bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table 3 from RAD51 foci as a biomarker predictive of platinum chemotherapy response in ovarian cancer
Authors: Compadre Amanda J. , van Biljon Lillian N. , Valentine Mark C. , Llop-Guevara Alba , Graham Emily , Fashemi Bisiayo , Herencia-Ropero Andrea , Kotnik Emilee N. , Cooper Isaac , Harrington Shariska P. , Kuroki Lindsay M. , McCourt Carolyn K. , Hagemann Andrea R. , Thaker Premal H. , Mutch David G. , Powell Matthew A. , Sun Lulu , Mosammaparast Nima , Serra Violeta , Zhao Peinan , Lomonosova Elena , Khabele Dineo , Mullen Mary M.
Published: September 2024

Patient characteristics of patient-derived ovarian cancer organoids
Supplementary Table 2 from RAD51 foci as a biomarker predictive of platinum chemotherapy response in ovarian cancer
Authors: Compadre Amanda J. , van Biljon Lillian N. , Valentine Mark C. , Llop-Guevara Alba , Graham Emily , Fashemi Bisiayo , Herencia-Ropero Andrea , Kotnik Emilee N. , Cooper Isaac , Harrington Shariska P. , Kuroki Lindsay M. , McCourt Carolyn K. , Hagemann Andrea R. , Thaker Premal H. , Mutch David G. , Powell Matthew A. , Sun Lulu , Mosammaparast Nima , Serra Violeta , Zhao Peinan , Lomonosova Elena , Khabele Dineo , Mullen Mary M.
Published: September 2024

Patient characteristics of patient-derived ovarian cancer cells
Supplementary Table 1 from RAD51 foci as a biomarker predictive of platinum chemotherapy response in ovarian cancer
Authors: Compadre Amanda J. , van Biljon Lillian N. , Valentine Mark C. , Llop-Guevara Alba , Graham Emily , Fashemi Bisiayo , Herencia-Ropero Andrea , Kotnik Emilee N. , Cooper Isaac , Harrington Shariska P. , Kuroki Lindsay M. , McCourt Carolyn K. , Hagemann Andrea R. , Thaker Premal H. , Mutch David G. , Powell Matthew A. , Sun Lulu , Mosammaparast Nima , Serra Violeta , Zhao Peinan , Lomonosova Elena , Khabele Dineo , Mullen Mary M.
Published: September 2024

Summary of Antibodies
Supplementary Figure S1 from RAD51 foci as a biomarker predictive of platinum chemotherapy response in ovarian cancer
Authors: Compadre Amanda J. , van Biljon Lillian N. , Valentine Mark C. , Llop-Guevara Alba , Graham Emily , Fashemi Bisiayo , Herencia-Ropero Andrea , Kotnik Emilee N. , Cooper Isaac , Harrington Shariska P. , Kuroki Lindsay M. , McCourt Carolyn K. , Hagemann Andrea R. , Thaker Premal H. , Mutch David G. , Powell Matthew A. , Sun Lulu , Mosammaparast Nima , Serra Violeta , Zhao Peinan , Lomonosova Elena , Khabele Dineo , Mullen Mary M.
Published: September 2024

Flow diagram of HGSOC patient-derived samples used for RAD51 foci assay
Supplementary Table 5 from Clinicopathologic, genomic, and immunophenotypic landscape of ATM mutations in non-small cell lung cancer
Authors: Ricciuti Biagio , Elkrief Arielle , Alessi Joao , Wang Xinan , Li Yvonne , Gupta Hersh , Muldoon Daniel M. , Bertram Arrien A. , Pecci Federica , Lamberti Giuseppe , Di Federico Alessandro , Barrichello Adriana , Vaz Victor R. , Gandhi Malini , Lee Elinton , Shapiro Geoffrey I. , Park Hyesun , Nishino Mizuki , Lindsay James , Felt Kristen D. , Sharma Bijaya , Cherniack Andrew D. , Rodig Scott , Gomez Daniel R. , Shaverdian Narek , Rakaee Mehrdad , Bandlamudi Chaitanya , Ladanyi Marc , Janne Pasi A. , Schoenfeld Adam J. , Sholl Lynette M. , Awad Mark M. , Cheng Michael L.
Published: September 2024

Supplementary Table 5. List of ATM mutations with matched IHC
Supplementary Table 4 from Clinicopathologic, genomic, and immunophenotypic landscape of ATM mutations in non-small cell lung cancer
Authors: Ricciuti Biagio , Elkrief Arielle , Alessi Joao , Wang Xinan , Li Yvonne , Gupta Hersh , Muldoon Daniel M. , Bertram Arrien A. , Pecci Federica , Lamberti Giuseppe , Di Federico Alessandro , Barrichello Adriana , Vaz Victor R. , Gandhi Malini , Lee Elinton , Shapiro Geoffrey I. , Park Hyesun , Nishino Mizuki , Lindsay James , Felt Kristen D. , Sharma Bijaya , Cherniack Andrew D. , Rodig Scott , Gomez Daniel R. , Shaverdian Narek , Rakaee Mehrdad , Bandlamudi Chaitanya , Ladanyi Marc , Janne Pasi A. , Schoenfeld Adam J. , Sholl Lynette M. , Awad Mark M. , Cheng Michael L.
Published: September 2024

Supplementary Table 4. Baseline clinicopathologic features of patients with ATM mutated NSCLC according ATM protein expression by immunohistochemistry.
Supplementary Figure 9 from Clinicopathologic, genomic, and immunophenotypic landscape of ATM mutations in non-small cell lung cancer
Authors: Ricciuti Biagio , Elkrief Arielle , Alessi Joao , Wang Xinan , Li Yvonne , Gupta Hersh , Muldoon Daniel M. , Bertram Arrien A. , Pecci Federica , Lamberti Giuseppe , Di Federico Alessandro , Barrichello Adriana , Vaz Victor R. , Gandhi Malini , Lee Elinton , Shapiro Geoffrey I. , Park Hyesun , Nishino Mizuki , Lindsay James , Felt Kristen D. , Sharma Bijaya , Cherniack Andrew D. , Rodig Scott , Gomez Daniel R. , Shaverdian Narek , Rakaee Mehrdad , Bandlamudi Chaitanya , Ladanyi Marc , Janne Pasi A. , Schoenfeld Adam J. , Sholl Lynette M. , Awad Mark M. , Cheng Michael L.
Published: September 2024

Supplementary Figure 9. (A) Disease free- and overall survival among patients with (A) stage I, and (B) stage II NSCLC according to ATM mutation status.
Supplementary Figure 4. from Clinicopathologic, genomic, and immunophenotypic landscape of ATM mutations in non-small cell lung cancer
Authors: Ricciuti Biagio , Elkrief Arielle , Alessi Joao , Wang Xinan , Li Yvonne , Gupta Hersh , Muldoon Daniel M. , Bertram Arrien A. , Pecci Federica , Lamberti Giuseppe , Di Federico Alessandro , Barrichello Adriana , Vaz Victor R. , Gandhi Malini , Lee Elinton , Shapiro Geoffrey I. , Park Hyesun , Nishino Mizuki , Lindsay James , Felt Kristen D. , Sharma Bijaya , Cherniack Andrew D. , Rodig Scott , Gomez Daniel R. , Shaverdian Narek , Rakaee Mehrdad , Bandlamudi Chaitanya , Ladanyi Marc , Janne Pasi A. , Schoenfeld Adam J. , Sholl Lynette M. , Awad Mark M. , Cheng Michael L.
Published: September 2024

Supplementary Figure 4. (A) Volcano plot showing gene mutations significantly enriched among NSCLCs harboring ATM missense mutations that were predicted to benign in silico versus NSCLCs without any ATM mutation. (B) Volcano plot showing gene mutations significantly enriched among ATMWT and ATMMUT samples in the TCGA-NSCLC cohort.
Supplementary Figure 21 from Clinicopathologic, genomic, and immunophenotypic landscape of ATM mutations in non-small cell lung cancer
Authors: Ricciuti Biagio , Elkrief Arielle , Alessi Joao , Wang Xinan , Li Yvonne , Gupta Hersh , Muldoon Daniel M. , Bertram Arrien A. , Pecci Federica , Lamberti Giuseppe , Di Federico Alessandro , Barrichello Adriana , Vaz Victor R. , Gandhi Malini , Lee Elinton , Shapiro Geoffrey I. , Park Hyesun , Nishino Mizuki , Lindsay James , Felt Kristen D. , Sharma Bijaya , Cherniack Andrew D. , Rodig Scott , Gomez Daniel R. , Shaverdian Narek , Rakaee Mehrdad , Bandlamudi Chaitanya , Ladanyi Marc , Janne Pasi A. , Schoenfeld Adam J. , Sholl Lynette M. , Awad Mark M. , Cheng Michael L.
Published: September 2024

Supplementary Figure 21. (A) Intratumoral, (B) tumor-stroma interface, and (C) total CD8+ PD1+ T cells in ATMMUT and ATMWT NSCLCs. (D) Intratumoral, (E) tumor-stroma interface, and (F) total FOXP3+ immune cells in ATMMUT and ATMWT NSCLCs.
Supplementary Figure 12 from Clinicopathologic, genomic, and immunophenotypic landscape of ATM mutations in non-small cell lung cancer
Authors: Ricciuti Biagio , Elkrief Arielle , Alessi Joao , Wang Xinan , Li Yvonne , Gupta Hersh , Muldoon Daniel M. , Bertram Arrien A. , Pecci Federica , Lamberti Giuseppe , Di Federico Alessandro , Barrichello Adriana , Vaz Victor R. , Gandhi Malini , Lee Elinton , Shapiro Geoffrey I. , Park Hyesun , Nishino Mizuki , Lindsay James , Felt Kristen D. , Sharma Bijaya , Cherniack Andrew D. , Rodig Scott , Gomez Daniel R. , Shaverdian Narek , Rakaee Mehrdad , Bandlamudi Chaitanya , Ladanyi Marc , Janne Pasi A. , Schoenfeld Adam J. , Sholl Lynette M. , Awad Mark M. , Cheng Michael L.
Published: September 2024

Supplementary Figure 12. Disease-free survival and overall survival among patients with (A) stage I, (B) stage II, and (C) stage III NSCLC according to ATM expression by immunohistochemistry.
Supplementary Figure 1. from Clinicopathologic, genomic, and immunophenotypic landscape of ATM mutations in non-small cell lung cancer
Authors: Ricciuti Biagio , Elkrief Arielle , Alessi Joao , Wang Xinan , Li Yvonne , Gupta Hersh , Muldoon Daniel M. , Bertram Arrien A. , Pecci Federica , Lamberti Giuseppe , Di Federico Alessandro , Barrichello Adriana , Vaz Victor R. , Gandhi Malini , Lee Elinton , Shapiro Geoffrey I. , Park Hyesun , Nishino Mizuki , Lindsay James , Felt Kristen D. , Sharma Bijaya , Cherniack Andrew D. , Rodig Scott , Gomez Daniel R. , Shaverdian Narek , Rakaee Mehrdad , Bandlamudi Chaitanya , Ladanyi Marc , Janne Pasi A. , Schoenfeld Adam J. , Sholl Lynette M. , Awad Mark M. , Cheng Michael L.
Published: September 2024

Supplementary Figure 1. (A) ATM mutation classification schema (B) Lollipop plot of all 714 mutations in the ATM gene identified in the combined DFCI/MSK cohort. (C) Lollipop plot of all 152 benign mutations in the ATM gene identified in the combined DFCI/MSK cohort.
Supplementary Table S4 from Devimistat in combination with gemcitabine and cisplatin in biliary tract cancer: Pre-clinical evaluation and phase 1b multicenter clinical trial (BilT-04)
Authors: Mohan Arathi , Griffith Kent A. , Wuchu Fulei , Zhen David B. , Kumar-Sinha Chandan , Crysler Oxana , Hsiehchen David , Enzler Thomas , Dippman Dominique , Gunchick Valerie , Achreja Abhinav , Animasahun Olamide , Choppara Srinadh , Nenwani Minal , Chinnaiyan Arul M. , Nagrath Deepak , Zalupski Mark M. , Sahai Vaibhav
Published: September 2024

Genomics data
Supplementary Table S2 from Devimistat in combination with gemcitabine and cisplatin in biliary tract cancer: Pre-clinical evaluation and phase 1b multicenter clinical trial (BilT-04)
Authors: Mohan Arathi , Griffith Kent A. , Wuchu Fulei , Zhen David B. , Kumar-Sinha Chandan , Crysler Oxana , Hsiehchen David , Enzler Thomas , Dippman Dominique , Gunchick Valerie , Achreja Abhinav , Animasahun Olamide , Choppara Srinadh , Nenwani Minal , Chinnaiyan Arul M. , Nagrath Deepak , Zalupski Mark M. , Sahai Vaibhav
Published: September 2024

Representativeness of Study Participants
Supplemental Fig. S3 from Clonal Hematopoiesis in Young Women Treated for Breast Cancer
Authors: Gibson Christopher J. , Fell Geoffrey G. , Sella Tal , Sperling Adam S. , Snow Craig , Rosenberg Shoshana M. , Kirkner Gregory , Patel Ashka , Dillon Deborah , Bick Alexander G. , Neuberg Donna , Partridge Ann H. , Miller Peter G.
Published: September 2024

Longitudinal Mutation Analysis in the YWS
Supplemental Fig. S2 from Clonal Hematopoiesis in Young Women Treated for Breast Cancer
Authors: Gibson Christopher J. , Fell Geoffrey G. , Sella Tal , Sperling Adam S. , Snow Craig , Rosenberg Shoshana M. , Kirkner Gregory , Patel Ashka , Dillon Deborah , Bick Alexander G. , Neuberg Donna , Partridge Ann H. , Miller Peter G.
Published: September 2024

Associations between Clonal Hematopoiesis (CH) and Survival
in the YWS
Supplementary Table S9 from Type 2 diabetes mellitus and efficacy outcomes from imune checkpoint blockade in patients with cancer
Authors: Cortellini Alessio , D'Alessio Antonio , Cleary Siobhan , Buti Sebastiano , Bersanelli Melissa , Bordi Paola , Tonini Giuseppe , Vincenzi Bruno , Tucci Marco , Russo Alessandro , Pantano Francesco , Russano Marco , Stucci Luigia Stefania , Sergi Maria Chiara , Falconi Martina , Zarzana Maria Antonietta. , Santini Daniele , Spagnolo Francesco , Tanda Enrica T. , Rastelli Francesca , Giorgi Francesca Chiara. , Pergolesi Federica , Giusti Raffaele , Filetti Marco , Lo Bianco Francesca , Marchetti Paolo , Botticelli Andrea , Gelibter Alain , Siringo Marco , Ferrari Marco , Marconcini Riccardo , Vitale Maria Giuseppa. , Nicolardi Linda , Chiari Rita , Ghidini Michele , Nigro Olga , Grossi Francesco , De Tursi Michele , Di Marino Pietro , Queirolo Paola , Bracarda Sergio , Macrini Serena , Inno Alessandro , Zoratto Federica , Veltri Enzo , Spoto Chiara , Vitale Maria Grazia. , Cannita Katia , Gennari Alessandra , Morganstein Daniel L. , Mallardo Domenico , Nibid Lorenzo , Sabarese Giovanna , Brunetti Leonardo , Perrone Giuseppe , Ascierto Paolo A. , Ficorella Corrado , Pinato David J.
Published: September 2024

Summary of baseline characteristics’ distribution after the propensity score matching procedure between patients on other antidiabetic drugs/insulin only and those who were not on diabetes medications (ratio 1:3, caliper 0.1).
Supplementary Table S6 from Type 2 diabetes mellitus and efficacy outcomes from imune checkpoint blockade in patients with cancer
Authors: Cortellini Alessio , D'Alessio Antonio , Cleary Siobhan , Buti Sebastiano , Bersanelli Melissa , Bordi Paola , Tonini Giuseppe , Vincenzi Bruno , Tucci Marco , Russo Alessandro , Pantano Francesco , Russano Marco , Stucci Luigia Stefania , Sergi Maria Chiara , Falconi Martina , Zarzana Maria Antonietta. , Santini Daniele , Spagnolo Francesco , Tanda Enrica T. , Rastelli Francesca , Giorgi Francesca Chiara. , Pergolesi Federica , Giusti Raffaele , Filetti Marco , Lo Bianco Francesca , Marchetti Paolo , Botticelli Andrea , Gelibter Alain , Siringo Marco , Ferrari Marco , Marconcini Riccardo , Vitale Maria Giuseppa. , Nicolardi Linda , Chiari Rita , Ghidini Michele , Nigro Olga , Grossi Francesco , De Tursi Michele , Di Marino Pietro , Queirolo Paola , Bracarda Sergio , Macrini Serena , Inno Alessandro , Zoratto Federica , Veltri Enzo , Spoto Chiara , Vitale Maria Grazia. , Cannita Katia , Gennari Alessandra , Morganstein Daniel L. , Mallardo Domenico , Nibid Lorenzo , Sabarese Giovanna , Brunetti Leonardo , Perrone Giuseppe , Ascierto Paolo A. , Ficorella Corrado , Pinato David J.
Published: September 2024

Summary of baseline characteristics’ distribution between patients on metformin only and those who were not on diabetes medications.
Supplementary Table S3 from Type 2 diabetes mellitus and efficacy outcomes from imune checkpoint blockade in patients with cancer
Authors: Cortellini Alessio , D'Alessio Antonio , Cleary Siobhan , Buti Sebastiano , Bersanelli Melissa , Bordi Paola , Tonini Giuseppe , Vincenzi Bruno , Tucci Marco , Russo Alessandro , Pantano Francesco , Russano Marco , Stucci Luigia Stefania , Sergi Maria Chiara , Falconi Martina , Zarzana Maria Antonietta. , Santini Daniele , Spagnolo Francesco , Tanda Enrica T. , Rastelli Francesca , Giorgi Francesca Chiara. , Pergolesi Federica , Giusti Raffaele , Filetti Marco , Lo Bianco Francesca , Marchetti Paolo , Botticelli Andrea , Gelibter Alain , Siringo Marco , Ferrari Marco , Marconcini Riccardo , Vitale Maria Giuseppa. , Nicolardi Linda , Chiari Rita , Ghidini Michele , Nigro Olga , Grossi Francesco , De Tursi Michele , Di Marino Pietro , Queirolo Paola , Bracarda Sergio , Macrini Serena , Inno Alessandro , Zoratto Federica , Veltri Enzo , Spoto Chiara , Vitale Maria Grazia. , Cannita Katia , Gennari Alessandra , Morganstein Daniel L. , Mallardo Domenico , Nibid Lorenzo , Sabarese Giovanna , Brunetti Leonardo , Perrone Giuseppe , Ascierto Paolo A. , Ficorella Corrado , Pinato David J.
Published: September 2024

Summary of baseline characteristics’ distribution after the propensity score matching procedure between patients on diabetes medications and those who were not receiving diabetes medications (ratio 1:2, caliper 0.1).
Supplementary Table S10 from Type 2 diabetes mellitus and efficacy outcomes from imune checkpoint blockade in patients with cancer
Authors: Cortellini Alessio , D'Alessio Antonio , Cleary Siobhan , Buti Sebastiano , Bersanelli Melissa , Bordi Paola , Tonini Giuseppe , Vincenzi Bruno , Tucci Marco , Russo Alessandro , Pantano Francesco , Russano Marco , Stucci Luigia Stefania , Sergi Maria Chiara , Falconi Martina , Zarzana Maria Antonietta. , Santini Daniele , Spagnolo Francesco , Tanda Enrica T. , Rastelli Francesca , Giorgi Francesca Chiara. , Pergolesi Federica , Giusti Raffaele , Filetti Marco , Lo Bianco Francesca , Marchetti Paolo , Botticelli Andrea , Gelibter Alain , Siringo Marco , Ferrari Marco , Marconcini Riccardo , Vitale Maria Giuseppa. , Nicolardi Linda , Chiari Rita , Ghidini Michele , Nigro Olga , Grossi Francesco , De Tursi Michele , Di Marino Pietro , Queirolo Paola , Bracarda Sergio , Macrini Serena , Inno Alessandro , Zoratto Federica , Veltri Enzo , Spoto Chiara , Vitale Maria Grazia. , Cannita Katia , Gennari Alessandra , Morganstein Daniel L. , Mallardo Domenico , Nibid Lorenzo , Sabarese Giovanna , Brunetti Leonardo , Perrone Giuseppe , Ascierto Paolo A. , Ficorella Corrado , Pinato David J.
Published: September 2024

Detailed random blood sugar test results used to compute the median baseline glycaemia (MBG). 133 patients included (30 from the Pascale Cancer Institute and 103 from Imperial College London Cohort.
Supplementary Table 2 from Metastatic Prostate Cancers with BRCA2 versus ATM Mutations Exhibit Divergent Molecular Features and Clinical Outcomes
Authors: Hwang Justin , Shi Xiaolei , Elliott Andrew , Arnoff Taylor E. , McGrath Julie , Xiu Joanne , Walker Phillip , Bergom Hannah E. , Day Abderrahman , Ahmed Shihab , Tape Sydney , Makovec Allison , Ali Atef , Shaker Rami M. , Toye Eamon , Passow Rachel , Lozada John R. , Wang Jinhua , Lou Emil , Mouw Kent W. , Carneiro Benedito A. , Heath Elisabeth I. , McKay Rana R. , Korn W. Michael , Nabhan Chadi , Ryan Charles J. , Antonarakis Emmanuel S.
Published: September 2024

Comparison of the frequencies of additional molecular features between non-castrate (NC) and castrate (C) samples in ATMm, BRCA2m, HRDother, and HRP groups. The significant differences between the two groups are highlighted (red box).
Trial protocol 1 from Efficacy of nivolumab in pediatric cancers with high mutation burden and mismatch-repair deficiency
Authors: Das Anirban , Tabori Uri , Sambira Nahum Lauren C. , Collins Natalie B. , Deyell Rebecca , Dvir Rina , Faure-Conter Cecile , Hassall Timothy E. , Minturn Jane E. , Edwards Melissa , Brookes Elissa , Bianchi Vanessa , Levine Adrian , Stone Simone C. , Sudhaman Sumedha , Sanchez-Ramirez Santiago , Ercan Ayse B. , Stengs Lucie , Chung Jiil , Negm Logine , Getz Gad , Maruvka Yosef E. , Ertl-Wagner Birgit , Ohashi Pamela S. , Pugh Trevor , Hawkins Cynthia , Bouffet Eric , Morgenstern Daniel A.
Published: September 2024

Full trial protocol NCT02992964
Suppl Table S2 from Efficacy of nivolumab in pediatric cancers with high mutation burden and mismatch-repair deficiency
Authors: Das Anirban , Tabori Uri , Sambira Nahum Lauren C. , Collins Natalie B. , Deyell Rebecca , Dvir Rina , Faure-Conter Cecile , Hassall Timothy E. , Minturn Jane E. , Edwards Melissa , Brookes Elissa , Bianchi Vanessa , Levine Adrian , Stone Simone C. , Sudhaman Sumedha , Sanchez-Ramirez Santiago , Ercan Ayse B. , Stengs Lucie , Chung Jiil , Negm Logine , Getz Gad , Maruvka Yosef E. , Ertl-Wagner Birgit , Ohashi Pamela S. , Pugh Trevor , Hawkins Cynthia , Bouffet Eric , Morgenstern Daniel A.
Published: September 2024

Results of time-dependent co-variate and landmark analyses at time-points 3 and 6 months of the trial
Supplementary Fig. 1 from Monitoring sarcoma response to immune checkpoint inhibition and local cryotherapy with circulating tumor DNA analysis
Authors: Bui Nam Q. , Nemat-Gorgani Neda , Subramanian Ajay , Torres Ileana A. , Lohman Marta , Sears Timothy J. , van de Rijn Matt , Charville Gregory W. , Becker Hans-Christoph , Wang David S. , Hwang Gloria L. , Ganjoo Kristen N. , Moding Everett J.
Published: September 2024

Supplementary Fig. 1
Supplementary Data 1 from Monitoring sarcoma response to immune checkpoint inhibition and local cryotherapy with circulating tumor DNA analysis
Authors: Bui Nam Q. , Nemat-Gorgani Neda , Subramanian Ajay , Torres Ileana A. , Lohman Marta , Sears Timothy J. , van de Rijn Matt , Charville Gregory W. , Becker Hans-Christoph , Wang David S. , Hwang Gloria L. , Ganjoo Kristen N. , Moding Everett J.
Published: September 2024

Supplementary Tables S1-S5
Supplementary Fig. 3 from INTRAVENOUS N-ACETYLCYSTEINE TO PREVENT CISPLATIN-INDUCED HEARING LOSS IN CHILDREN: A NONRANDOMIZED CONTROLLED PHASE 1 TRIAL
Authors: Orgel Etan , Knight Kristin R. , Chi Yueh-Yun , Malvar Jemily , Rushing Teresa , Mena Victoria , Eisenberg Laurie S. , Rassekh Shahrad R. , Ross Colin JD. , Scott Erika N. , Neely Michael , Neuwelt Edward A. , Muldoon Leslie L. , Freyer David R.
Published: September 2024

Supplementary Fig. 3 Change in serum glutathione concentrations following NAC infusion
Supplementary Data 1 from INTRAVENOUS N-ACETYLCYSTEINE TO PREVENT CISPLATIN-INDUCED HEARING LOSS IN CHILDREN: A NONRANDOMIZED CONTROLLED PHASE 1 TRIAL
Authors: Orgel Etan , Knight Kristin R. , Chi Yueh-Yun , Malvar Jemily , Rushing Teresa , Mena Victoria , Eisenberg Laurie S. , Rassekh Shahrad R. , Ross Colin JD. , Scott Erika N. , Neely Michael , Neuwelt Edward A. , Muldoon Leslie L. , Freyer David R.
Published: September 2024

Supplemental Tables and Files
Table S4 from Resolving the pathogenesis of anaplastic Wilms tumors through spatial mapping of cancer cell evolution
Authors: Rastegar Bahar , Andersson Natalie , Petersson Alexandra , Karlsson Jenny , Chattopadhyay Subhayan , Valind Anders , Jansson Caroline , Durand Geoffroy , Romerius Patrik , Jirstrom Karin , Holmquist Mengelbier Linda , Gisselsson David
Published: September 2024

Supplementary Table 4. Segmental aberrations. All 20 Wilms tumor (WT) cases and their corresponding samples are listed. ‘Sample position’ refers to the individual sample and its position in a certain paraffin block (see Figure 1 for details.) For each genetic event the following information is given: the ploidy level (Ploidy), chromosome (chr), the genomic start and end positions, genetic events annotated as gain, loss, CNNI (copy neutral imbalance) or homozygous loss, the length of the aberration (bp), which chromosomal cytoband, the median log2 ratio, allelic composition and mutated cell fraction (MCF). IR= intermediate risk, BT= blastemal type, DA= diffuse anaplasia. Genomic positions accordning to hg19.
Supplementary Table S5 from TIGIT expression delineates T cell populations with distinct functional and prognostic impact in pancreatic cancer
Authors: Heiduk Max , Klimova Anna , Reiche Charlotte , Digomann David , Beer Carolin , Aust Daniela E. , Distler Marius , Weitz Jürgen , Seifert Adrian M. , Seifert Lena
Published: September 2024

Proportion of PD-1+ or TIGIT+ cells of CD8+ T cells, Tconv or Treg ± standard deviation in PDAC according to clinicopathological parameters. Statistics (Stat.) with unpaired two-sided t-test or one-way ANOVA, respectively. *, P < 0.05; **, P < 0.01
Supplementary Table S2 from TIGIT expression delineates T cell populations with distinct functional and prognostic impact in pancreatic cancer
Authors: Heiduk Max , Klimova Anna , Reiche Charlotte , Digomann David , Beer Carolin , Aust Daniela E. , Distler Marius , Weitz Jürgen , Seifert Adrian M. , Seifert Lena
Published: September 2024

Antibodies used for flow cytometry.
Supplementary Figure S9 from TIGIT expression delineates T cell populations with distinct functional and prognostic impact in pancreatic cancer
Authors: Heiduk Max , Klimova Anna , Reiche Charlotte , Digomann David , Beer Carolin , Aust Daniela E. , Distler Marius , Weitz Jürgen , Seifert Adrian M. , Seifert Lena
Published: September 2024

General EOMES expression and expression as a function of PD-1 and TIGIT in blood.
Supplementary Figure S8 from TIGIT expression delineates T cell populations with distinct functional and prognostic impact in pancreatic cancer
Authors: Heiduk Max , Klimova Anna , Reiche Charlotte , Digomann David , Beer Carolin , Aust Daniela E. , Distler Marius , Weitz Jürgen , Seifert Adrian M. , Seifert Lena
Published: September 2024

General CD39 and CD103 expression and expression as a function of PD-1 and TIGIT in blood.
Supplementary Figure S6 from TIGIT expression delineates T cell populations with distinct functional and prognostic impact in pancreatic cancer
Authors: Heiduk Max , Klimova Anna , Reiche Charlotte , Digomann David , Beer Carolin , Aust Daniela E. , Distler Marius , Weitz Jürgen , Seifert Adrian M. , Seifert Lena
Published: September 2024

Cytokine expression in blood and matched PDAC.
Supplementary Figure S4 from TIGIT expression delineates T cell populations with distinct functional and prognostic impact in pancreatic cancer
Authors: Heiduk Max , Klimova Anna , Reiche Charlotte , Digomann David , Beer Carolin , Aust Daniela E. , Distler Marius , Weitz Jürgen , Seifert Adrian M. , Seifert Lena
Published: September 2024

Distribution of PD-1 and TIGIT co-expression and expression as a function of the differentiation status in blood.
Supplementary Figure S13 from TIGIT expression delineates T cell populations with distinct functional and prognostic impact in pancreatic cancer
Authors: Heiduk Max , Klimova Anna , Reiche Charlotte , Digomann David , Beer Carolin , Aust Daniela E. , Distler Marius , Weitz Jürgen , Seifert Adrian M. , Seifert Lena
Published: September 2024

. Illustration depicting T cell subsets that enable dichotomization of PDAC patients with significantly different survival functions.
Supplementary Table S2 from Targeting Replication Stress and Chemotherapy Resistance with a Combination of Sacituzumab Govitecan and Berzosertib: A Phase I Clinical Trial
Authors: Abel Melissa L. , Takahashi Nobuyuki , Peer Cody , Redon Christophe E. , Nichols Samantha , Vilimas Rasa , Lee Min-Jung , Lee Sunmin , Shelat Meenakshi , Kattapuram Robbie , Sciuto Linda , Pinkiert Danielle , Graham Chante , Butcher Donna , Karim Baktiar , Sharma Ajit Kumar. , Malin Justin , Kumar Rajesh , Schultz Christopher W. , Goyal Shubhank , Del Rivero Jaydira , Krishnamurthy Manan , Upadhyay Deep , Schroeder Brett , Sissung Tristan , Tyagi Manoj , Kim Jung , Pommier Yves , Aladjem Mirit , Raffeld Mark , Figg William Douglas. , Trepel Jane , Xi Liqiang , Desai Parth , Thomas Anish
Published: September 2024

Study Representativeness
Supplementary Table S1 from Targeting Replication Stress and Chemotherapy Resistance with a Combination of Sacituzumab Govitecan and Berzosertib: A Phase I Clinical Trial
Authors: Abel Melissa L. , Takahashi Nobuyuki , Peer Cody , Redon Christophe E. , Nichols Samantha , Vilimas Rasa , Lee Min-Jung , Lee Sunmin , Shelat Meenakshi , Kattapuram Robbie , Sciuto Linda , Pinkiert Danielle , Graham Chante , Butcher Donna , Karim Baktiar , Sharma Ajit Kumar. , Malin Justin , Kumar Rajesh , Schultz Christopher W. , Goyal Shubhank , Del Rivero Jaydira , Krishnamurthy Manan , Upadhyay Deep , Schroeder Brett , Sissung Tristan , Tyagi Manoj , Kim Jung , Pommier Yves , Aladjem Mirit , Raffeld Mark , Figg William Douglas. , Trepel Jane , Xi Liqiang , Desai Parth , Thomas Anish
Published: September 2024

Whole exome sequencing results
Supplementary Figure S1 from Targeting Replication Stress and Chemotherapy Resistance with a Combination of Sacituzumab Govitecan and Berzosertib: A Phase I Clinical Trial
Authors: Abel Melissa L. , Takahashi Nobuyuki , Peer Cody , Redon Christophe E. , Nichols Samantha , Vilimas Rasa , Lee Min-Jung , Lee Sunmin , Shelat Meenakshi , Kattapuram Robbie , Sciuto Linda , Pinkiert Danielle , Graham Chante , Butcher Donna , Karim Baktiar , Sharma Ajit Kumar. , Malin Justin , Kumar Rajesh , Schultz Christopher W. , Goyal Shubhank , Del Rivero Jaydira , Krishnamurthy Manan , Upadhyay Deep , Schroeder Brett , Sissung Tristan , Tyagi Manoj , Kim Jung , Pommier Yves , Aladjem Mirit , Raffeld Mark , Figg William Douglas. , Trepel Jane , Xi Liqiang , Desai Parth , Thomas Anish
Published: September 2024

Berzosertib pharmacodynamic assessment
Supplementary Table S7 from CD49d expression identifies a biologically distinct subtype of chronic lymphocytic leukemia with inferior progression-free survival on BTK inhibitor therapy.
Authors: Alsadhan Anfal , Chen Jonathan , Gaglione Erika M. , Underbayev Chingiz , Tuma Pamela L. , Tian Xin , Freeman Lita A. , Baskar Sivasubramanian , Nierman Pia , Soto Susan , Itsara Andy , Ahn Inhye E. , Sun Clare , Bibikova Elena , Hartmann Tanja Nicole. , Mhibik Maissa , Wiestner Adrian
Published: September 2024

Supplementary Table S7. DEGs for 1 month Comparison of CD49d+ and CD49d-
Supplementary Table S10 from CD49d expression identifies a biologically distinct subtype of chronic lymphocytic leukemia with inferior progression-free survival on BTK inhibitor therapy.
Authors: Alsadhan Anfal , Chen Jonathan , Gaglione Erika M. , Underbayev Chingiz , Tuma Pamela L. , Tian Xin , Freeman Lita A. , Baskar Sivasubramanian , Nierman Pia , Soto Susan , Itsara Andy , Ahn Inhye E. , Sun Clare , Bibikova Elena , Hartmann Tanja Nicole. , Mhibik Maissa , Wiestner Adrian
Published: September 2024

Supplementary Table S10. Outcome Data
Figure S6 from A multiparameter molecular classifier to predict response to neoadjuvant lapatinib plus trastuzumab without chemotherapy in HER2+ breast cancer
Authors: Veeraraghavan Jamunarani , Gutierrez Carolina , De Angelis Carmine , Davis Robert , Wang Tao , Pascual Tomas , Selenica Pier , Sanchez Katherine , Nitta Hiroaki , Kapadia Monesh , Pavlick Anne C. , Galván Patricia , Rexer Brent , Forero-Torres Andres , Nanda Rita , Storniolo Anna M. , Krop Ian E. , Goetz Matthew P. , Nangia Julie R. , Wolff Antonio C. , Weigelt Britta , Reis-Filho Jorge S. , Hilsenbeck Susan G. , Prat Aleix , Osborne C. Kent , Schiff Rachel , Rimawi Mothaffar F.
Published: September 2024

Supplementary Figure S6. Distribution of HER2 gene ratio in relation to PIK3CA mutation status and HER2-enriched subtype.
Figure S4 from A multiparameter molecular classifier to predict response to neoadjuvant lapatinib plus trastuzumab without chemotherapy in HER2+ breast cancer
Authors: Veeraraghavan Jamunarani , Gutierrez Carolina , De Angelis Carmine , Davis Robert , Wang Tao , Pascual Tomas , Selenica Pier , Sanchez Katherine , Nitta Hiroaki , Kapadia Monesh , Pavlick Anne C. , Galván Patricia , Rexer Brent , Forero-Torres Andres , Nanda Rita , Storniolo Anna M. , Krop Ian E. , Goetz Matthew P. , Nangia Julie R. , Wolff Antonio C. , Weigelt Britta , Reis-Filho Jorge S. , Hilsenbeck Susan G. , Prat Aleix , Osborne C. Kent , Schiff Rachel , Rimawi Mothaffar F.
Published: September 2024

Supplementary Figure S4. Decision tree algorithm to construct the multiparameter classifier of response in TBCRC023.
Figure S3 from A multiparameter molecular classifier to predict response to neoadjuvant lapatinib plus trastuzumab without chemotherapy in HER2+ breast cancer
Authors: Veeraraghavan Jamunarani , Gutierrez Carolina , De Angelis Carmine , Davis Robert , Wang Tao , Pascual Tomas , Selenica Pier , Sanchez Katherine , Nitta Hiroaki , Kapadia Monesh , Pavlick Anne C. , Galván Patricia , Rexer Brent , Forero-Torres Andres , Nanda Rita , Storniolo Anna M. , Krop Ian E. , Goetz Matthew P. , Nangia Julie R. , Wolff Antonio C. , Weigelt Britta , Reis-Filho Jorge S. , Hilsenbeck Susan G. , Prat Aleix , Osborne C. Kent , Schiff Rachel , Rimawi Mothaffar F.
Published: September 2024

Supplementary Figure S3. Distribution of intrinsic subtypes in (A) TBCRC023 and (B) PAMELA cohort.
Figure S2 from A multiparameter molecular classifier to predict response to neoadjuvant lapatinib plus trastuzumab without chemotherapy in HER2+ breast cancer
Authors: Veeraraghavan Jamunarani , Gutierrez Carolina , De Angelis Carmine , Davis Robert , Wang Tao , Pascual Tomas , Selenica Pier , Sanchez Katherine , Nitta Hiroaki , Kapadia Monesh , Pavlick Anne C. , Galván Patricia , Rexer Brent , Forero-Torres Andres , Nanda Rita , Storniolo Anna M. , Krop Ian E. , Goetz Matthew P. , Nangia Julie R. , Wolff Antonio C. , Weigelt Britta , Reis-Filho Jorge S. , Hilsenbeck Susan G. , Prat Aleix , Osborne C. Kent , Schiff Rachel , Rimawi Mothaffar F.
Published: September 2024

Supplementary Figure S2. Distribution of HER2 gene ratio and protein in the two neoadjuvant cohorts.
Supplementary Table S1 from Genomic profiling of radiation-induced sarcomas reveals the immunological characteristics and its response to immune checkpoint blockade
Authors: Hong Dong-Chun , Yang Jing , Sun Cong , Liu Yuan-Tao , Shen Lu-Jun , Xu Bu-Shu , Que Yi , Xia Xiaojun , Zhang Xing
Published: September 2024

Clinical characteristics of patients in RIS group and SARC group as a whole, or for WES, or for mRNA- seq.
Supplementary Figure S4 from Genomic profiling of radiation-induced sarcomas reveals the immunological characteristics and its response to immune checkpoint blockade
Authors: Hong Dong-Chun , Yang Jing , Sun Cong , Liu Yuan-Tao , Shen Lu-Jun , Xu Bu-Shu , Que Yi , Xia Xiaojun , Zhang Xing
Published: September 2024

The landscape of copy number variants and results for blood detection.
（A）Top genes in copy number changes in RIS and SARC groups filtered by COSMIC gene list.
（B）Top genes in copy number changes in RIFS and FS subtypes.
（C）Top genes in copy number changes in RIOS and OS subtypes.
(D and E）Flow cytometry (D) and ELISA (E) results of immune cells and cytokines in peripheral blood from patients.
Supplementary Figure S3 from Genomic profiling of radiation-induced sarcomas reveals the immunological characteristics and its response to immune checkpoint blockade
Authors: Hong Dong-Chun , Yang Jing , Sun Cong , Liu Yuan-Tao , Shen Lu-Jun , Xu Bu-Shu , Que Yi , Xia Xiaojun , Zhang Xing
Published: September 2024

Comparison between RIS group and SARC group in mRNA-seq and WES data.
(A) Expression levels of IDO and CTLA-4 in the RIS group and SARC group in mRNA-seq.
(B) The anti-tumor immunity score and the proliferation module score of the RIFS group and the RIOS group.
(C) The comparison of the anti-tumor immunity score and the proliferation module score between subtypes RIFS vs FS and between RIOS vs OS.
(D) Mutation summary of WES data in the RIS and SARC groups.
(E) Top 50 mutated genes in RIFS, FS, RIOS and OS subtype groups.
Supplementary Figure S1 from Genomic profiling of radiation-induced sarcomas reveals the immunological characteristics and its response to immune checkpoint blockade
Authors: Hong Dong-Chun , Yang Jing , Sun Cong , Liu Yuan-Tao , Shen Lu-Jun , Xu Bu-Shu , Que Yi , Xia Xiaojun , Zhang Xing
Published: September 2024

The flowchart showing patient screening and identification, and analysis steps for mRNA-seq and WES data. FS: fibrosarcoma; OS: osteosarcoma.
Supplementary Table S2 from The impact of germline alterations in appendiceal adenocarcinoma
Authors: Foote Michael B. , Walch Henry , Kemel Yelena , Vakiani Efsevia , Johannet Paul , Sheehan Margaret , Chatila Walid , Chung Sebastian , NASH Garrett , Maio Anna , Shia Jinru , Mandelker Diana , Berger Michael , Schultz Nikolaus , Diaz Luis A. , Cercek Andrea , Stadler Zsofia K.
Published: September 2024

Germline mutations present in the assessed cohort of patients with appendiceal adenocarcinoma.
Supplementary Table S1 from The impact of germline alterations in appendiceal adenocarcinoma
Authors: Foote Michael B. , Walch Henry , Kemel Yelena , Vakiani Efsevia , Johannet Paul , Sheehan Margaret , Chatila Walid , Chung Sebastian , NASH Garrett , Maio Anna , Shia Jinru , Mandelker Diana , Berger Michael , Schultz Nikolaus , Diaz Luis A. , Cercek Andrea , Stadler Zsofia K.
Published: September 2024

Genes evaluated by the MSK IMPACT germline sequencing panel
Supplementary Figure S7 from HLA class II loss and JAK1/2 deficiency coevolve in melanoma leading to CD4 T cell and IFNγ cross-resistance
Authors: Stupia Simone , Heeke Christina , Brüggemann Alicia , Zaremba Anne , Thier Beatrice , Kretz Julia , Sucker Antje , Philip Manuel , Zelinskyy Gennadiy , Ferrone Soldano , Roesch Alexander , Horn Susanne , Hadaschik Eva , Schadendorf Dirk , Trilling Mirko , Dittmer Ulf , Griewank Klaus , Zhao Fang , Paschen Annette
Published: September 2024

HLA-II APM transcript levels in melanoma biopsies from ICB-treated patients
Supplementary Figure S3 from HLA class II loss and JAK1/2 deficiency coevolve in melanoma leading to CD4 T cell and IFNγ cross-resistance
Authors: Stupia Simone , Heeke Christina , Brüggemann Alicia , Zaremba Anne , Thier Beatrice , Kretz Julia , Sucker Antje , Philip Manuel , Zelinskyy Gennadiy , Ferrone Soldano , Roesch Alexander , Horn Susanne , Hadaschik Eva , Schadendorf Dirk , Trilling Mirko , Dittmer Ulf , Griewank Klaus , Zhao Fang , Paschen Annette
Published: September 2024

ConstHLA-II melanoma cells lack endogenous interferon expression
Figure S8 from Subsets of interferon signaling predict response to immune checkpoint blockade in melanoma patients
Authors: Horowitch Brooke , Lee Daniel Y. , Ding Min , Martinez-Morilla Sandra , Aung Thazin Nwe. , Ouerghi Feriel , Wang Xueting , Wei Wei , Damsky William , Sznol Mario , Kluger Harriet , Rimm David L. , Ishizuka Jeffrey
Published: September 2024

Supplementary Figure 8: Members of the interferon signaling pathway and ICI treatment regimen predict survival in Gide et al
Supplementary Fig. 2 from Anti-tumor efficacy of the novel KIT inhibitor IDRX-42 (formerly M4205) in patient- and cell line-derived xenograft models of gastrointestinal stromal tumor (GIST)
Authors: De Sutter Luna , Wozniak Agnieszka , Verreet Jasper , Vanleeuw Ulla , De Cock Lore , Linde Nina , Drechsler Christine , Esdar Christina , Sciot Raf , Schöffski Patrick
Published: September 2024

Supplementary Fig. 2. Individual absolute tumor volumes per experiment and per treatment group on the first and last day of experiment.
Supplementary Figure S2 from The DRD2 antagonist haloperidol mediates autophagy-induced ferroptosis to increase temozolomide sensitivity by promoting endoplasmic reticulum stress in glioblastoma
Authors: Shi Linyong , Chen Hanning , Chen Kunxiang , Zhong Chengzong , Song Chong , Huang Yifeng , Wang Tong , Chen Lei , Li Chiyang , Huang Annie , Li Hong , Lu Yuntao
Published: September 2024

Fig. S2. TMZ+HP Hp induces ferroptosis in GBM cells.
Supplementary Fig. 6 from An open-label phase I study of GDC-0927 in postmenopausal women with locally advanced or metastatic estrogen receptor positive breast cancer
Authors: Chandarlapaty Sarat , Dickler Maura N. , Perez Fidalgo Jose Alejandro , Villanueva-Vázquez Rafael , Giltnane Jennifer , Gates Mary , Chang Ching-Wei , Cheeti Sravanthi , Fredrickson Jill , Wang Xiaojing , Collier Ann , Moore Heather M. , Metcalfe Ciara , Lauchle Jennifer , Humke Eric W. , Bardia Aditya
Published: September 2024

Supplementary Fig. S6. Detection of short variant gene alterations using the FACT next generation sequencing assay on ctDNA samples from patients dosed at 1400 mg dose (n=23).
Supplementary Fig. 5 from An open-label phase I study of GDC-0927 in postmenopausal women with locally advanced or metastatic estrogen receptor positive breast cancer
Authors: Chandarlapaty Sarat , Dickler Maura N. , Perez Fidalgo Jose Alejandro , Villanueva-Vázquez Rafael , Giltnane Jennifer , Gates Mary , Chang Ching-Wei , Cheeti Sravanthi , Fredrickson Jill , Wang Xiaojing , Collier Ann , Moore Heather M. , Metcalfe Ciara , Lauchle Jennifer , Humke Eric W. , Bardia Aditya
Published: September 2024

Supplementary Fig. S5. Kaplan-Meier estimate of progression-free survival for patients with and without ESR1 mutations in baseline ctDNA samples collected from the 1400 mg dose group.
ESR1 data was available for 36 of 36 patients dosed at 1400 mg.
Supplementary Fig. 2 from An open-label phase I study of GDC-0927 in postmenopausal women with locally advanced or metastatic estrogen receptor positive breast cancer
Authors: Chandarlapaty Sarat , Dickler Maura N. , Perez Fidalgo Jose Alejandro , Villanueva-Vázquez Rafael , Giltnane Jennifer , Gates Mary , Chang Ching-Wei , Cheeti Sravanthi , Fredrickson Jill , Wang Xiaojing , Collier Ann , Moore Heather M. , Metcalfe Ciara , Lauchle Jennifer , Humke Eric W. , Bardia Aditya
Published: September 2024

Supplementary Fig. S2. The PGR z-score for six patients analyzed in Fig. 4.
Supplementary Figure S1 from A bi-functional PARP-HDAC inhibitor with activity in Ewing sarcoma
Authors: Ramos Louise , Truong Sarah , Zhai Beibei , Joshi Jay , Ghaidi Fariba , Lizardo Michael M. , Shyp Taras , Kung Sonia H.Y. , Rezakhanlou Alireza M. , Oo Htoo Zarni , Adomat Hans , Le Bihan Stephane , Collins Colin , Bacha Jeffrey , Brown Dennis , Langlands John , Shen Wang , Lallous Nada , Sorensen Poul H. , Daugaard Mads
Published: September 2024

Replicate graphs of HDAC, PARP1, PARP2 and PARylation assays
Supplementary Figure S16 from Autocrine 17-β-estradiol/estrogen receptor-α loop determines the response to immune-checkpoint inhibitors in non-small cell lung cancer
Authors: Anobile Dario P. , Salaroglio Iris C. , Tabbò Fabrizio , La Vecchia Sofia , Akman Muhlis , Napoli Francesca , Bungaro Maristella , Benso Federica , Aldieri Elisabetta , Bironzo Paolo , Kopecka Joanna , Passiglia Francesco , Righi Luisella , Novello Silvia , Scagliotti Giorgio V. , Riganti Chiara
Published: September 2024

Molecular circuitries linking ERα and PD-L1.
ERα, activated by the binding of 17-β-estradiol and by the phosphorylation on Ser118 via the EGFR/Akt and EGFR/ERK1/2 axes, upregulates PD-L1 and predicts a better response to pembrolizumab. However, lowering the synthesis of 17-β-estradiol with letrozole or the activity of ERα with fulvestrant sensitizes non-small cell lung cancer to pembrolizumab, relieving the PD-L1-dependent immune-suppression, allowing the expansion and activity of anti-tumor infiltrating lymphocytes, such as CD8+T-cells, NK cells and Vγ9Vδ2+T cells. We suggest the existence of four possible scenarios, depending on sex, EGFR activity, 17-β-estradiol/ERα and PD-L1 status, with a differential sensitivity to pembrolizumab and aromatase inhibitors:1) male patients with low 17-β-estradiol synthesis, low EGFR signaling, low ERα amount/activity and low PD-L1 amount; 2) male patients with high EGFR signaling, high ERα amount/activity but low 17-β-estradiol synthesis, with intermediate PD-L1 amount; 3) female patients with low EGFR signaling, low ERα amount/activity but high 17-β-estradiol synthesis, with intermediate PD-L1 amount; 4) female patients with high EGFR signaling, high ERα amount/activity, high 17-β-estradiol synthesis and high PD-L1 amount. The efficacy of pembrolizumab and the additional benefit of aromatase inhibitors increased progressively from scenario 1 to 4.
Supplementary Table S1 from B-cell receptor pathway mutations are infrequent in patients with chronic lymphocytic leukemia on continuous ibrutinib therapy
Authors: Woyach Jennifer A. , Ghia Paolo , Byrd John C. , Ahn Inhye E. , Moreno Carol , O'Brien Susan M. , Jones Daniel , Cheung Leo W.K. , Chong Elizabeth , Kwei Kevin , Dean James P. , James Danelle F. , Wiestner Adrian
Published: September 2024

Supplemental Table 1 Listing of all detected BTK mutations (by NGS) in samples from
previously untreated patients or those with relapsed/refractory disease
Supplementary Table S2 from Activin A-mediated polarization of cancer-associated fibroblasts and macrophages confers resistance to checkpoint immunotherapy in skin cancer
Authors: Pich-Bavastro Christine , Yerly Laura , Di Domizio Jeremy , Tissot-Renaud Stéphanie , Gilliet Michel , Kuonen François
Published: September 2024

Supplementary Table S2. Spatial TME1 (STME1) and TME2 (STME2) gene signatures.
Supplementary Table S5 from Identifying mechanisms of resistance by circulating tumour DNA in EVOLVE, a Phase II Trial of Cediranib Plus Olaparib for Ovarian Cancer at time of PARP Inhibitor Progression
Authors: Lheureux Stephanie , Prokopec Stephenie D. , Oldfield Leslie E. , Gonzalez-Ochoa Eduardo , Bruce Jeff P. , Wong Derek , Danesh Arnavaz , Torti Dax , Torchia Jonathan , Fortuna Alexander , Singh Sharanjit , Irving Matthew , Marsh Kayla , Lam Bernard , Speers Vanessa , Yosifova Aleksandra , Oaknin Ana , Madariaga Ainhoa , Dhani Neesha C. , Bowering Valerie , Oza Amit M. , Pugh Trevor J.
Published: September 2024

Supplementary Table S5: Novel pathogenic mutations discovered in cfDNA. List of novel pathogenic mutations found in cfDNA samples that were not detected in the bulk tumour tissue by whole exome sequencing. For each mutation, both the variant allele frequency (VAF), median fragment size and total fragment count for ALT and REF reads (only available for SNVs), and inferred status (somatic or CHIP mutation) are shown.
Supplementary Table S3 from Identifying mechanisms of resistance by circulating tumour DNA in EVOLVE, a Phase II Trial of Cediranib Plus Olaparib for Ovarian Cancer at time of PARP Inhibitor Progression
Authors: Lheureux Stephanie , Prokopec Stephenie D. , Oldfield Leslie E. , Gonzalez-Ochoa Eduardo , Bruce Jeff P. , Wong Derek , Danesh Arnavaz , Torti Dax , Torchia Jonathan , Fortuna Alexander , Singh Sharanjit , Irving Matthew , Marsh Kayla , Lam Bernard , Speers Vanessa , Yosifova Aleksandra , Oaknin Ana , Madariaga Ainhoa , Dhani Neesha C. , Bowering Valerie , Oza Amit M. , Pugh Trevor J.
Published: September 2024

Supplementary Table S3: Targeted Sequencing Panel. List of regions included in the CHARM+EVOLVE panel used for targeted sequencing; coordinates are for human reference hg38.
Supplementary Figure S4 from Identifying mechanisms of resistance by circulating tumour DNA in EVOLVE, a Phase II Trial of Cediranib Plus Olaparib for Ovarian Cancer at time of PARP Inhibitor Progression
Authors: Lheureux Stephanie , Prokopec Stephenie D. , Oldfield Leslie E. , Gonzalez-Ochoa Eduardo , Bruce Jeff P. , Wong Derek , Danesh Arnavaz , Torti Dax , Torchia Jonathan , Fortuna Alexander , Singh Sharanjit , Irving Matthew , Marsh Kayla , Lam Bernard , Speers Vanessa , Yosifova Aleksandra , Oaknin Ana , Madariaga Ainhoa , Dhani Neesha C. , Bowering Valerie , Oza Amit M. , Pugh Trevor J.
Published: September 2024

Supplementary Figure 4: Distribution of cfDNA fragment length
Supplementary Fig. 5 from Discovery and targeting of a noncanonical mechanism of sarcoma resistance to ADI-PEG20 mediated by the microenvironment
Authors: Rogers Leonard C. , Kremer Jeff C. , Brashears Caitlyn B. , Lin Zongtao , Hu Zhixian , Bastos Alliny C. S. , Baker Adriana , Fettig Nicole , Zhou Dong , Shoghi Kooresh I. , Dehner Carina A. , Chrisinger John S. A. , Bomalaski John S. , Garcia Benjamin A. , Oyama Toshinao , White Eileen P. , Van Tine Brian A.
Published: September 2024

Supplemental Figure 5. Evidence against other possible growth support mechanisms and MEF toxicity.
Supplementary Data S7 from Genomic profiling of metastatic castration-resistant prostate cancer samples resistant to androgen-receptor pathway inhibitors
Authors: Menssouri Naoual , Poiraudeau Loic , Helissey Carole , Bigot Ludovic , Sabio Jonathan , Ibrahim Tony , Pobel Cedric , Nicotra Claudio , Ngo-Camus Maud , Lacroix Ludovic , Rouleau Etienne , Tselikas Lambros , CHAUCHEREAU Anne , Blanc-Durand Félix , Bernard-Tessier Alice , Patrikidou Anna , Naoun Natacha , Flippot Ronan , Colomba Emeline , Fuerea Alina , Albiges Laurence , Lavaud Pernelle , van de Wiel Paul , den Biezen-Timmermans Eveline , Wesseling-Rozendaal Yvonne , Ponce-Aix Santiago , Michiels Stefan , Massard Christophe , Gautheret Daniel , Barlesi Fabrice , Andre Fabrice , Besse Benjamin , Scoazec Jean-Yves , Friboulet Luc , Fizazi Karim , Loriot Yohann
Published: September 2024

Supplementary Data 7 describes the molecular features associated with response and primary resistance to ARPI.
Supplementary Data S3 from Genomic profiling of metastatic castration-resistant prostate cancer samples resistant to androgen-receptor pathway inhibitors
Authors: Menssouri Naoual , Poiraudeau Loic , Helissey Carole , Bigot Ludovic , Sabio Jonathan , Ibrahim Tony , Pobel Cedric , Nicotra Claudio , Ngo-Camus Maud , Lacroix Ludovic , Rouleau Etienne , Tselikas Lambros , CHAUCHEREAU Anne , Blanc-Durand Félix , Bernard-Tessier Alice , Patrikidou Anna , Naoun Natacha , Flippot Ronan , Colomba Emeline , Fuerea Alina , Albiges Laurence , Lavaud Pernelle , van de Wiel Paul , den Biezen-Timmermans Eveline , Wesseling-Rozendaal Yvonne , Ponce-Aix Santiago , Michiels Stefan , Massard Christophe , Gautheret Daniel , Barlesi Fabrice , Andre Fabrice , Besse Benjamin , Scoazec Jean-Yves , Friboulet Luc , Fizazi Karim , Loriot Yohann
Published: September 2024

Supplementary Data 3 reports the gene fusions data from the whole cohort.