bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Fig 1 from Synthetic Lethal Screens Reveal Cotargeting FAK and MEK as a Multimodal Precision Therapy for GNAQ-Driven Uveal Melanoma
Authors: Paradis Justine S. , Acosta Monica , Saddawi-Konefka Robert , Kishore Ayush , Lubrano Simone , Gomes Frederico , Arang Nadia , Tiago Manoela , Coma Silvia , Wu Xingyu , Ford Kyle , Day Chi-Ping , Merlino Glenn , Mali Prashant , Pachter Jonathan A. , Sato Takami , Aplin Andrew E. , Gutkind J. Silvio
Published: April 2023

Supplementary figure S1. Synthetic lethality of FAK and ERK/MAPK pathway inhibition.
Supplementary Figure 1 from Vertical Pathway Inhibition Overcomes Adaptive Feedback Resistance to KRASG12C Inhibition
Authors: Ryan Meagan B. , Fece de la Cruz Ferran , Phat Sarah , Myers David T. , Wong Edmond , Shahzade Heather A. , Hong Catriona B. , Corcoran Ryan B.
Published: April 2023

Supplementary Figure S1. AMG 510 demonstrates cooperativity with SHP2 and RTK inhibition
Supplementary Data from Spatial Analysis and Clinical Significance of HLA Class-I and Class-II Subunit Expression in Non–Small Cell Lung Cancer
Authors: Datar Ila J. , Hauc Sacha C. , Desai Shruti , Gianino Nicole , Henick Brian , Liu Yuting , Syrigos Kostas , Rimm David L. , Kavathas Paula , Ferrone Soldano , Schalper Kurt A.
Published: April 2023

Supplementary figures and tables.
Supplemental data from BET Inhibition Enhances the Antileukemic Activity of Low-dose Venetoclax in Acute Myeloid Leukemia
Authors: Ramsey Haley E. , Greenwood Dalton , Zhang Susu , Childress Merrida , Arrate Maria P. , Gorska Agnieszka E. , Fuller Londa , Zhao Yue , Stengel Kristy , Fischer Melissa A. , Stubbs Matthew C. , Liu Phillip C.C. , Boyd Kelli , Rathmell Jeffrey C. , Hiebert Scott W. , Savona Michael R.
Published: April 2023

Supplemental data
Supplementary Table 1 from Combinations with Allosteric SHP2 Inhibitor TNO155 to Block Receptor Tyrosine Kinase Signaling
Authors: Liu Chen , Lu Hengyu , Wang Hongyun , Loo Alice , Zhang Xiamei , Yang Guizhi , Kowal Colleen , Delach Scott , Wang Ye , Goldoni Silvia , Hastings William D. , Wong Karrie , Gao Hui , Meyer Matthew J. , Moody Susan E. , LaMarche Matthew J. , Engelman Jeffrey A. , Williams Juliet A. , Hammerman Peter S. , Abrams Tinya J. , Mohseni Morvarid , Caponigro Giordano , Hao Huai-Xiang
Published: April 2023

The activity of nazartinib, TNO155, and their combination in EGFR mutant NSCLC cell lines.
Supplementary Fig. S9 from Proteasome Inhibition Overcomes ALK-TKI Resistance in ALK-Rearranged/TP53-Mutant NSCLC via Noxa Expression
Authors: Tanimoto Azusa , Matsumoto Shingo , Takeuchi Shinji , Arai Sachiko , Fukuda Koji , Nishiyama Akihiro , Yoh Kiyotaka , Ikeda Takaya , Furuya Naoki , Nishino Kazumi , Ohe Yuichiro , Goto Koichi , Yano Seiji
Published: April 2023

Graphical schema showing the mechanism for overcoming intrinsic resistance to ALK-TKIs owing to TP53 mutations
Supplementary Figure 8 from Sensitive Detection of Minimal Residual Disease in Patients Treated for Early-Stage Breast Cancer
Authors: Parsons Heather A. , Rhoades Justin , Reed Sarah C. , Gydush Gregory , Ram Priyanka , Exman Pedro , Xiong Kan , Lo Christopher C. , Li Tianyu , Fleharty Mark , Kirkner Gregory J. , Rotem Denisse , Cohen Ofir , Yu Fangyan , Fitarelli-Kiehl Mariana , Leong Ka Wai , Hughes Melissa E. , Rosenberg Shoshana M. , Collins Laura C. , Miller Kathy D. , Blumenstiel Brendan , Trippa Lorenzo , Cibulskis Carrie , Neuberg Donna S. , DeFelice Matthew , Freeman Samuel S. , Lennon Niall J. , Wagle Nikhil , Ha Gavin , Stover Daniel G. , Choudhury Atish D. , Getz Gad , Winer Eric P. , Meyerson Matthew , Lin Nancy U. , Krop Ian , Love J. Christopher , Makrigiorgos G. Mike , Partridge Ann H. , Mayer Erica L. , Golub Todd R. , Adalsteinsson Viktor A.
Published: April 2023

Application of MRD testing to healthy donor cfDNA samples. Patient specific panels designed for 14 different patients were pooled together and applied to cfDNA collected from four different healthy donors. Reported are the number of sites where ctDNA was detected. We required at least two sites to call a sample MRD+.
Supplementary Figure 7 from Sensitive Detection of Minimal Residual Disease in Patients Treated for Early-Stage Breast Cancer
Authors: Parsons Heather A. , Rhoades Justin , Reed Sarah C. , Gydush Gregory , Ram Priyanka , Exman Pedro , Xiong Kan , Lo Christopher C. , Li Tianyu , Fleharty Mark , Kirkner Gregory J. , Rotem Denisse , Cohen Ofir , Yu Fangyan , Fitarelli-Kiehl Mariana , Leong Ka Wai , Hughes Melissa E. , Rosenberg Shoshana M. , Collins Laura C. , Miller Kathy D. , Blumenstiel Brendan , Trippa Lorenzo , Cibulskis Carrie , Neuberg Donna S. , DeFelice Matthew , Freeman Samuel S. , Lennon Niall J. , Wagle Nikhil , Ha Gavin , Stover Daniel G. , Choudhury Atish D. , Getz Gad , Winer Eric P. , Meyerson Matthew , Lin Nancy U. , Krop Ian , Love J. Christopher , Makrigiorgos G. Mike , Partridge Ann H. , Mayer Erica L. , Golub Todd R. , Adalsteinsson Viktor A.
Published: April 2023

Serial dilution benchmarking of a cancer patient's cfDNA spiked into healthy donor cfDNA using a patient specific panel. (A) Detection power for a range of tumor fractions using our MRD assay. (B) Fraction of replicate dilutions detected by our MRD assay and the median detection power for those samples. (C) Tumor fraction estimation benchmarking for several replicates across a range of tumor fractions.
Supplementary Table-3 from Development and Validation of a Gene Signature Classifier for Consensus Molecular Subtyping of Colorectal Carcinoma in a CLIA-Certified Setting
Authors: Morris Jeffrey S. , Luthra Rajyalakshmi , Liu Yusha , Duose Dzifa Y. , Lee Wonyul , Reddy Neelima G. , Windham Justin , Chen Huiqin , Tong Zhimin , Zhang Baili , Wei Wei , Ganiraju Manyam , Broom Bradley M. , Alvarez Hector A. , Mejia Alicia , Veeranki Omkara , Routbort Mark J. , Morris Van K. , Overman Michael J. , Menter David , Katkhuda Riham , Wistuba Ignacio I. , Davis Jennifer S. , Kopetz Scott , Maru Dipen M.
Published: April 2023

3A. Classification accuracy of CMS1 samples on training data set V1 using 4-fold cross validation as function of number of genes.3B.able-3B: Classification accuracy of CMS1 samples on validation data set (V2) as function of number of genes.3C. Classification accuracy CMS1 samples with out of sample (V2o) prediction set as function of number of genes.3D. Classification accuracy CMS1 samples with TCGA dataset (RNA-seq subset) as function of number of genes. 3E. Classification accuracy CMS1 samples with Affymetrix set (V2a) as function of number of genes.
Supplementary Figure 5 from Sensitive Detection of Minimal Residual Disease in Patients Treated for Early-Stage Breast Cancer
Authors: Parsons Heather A. , Rhoades Justin , Reed Sarah C. , Gydush Gregory , Ram Priyanka , Exman Pedro , Xiong Kan , Lo Christopher C. , Li Tianyu , Fleharty Mark , Kirkner Gregory J. , Rotem Denisse , Cohen Ofir , Yu Fangyan , Fitarelli-Kiehl Mariana , Leong Ka Wai , Hughes Melissa E. , Rosenberg Shoshana M. , Collins Laura C. , Miller Kathy D. , Blumenstiel Brendan , Trippa Lorenzo , Cibulskis Carrie , Neuberg Donna S. , DeFelice Matthew , Freeman Samuel S. , Lennon Niall J. , Wagle Nikhil , Ha Gavin , Stover Daniel G. , Choudhury Atish D. , Getz Gad , Winer Eric P. , Meyerson Matthew , Lin Nancy U. , Krop Ian , Love J. Christopher , Makrigiorgos G. Mike , Partridge Ann H. , Mayer Erica L. , Golub Todd R. , Adalsteinsson Viktor A.
Published: April 2023

Verification of detection power calculation. Comparison between the predicted detection power of 18 replicates and the actual fraction of those replicates that were called MRD+. 18 independent samples from a 1:100k dilution were probed with a 488 SNV panel (see methods). Replicates had their duplex consensus reads downsampled in increments of 10% and detection power was recalculated. Reported are the median and range of predicted detection powers for all replicates at each downsampling.
Supplementary Figure-6 from Development and Validation of a Gene Signature Classifier for Consensus Molecular Subtyping of Colorectal Carcinoma in a CLIA-Certified Setting
Authors: Morris Jeffrey S. , Luthra Rajyalakshmi , Liu Yusha , Duose Dzifa Y. , Lee Wonyul , Reddy Neelima G. , Windham Justin , Chen Huiqin , Tong Zhimin , Zhang Baili , Wei Wei , Ganiraju Manyam , Broom Bradley M. , Alvarez Hector A. , Mejia Alicia , Veeranki Omkara , Routbort Mark J. , Morris Van K. , Overman Michael J. , Menter David , Katkhuda Riham , Wistuba Ignacio I. , Davis Jennifer S. , Kopetz Scott , Maru Dipen M.
Published: April 2023

Nanostring CMS Classifier Performance: Performance of Nanostring 100 gene CMS classifier applied to FFPE samples (6A and 6C) and FF samples (6B and 63D). The top two figures plot 4-class accuracy vs. classification confidence, with the dots marking individual samples either correctly (1.0) or incorrectly (0.0), with color indicat-ing correct CMS. The line contains a generalized additive model (GAM) fit to these data with 95% pointwise confidence bands, and demonstrates that samples classified with greater confidence were more likely to be cor-rectly classified. Figure 6C and 6D plot 4-class accuracy vs. RNA quality, defined as 0nt (FFPE) or RIN (FF). Note that there is little if any association of CMS accuracy with RNA quality, suggesting that the perfor-mance of classifier is robust to RNA quality in this study.
Supplementary Figure-5 from Development and Validation of a Gene Signature Classifier for Consensus Molecular Subtyping of Colorectal Carcinoma in a CLIA-Certified Setting
Authors: Morris Jeffrey S. , Luthra Rajyalakshmi , Liu Yusha , Duose Dzifa Y. , Lee Wonyul , Reddy Neelima G. , Windham Justin , Chen Huiqin , Tong Zhimin , Zhang Baili , Wei Wei , Ganiraju Manyam , Broom Bradley M. , Alvarez Hector A. , Mejia Alicia , Veeranki Omkara , Routbort Mark J. , Morris Van K. , Overman Michael J. , Menter David , Katkhuda Riham , Wistuba Ignacio I. , Davis Jennifer S. , Kopetz Scott , Maru Dipen M.
Published: April 2023

Sample-wise and Gene-wise correlation of FF/FFPE paired Samples: Scatterplot of gene-specific Spearman correlation of FF/FFPE computed separately for CRCSC samples and non-CRCSC samples , with red and blue marking the overall top 100 and top 200 genes, respectively, in terms of FF/FFPE correlation computed across all samples. Note the high level of agreement across batches that genes with high FF/FFPE correlations for one batch tended to also have high FF/FFPE correlation in the other batch, suggesting high FF/FFPE correla-tion is a characteristic of the gene/probe set.
Supplementary Figure 14 from Sensitive Detection of Minimal Residual Disease in Patients Treated for Early-Stage Breast Cancer
Authors: Parsons Heather A. , Rhoades Justin , Reed Sarah C. , Gydush Gregory , Ram Priyanka , Exman Pedro , Xiong Kan , Lo Christopher C. , Li Tianyu , Fleharty Mark , Kirkner Gregory J. , Rotem Denisse , Cohen Ofir , Yu Fangyan , Fitarelli-Kiehl Mariana , Leong Ka Wai , Hughes Melissa E. , Rosenberg Shoshana M. , Collins Laura C. , Miller Kathy D. , Blumenstiel Brendan , Trippa Lorenzo , Cibulskis Carrie , Neuberg Donna S. , DeFelice Matthew , Freeman Samuel S. , Lennon Niall J. , Wagle Nikhil , Ha Gavin , Stover Daniel G. , Choudhury Atish D. , Getz Gad , Winer Eric P. , Meyerson Matthew , Lin Nancy U. , Krop Ian , Love J. Christopher , Makrigiorgos G. Mike , Partridge Ann H. , Mayer Erica L. , Golub Todd R. , Adalsteinsson Viktor A.
Published: April 2023

Patients who experienced local recurrence only after treatment for early stage breast cancer. cfDNA time points for all patients who experienced local recurrence only. End points represent time of last follow up or death.
Supplementary Figure 12 from Sensitive Detection of Minimal Residual Disease in Patients Treated for Early-Stage Breast Cancer
Authors: Parsons Heather A. , Rhoades Justin , Reed Sarah C. , Gydush Gregory , Ram Priyanka , Exman Pedro , Xiong Kan , Lo Christopher C. , Li Tianyu , Fleharty Mark , Kirkner Gregory J. , Rotem Denisse , Cohen Ofir , Yu Fangyan , Fitarelli-Kiehl Mariana , Leong Ka Wai , Hughes Melissa E. , Rosenberg Shoshana M. , Collins Laura C. , Miller Kathy D. , Blumenstiel Brendan , Trippa Lorenzo , Cibulskis Carrie , Neuberg Donna S. , DeFelice Matthew , Freeman Samuel S. , Lennon Niall J. , Wagle Nikhil , Ha Gavin , Stover Daniel G. , Choudhury Atish D. , Getz Gad , Winer Eric P. , Meyerson Matthew , Lin Nancy U. , Krop Ian , Love J. Christopher , Makrigiorgos G. Mike , Partridge Ann H. , Mayer Erica L. , Golub Todd R. , Adalsteinsson Viktor A.
Published: April 2023

Patients who experienced distant recurrence after treatment for early stage breast cancer. cfDNA time points for patients who ultimately experienced distant recurrence. Those marked with poor detection limits had an estimated detection limit worse than 1/1,000. End points represent time of distant clinical recurrence. Patients 05055_81 and YWBC_202 were excluded from this plot due to missing time of recurrence.
Table S2 from Characterization of Immune Dysfunction and Identification of Prognostic Immune-Related Risk Factors in Acute Myeloid Leukemia
Authors: Tang Lu , Wu Jianghua , Li Cheng-Gong , Jiang Hui-Wen , Xu Min , Du Mengyi , Yin Zhinan , Mei Heng , Hu Yu
Published: April 2023

Table S2 shows a list of antibodies used for flow cytometric analysis.
Supplementary Figure S3 from Interventional Radiology for Local Immunotherapy in Oncology
Authors: Tselikas Lambros , Champiat Stephane , Sheth Rahul A. , Yevich Steve , Ammari Samy , Deschamps Frederic , Farhane Siham , Roux Charles , Susini Sandrine , Mouraud Severine , Delpla Alexandre , Raoult Thibault , Robert Caroline , Massard Christophe , Barlesi Fabrice , Soria Jean-Charles , Marabelle Aurélien , de Baere Thierry
Published: April 2023

Devices for direct intratumoral immunotherapy
Table S1 from Characterization of Immune Dysfunction and Identification of Prognostic Immune-Related Risk Factors in Acute Myeloid Leukemia
Authors: Tang Lu , Wu Jianghua , Li Cheng-Gong , Jiang Hui-Wen , Xu Min , Du Mengyi , Yin Zhinan , Mei Heng , Hu Yu
Published: April 2023

Table S1 shows detailed clinical characteristics of AML participants.
Supplemental Legend from Characterization of Immune Dysfunction and Identification of Prognostic Immune-Related Risk Factors in Acute Myeloid Leukemia
Authors: Tang Lu , Wu Jianghua , Li Cheng-Gong , Jiang Hui-Wen , Xu Min , Du Mengyi , Yin Zhinan , Mei Heng , Hu Yu
Published: April 2023

Supplemental Legend
Supplementary Data from The Use of Serial Circulating Tumor DNA to Detect Resistance Alterations in Progressive Metastatic Breast Cancer
Authors: Jacob Saya , Davis Andrew A. , Gerratana Lorenzo , Velimirovic Marko , Shah Ami N. , Wehbe Firas , Katam Neelima , Zhang Qiang , Flaum Lisa , Siziopikou Kalliopi P. , Platanias Leonidas C. , Gradishar William J. , Behdad Amir , Bardia Aditya , Cristofanilli Massimo
Published: April 2023

Supplemental Table 1: Treatments by subgroup. Supplemental Figure 1A-D: Association of baseline MAF and NOA with survival
Figure S3 from Characterization of Immune Dysfunction and Identification of Prognostic Immune-Related Risk Factors in Acute Myeloid Leukemia
Authors: Tang Lu , Wu Jianghua , Li Cheng-Gong , Jiang Hui-Wen , Xu Min , Du Mengyi , Yin Zhinan , Mei Heng , Hu Yu
Published: April 2023

Figure S3 shows the analysis of cytokines production and degranulation capacity in T and NK cells.
Figure S2 from Characterization of Immune Dysfunction and Identification of Prognostic Immune-Related Risk Factors in Acute Myeloid Leukemia
Authors: Tang Lu , Wu Jianghua , Li Cheng-Gong , Jiang Hui-Wen , Xu Min , Du Mengyi , Yin Zhinan , Mei Heng , Hu Yu
Published: April 2023

Figure S2 shows the coexistence of senescence and exhaustion phenotypic signatures in CD4+ and CD8+ T cells.
Supplementary Data from Predicting Therapeutic Antibody Delivery into Human Head and Neck Cancers
Authors: Lu Guolan , Fakurnejad Shayan , Martin Brock A. , van den Berg Nynke S. , van Keulen Stan , Nishio Naoki , Zhu Ashley J. , Chirita Stefania U. , Zhou Quan , Gao Rebecca W. , Kong Christina S. , Fischbein Nancy , Penta Mrudula , Colevas Alexander D. , Rosenthal Eben L.
Published: April 2023

Supplementary tables and figures
Figure S1 from Characterization of Immune Dysfunction and Identification of Prognostic Immune-Related Risk Factors in Acute Myeloid Leukemia
Authors: Tang Lu , Wu Jianghua , Li Cheng-Gong , Jiang Hui-Wen , Xu Min , Du Mengyi , Yin Zhinan , Mei Heng , Hu Yu
Published: April 2023

Figure S1 shows specific gating strategy of flow cytometric analysis.
Supplementary Data from Circulating Tumor DNA Genomics Reveal Potential Mechanisms of Resistance to BRAF-Targeted Therapies in Patients with BRAF-Mutant Metastatic Non–Small Cell Lung Cancer
Authors: Ortiz-Cuaran Sandra , Mezquita Laura , Swalduz Aurélie , Aldea Mihalea , Mazieres Julien , Leonce Camille , Jovelet Cecile , Pradines Anne , Avrillon Virginie , Chumbi Flores Washington R. , Lacroix Ludovic , Loriot Yohann , Westeel Virginie , Ngo-Camus Maud , Tissot Claire , Raynaud Christine , Gervais Radj , Brain Etienne , Monnet Isabelle , Giroux Leprieur Etienne , Caramella Caroline , Mahier-Aït Oukhatar Celine , Hoog-Labouret Natalie , de Kievit Frank , Howarth Karen , Morris Clive , Green Emma , Friboulet Luc , Chabaud Sylvie , Guichou Jean-François , Perol Maurice , Besse Benjamin , Blay Jean-Yves , Saintigny Pierre , Planchard David
Published: April 2023

Supplementary Tables and Supplementary Figures
Figure S2 from Analysis of Pre- and Posttreatment Tissues from the SWOG S0800 Trial Reveals an Effect of Neoadjuvant Chemotherapy on the Breast Cancer Genome
Authors: Powles Ryan L. , Wali Vikram B. , Li Xiaotong , Barlow William E. , Nahleh Zeina , Thompson Alastair M. , Godwin Andrew K. , Hatzis Christos , Pusztai Lajos
Published: April 2023

Supplementary Figure 2. HFI mutations affecting individual recurrent genes in pre-treatment samples. Only genes affected in a minimum of 10% of the cohort are shown.
Supplementary Tables S1-S6 from Predictive Biomarkers for Adjuvant Capecitabine Benefit in Early-Stage Triple-Negative Breast Cancer in the FinXX Clinical Trial
Authors: Asleh Karama , Brauer Heather Ann , Sullivan Amy , Lauttia Susanna , Lindman Henrik , Nielsen Torsten O. , Joensuu Heikki , Thompson E. Aubrey , Chumsri Saranya
Published: April 2023

Supplementary Table S1 includes biological description of the 30 custom genes, Supplementary Tables S2-S3 show patient characteristics, Supplementary Table S4 shows biological classification of the study cohort, Supplementary Tables S5-6 show survival analysis and interaction tests for selected genes and metagenes
Figure S1 from Analysis of Pre- and Posttreatment Tissues from the SWOG S0800 Trial Reveals an Effect of Neoadjuvant Chemotherapy on the Breast Cancer Genome
Authors: Powles Ryan L. , Wali Vikram B. , Li Xiaotong , Barlow William E. , Nahleh Zeina , Thompson Alastair M. , Godwin Andrew K. , Hatzis Christos , Pusztai Lajos
Published: April 2023

Supplementary Figure 1. Flow diagram of patients and samples used in analysis. Blue boxes represent sub-cohorts used for various parts of the study.
Supplementary Figure S7 from Predictive Biomarkers for Adjuvant Capecitabine Benefit in Early-Stage Triple-Negative Breast Cancer in the FinXX Clinical Trial
Authors: Asleh Karama , Brauer Heather Ann , Sullivan Amy , Lauttia Susanna , Lindman Henrik , Nielsen Torsten O. , Joensuu Heikki , Thompson E. Aubrey , Chumsri Saranya
Published: April 2023

Supplementary Figure S7 shows scatter plots for TYMP expression against selected genes and metagenes
Supplemental Table from Differential Outcomes in Codon 12/13 and Codon 61 NRAS-Mutated Cancers in the Phase II NCI-MATCH Trial of Binimetinib in Patients with NRAS-Mutated Tumors
Authors: Cleary James M. , Wang Victoria , Heist Rebecca S. , Kopetz E. Scott , Mitchell Edith P. , Zwiebel James A. , Kapner Kevin S. , Chen Helen X. , Li Shuli , Gray Robert J. , McShane Lisa M. , Rubinstein Larry V. , Patton David R. , Meric-Bernstam Funda , Dillmon Melissa S. , Williams P. Mickey , Hamilton Stanley R. , Conley Barbara A. , Aguirre Andrew J. , O'Dwyer Peter J. , Harris Lyndsay N. , Arteaga Carlos L. , Chen Alice P. , Flaherty Keith T.
Published: April 2023

Supplemental Table
Supplementary Figure S5 from Predictive Biomarkers for Adjuvant Capecitabine Benefit in Early-Stage Triple-Negative Breast Cancer in the FinXX Clinical Trial
Authors: Asleh Karama , Brauer Heather Ann , Sullivan Amy , Lauttia Susanna , Lindman Henrik , Nielsen Torsten O. , Joensuu Heikki , Thompson E. Aubrey , Chumsri Saranya
Published: April 2023

Supplementary Figure S5 shows a forest plot of the categorical expression of selected genes and metagenes and their association with survival in each treatment arm
Supplemental Figures from Differential Outcomes in Codon 12/13 and Codon 61 NRAS-Mutated Cancers in the Phase II NCI-MATCH Trial of Binimetinib in Patients with NRAS-Mutated Tumors
Authors: Cleary James M. , Wang Victoria , Heist Rebecca S. , Kopetz E. Scott , Mitchell Edith P. , Zwiebel James A. , Kapner Kevin S. , Chen Helen X. , Li Shuli , Gray Robert J. , McShane Lisa M. , Rubinstein Larry V. , Patton David R. , Meric-Bernstam Funda , Dillmon Melissa S. , Williams P. Mickey , Hamilton Stanley R. , Conley Barbara A. , Aguirre Andrew J. , O'Dwyer Peter J. , Harris Lyndsay N. , Arteaga Carlos L. , Chen Alice P. , Flaherty Keith T.
Published: April 2023

Supplemental Figures
Supplementary Figure S4 from Predictive Biomarkers for Adjuvant Capecitabine Benefit in Early-Stage Triple-Negative Breast Cancer in the FinXX Clinical Trial
Authors: Asleh Karama , Brauer Heather Ann , Sullivan Amy , Lauttia Susanna , Lindman Henrik , Nielsen Torsten O. , Joensuu Heikki , Thompson E. Aubrey , Chumsri Saranya
Published: April 2023

Supplementary Figure S4 shows a Kaplan Meier survival curve of the study cohort
Supplementary Figure S3 from Predictive Biomarkers for Adjuvant Capecitabine Benefit in Early-Stage Triple-Negative Breast Cancer in the FinXX Clinical Trial
Authors: Asleh Karama , Brauer Heather Ann , Sullivan Amy , Lauttia Susanna , Lindman Henrik , Nielsen Torsten O. , Joensuu Heikki , Thompson E. Aubrey , Chumsri Saranya
Published: April 2023

Supplementary Figure S3 shows the expression levels of immune-related genes and metagenes against basal status
Protocol from A Randomized Phase IIb Study of Low-dose Tamoxifen in Chest-irradiated Cancer Survivors at Risk for Breast Cancer
Authors: Bhatia Smita , Palomares Melanie R. , Hageman Lindsey , Chen Yanjun , Landier Wendy , Smith Kandice , Umphrey Heidi , Reich Caroline A. , Zamora Kathryn W. , Armenian Saro H. , Bevers Therese B. , Blaes Anne , Henderson Tara , Hodgson David , Hudson Melissa M. , Korde Larissa A. , Melin Susan A. , Merajver Sofia D. , Overholser Linda , Pruthi Sandhya , Wong F. Lennie , Garber Judy E.
Published: April 2023

Protocol
Figure S5 from Preclinical Evaluation of B7-H3–specific Chimeric Antigen Receptor T Cells for the Treatment of Acute Myeloid Leukemia
Authors: Lichtman Eben I. , Du Hongwei , Shou Peishun , Song Feifei , Suzuki Kyogo , Ahn Sarah , Li Guangming , Ferrone Soldano , Su Lishan , Savoldo Barbara , Dotti Gianpietro
Published: April 2023

B7-H3.CAR-Ts control leukemia growth in a patient-derived xenograft model of AML.
Figure S2 from Preclinical Evaluation of B7-H3–specific Chimeric Antigen Receptor T Cells for the Treatment of Acute Myeloid Leukemia
Authors: Lichtman Eben I. , Du Hongwei , Shou Peishun , Song Feifei , Suzuki Kyogo , Ahn Sarah , Li Guangming , Ferrone Soldano , Su Lishan , Savoldo Barbara , Dotti Gianpietro
Published: April 2023

B7-H3 expression is retained on THP1 cells and patient-derived AML blasts after B7-H3.CAR-T treatment
Supplementary Figure 3 from Pacritinib Combined with Sirolimus and Low-Dose Tacrolimus for GVHD Prevention after Allogeneic Hematopoietic Cell Transplantation: Preclinical and Phase I Trial Results
Authors: Pidala Joseph , Walton Kelly , Elmariah Hany , Kim Jongphil , Mishra Asmita , Bejanyan Nelli , Nishihori Taiga , Khimani Farhad , Perez Lia , Faramand Rawan G. , Davila Marco L. , Nieder Michael L. , Sagatys Elizabeth M. , Holtan Shernan G. , Lawrence Nicholas J. , Lawrence Harshani R. , Blazar Bruce R. , Anasetti Claudio , Sebti Said M. , Betts Brian C.
Published: April 2023

Serial measures of absolute neutrophil count (ANC), hemoglobin (Hgb) and platelet counts (PLT) through complete pacritinib treatment period
Supplementary Figure 2 from Pacritinib Combined with Sirolimus and Low-Dose Tacrolimus for GVHD Prevention after Allogeneic Hematopoietic Cell Transplantation: Preclinical and Phase I Trial Results
Authors: Pidala Joseph , Walton Kelly , Elmariah Hany , Kim Jongphil , Mishra Asmita , Bejanyan Nelli , Nishihori Taiga , Khimani Farhad , Perez Lia , Faramand Rawan G. , Davila Marco L. , Nieder Michael L. , Sagatys Elizabeth M. , Holtan Shernan G. , Lawrence Nicholas J. , Lawrence Harshani R. , Blazar Bruce R. , Anasetti Claudio , Sebti Said M. , Betts Brian C.
Published: April 2023

Safety measures monitored on trial including (A) QTcF, (B) cardiac ejection fraction, (C) prothrombin time, (D) partial thromboplastin time, (E) and thrombin time
Supplementary table 3 from Gene Expression Signatures Identify Novel Therapeutics for Metastatic Pancreatic Neuroendocrine Tumors
Authors: Scott Aaron T. , Weitz Michelle , Breheny Patrick J. , Ear Po Hien , Darbro Benjamin , Brown Bart J. , Braun Terry A. , Li Guiying , Umesalma Shaikamjad , Kaemmer Courtney A. , Maharjan Chandra K. , Quelle Dawn E. , Bellizzi Andrew M. , Chandrasekharan Chandrikha , Dillon Joseph S. , O'Dorisio Thomas M. , Howe James R.
Published: April 2023

Supplementary table 3
Supplementary Data Clean from Anastrozole has an Association between Degree of Estrogen Suppression and Outcomes in Early Breast Cancer and is a Ligand for Estrogen Receptor α
Authors: Ingle James N. , Cairns Junmei , Suman Vera J. , Shepherd Lois E. , Fasching Peter A. , Hoskin Tanya L. , Singh Ravinder J. , Desta Zeruesenay , Kalari Krishna R. , Ellis Matthew J. , Goss Paul E. , Chen Bingshu E. , Volz Bernhard , Barman Poulami , Carlson Erin E. , Haddad Tufia , Goetz Matthew P. , Goodnature Barbara , Cuellar Matthew E. , Walters Michael A. , Correia Cristina , Kaufmann Scott H. , Weinshilboum Richard M. , Wang Liewei
Published: April 2023

This file is the revised clean Supplementary Data
Supplementary Data from Combination of PARP Inhibitor Olaparib, and PD-L1 Inhibitor Durvalumab, in Recurrent Ovarian Cancer: a Proof-of-Concept Phase II Study
Authors: Lampert Erika J. , Zimmer Alexandra , Padget Michelle , Cimino-Mathews Ashley , Nair Jayakumar R. , Liu Yingmiao , Swisher Elizabeth M. , Hodge James W. , Nixon Andrew B. , Nichols Erin , Bagheri Mohammad H. , Levy Elliott , Radke Marc R. , Lipkowitz Stanley , Annunziata Christina M. , Taube Janis M. , Steinberg Seth M. , Lee Jung-Min
Published: April 2023

Supplementary methods, tables, figures 1-5 with corresponding figure legends, and references
Supplementary Data 3 from Chromatin Accessibility Identifies Regulatory Elements Predictive of Gene Expression and Disease Outcome in Multiple Myeloma
Authors: Barwick Benjamin G. , Gupta Vikas A. , Matulis Shannon M. , Patton Jonathan C. , Powell Doris R. , Gu Yanyan , Jaye David L. , Conneely Karen N. , Lin Yin C. , Hofmeister Craig C. , Nooka Ajay K. , Keats Jonathan J. , Lonial Sagar , Vertino Paula M. , Boise Lawrence H.
Published: April 2023

Gene set enrichment analysis of transcribed regulatory elements in CoMMpass.
Supplementary Data from A Biparatopic Antibody That Modulates MET Trafficking Exhibits Enhanced Efficacy Compared with Parental Antibodies in MET-Driven Tumor Models
Authors: DaSilva John O. , Yang Katie , Perez Bay Andres E. , Andreev Julian , Ngoi Peter , Pyles Erica , Franklin Matthew C. , Dudgeon Drew , Rafique Ashique , Dore Anthony , Delfino Frank J. , Potocky Terra B. , Babb Robert , Chen Gang , MacDonald Douglas , Olson William C. , Thurston Gavin , Daly Christopher
Published: April 2023

supplementary figures and tables
Supplementary Data 1 from Chromatin Accessibility Identifies Regulatory Elements Predictive of Gene Expression and Disease Outcome in Multiple Myeloma
Authors: Barwick Benjamin G. , Gupta Vikas A. , Matulis Shannon M. , Patton Jonathan C. , Powell Doris R. , Gu Yanyan , Jaye David L. , Conneely Karen N. , Lin Yin C. , Hofmeister Craig C. , Nooka Ajay K. , Keats Jonathan J. , Lonial Sagar , Vertino Paula M. , Boise Lawrence H.
Published: April 2023

Correlation of chromatin accessibility and gene expression for the 5% most variably expressed genes.
Supplementary Data from A Biparatopic Antibody That Modulates MET Trafficking Exhibits Enhanced Efficacy Compared with Parental Antibodies in MET-Driven Tumor Models
Authors: DaSilva John O. , Yang Katie , Perez Bay Andres E. , Andreev Julian , Ngoi Peter , Pyles Erica , Franklin Matthew C. , Dudgeon Drew , Rafique Ashique , Dore Anthony , Delfino Frank J. , Potocky Terra B. , Babb Robert , Chen Gang , MacDonald Douglas , Olson William C. , Thurston Gavin , Daly Christopher
Published: April 2023

Supplementary figure legends and methods
Table S3 from Circulating T-cell Immunosenescence in Patients with Advanced Non–small Cell Lung Cancer Treated with Single-agent PD-1/PD-L1 Inhibitors or Platinum-based Chemotherapy
Authors: Ferrara Roberto , Naigeon Marie , Auclin Edouard , Duchemann Boris , Cassard Lydie , Jouniaux Jean-Mehdi , Boselli Lisa , Grivel Jonathan , Desnoyer Aude , Mezquita Laura , Texier Matthieu , Caramella Caroline , Hendriks Lizza , Planchard David , Remon Jordi , Sangaletti Sabina , Proto Claudia , Garassino Marina C. , Soria Jean-Charles , Marabelle Aurelien , Voisin Anne-Laure , Farhane Siham , Besse Benjamin , Chaput Nathalie
Published: April 2023

Patients characteristics according to SIP status (PCT cohort)
Table S3 from Deep Learning Predicts HPV Association in Oropharyngeal Squamous Cell Carcinomas and Identifies Patients with a Favorable Prognosis Using Regular H&E Stains
Authors: Klein Sebastian , Quaas Alexander , Quantius Jennifer , Löser Heike , Meinel Jörn , Peifer Martin , Wagner Steffen , Gattenlöhner Stefan , Wittekindt Claus , von Knebel Doeberitz Magnus , Prigge Elena-Sophie , Langer Christine , Noh Ka-Won , Maltseva Margaret , Reinhardt Hans Christian , Büttner Reinhard , Klussmann Jens Peter , Wuerdemann Nora
Published: April 2023

Patient characteristics TCGA HNSCC cohort
Figure S8 from Circulating T-cell Immunosenescence in Patients with Advanced Non–small Cell Lung Cancer Treated with Single-agent PD-1/PD-L1 Inhibitors or Platinum-based Chemotherapy
Authors: Ferrara Roberto , Naigeon Marie , Auclin Edouard , Duchemann Boris , Cassard Lydie , Jouniaux Jean-Mehdi , Boselli Lisa , Grivel Jonathan , Desnoyer Aude , Mezquita Laura , Texier Matthieu , Caramella Caroline , Hendriks Lizza , Planchard David , Remon Jordi , Sangaletti Sabina , Proto Claudia , Garassino Marina C. , Soria Jean-Charles , Marabelle Aurelien , Voisin Anne-Laure , Farhane Siham , Besse Benjamin , Chaput Nathalie
Published: April 2023

Scatter plot of tumor growth rate variation and hyperprogressive disease according to SIP status (27 patients, ICI validation cohort)
Supplementary Tables 1-4 from Trametinib Activity in Patients with Solid Tumors and Lymphomas Harboring BRAF Non-V600 Mutations or Fusions: Results from NCI-MATCH (EAY131)
Authors: Johnson Douglas B. , Zhao Fengmin , Noel Marcus , Riely Gregory J. , Mitchell Edith P. , Wright John J. , Chen Helen X. , Gray Robert J. , Li Shuli , McShane Lisa M. , Rubinstein Larry V. , Patton David , Williams P. Mickey , Hamilton Stanly R. , Conley Barbara A. , Arteaga Carlos L. , Harris Lyndsay N. , O'Dwyer Peter J. , Chen Alice P. , Flaherty Keith T.
Published: April 2023

1) Eligible mutations/fusions, 2) identified mutations/fusions, 3) Treatment-related toxicities, 4) Number of treatment cycles and reasons for discontinuation
Supplementary Data from Trametinib Activity in Patients with Solid Tumors and Lymphomas Harboring BRAF Non-V600 Mutations or Fusions: Results from NCI-MATCH (EAY131)
Authors: Johnson Douglas B. , Zhao Fengmin , Noel Marcus , Riely Gregory J. , Mitchell Edith P. , Wright John J. , Chen Helen X. , Gray Robert J. , Li Shuli , McShane Lisa M. , Rubinstein Larry V. , Patton David , Williams P. Mickey , Hamilton Stanly R. , Conley Barbara A. , Arteaga Carlos L. , Harris Lyndsay N. , O'Dwyer Peter J. , Chen Alice P. , Flaherty Keith T.
Published: April 2023

Supplementary Figure 4: (A) PFS and (B) OS of patients based on location of BRAF mutation (exon 11 vs. 15)
Figure S2 from Circulating T-cell Immunosenescence in Patients with Advanced Non–small Cell Lung Cancer Treated with Single-agent PD-1/PD-L1 Inhibitors or Platinum-based Chemotherapy
Authors: Ferrara Roberto , Naigeon Marie , Auclin Edouard , Duchemann Boris , Cassard Lydie , Jouniaux Jean-Mehdi , Boselli Lisa , Grivel Jonathan , Desnoyer Aude , Mezquita Laura , Texier Matthieu , Caramella Caroline , Hendriks Lizza , Planchard David , Remon Jordi , Sangaletti Sabina , Proto Claudia , Garassino Marina C. , Soria Jean-Charles , Marabelle Aurelien , Voisin Anne-Laure , Farhane Siham , Besse Benjamin , Chaput Nathalie
Published: April 2023

Flow diagram of patients evaluable for SIP, other flow cytometry panels and response to ICI (discovery and validation cohort) or PCT
Figure S1 from Circulating T-cell Immunosenescence in Patients with Advanced Non–small Cell Lung Cancer Treated with Single-agent PD-1/PD-L1 Inhibitors or Platinum-based Chemotherapy
Authors: Ferrara Roberto , Naigeon Marie , Auclin Edouard , Duchemann Boris , Cassard Lydie , Jouniaux Jean-Mehdi , Boselli Lisa , Grivel Jonathan , Desnoyer Aude , Mezquita Laura , Texier Matthieu , Caramella Caroline , Hendriks Lizza , Planchard David , Remon Jordi , Sangaletti Sabina , Proto Claudia , Garassino Marina C. , Soria Jean-Charles , Marabelle Aurelien , Voisin Anne-Laure , Farhane Siham , Besse Benjamin , Chaput Nathalie
Published: April 2023

Gating strategy for the T-cell immunosenescence flow cytometry panel
Table S2 from An Immune-Related Gene Prognostic Index for Head and Neck Squamous Cell Carcinoma
Authors: Chen Yue , Li Zhi-Yong , Zhou Guan-Qun , Sun Ying
Published: April 2023

GO terms and KEGG pathways enriched in the turquoise and blue modules
Supplementary Table S3 from Breast Cancer Index Predicts Extended Endocrine Benefit to Individualize Selection of Patients with HR+ Early-stage Breast Cancer for 10 Years of Endocrine Therapy
Authors: Noordhoek Iris , Treuner Kai , Putter Hein , Zhang Yi , Wong Jenna , Meershoek-Klein Kranenbarg Elma , Duijm-de Carpentier Marjolijn , van de Velde Cornelis J.H. , Schnabel Catherine A. , Liefers Gerrit-Jan
Published: April 2023

Summary of BCI (H/I) as predictive biomarker of endocrine benefit.
Supplementary Data from Proliferation and AKT Activity Biomarker Analyses after Capivasertib (AZD5363) Treatment of Patients with ER+ Invasive Breast Cancer (STAKT)
Authors: Robertson John F.R. , Coleman Robert E. , Cheung Kwok-Leung , Evans Abigail , Holcombe Chris , Skene Anthony , Rea Daniel , Ahmed Samreen , Jahan Ali , Horgan Kieran , Rauchhaus Petra , Littleford Roberta , Cheung S.Y. Amy , Cullberg Marie , de Bruin Elza C. , Koulai Loumpiana , Lindemann Justin P.O. , Pass Martin , Rugman Paul , Schiavon Gaia , Deb Rahul , Finlay Pauline , Foxley Andrew , Gee Julia M.W.
Published: April 2023

Supplementary Data from Proliferation and AKT Activity Biomarker Analyses after Capivasertib (AZD5363) Treatment of Patients with ER+ Invasive Breast Cancer (STAKT)
Supplementary Table S1 from Breast Cancer Index Predicts Extended Endocrine Benefit to Individualize Selection of Patients with HR+ Early-stage Breast Cancer for 10 Years of Endocrine Therapy
Authors: Noordhoek Iris , Treuner Kai , Putter Hein , Zhang Yi , Wong Jenna , Meershoek-Klein Kranenbarg Elma , Duijm-de Carpentier Marjolijn , van de Velde Cornelis J.H. , Schnabel Catherine A. , Liefers Gerrit-Jan
Published: April 2023

Kaplan-Meier estimates of risk of recurrence at year 10 since randomization for patients treated with 5 years vs 2.5 years of additional letrozole in the overall cohort and in the Primary AI subset.
Supplementary Figures from Designing Evolutionary-based Interception Strategies to Block the Transition from Precursor Phases to Multiple Myeloma
Authors: Maura Francesco , Landgren Ola , Morgan Gareth J.
Published: April 2023

All Supplementary Figures
Table S2 from Phase I Clinical Trial of Combination Propranolol and Pembrolizumab in Locally Advanced and Metastatic Melanoma: Safety, Tolerability, and Preliminary Evidence of Antitumor Activity
Authors: Gandhi Shipra , Pandey Manu R. , Attwood Kristopher , Ji Wenyan , Witkiewicz Agnieszka K. , Knudsen Erik S. , Allen Cheryl , Tario Joseph D. , Wallace Paul K. , Cedeno Carlos D. , Levis Maria , Stack Suzanne , Funchain Pauline , Drabick Joseph J. , Bucsek Mark J. , Puzanov Igor , Mohammadpour Hemn , Repasky Elizabeth A. , Ernstoff Marc S.
Published: April 2023

A. Absolute quantitative change in peripheral blood chemokines* from baseline to week 3 (week 3 minus baseline; change in mean value +/- standard deviation). B. Quantitative change in peripheral blood cellular fractions expressed as percentage of total CD45+ cells from baseline to 3 weeks (week 3 minus baseline).
Figure S5 from Phase I Clinical Trial of Combination Propranolol and Pembrolizumab in Locally Advanced and Metastatic Melanoma: Safety, Tolerability, and Preliminary Evidence of Antitumor Activity
Authors: Gandhi Shipra , Pandey Manu R. , Attwood Kristopher , Ji Wenyan , Witkiewicz Agnieszka K. , Knudsen Erik S. , Allen Cheryl , Tario Joseph D. , Wallace Paul K. , Cedeno Carlos D. , Levis Maria , Stack Suzanne , Funchain Pauline , Drabick Joseph J. , Bucsek Mark J. , Puzanov Igor , Mohammadpour Hemn , Repasky Elizabeth A. , Ernstoff Marc S.
Published: April 2023

10x magnification of hematoxylin and eosin stained slides of archival tissue biopsies of patients at dose level 1, 2 and 3 on the study. Dose level 1 is propranolol 10 mg BID, dose level 2 is propranolol 20 mg BID, dose level 3 is propranolol 30 mg BID
Figure S4 from Phase I Clinical Trial of Combination Propranolol and Pembrolizumab in Locally Advanced and Metastatic Melanoma: Safety, Tolerability, and Preliminary Evidence of Antitumor Activity
Authors: Gandhi Shipra , Pandey Manu R. , Attwood Kristopher , Ji Wenyan , Witkiewicz Agnieszka K. , Knudsen Erik S. , Allen Cheryl , Tario Joseph D. , Wallace Paul K. , Cedeno Carlos D. , Levis Maria , Stack Suzanne , Funchain Pauline , Drabick Joseph J. , Bucsek Mark J. , Puzanov Igor , Mohammadpour Hemn , Repasky Elizabeth A. , Ernstoff Marc S.
Published: April 2023

Multispectral analysis of T-cell activation and exhaustion markers using antibodies for CD8, OX40, CTLA4, PD1, LAG3 and TIM3. A, Representative multiplex and monoplex images for a patient on the study using pre-treatment biopsy. B, Phenotyping was performed using InForm software to delineate activated T-cells, cytotoxic T-cells, partially exhausted T-cells and exhausted T-cells with the underlying marker analysis illustrated for a representative tumor.
Supplementary Data from NRF2 Activation Promotes Aggressive Lung Cancer and Associates with Poor Clinical Outcomes
Authors: Singh Anju , Daemen Anneleen , Nickles Dorothee , Jeon Sang-Min , Foreman Oded , Sudini Kuladeep , Gnad Florian , Lajoie Stephane , Gour Naina , Mitzner Wayne , Chatterjee Samit , Choi Eun-Ji , Ravishankar Buvana , Rappaport Amy , Patil Namrata , McCleland Mark , Johnson Leisa , Acquaah-Mensah George , Gabrielson Edward , Biswal Shyam , Hatzivassiliou Georgia
Published: April 2023

Supplementary Legends, Materials and Methods
Figure S5 from NRF2 Activation Promotes Aggressive Lung Cancer and Associates with Poor Clinical Outcomes
Authors: Singh Anju , Daemen Anneleen , Nickles Dorothee , Jeon Sang-Min , Foreman Oded , Sudini Kuladeep , Gnad Florian , Lajoie Stephane , Gour Naina , Mitzner Wayne , Chatterjee Samit , Choi Eun-Ji , Ravishankar Buvana , Rappaport Amy , Patil Namrata , McCleland Mark , Johnson Leisa , Acquaah-Mensah George , Gabrielson Edward , Biswal Shyam , Hatzivassiliou Georgia
Published: April 2023

Fig. S5, related to Fig. 5.
Figure S4 from NRF2 Activation Promotes Aggressive Lung Cancer and Associates with Poor Clinical Outcomes
Authors: Singh Anju , Daemen Anneleen , Nickles Dorothee , Jeon Sang-Min , Foreman Oded , Sudini Kuladeep , Gnad Florian , Lajoie Stephane , Gour Naina , Mitzner Wayne , Chatterjee Samit , Choi Eun-Ji , Ravishankar Buvana , Rappaport Amy , Patil Namrata , McCleland Mark , Johnson Leisa , Acquaah-Mensah George , Gabrielson Edward , Biswal Shyam , Hatzivassiliou Georgia
Published: April 2023

Fig. S4, related to Fig. 4.
Table S3 from TIGIT Expression Is Associated with T-cell Suppression and Exhaustion and Predicts Clinical Outcome and Anti–PD-1 Response in Follicular Lymphoma
Authors: Yang Zhi-Zhang , Kim Hyo Jin , Wu Hongyan , Jalali Shahrzad , Tang Xinyi , Krull Jordan E. , Ding Wei , Novak Anne J. , Ansell Stephen M.
Published: April 2023

Cox analysis for TIGIT subsets
Table S1 from TIGIT Expression Is Associated with T-cell Suppression and Exhaustion and Predicts Clinical Outcome and Anti–PD-1 Response in Follicular Lymphoma
Authors: Yang Zhi-Zhang , Kim Hyo Jin , Wu Hongyan , Jalali Shahrzad , Tang Xinyi , Krull Jordan E. , Ding Wei , Novak Anne J. , Ansell Stephen M.
Published: April 2023

Patient characteristics
Supplementary Figures and Tables from A Novel Neoplastic Fusion Transcript, RAD51AP1-DYRK4, Confers Sensitivity to the MEK Inhibitor Trametinib in Aggressive Breast Cancers
Authors: Liu Chia-Chia , Veeraraghavan Jamunarani , Tan Ying , Kim Jin-Ah , Wang Xian , Loo Suet Kee , Lee Sanghoon , Hu Yiheng , Wang Xiao-Song
Published: April 2023

Supplementary file containing supplementary figures and tables.
Figure S5 from TIGIT Expression Is Associated with T-cell Suppression and Exhaustion and Predicts Clinical Outcome and Anti–PD-1 Response in Follicular Lymphoma
Authors: Yang Zhi-Zhang , Kim Hyo Jin , Wu Hongyan , Jalali Shahrzad , Tang Xinyi , Krull Jordan E. , Ding Wei , Novak Anne J. , Ansell Stephen M.
Published: April 2023

(A) The viSNE plots showing TIGIT expression by CD3+ cells from FL patients before or after therapy with pembrolizumab. Graphs showing number (%) of TIGIT+ or TIGIT expression level (mean) in CD3+ population in each group. (B) Histograms showing expression of PD-1, TIM-3, ICOS, LAG-3, CTLA-4, CD127, CCR7 and CD28 by subsets 3, 8, 5 and 6 that differed in numbers between groups of before and after pembrolizumab treatment. Graphs below showing expression level (mean) of PD-1, TIM-3, ICOS, LAG-3, CTLA-4, CD127, CCR7 and CD28 by subsets 3, 8, 5 and 6. (C) The viSNE plot from a representative FL sample showing CD28 expression by CD4+ or CD8+TIGIT+ cells. Graph showing number (%) of CD28+ cells in CD4+ or CD8+TIGIT+.
Supplementary Table 4 from A Performance Comparison of Commonly Used Assays to Detect RET Fusions
Authors: Yang Soo-Ryum , Aypar Umut , Rosen Ezra Y. , Mata Douglas A. , Benayed Ryma , Mullaney Kerry , Jayakumaran Gowtham , Zhang Yanming , Frosina Denise , Drilon Alexander , Ladanyi Marc , Jungbluth Achim A. , Rekhtman Natasha , Hechtman Jaclyn F.
Published: April 2023

Supplementary Table 4: RET inhibition in fusion-positive tumors with low or absent RET IHC expression.
Supplementary Table 3 from A Performance Comparison of Commonly Used Assays to Detect RET Fusions
Authors: Yang Soo-Ryum , Aypar Umut , Rosen Ezra Y. , Mata Douglas A. , Benayed Ryma , Mullaney Kerry , Jayakumaran Gowtham , Zhang Yanming , Frosina Denise , Drilon Alexander , Ladanyi Marc , Jungbluth Achim A. , Rekhtman Natasha , Hechtman Jaclyn F.
Published: April 2023

Supplementary Table 3: Prevalence of oncogenic RET fusions in solid tumors analyzed by MSK-IMPACT.
Legends for Supplementary Figure S1 from A Performance Comparison of Commonly Used Assays to Detect RET Fusions
Authors: Yang Soo-Ryum , Aypar Umut , Rosen Ezra Y. , Mata Douglas A. , Benayed Ryma , Mullaney Kerry , Jayakumaran Gowtham , Zhang Yanming , Frosina Denise , Drilon Alexander , Ladanyi Marc , Jungbluth Achim A. , Rekhtman Natasha , Hechtman Jaclyn F.
Published: April 2023

Supplementary Figure 1: (A) RET SVUS that did not express RET fusion transcripts on RNA sequencing (group D cases). (B) Location of KIF5B (NM_004521), RET (NM_020975), NCOA4 (NM_001145260), and CCDC6 (NM_005436) in relation to the break-apart FISH probes on chromosome 10. Red (5') and green (3') probes for FISH are provided. The distance between KIF5B and RET is approximately 11.2 Mb, whereas the distance between NCOA4 and RET is approximately 7.9 Mb.
Figure S5 from The Genetic Evolution of Treatment-Resistant Cutaneous, Acral, and Uveal Melanomas
Authors: Makohon-Moore Alvin P. , Lipson Evan J. , Hooper Jody E. , Zucker Amanda , Hong Jungeui , Bielski Craig M. , Hayashi Akimasa , Tokheim Collin , Baez Priscilla , Kappagantula Rajya , Kohutek Zachary , Makarov Vladimir , Riaz Nadeem , Postow Michael A. , Chapman Paul B. , Karchin Rachel , Socci Nicholas D. , Solit David B. , Chan Timothy A. , Taylor Barry S. , Topalian Suzanne L. , Iacobuzio-Donahue Christine A.
Published: April 2023

Figure S5 shows the Jaccard similarity coefficients across the seven melanoma cases.
Figure S3 from The Genetic Evolution of Treatment-Resistant Cutaneous, Acral, and Uveal Melanomas
Authors: Makohon-Moore Alvin P. , Lipson Evan J. , Hooper Jody E. , Zucker Amanda , Hong Jungeui , Bielski Craig M. , Hayashi Akimasa , Tokheim Collin , Baez Priscilla , Kappagantula Rajya , Kohutek Zachary , Makarov Vladimir , Riaz Nadeem , Postow Michael A. , Chapman Paul B. , Karchin Rachel , Socci Nicholas D. , Solit David B. , Chan Timothy A. , Taylor Barry S. , Topalian Suzanne L. , Iacobuzio-Donahue Christine A.
Published: April 2023

Figure S3 shows mutation signatures identified.
Supplemental Figure 8 from Blocking IL1 Beta Promotes Tumor Regression and Remodeling of the Myeloid Compartment in a Renal Cell Carcinoma Model: Multidimensional Analyses
Authors: Aggen David H. , Ager Casey R. , Obradovic Aleksandar Z. , Chowdhury Nivedita , Ghasemzadeh Ali , Mao Wendy , Chaimowitz Matthew G. , Lopez-Bujanda Zoila A. , Spina Catherine S. , Hawley Jessica E. , Dallos Matthew C. , Zhang Cheng , Wang Vinson , Li Hu , Guo Xinzheng V. , Drake Charles G.
Published: April 2023

Evaluation of T cell depletion on the efficacy of combination cabozantinib and anti-interleukin-1b immunotherapy.
Supplemental Figure 6 from Blocking IL1 Beta Promotes Tumor Regression and Remodeling of the Myeloid Compartment in a Renal Cell Carcinoma Model: Multidimensional Analyses
Authors: Aggen David H. , Ager Casey R. , Obradovic Aleksandar Z. , Chowdhury Nivedita , Ghasemzadeh Ali , Mao Wendy , Chaimowitz Matthew G. , Lopez-Bujanda Zoila A. , Spina Catherine S. , Hawley Jessica E. , Dallos Matthew C. , Zhang Cheng , Wang Vinson , Li Hu , Guo Xinzheng V. , Drake Charles G.
Published: April 2023

Visualization of top 5 upregulated RNA transcripts associated with each cluster.
Supplementary Appendix from Integration of Genomic and Transcriptomic Markers Improves the Prognosis Prediction of Acute Promyelocytic Leukemia
Authors: Lin Xiaojing , Qiao Niu , Shen Yang , Fang Hai , Xue Qing , Cui Bowen , Chen Li , Zhu Hongming , Zhang Sujiang , Chen Yu , Jiang Lu , Wang Shengyue , Li Junmin , Wang Bingshun , Chen Bing , Chen Zhu , Chen Saijuan
Published: April 2023

Supplementary methods
Supplemental Figure 3 from Blocking IL1 Beta Promotes Tumor Regression and Remodeling of the Myeloid Compartment in a Renal Cell Carcinoma Model: Multidimensional Analyses
Authors: Aggen David H. , Ager Casey R. , Obradovic Aleksandar Z. , Chowdhury Nivedita , Ghasemzadeh Ali , Mao Wendy , Chaimowitz Matthew G. , Lopez-Bujanda Zoila A. , Spina Catherine S. , Hawley Jessica E. , Dallos Matthew C. , Zhang Cheng , Wang Vinson , Li Hu , Guo Xinzheng V. , Drake Charles G.
Published: April 2023

Immune cell phenotyping of tumor draining lymph nodes from RENCA tumor bearing mice.