained cells.
Supplementary Figure S2 from Chemoprevention with Cyclooxygenase and Epidermal Growth Factor Receptor Inhibitors in Familial Adenomatous Polyposis Patients: mRNA Signatures of Duodenal Neoplasia
Authors: Delker Don A. , Wood Austin C. , Snow Angela K. , Samadder N. Jewel , Samowitz Wade S. , Affolter Kajsa E. , Boucher Kenneth M. , Pappas Lisa M. , Stijleman Inge J. , Kanth Priyanka , Byrne Kathryn R. , Burt Randall W. , Bernard Philip S. , Neklason Deborah W.
Published: April 2023

Linear correlation of RNASeq (RPKM value) versus RT-qPCR of each gene transcript represented in Figure 3. Each data point represents a distinct sample used in the experiments described in this manuscript.
Supplementary Figure from Association between Statins and Incidence of Cancer in Patients with Dyslipidemia Using Large-Scale Health Insurance Claims Data
Authors: Maeda-Minami Ayako , Takagi Masayuki , Mano Yasunari , Ishikawa Hideki , Matsuyama Yutaka , Mutoh Michihiro
Published: April 2023

Supplementary Figure from Association between Statins and Incidence of Cancer in Patients with Dyslipidemia Using Large-Scale Health Insurance Claims Data
Supplementary Figure 5 from Identification of Luminal Breast Cancers That Establish a Tumor-Supportive Macroenvironment Defined by Proangiogenic Platelets and Bone Marrow–Derived Cells
Authors: Kuznetsov Hanna S. , Marsh Timothy , Markens Beth A. , Castaño Zafira , Greene-Colozzi April , Hay Samantha A. , Brown Victoria E. , Richardson Andrea L. , Signoretti Sabina , Battinelli Elisabeth M. , McAllister Sandra S.
Published: April 2023

PDF file - 490K, Images used for quantification of responding tumor vessel density under indicated systemic environments; analysis reveals enhanced vascularization in the instigating LBC environment
Supplementary Figure 6 from Gene Signatures Associated with Mouse Postnatal Hindbrain Neural Stem Cells and Medulloblastoma Cancer Stem Cells Identify Novel Molecular Mediators and Predict Human Medulloblastoma Molecular Classification
Authors: Corno Daniela , Pala Mauro , Cominelli Manuela , Cipelletti Barbara , Leto Ketty , Croci Laura , Barili Valeria , Brandalise Federico , Melzi Raffaella , Di Gregorio Alessandra , Sergi Lucia Sergi , Politi Letterio Salvatore , Piemonti Lorenzo , Bulfone Alessandro , Rossi Paola , Rossi Ferdinando , Consalez Gian Giacomo , Poliani Pietro Luigi , Galli Rossella
Published: April 2023

PDF file - 130K, EBF3 expression can be retrieved in silico in human MBs by exploiting publicly available human data sets
Supplementary Figure 5 from Senescence Sensitivity of Breast Cancer Cells Is Defined by Positive Feedback Loop between CIP2A and E2F1
Authors: Laine Anni , Sihto Harri , Come Christophe , Rosenfeldt Mathias T. , Zwolinska Aleksandra , Niemelä Minna , Khanna Anchit , Chan Edward K. , Kähäri Veli-Matti , Kellokumpu-Lehtinen Pirkko-Liisa , Sansom Owen J. , Evan Gerard I. , Junttila Melissa R. , Ryan Kevin M. , Marine Jean-Christophe , Joensuu Heikki , Westermarck Jukka
Published: April 2023

Supplementary Figure 5 PDF file - 82K, Prognostic value of CIP2A in advanced human breast cancer patient material and characterization of vinorelbine effects
Supplementary Figure 1 from Hypoxia-Dependent Modification of Collagen Networks Promotes Sarcoma Metastasis
Authors: Eisinger-Mathason T.S. Karin , Zhang Minsi , Qiu Qiong , Skuli Nicolas , Nakazawa Michael S. , Karakasheva Tatiana , Mucaj Vera , Shay Jessica E.S. , Stangenberg Lars , Sadri Navid , Puré Ellen , Yoon Sam S. , Kirsch David G. , Simon M. Celeste
Published: April 2023

Supplementary Figure 1 - PDF file 122K, Sarcoma cell lung colonization is dependent on HIF1{alpha} and PLOD2
Supplementary Figure 7 from The OPCML Tumor Suppressor Functions as a Cell Surface Repressor–Adaptor, Negatively Regulating Receptor Tyrosine Kinases in Epithelial Ovarian Cancer
Authors: McKie Arthur B. , Vaughan Sebastian , Zanini Elisa , Okon Imoh S. , Louis Louay , de Sousa Camila , Greene Mark I. , Wang Qiang , Agarwal Roshan , Shaposhnikov Dmitry , Wong Joshua L. C. , Gungor Hatice , Janczar Szymon , El-Bahrawy Mona , Lam Eric W-F. , Chayen Naomi E. , Gabra Hani
Published: April 2023

PDF file - 88K
Figure S5 from Autophagy Sustains Mitochondrial Glutamine Metabolism and Growth of BrafV600E–Driven Lung Tumors
Authors: Strohecker Anne M. , Guo Jessie Yanxiang , Karsli-Uzunbas Gizem , Price Sandy M. , Chen Guanghua Jim , Mathew Robin , McMahon Martin , White Eileen
Published: April 2023

Figure S5 - PDF file 1330K, Loss of ATG7 is associated with increased ?H2AX staining
Supplementary Figure S2 from Relief of Feedback Inhibition of HER3 Transcription by RAF and MEK Inhibitors Attenuates Their Antitumor Effects in BRAF-Mutant Thyroid Carcinomas
Authors: Montero-Conde Cristina , Ruiz-Llorente Sergio , Dominguez Jose M. , Knauf Jeffrey A. , Viale Agnes , Sherman Eric J. , Ryder Mabel , Ghossein Ronald A. , Rosen Neal , Fagin James A.
Published: April 2023

Supplementary Figure S2 PDF file - 112K, PLX4032-treated BRAF mutant thyroid cancer cells show induction or high basal expression of several RTKs compared to melanoma cell lines. A, gene expression profiles (Illumina HT-12 v4) of thyroid (SW1736; red) vs melanoma (SK-MEL-28; green) cells at the indicated times after treatment with 2 �gM PLX4032. Graphs represent the median profiles of gene clusters that are significantly different between the lines. B, table shows KEGG terms significantly over-represented in the stated gene clusters vs the rest of the genome by Fisher's exact test. The p-values are adjusted by FDR (B & H). C, Technical validation of differentially expressed RTKs identified by expression profiling analysis of SW1736 vs SK-3 MEL-28 cells. Cells were treated with 2 �gM PLX4032 for 1, 6 or 48 h. Points represent RTK/GAPDH Q-RT-PCR values of triplicates assays (mean +/- SD)
Supplementary Figures 1 - 5 from An Oncogenic NTRK Fusion in a Patient with Soft-Tissue Sarcoma with Response to the Tropomyosin-Related Kinase Inhibitor LOXO-101
Authors: Doebele Robert C. , Davis Lara E. , Vaishnavi Aria , Le Anh T. , Estrada-Bernal Adriana , Keysar Stephen , Jimeno Antonio , Varella-Garcia Marileila , Aisner Dara L. , Li Yali , Stephens Philip J. , Morosini Deborah , Tuch Brian B. , Fernandes Michele , Nanda Nisha , Low Jennifer A.
Published: April 2023

Supplementary Figure 1. Structure of LOXO-101. Supplementary Figure 2. Schematic for TRK-SHC1 proximity ligation assay (PLA). Supplementary Figure 3. Validation of the TRK-SHC1 PLA. Supplementary Figure 4. TRK and ALK PLA in an ALK+ tumor sample. Supplementary Figure 5. Serum tumor marker response.
Supplementary Figures from Haploinsufficiency of an RB–E2F1–Condensin II Complex Leads to Aberrant Replication and Aneuploidy
Authors: Coschi Courtney H. , Ishak Charles A. , Gallo David , Marshall Aren , Talluri Srikanth , Wang Jianxin , Cecchini Matthew J. , Martens Alison L. , Percy Vanessa , Welch Ian , Boutros Paul C. , Brown Grant W. , Dick Frederick A.
Published: April 2023

PDF file 3766K, Analysis of gammaH2AX distribution, chromosomal instability phenotypes in heterozygous cells, and verification of genotypes in human cells
Supplementary Table S1 from EPHA2 Is a Mediator of Vemurafenib Resistance and a Novel Therapeutic Target in Melanoma
Authors: Miao Benchun , Ji Zhenyu , Tan Li , Taylor Michael , Zhang Jianming , Choi Hwan Geun , Frederick Dennie T. , Kumar Raj , Wargo Jennifer A. , Flaherty Keith T. , Gray Nathanael S. , Tsao Hensin
Published: April 2023

Supplementary Table S1. The information of the melanoma patients for EphA2 analysis.
Supplementary Table 2 from MEK-Dependent Negative Feedback Underlies BCR–ABL-Mediated Oncogene Addiction
Authors: Asmussen Jennifer , Lasater Elisabeth A. , Tajon Cheryl , Oses-Prieto Juan , Jun Young-wook , Taylor Barry S. , Burlingame Alma , Craik Charles S. , Shah Neil P.
Published: April 2023

XLSX file 50K, DAVID analysis of durably dephosphorylated peptides
Supplementary Figure 2 from A Diverse Array of Cancer-Associated MTOR Mutations Are Hyperactivating and Can Predict Rapamycin Sensitivity
Authors: Grabiner Brian C. , Nardi Valentina , Birsoy Kıvanç , Possemato Richard , Shen Kuang , Sinha Sumi , Jordan Alexander , Beck Andrew H. , Sabatini David M.
Published: April 2023

PDF file 106K, S2215Y mTOR activates mTORC1 signaling similar to WT and mutant PI3K-p110alpha
Supplementary Table S1 from RNA Helicase A Is a Downstream Mediator of KIF1Bβ Tumor-Suppressor Function in Neuroblastoma
Authors: Chen Zhi Xiong , Wallis Karin , Fell Stuart M. , Sobrado Veronica R. , Hemmer Marie C. , Ramsköld Daniel , Hellman Ulf , Sandberg Rickard , Kenchappa Rajappa S. , Martinson Tommy , Johnsen John I. , Kogner Per , Schlisio Susanne
Published: April 2023

PDF file 53K, Table S1, related to Figure 5. List of genes generated by DESeq analysis of RNA-SEQ results shown in Figure 5
Supplementary Figures 1 - 8 from Multifunctional T-cell Analyses to Study Response and Progression in Adoptive Cell Transfer Immunotherapy
Authors: Ma Chao , Cheung Ann F. , Chodon Thinle , Koya Richard C. , Wu Zhongqi , Ng Charles , Avramis Earl , Cochran Alistair J. , Witte Owen N. , Baltimore David , Chmielowski Bartosz , Economou James S. , Comin-Anduix Begonya , Ribas Antoni , Heath James R.
Published: April 2023

PDF file - 1292K, Study scheme, assay validation, functional changes of patients F5-2 and F5-8.
Supplementary Tables S1 and S2 from Reduced NF1 Expression Confers Resistance to EGFR Inhibition in Lung Cancer
Authors: de Bruin Elza C. , Cowell Catherine , Warne Patricia H. , Jiang Ming , Saunders Rebecca E. , Melnick Mary Ann , Gettinger Scott , Walther Zenta , Wurtz Anna , Heynen Guus J. , Heideman Daniëlle A.M. , Gómez-Román Javier , García-Castaño Almudena , Gong Yixuan , Ladanyi Marc , Varmus Harold , Bernards René , Smit Egbert F. , Politi Katerina , Downward Julian
Published: April 2023

XLSX file 2064K, Table S1. Tabulated complete data from the first genome-wide screen. Table S2. Tabulated data from the 242 siRNA pools identified in the first genome-wide screen with the Z-scores obtained in the repeat genome-wide screen
Supplementary Table 4 from Cell-Free DNA Next-Generation Sequencing in Pancreatobiliary Carcinomas
Authors: Zill Oliver A. , Greene Claire , Sebisanovic Dragan , Siew Lai Mun , Leng Jim , Vu Mary , Hendifar Andrew E. , Wang Zhen , Atreya Chloe E. , Kelley Robin K. , Van Loon Katherine , Ko Andrew H. , Tempero Margaret A. , Bivona Trever G. , Munster Pamela N. , Talasaz AmirAli , Collisson Eric A.
Published: April 2023

List of genes and exons captured in the Guardant360 cfDNA sequencing test.
Supplementary Figure S3 from Mutant N-RAS Protects Colorectal Cancer Cells from Stress-Induced Apoptosis and Contributes to Cancer Development and Progression
Authors: Wang Yufang , Velho Sérgia , Vakiani Efsevia , Peng Shouyong , Bass Adam J. , Chu Gerald C. , Gierut Jessica , Bugni James M. , Der Channing J. , Philips Mark , Solit David B. , Haigis Kevin M.
Published: April 2023

Supplementary Figure S3 PDF file 66K,Additional data related to the proliferative and apoptotic phenotypes of CRC cells expressing mutant Ras
Supplementary Figure 4 from Mcl-1 and FBW7 Control a Dominant Survival Pathway Underlying HDAC and Bcl-2 Inhibitor Synergy in Squamous Cell Carcinoma
Authors: He Lei , Torres-Lockhart Kristine , Forster Nicole , Ramakrishnan Saranya , Greninger Patricia , Garnett Mathew J. , McDermott Ultan , Rothenberg Stephen M. , Benes Cyril H. , Ellisen Leif W.
Published: April 2023

Supplementary Figure 4 PDF file 107K, Strong synergy between vorinostat and ABT-737 in vitro and in vivo
Supplementary Table 2 from Combined Inhibition of MAP Kinase and KIT Signaling Synergistically Destabilizes ETV1 and Suppresses GIST Tumor Growth
Authors: Ran Leili , Sirota Inna , Cao Zhen , Murphy Devan , Chen Yuedan , Shukla Shipra , Xie Yuanyuan , Kaufmann Michael C. , Gao Dong , Zhu Sinan , Rossi Ferdinando , Wongvipat John , Taguchi Takahiro , Tap William D. , Mellinghoff Ingo K. , Besmer Peter , Antonescu Cristina R. , Chen Yu , Chi Ping
Published: April 2023

Supplementary Table 2: Gene sets enriched among genes DOWNregulated by tamoxifen treatment (Etv1 ablation) in murine GIST-like tumors.
Supplemental Figures S1-S5, Table S1 from Development of siRNA Payloads to Target KRAS-Mutant Cancer
Authors: Yuan Tina L. , Fellmann Christof , Lee Chih-Shia , Ritchie Cayde D. , Thapar Vishal , Lee Liam C. , Hsu Dennis J. , Grace Danielle , Carver Joseph O. , Zuber Johannes , Luo Ji , McCormick Frank , Lowe Scott W.
Published: April 2023

Supplemental Figure S1. Sensor-based generation of a functionally validated sh/siRNA library targeting Ras pathway genes. Figure S2. Validation of Sensor siRNAs targeting components in the MAPK pathway. Figure S3. Dose dependent off-target effects of sh/siRNAs. Figure S4. Sensor siRNA pooling effects. Figure S5. In vivo fluorescence reporter system. Table S1. Correlation of library reads and Sensor score.
Supplementary Tables from Identification of Targetable FGFR Gene Fusions in Diverse Cancers
Authors: Wu Yi-Mi , Su Fengyun , Kalyana-Sundaram Shanker , Khazanov Nickolay , Ateeq Bushra , Cao Xuhong , Lonigro Robert J. , Vats Pankaj , Wang Rui , Lin Su-Fang , Cheng Ann-Joy , Kunju Lakshmi P. , Siddiqui Javed , Tomlins Scott A. , Wyngaard Peter , Sadis Seth , Roychowdhury Sameek , Hussain Maha H. , Feng Felix Y. , Zalupski Mark M. , Talpaz Moshe , Pienta Kenneth J. , Rhodes Daniel R. , Robinson Dan R. , Chinnaiyan Arul M.
Published: April 2023

Supplementary Tables - PDF file 753K, Supplementary Tables S1-S15 include transcriptome and exome sequencing results for the FGFR fusion positive index cases, and summaries of sequencing cohorts
Supplementary Figure 5 from A Small-Molecule c-Rel Inhibitor Reduces Alloactivation of T Cells without Compromising Antitumor Activity
Authors: Shono Yusuke , Tuckett Andrea Z. , Ouk Samedy , Liou Hsiou-Chi , Altan-Bonnet Grégoire , Tsai Jennifer J. , Oyler Jennifer E. , Smith Odette M. , West Mallory L. , Singer Natalie V. , Doubrovina Ekaterina , Pankov Dmitry , Undhad Chandresh V. , Murphy George F. , Lezcano Cecilia , Liu Chen , O'Reilly Richard J. , van den Brink Marcel R.M. , Zakrzewski Johannes L.
Published: April 2023

PDF file 135KB, Non-specific negative effect of DMSO on the GVT activity of T-cells
Supplementary Figure 2 from A Small-Molecule c-Rel Inhibitor Reduces Alloactivation of T Cells without Compromising Antitumor Activity
Authors: Shono Yusuke , Tuckett Andrea Z. , Ouk Samedy , Liou Hsiou-Chi , Altan-Bonnet Grégoire , Tsai Jennifer J. , Oyler Jennifer E. , Smith Odette M. , West Mallory L. , Singer Natalie V. , Doubrovina Ekaterina , Pankov Dmitry , Undhad Chandresh V. , Murphy George F. , Lezcano Cecilia , Liu Chen , O'Reilly Richard J. , van den Brink Marcel R.M. , Zakrzewski Johannes L.
Published: April 2023

PDF file 191K, Recipients of c-Rel-deficient T-cells exhibit reduced damage of GVHD target organs
Supplementary Figure S6 from Comprehensive Genomic Analysis of Rhabdomyosarcoma Reveals a Landscape of Alterations Affecting a Common Genetic Axis in Fusion-Positive and Fusion-Negative Tumors
Authors: Shern Jack F. , Chen Li , Chmielecki Juliann , Wei Jun S. , Patidar Rajesh , Rosenberg Mara , Ambrogio Lauren , Auclair Daniel , Wang Jianjun , Song Young K. , Tolman Catherine , Hurd Laura , Liao Hongling , Zhang Shile , Bogen Dominik , Brohl Andrew S. , Sindiri Sivasish , Catchpoole Daniel , Badgett Thomas , Getz Gad , Mora Jaume , Anderson James R. , Skapek Stephen X. , Barr Frederic G. , Meyerson Matthew , Hawkins Douglas S. , Khan Javed
Published: April 2023

PDF file 145K, Recurrent Recurrence peaks of focal copy number change
Figure S6 from Mechanism-Based Epigenetic Chemosensitization Therapy of Diffuse Large B-Cell Lymphoma
Authors: Clozel Thomas , Yang ShaoNing , Elstrom Rebecca L. , Tam Wayne , Martin Peter , Kormaksson Matthias , Banerjee Samprit , Vasanthakumar Aparna , Culjkovic Biljana , Scott David W. , Wyman Sarah , Leser Micheal , Shaknovich Rita , Chadburn Amy , Tabbo Fabrizio , Godley Lucy A. , Gascoyne Randy D. , Borden Katherine L. , Inghirami Giorgio , Leonard John P. , Melnick Ari , Cerchietti Leandro
Published: April 2023

Figure S6 - PDF file 110K, Daunorubicin uptake in DLBCL cell lines
Supplementary Table S5 from Systematic Interrogation of 3q26 Identifies TLOC1 and SKIL as Cancer Drivers
Authors: Hagerstrand Daniel , Tong Alexander , Schumacher Steven E. , Ilic Nina , Shen Rhine R. , Cheung Hiu Wing , Vazquez Francisca , Shrestha Yashaswi , Kim So Young , Giacomelli Andrew O. , Rosenbluh Joseph , Schinzel Anna C. , Spardy Nicole A. , Barbie David A. , Mermel Craig H. , Weir Barbara A. , Garraway Levi A. , Tamayo Pablo , Mesirov Jill P. , Beroukhim Rameen , Hahn William C.
Published: April 2023

Supplementary Table S5 - XLSX file 48K, Intersection of gene expression signatures that correlate with either high SKIL or low SMAD4 gene expression
Supplementary Figure 4 from Dominant Role of Oncogene Dosage and Absence of Tumor Suppressor Activity in Nras-Driven Hematopoietic Transformation
Authors: Xu Jin , Haigis Kevin M. , Firestone Ari J. , McNerney Megan E. , Li Qing , Davis Elizabeth , Chen Shann-Ching , Nakitandwe Joy , Downing James , Jacks Tyler , Le Beau Michelle M. , Shannon Kevin
Published: April 2023

Supplementary Figure 4 - PDF file 64K, Data showing the molecular Analysis of AMLs from NrasG12D/+ Mice
Supplementary Table S1 from Polarization of Tissue-Resident TFH-Like Cells in Human Hepatoma Bridges Innate Monocyte Inflammation and M2b Macrophage Polarization
Authors: Chen Min-Min , Xiao Xiao , Lao Xiang-Ming , Wei Yuan , Liu Rui-Xian , Zeng Qiu-Hui , Wang Jun-Cheng , Ouyang Fang-Zhu , Chen Dong-Ping , Chan Ka-Wo , Shi Dai-Chao , Zheng Limin , Kuang Dong-Ming
Published: April 2023

Supplementary Table S1. Characteristics of Patients Contributing Samples in Figures 1, 2, 4 and 5.
Supplementary Table S2 from Targeting YAP-Dependent MDSC Infiltration Impairs Tumor Progression
Authors: Wang Guocan , Lu Xin , Dey Prasenjit , Deng Pingna , Wu Chia Chin , Jiang Shan , Fang Zhuangna , Zhao Kun , Konaparthi Ramakrishna , Hua Sujun , Zhang Jianhua , Li-Ning-Tapia Elsa M. , Kapoor Avnish , Wu Chang-Jiun , Patel Neelay Bhaskar , Guo Zhenglin , Ramamoorthy Vandhana , Tieu Trang N. , Heffernan Tim , Zhao Di , Shang Xiaoying , Khadka Sunada , Hou Pingping , Hu Baoli , Jin Eun-Jung , Yao Wantong , Pan Xiaolu , Ding Zhihu , Shi Yanxia , Li Liren , Chang Qing , Troncoso Patricia , Logothetis Christopher J. , McArthur Mark J. , Chin Lynda , Wang Y. Alan , DePinho Ronald A.
Published: April 2023

Detailed pathology description of the Gr1 treated mice and Cxcr2 inhibitor treated mice.
Supplementary Figure S7 from Suppression of Metastases Using a New Lymphocyte Checkpoint Target for Cancer Immunotherapy
Authors: Blake Stephen J. , Stannard Kimberley , Liu Jing , Allen Stacey , Yong Michelle C.R. , Mittal Deepak , Aguilera Amelia Roman , Miles John J. , Lutzky Viviana P. , de Andrade Lucas Ferrari , Martinet Ludovic , Colonna Marco , Takeda Kazuyoshi , Kühnel Florian , Gurlevik Engin , Bernhardt Günter , Teng Michele W.L. , Smyth Mark J.
Published: April 2023

Supplementary Figure S7. Reduction in B16F10 lung metastases by anti-CD96/anti-PD1 is dependent on NK cells.
Supplementary Table S6 from Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles
Authors: Kim Eejung , Ilic Nina , Shrestha Yashaswi , Zou Lihua , Kamburov Atanas , Zhu Cong , Yang Xiaoping , Lubonja Rakela , Tran Nancy , Nguyen Cindy , Lawrence Michael S. , Piccioni Federica , Bagul Mukta , Doench John G. , Chouinard Candace R. , Wu Xiaoyun , Hogstrom Larson , Natoli Ted , Tamayo Pablo , Horn Heiko , Corsello Steven M. , Lage Kasper , Root David E. , Subramanian Aravind , Golub Todd R. , Getz Gad , Boehm Jesse S. , Hahn William C.
Published: April 2023

Comparison to in silico methods.
Supplementary Figure S2 from Loss of PTEN Promotes Resistance to T Cell–Mediated Immunotherapy
Authors: Peng Weiyi , Chen Jie Qing , Liu Chengwen , Malu Shruti , Creasy Caitlin , Tetzlaff Michael T. , Xu Chunyu , McKenzie Jodi A. , Zhang Chunlei , Liang Xiaoxuan , Williams Leila J. , Deng Wanleng , Chen Guo , Mbofung Rina , Lazar Alexander J. , Torres-Cabala Carlos A. , Cooper Zachary A. , Chen Pei-Ling , Tieu Trang N. , Spranger Stefani , Yu Xiaoxing , Bernatchez Chantale , Forget Marie-Andree , Haymaker Cara , Amaria Rodabe , McQuade Jennifer L. , Glitza Isabella C. , Cascone Tina , Li Haiyan S. , Kwong Lawrence N. , Heffernan Timothy P. , Hu Jianhua , Bassett Roland L. , Bosenberg Marcus W. , Woodman Scott E. , Overwijk Willem W. , Lizée Gregory , Roszik Jason , Gajewski Thomas F. , Wargo Jennifer A. , Gershenwald Jeffrey E. , Radvanyi Laszlo , Davies Michael A. , Hwu Patrick
Published: April 2023

Lymphocyte infiltration status and the expression level of MHC class I in tumors from patients with melanoma.
Supplementary Table S1 from Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles
Authors: Kim Eejung , Ilic Nina , Shrestha Yashaswi , Zou Lihua , Kamburov Atanas , Zhu Cong , Yang Xiaoping , Lubonja Rakela , Tran Nancy , Nguyen Cindy , Lawrence Michael S. , Piccioni Federica , Bagul Mukta , Doench John G. , Chouinard Candace R. , Wu Xiaoyun , Hogstrom Larson , Natoli Ted , Tamayo Pablo , Horn Heiko , Corsello Steven M. , Lage Kasper , Root David E. , Subramanian Aravind , Golub Todd R. , Getz Gad , Boehm Jesse S. , Hahn William C.
Published: April 2023

Genes and alleles selected for the project.
Supplementary Figures 1 - 16 from ARID1A Deficiency Impairs the DNA Damage Checkpoint and Sensitizes Cells to PARP Inhibitors
Authors: Shen Jianfeng , Peng Yang , Wei Leizhen , Zhang Wei , Yang Lin , Lan Li , Kapoor Prabodh , Ju Zhenlin , Mo Qianxing , Shih Ie-Ming , Uray Ivan P. , Wu Xiangwei , Brown Powel H. , Shen Xuetong , Mills Gordon B. , Peng Guang
Published: April 2023

Supplementary Figure 1. Proteomic analysis of ATR-interacting proteins. Supplementary Figure 2. ARID1A interacts with ATR in MDA-MB-231 Cells. Supplementary Figure 3. ARID1A recruitment to I-SceI-induced DSBs analyzed by ChIP assay. Supplementary Figure 4. Schematic diagram of KillerRed system in U2OS TRE cells. Supplementary Figure 5. Expression of ARID1A mutants. Supplementary Figure 6. Knockdown BRG1, BRM, or ARID1A in U2OS cells. Supplementary Figure 7. ARID1A depletion did not affect the number of ATM foci after exposure to IR. Supplementary Figure 8. (A) ARID1A depletion did not affect the presence of DSBs after exposure to IR. Supplementary Figure 9. ARID1A depletion did not affect the expression of DSB end resection factors. Supplementary Figure 10. ARID1A depletion did not affect the expression of ATM and MRN complex. Supplementary Figure 11. (A) ARID1A depletion sensitize MDA-MB-231 cells to PARP inhibitor. Supplementary Figure 12. ARID1A knockdown sensitizes ovarian cancer cell line HOC8 to PARP inhibitor. Supplementary Figure 13. Ovarian cancer cells with lower expression levels of ARID1A are more sensitive to PARP inhibitor treatment than cells with higher ARID1A expression levels. Supplementary Figure 14. Rescuing experiments were conducted with ARID1A wild-type and mutant constructs (deletion mutants/patient-derived mutants). Supplementary Figure 15. ATR inhibitor sensitizes cells to PAPR Inhibitor treatment. Supplementary Figure 16. Proposed model for ARID1A function in DSB End Resection and repair.
Supplementary Methods, Figure Legends from Macrophage PI3Kγ Drives Pancreatic Ductal Adenocarcinoma Progression
Authors: Kaneda Megan M. , Cappello Paola , Nguyen Abraham V. , Ralainirina Natacha , Hardamon Chanae R. , Foubert Philippe , Schmid Michael C. , Sun Ping , Mose Evangeline , Bouvet Michael , Lowy Andrew M. , Valasek Mark A. , Sasik Roman , Novelli Francesco , Hirsch Emilio , Varner Judith A.
Published: April 2023

Supplementary Methods, Figure Legends
Supplementary Table S7 from DNMT3A Haploinsufficiency Transforms FLT3ITD Myeloproliferative Disease into a Rapid, Spontaneous, and Fully Penetrant Acute Myeloid Leukemia
Authors: Meyer Sara E. , Qin Tingting , Muench David E. , Masuda Kohei , Venkatasubramanian Meenakshi , Orr Emily , Suarez Lauren , Gore Steven D. , Delwel Ruud , Paietta Elisabeth , Tallman Martin S. , Fernandez Hugo , Melnick Ari , Le Beau Michelle M. , Kogan Scott , Salomonis Nathan , Figueroa Maria E. , Grimes H. Leighton
Published: April 2023

Clinical mutation data on primary human AML samples.
Supplementary Table S1 from DNMT3A Haploinsufficiency Transforms FLT3ITD Myeloproliferative Disease into a Rapid, Spontaneous, and Fully Penetrant Acute Myeloid Leukemia
Authors: Meyer Sara E. , Qin Tingting , Muench David E. , Masuda Kohei , Venkatasubramanian Meenakshi , Orr Emily , Suarez Lauren , Gore Steven D. , Delwel Ruud , Paietta Elisabeth , Tallman Martin S. , Fernandez Hugo , Melnick Ari , Le Beau Michelle M. , Kogan Scott , Salomonis Nathan , Figueroa Maria E. , Grimes H. Leighton
Published: April 2023

Peripheral blood findings in moribund Flt3ITD/ITD;Dnmt3afl/fl MxCre mice and age-matched Flt3ITD/ITD;Dnmt3afl/fl and wild-type control mice.
Supplementary Table 1 from Chronic Myelogenous Leukemia– Initiating Cells Require Polycomb Group Protein EZH2
Authors: Xie Huafeng , Peng Cong , Huang Jialiang , Li Bin E. , Kim Woojin , Smith Elenoe C. , Fujiwara Yuko , Qi Jun , Cheloni Giulia , Das Partha P. , Nguyen Minh , Li Shaoguang , Bradner James E. , Orkin Stuart H.
Published: April 2023

List of gene sets.
Supplementary Figure 7 from Combined EGFR/MEK Inhibition Prevents the Emergence of Resistance in EGFR-Mutant Lung Cancer
Authors: Tricker Erin M. , Xu Chunxiao , Uddin Sharmeen , Capelletti Marzia , Ercan Dalia , Ogino Atsuko , Pratilas Christine A. , Rosen Neal , Gray Nathanael S. , Wong Kwok-Kin , Jänne Pasi A.
Published: April 2023

Supplementary Figure S7. Effect of Torin2 on PC9 and PC9 derived WZ4002 + trametinib resistant cell lines. (A) Inhibition of S6 was assessed at the indicated concentration by immunoblot. (B) Viability was assessed by MTS assay after 72 hours of the indicated concentration of Torin2 (mean +/- SD, n = 6 technical replicates). (C) PC9 W+T resistant clone was treated with WZ4002 + trametinib for 72 hours and viability was assessed by MTS (mean +/- SD, n = 6 technical replicates).
Supplementary Figure 4 from Cancer Immunotherapy with Immunomodulatory Anti-CD137 and Anti–PD-1 Monoclonal Antibodies Requires BATF3-Dependent Dendritic Cells
Authors: Sánchez-Paulete Alfonso R. , Cueto Francisco J. , Martínez-López María , Labiano Sara , Morales-Kastresana Aizea , Rodríguez-Ruiz María E. , Jure-Kunkel Maria , Azpilikueta Arantza , Aznar M. Angela , Quetglas José I. , Sancho David , Melero Ignacio
Published: April 2023

Combinations of immunomodulatory anti-CD137 and anti-PD-1 mAbs synergize with sFlt3L and poly-ICLC against grafted B16F10 and B16-OVA melanomas.
Supplementary Figure 2 from Combined EGFR/MEK Inhibition Prevents the Emergence of Resistance in EGFR-Mutant Lung Cancer
Authors: Tricker Erin M. , Xu Chunxiao , Uddin Sharmeen , Capelletti Marzia , Ercan Dalia , Ogino Atsuko , Pratilas Christine A. , Rosen Neal , Gray Nathanael S. , Wong Kwok-Kin , Jänne Pasi A.
Published: April 2023

Supplementary Figure S2. Comparison of WZ4002 + crizotinib and WZ4002 + trametinib combinations in TKI resistant cell lines. HCC827 GR6 and HCC827 + HGF were treated with DMSO control (Media), 100 nM WZ4002, 30 nM trametinib, 100 nM crizotinib or WZ4002 combinations weekly. Positive wells were tallied weekly (mean +/- SD, n = 3 biological replicates of 60 wells each). Arrow indicates that confluence was not reached at 9 weeks.
Supplementary Table 5 from Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine
Authors: Pauli Chantal , Hopkins Benjamin D. , Prandi Davide , Shaw Reid , Fedrizzi Tarcisio , Sboner Andrea , Sailer Verena , Augello Michael , Puca Loredana , Rosati Rachele , McNary Terra J. , Churakova Yelena , Cheung Cynthia , Triscott Joanna , Pisapia David , Rao Rema , Mosquera Juan Miguel , Robinson Brian , Faltas Bishoy M. , Emerling Brooke E. , Gadi Vijayakrishna K. , Bernard Brady , Elemento Olivier , Beltran Himisha , Demichelis Francesca , Kemp Christopher J. , Grandori Carla , Cantley Lewis C. , Rubin Mark A.
Published: April 2023

Supplementary Table 5. Patient B Single and buparlisib Combination High Throughput Drug Screen.
Supplementary Figures 1 - 6 from Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine
Authors: Pauli Chantal , Hopkins Benjamin D. , Prandi Davide , Shaw Reid , Fedrizzi Tarcisio , Sboner Andrea , Sailer Verena , Augello Michael , Puca Loredana , Rosati Rachele , McNary Terra J. , Churakova Yelena , Cheung Cynthia , Triscott Joanna , Pisapia David , Rao Rema , Mosquera Juan Miguel , Robinson Brian , Faltas Bishoy M. , Emerling Brooke E. , Gadi Vijayakrishna K. , Bernard Brady , Elemento Olivier , Beltran Himisha , Demichelis Francesca , Kemp Christopher J. , Grandori Carla , Cantley Lewis C. , Rubin Mark A.
Published: April 2023

Supplementary Figures 1 - 6
Supplemental Methods, Supplemental Tables 1-2, Supplemental Figures 1-4 from AACR Project GENIE: Powering Precision Medicine through an International Consortium
Authors: André Fabrice , Arnedos Monica , Baras Alexander S. , Baselga José , Bedard Philippe L. , Berger Michael F. , Bierkens Mariska , Calvo Fabien , Cerami Ethan , Chakravarty Debyani , Dang Kristen K. , Davidson Nancy E. , Del Vecchio Fitz Catherine , Dogan Semih , DuBois Raymond N. , Ducar Matthew D. , Futreal P. Andrew , Gao Jianjiong , Garcia Francisco , Gardos Stu , Gocke Christopher D. , Gross Benjamin E. , Guinney Justin , Heins Zachary J. , Hintzen Stephanie , Horlings Hugo , Hudeček Jan , Hyman David M. , Kamel-Reid Suzanne , Kandoth Cyriac , Kinyua Walter , Kumari Priti , Kundra Ritika , Ladanyi Marc , Lefebvre Céline , LeNoue-Newton Michele L. , Lepisto Eva M. , Levy Mia A. , Lindeman Neal I. , Lindsay James , Liu David , Lu Zhibin , MacConaill Laura E. , Maurer Ian , Maxwell David S. , Meijer Gerrit A. , Meric-Bernstam Funda , Micheel Christine M. , Miller Clinton , Mills Gordon , Moore Nathanael D. , Nederlof Petra M. , Omberg Larsson , Orechia John A. , Park Ben Ho , Pugh Trevor J. , Reardon Brendan , Rollins Barrett J. , Routbort Mark J. , Sawyers Charles L. , Schrag Deborah , Schultz Nikolaus , Shaw Kenna R Mills , Shivdasani Priyanka , Siu Lillian L. , Solit David B. , Sonke Gabe S. , Soria Jean Charles , Sripakdeevong Parin , Stickle Natalie H. , Stricker Thomas P. , Sweeney Shawn M. , Taylor Barry S. , ten Hoeve Jelle J. , Thomas Stacy B. , Van Allen Eliezer M. , Van 'T Veer Laura J. , van de Velde Tony , van Tinteren Harm , Velculescu Victor E. , Virtanen Carl , Voest Emile E. , Wang Lucy L. , Wathoo Chetna , Watt Stuart , Yu Celeste , Yu Thomas V. , Yu Emily , Zehir Ahmet , Zhang Hongxin
Published: April 2023

Supplemental Methods. Supplemental Table 1: Ã¢â,¬â€¹Genomic Data Characterization by Center. Supplemental Table 2: Ã¢â,¬â€¹Gene Panels Submitted by Each Center. Figure S1: Number of putative germline SNPs per sample, before and after uniform germline filtering. Figure S2Ã¢â,¬â€¹. Distribution of total somatic mutation burden per sample stratified by sequencing panel. Figure S3: Ã¢â,¬â€¹Log-scale comparison of mutation frequencies at hotspot sites between GENIE (data aggregated from all sequencing panels) and cancerhotspots.org (CHS) using a binomial test. Figure S4:Ã¢â,¬â€¹ Comparison of mutation frequencies at hotspot sites in each GENIE sequencing panel with cancerhotspots.org (CHS) using a binomial test.
Supplemental File 1 from AACR Project GENIE: Powering Precision Medicine through an International Consortium
Authors: André Fabrice , Arnedos Monica , Baras Alexander S. , Baselga José , Bedard Philippe L. , Berger Michael F. , Bierkens Mariska , Calvo Fabien , Cerami Ethan , Chakravarty Debyani , Dang Kristen K. , Davidson Nancy E. , Del Vecchio Fitz Catherine , Dogan Semih , DuBois Raymond N. , Ducar Matthew D. , Futreal P. Andrew , Gao Jianjiong , Garcia Francisco , Gardos Stu , Gocke Christopher D. , Gross Benjamin E. , Guinney Justin , Heins Zachary J. , Hintzen Stephanie , Horlings Hugo , Hudeček Jan , Hyman David M. , Kamel-Reid Suzanne , Kandoth Cyriac , Kinyua Walter , Kumari Priti , Kundra Ritika , Ladanyi Marc , Lefebvre Céline , LeNoue-Newton Michele L. , Lepisto Eva M. , Levy Mia A. , Lindeman Neal I. , Lindsay James , Liu David , Lu Zhibin , MacConaill Laura E. , Maurer Ian , Maxwell David S. , Meijer Gerrit A. , Meric-Bernstam Funda , Micheel Christine M. , Miller Clinton , Mills Gordon , Moore Nathanael D. , Nederlof Petra M. , Omberg Larsson , Orechia John A. , Park Ben Ho , Pugh Trevor J. , Reardon Brendan , Rollins Barrett J. , Routbort Mark J. , Sawyers Charles L. , Schrag Deborah , Schultz Nikolaus , Shaw Kenna R Mills , Shivdasani Priyanka , Siu Lillian L. , Solit David B. , Sonke Gabe S. , Soria Jean Charles , Sripakdeevong Parin , Stickle Natalie H. , Stricker Thomas P. , Sweeney Shawn M. , Taylor Barry S. , ten Hoeve Jelle J. , Thomas Stacy B. , Van Allen Eliezer M. , Van 'T Veer Laura J. , van de Velde Tony , van Tinteren Harm , Velculescu Victor E. , Virtanen Carl , Voest Emile E. , Wang Lucy L. , Wathoo Chetna , Watt Stuart , Yu Celeste , Yu Thomas V. , Yu Emily , Zehir Ahmet , Zhang Hongxin
Published: April 2023

AACR GENIE Data Guide