bluuebunny/crossref_metadata_2025 huggingface dataset:
Online Supplementary Materials from Genomics-Driven Precision Medicine for Advanced Pancreatic Cancer: Early Results from the COMPASS Trial
Authors: Aung Kyaw L. , Fischer Sandra E. , Denroche Robert E. , Jang Gun-Ho , Dodd Anna , Creighton Sean , Southwood Bernadette , Liang Sheng-Ben , Chadwick Dianne , Zhang Amy , O'Kane Grainne M. , Albaba Hamzeh , Moura Shari , Grant Robert C. , Miller Jessica K. , Mbabaali Faridah , Pasternack Danielle , Lungu Ilinca M. , Bartlett John M.S. , Ghai Sangeet , Lemire Mathieu , Holter Spring , Connor Ashton A. , Moffitt Richard A. , Yeh Jen Jen , Timms Lee , Krzyzanowski Paul M. , Dhani Neesha , Hedley David , Notta Faiyaz , Wilson Julie M. , Moore Malcolm J. , Gallinger Steven , Knox Jennifer J.
Published: April 2023

Supplementary Methods, Tables and Figures Supplementary Table 1: Summary of whole genome sequencing results including performance metrics and time to reporting (N=62). Supplementary Table 2: Summary of GATA6 RNA in situ results and its correlation with RNA subtype and histologic grade. Supplementary Figure 1: WGS Performance Characteristics. Supplementary Figure 2: Both COMP-0037 and COMP-0057 had germline BRCA2 p.S1982fs mutations but only COMP-0037 had a second hit (somatic LOH of wild type allele) and showed hallmarks of double strand break repair deficiency. Supplementary Figure 3: BRCA2 mutation status of COMP-0057. Supplementary Figure 4: Subtypes of advanced PDAC by Moffitt tumour classification Supplementary Figure 5: Correlation between Moffitt tumor RNA subtypes and GATA6 gene expression. Supplementary Figure 6: Correlation between GATA6 expression measured by RNASeq and RNA in situ hybridization. Supplementary Figure 7: Differentially expressed pathways between Moffitt's basal like and classical RNA subtypes Supplementary Figure 8: CDK4 amplification identified in COMP-0008 (A) and CDK6 amplification identified in COMP-0010 (B) validated by fluorescence in-situ hybridization.
Efficacy of estrogen releasing pellets. from Preclinical Efficacy of Ron Kinase Inhibitors Alone and in Combination with PI3K Inhibitors for Treatment of sfRon-Expressing Breast Cancer Patient-Derived Xenografts
Authors: Bieniasz Magdalena , Radhakrishnan Parvathi , Faham Najme , De La O Jean-Paul , Welm Alana L.
Published: April 2023

A. MCF7 tumor growth rate in NOD/SCID mice implanted with beeswax E2 pellets, commercial 0.72 mg/60 days E2 pellets (Innovative Research of America) and control mice. Both, 0.72 mg/60 days E2 and beeswax E2 pellets equally supported estrogen dependent tumor growth. In contrast, control mice not supplemented with E2 pellets failed to grow tumors. B. Quantification of E2 plasma levels 10 days post implantation of E2 pellets in NOD/SCID mice. The beeswax pellets yielded mean E2 plasma levels of 84 pg/ml with very little variation, which are comparable plasma estrogen levels released from commercially available E2 pellets.
Supplementary Tables from DNMT1–MicroRNA126 Epigenetic Circuit Contributes to Esophageal Squamous Cell Carcinoma Growth via ADAM9–EGFR–AKT Signaling
Authors: Liu Ronghua , Gu Jie , Jiang Pei , Zheng Yijie , Liu Xiaoming , Jiang Xuechao , Huang Enyu , Xiong Shudao , Xu Fengkai , Liu Guangwei , Ge Di , Chu Yiwei
Published: April 2023

The file included six supplementary tables as following: Table S1.Clinicopathological Characteristics; Table S2. Differently expressed miRNAs between ECs and NMs; Table S3. Univariate and Multivariate analysis of factors associated with disease-specific survival; Table S4. A short list of functionally relevant genes significantly downredulated in 126-EC cells vs. NC-EC cells; Table S5. Primer sequences (5'-3'), Table S6. The primary antibodies for western blot and IHC.
Supplementary Figure S6 from DNMT1–MicroRNA126 Epigenetic Circuit Contributes to Esophageal Squamous Cell Carcinoma Growth via ADAM9–EGFR–AKT Signaling
Authors: Liu Ronghua , Gu Jie , Jiang Pei , Zheng Yijie , Liu Xiaoming , Jiang Xuechao , Huang Enyu , Xiong Shudao , Xu Fengkai , Liu Guangwei , Ge Di , Chu Yiwei
Published: April 2023

Supplementary Figure S6.Other targets of miR-126 in ESCC.
Data Supplement from Activating FGFR2–RAS–BRAF Mutations in Ameloblastoma
Authors: Brown Noah A. , Rolland Delphine , McHugh Jonathan B. , Weigelin Helmut C. , Zhao Lili , Lim Megan S. , Elenitoba-Johnson Kojo S.J. , Betz Bryan L.
Published: April 2023

Supplemental Figure S2. CTNNB1 and SMARCB1 immunohistochemistry.
Supplementary Table (S1) from HAGE in Triple-Negative Breast Cancer Is a Novel Prognostic, Predictive, and Actionable Biomarker: A Transcriptomic and Protein Expression Analysis
Authors: Abdel-Fatah Tarek M.A. , McArdle Stephanie E.B. , Agarwal Devika , Moseley Paul M. , Green Andrew R. , Ball Graham R. , Pockley A. Graham , Ellis Ian O. , Rees Robert C. , Chan Stephen Y.T.
Published: April 2023

Supplementary Table (S1). Clinico-pathological characteristics of early primary triple negative breast cancer (EP-TNBC; n=520)
Supplemental Figure 2 from The MET Inhibitor AZD6094 (Savolitinib, HMPL-504) Induces Regression in Papillary Renal Cell Carcinoma Patient–Derived Xenograft Models
Authors: Schuller Alwin G. , Barry Evan R. , Jones Rhys D.O. , Henry Ryan E. , Frigault Melanie M. , Beran Garry , Linsenmayer David , Hattersley Maureen , Smith Aaron , Wilson Joanne , Cairo Stefano , Déas Olivier , Nicolle Delphine , Adam Ammar , Zinda Michael , Reimer Corinne , Fawell Stephen E. , Clark Edwin A. , D'Cruz Celina M.
Published: April 2023

Supplemental Figure 2. MET copy number in RCC-43 tumors from passage 6 and 9, and in RCC-47 tumors from passage 5 and 10 by qPCR
Supplementary Table 4 from Gemtuzumab Ozogamicin Reduces Relapse Risk in FLT3/ITD Acute Myeloid Leukemia: A Report from the Children's Oncology Group
Authors: Tarlock Katherine , Alonzo Todd A. , Gerbing Robert B. , Raimondi Susana C. , Hirsch Betsy A. , Sung Lillian , Pollard Jessica A. , Aplenc Richard , Loken Michael R. , Gamis Alan S. , Meshinchi Soheil
Published: April 2023

CTC v3.0 toxicities grade 3 or higher for patients in the No-GO and GO cohorts treated on AAML03P1 and AAML0531.
Supplementary Table 2 from Gemtuzumab Ozogamicin Reduces Relapse Risk in FLT3/ITD Acute Myeloid Leukemia: A Report from the Children's Oncology Group
Authors: Tarlock Katherine , Alonzo Todd A. , Gerbing Robert B. , Raimondi Susana C. , Hirsch Betsy A. , Sung Lillian , Pollard Jessica A. , Aplenc Richard , Loken Michael R. , Gamis Alan S. , Meshinchi Soheil
Published: April 2023

Clinical outcomes for FLT3/ITD patients according to treatment by GO or No-GO, stratified by low or high allelic ratio (AR) and high AR receiving HCT
Supplementary Figure Legends from Upregulation of IGF1R by Mutant RAS in Leukemia and Potentiation of RAS Signaling Inhibitors by Small-Molecule Inhibition of IGF1R
Authors: Weisberg Ellen , Nonami Atsushi , Chen Zhao , Nelson Erik , Chen Yongfei , Liu Feiyang , Cho HaeYeon , Zhang Jianming , Sattler Martin , Mitsiades Constantine , Wong Kwok-Kin , Liu Qingsong , Gray Nathanael S. , Griffin James D.
Published: April 2023

Figure Legends for data shown in supplementary data section
Table S4 from Global Promoter Methylation Analysis Reveals Novel Candidate Tumor Suppressor Genes in Natural Killer Cell Lymphoma
Authors: Küçük Can , Hu Xiaozhou , Jiang Bei , Klinkebiel David , Geng Huimin , Gong Qiang , Bouska Alyssa , Iqbal Javeed , Gaulard Philippe , McKeithan Timothy W. , Chan Wing C.
Published: April 2023

Table S4. Significantly enriched functional groups for 174 hypermethylated genes in Ingeniuty Pathway Analysis
Table S2 from Global Promoter Methylation Analysis Reveals Novel Candidate Tumor Suppressor Genes in Natural Killer Cell Lymphoma
Authors: Küçük Can , Hu Xiaozhou , Jiang Bei , Klinkebiel David , Geng Huimin , Gong Qiang , Bouska Alyssa , Iqbal Javeed , Gaulard Philippe , McKeithan Timothy W. , Chan Wing C.
Published: April 2023

Table S2. Basic sequencing statistics of NK samples
Supplementary Table S1 from The Stat3/5 Signaling Biosignature in Hematopoietic Stem/Progenitor Cells Predicts Response and Outcome in Myelodysplastic Syndrome Patients Treated with Azacitidine
Authors: Miltiades Paraskevi , Lamprianidou Eleftheria , Vassilakopoulos Theodoros P. , Papageorgiou Sotirios G. , Galanopoulos Athanasios G. , Kontos Christos K. , Adamopoulos Panagiotis G. , Nakou Evangelia , Vakalopoulou Sofia , Garypidou Vassilia , Papaioannou Maria , Hatjiharissi Evdoxia , Papadaki Helen A. , Spanoudakis Emmanuil , Pappa Vassiliki , Scorilas Andreas , Tsatalas Constantinos , Kotsianidis Ioannis
Published: April 2023

Multivariate analysis of prognostic factors for overall survival in the patient cohort (n=74)
Supplementary Figure S4 from The Stat3/5 Signaling Biosignature in Hematopoietic Stem/Progenitor Cells Predicts Response and Outcome in Myelodysplastic Syndrome Patients Treated with Azacitidine
Authors: Miltiades Paraskevi , Lamprianidou Eleftheria , Vassilakopoulos Theodoros P. , Papageorgiou Sotirios G. , Galanopoulos Athanasios G. , Kontos Christos K. , Adamopoulos Panagiotis G. , Nakou Evangelia , Vakalopoulou Sofia , Garypidou Vassilia , Papaioannou Maria , Hatjiharissi Evdoxia , Papadaki Helen A. , Spanoudakis Emmanuil , Pappa Vassiliki , Scorilas Andreas , Tsatalas Constantinos , Kotsianidis Ioannis
Published: April 2023

Molecular characterization of the G-CSF-inducible Stat3/5 double positive (DP) and double negative (DN) subpopulations.
Supplementary figures S1-4 from Prognostic Impact of Novel Molecular Subtypes of Small Intestinal Neuroendocrine Tumor
Authors: Karpathakis Anna , Dibra Harpreet , Pipinikas Chistodoulos , Feber Andrew , Morris Tiffany , Francis Joshua , Oukrif Dahmane , Mandair Dalvinder , Pericleous Marinos , Mohmaduvesh Mullan , Serra Stefano , Ogunbiyi Olagunju , Novelli Marco , Luong TuVinh , Asa Sylvia L. , Kulke Matthew , Toumpanakis Christos , Meyer Tim , Caplin Martyn , Meyerson Matthew , Beck Stephan , Thirlwell Christina
Published: April 2023

Supplementary figures S1-4. Supplementary figure S1. Methylation variable positions distinguishing primary SI NET from normal small intestine. Supplementary figure S2. Kegg pathway analysis of differential methylated genes distinguishing primary SI NET from normal small intestine. Supplementary figure S3. Differentially expressed probes distinguishing subgroups of primary SI NET. Supplementary figure S4. Methylation and expression profiles of panel of 21 global driver candidate genes.
Supplementary Table 4 from Prognostic Impact of Novel Molecular Subtypes of Small Intestinal Neuroendocrine Tumor
Authors: Karpathakis Anna , Dibra Harpreet , Pipinikas Chistodoulos , Feber Andrew , Morris Tiffany , Francis Joshua , Oukrif Dahmane , Mandair Dalvinder , Pericleous Marinos , Mohmaduvesh Mullan , Serra Stefano , Ogunbiyi Olagunju , Novelli Marco , Luong TuVinh , Asa Sylvia L. , Kulke Matthew , Toumpanakis Christos , Meyer Tim , Caplin Martyn , Meyerson Matthew , Beck Stephan , Thirlwell Christina
Published: April 2023

Supplementary Table S4. Genes demonstrating concordant methylation and expression changes in SI NET primaries.
Supplementary Figure 1 Legend from Prospective Validation of Pooled Prognostic Factors in Women with Advanced Cervical Cancer Treated with Chemotherapy with/without Bevacizumab: NRG Oncology/GOG Study
Authors: Tewari Krishnansu S. , Sill Michael W. , Monk Bradley J. , Penson Richard T. , Long Harry J. , Poveda Andrés , Landrum Lisa M. , Leitao Mario M. , Brown Jubilee , Reid Thomas J.A. , Michael Helen E. , Moore David H.
Published: April 2023

The Figure Legend for the Supplemental Figure 1 describes the content of the 3 panels that make up this Supplemental Figure.
Supplementary Table 2 from Prognostic Impact of Novel Molecular Subtypes of Small Intestinal Neuroendocrine Tumor
Authors: Karpathakis Anna , Dibra Harpreet , Pipinikas Chistodoulos , Feber Andrew , Morris Tiffany , Francis Joshua , Oukrif Dahmane , Mandair Dalvinder , Pericleous Marinos , Mohmaduvesh Mullan , Serra Stefano , Ogunbiyi Olagunju , Novelli Marco , Luong TuVinh , Asa Sylvia L. , Kulke Matthew , Toumpanakis Christos , Meyer Tim , Caplin Martyn , Meyerson Matthew , Beck Stephan , Thirlwell Christina
Published: April 2023

Supplementary Table S2. Analysis cohort.
Supplementary Figure 4 from Heterogeneous Mechanisms of Primary and Acquired Resistance to Third-Generation EGFR Inhibitors
Authors: Ortiz-Cuaran Sandra , Scheffler Matthias , Plenker Dennis , Dahmen llona , Scheel Andreas H. , Fernandez-Cuesta Lynnette , Meder Lydia , Lovly Christine M. , Persigehl Thorsten , Merkelbach-Bruse Sabine , Bos Marc , Michels Sebastian , Fischer Rieke , Albus Kerstin , König Katharina , Schildhaus Hans-Ulrich , Fassunke Jana , Ihle Michaela A. , Pasternack Helen , Heydt Carina , Becker Christian , Altmüller Janine , Ji Hongbin , Müller Christian , Florin Alexandra , Heuckmann Johannes M. , Nuernberg Peter , Ansén Sascha , Heukamp Lukas C. , Berg Johannes , Pao William , Peifer Martin , Buettner Reinhard , Wolf Jürgen , Thomas Roman K. , Sos Martin L.
Published: April 2023

Concomitant inhibition of MEK and EGFR is synergistic in PC9KRAS-G12S and HCC827KRAS-G12S cells.
Supplementary Table S1: Original DTP for Cohorts 1 to 3 (with cohort size of 3) with all 64 pathways without stopping early for excessive toxicity in Viola from Dose Transition Pathways: The Missing Link Between Complex Dose-Finding Designs and Simple Decision-Making
Authors: Yap Christina , Billingham Lucinda J. , Cheung Ying Kuen , Craddock Charlie , O'Quigley John
Published: April 2023

Original DTP for Cohorts 1 to 3 (with cohort size of 3) with all 64 pathways without stopping early for excessive toxicity in Viola. The design will always recommend staying at the lowest dose even when high numbers of DLTs are observed at the lowest dose as no safety stopping criterion is applied.
Supplementary Figure S1: DTP-Heatmap of risk of lowest dose being too toxic from Dose Transition Pathways: The Missing Link Between Complex Dose-Finding Designs and Simple Decision-Making
Authors: Yap Christina , Billingham Lucinda J. , Cheung Ying Kuen , Craddock Charlie , O'Quigley John
Published: April 2023

DTP-Heatmap of risk of lowest dose being too toxic. This figure presents a heatmap to highlight any case where there is a high chance that the lowest dose is too toxic (greater than 0.3 DLT rate) based on the accumulated data in each pathway for the first three complete cohorts, C1-C3. This is computed for pathways where the current recommended dose is the lowest dose (Light Yellow, Yellow, Orange, Red represent increasing risks that the lowest dose is too toxic
Supplementary table 3b from Pan-Cancer Immunogenomic Perspective on the Tumor Microenvironment Based on PD-L1 and CD8 T-Cell Infiltration
Authors: Ock Chan-Young , Keam Bhumsuk , Kim Sehui , Lee Ju-Seog , Kim Miso , Kim Tae Min , Jeon Yoon Kyung , Kim Dong-Wan , Chung Doo Hyun , Heo Dae Seog
Published: April 2023

Supplementary table 3b. Specific amplification of cancer driver genes to predict tumor microenvironment immune types
Supplementary figures from Pan-Cancer Immunogenomic Perspective on the Tumor Microenvironment Based on PD-L1 and CD8 T-Cell Infiltration
Authors: Ock Chan-Young , Keam Bhumsuk , Kim Sehui , Lee Ju-Seog , Kim Miso , Kim Tae Min , Jeon Yoon Kyung , Kim Dong-Wan , Chung Doo Hyun , Heo Dae Seog
Published: April 2023

Supplementary Figure 1. Distribution of PD-L1 and CD8A expression in TCGA. Supplementary Figure 2. Significant correlation between CD8A and cytolytic activity, as well as PD-1. Supplementary Figure 3. Overall survival analysis according to tumor microenvironment immune types (TMIT). Supplementary Figure 4. Forest plot of hazards ratio (HR) and 95% confidence interval (CI) of overall survival according to tumor microenvironment immune type (TMIT). Supplementary Figure 5. The distribution of immune type sorted by mutational burden across cancer types. Supplementary Figure 6. Microsatellite-high tumor of colorectal adenocarcinoma and stomach adenocarcinoma has high proportion of tumor microenvironment immune type (TMIT) I. Supplementary Figure 7. POLE mutation is associated with tumor microenvironment immune type I. Supplementary Figure 8. Specific somatic mutation correlated with immune types. Supplementary Figure 9. Specific amplification (a) or deletion (b) of copy number correlated with immune types. Supplementary Figure 10. Virus detection and immune type across cancer types. Supplementary Figure 11. Virus detection and immune types in stomach adenocarcinoma (STAD), head and neck squamous cell carcinoma (HNSC), and hepatocellular carcinoma (LIHC). Supplementary Figure 12. Summary of tumor microenvironment immune types.
Supplemental Table S4: Probe sequences used for MLPA from Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group
Authors: Ooms Ariadne H.A.G. , Gadd Samantha , Gerhard Daniela S. , Smith Malcolm A. , Guidry Auvil Jaime M. , Meerzaman Daoud , Chen Qing-Rong , Hsu Chih Hao , Yan Chunhua , Nguyen Cu , Hu Ying , Ma Yussanne , Zong Zusheng , Mungall Andrew J. , Moore Richard A. , Marra Marco A. , Huff Vicki , Dome Jeffrey S. , Chi Yueh-Yun , Tian Jing , Geller James I. , Mullighan Charles G. , Ma Jing , Wheeler David A. , Hampton Oliver A. , Walz Amy L. , van den Heuvel-Eibrink Marry M. , de Krijger Ronald R. , Ross Nicole , Gastier-Foster Julie M. , Perlman Elizabeth J.
Published: April 2023

This table shows the sequences of the probes used for MLPA
Supplemental Table S1: TP53 variants identified in 118 DAWTs by WGS or WES from Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group
Authors: Ooms Ariadne H.A.G. , Gadd Samantha , Gerhard Daniela S. , Smith Malcolm A. , Guidry Auvil Jaime M. , Meerzaman Daoud , Chen Qing-Rong , Hsu Chih Hao , Yan Chunhua , Nguyen Cu , Hu Ying , Ma Yussanne , Zong Zusheng , Mungall Andrew J. , Moore Richard A. , Marra Marco A. , Huff Vicki , Dome Jeffrey S. , Chi Yueh-Yun , Tian Jing , Geller James I. , Mullighan Charles G. , Ma Jing , Wheeler David A. , Hampton Oliver A. , Walz Amy L. , van den Heuvel-Eibrink Marry M. , de Krijger Ronald R. , Ross Nicole , Gastier-Foster Julie M. , Perlman Elizabeth J.
Published: April 2023

This table shows all TP53 variant that were identified by Whole Genome or Exome Sequencing in all DAWTs included in this study
Supplementary Table S2 from A Complex Network of Tumor Microenvironment in Human High-Grade Serous Ovarian Cancer
Authors: Kreuzinger Caroline , Geroldinger Angelika , Smeets Dominiek , Braicu Elena Ioana , Sehouli Jalid , Koller Julia , Wolf Andrea , Darb-Esfahani Silvia , Joehrens Korinna , Vergote Ignace , Vanderstichele Adriaan , Boeckx Bram , Lambrechts Diether , Gabra Hani , Wisman G. Bea A. , Trillsch Fabian , Heinze Georg , Horvat Reinhard , Polterauer Stephan , Berns Els , Theillet Charles , Cacsire Castillo-Tong Dan
Published: April 2023

Functional assignment of the 142 genes with the highest expression difference in the two clusters revealed by unsupervised clustering of recurrent samples
Supplementary Table S1 from A Complex Network of Tumor Microenvironment in Human High-Grade Serous Ovarian Cancer
Authors: Kreuzinger Caroline , Geroldinger Angelika , Smeets Dominiek , Braicu Elena Ioana , Sehouli Jalid , Koller Julia , Wolf Andrea , Darb-Esfahani Silvia , Joehrens Korinna , Vergote Ignace , Vanderstichele Adriaan , Boeckx Bram , Lambrechts Diether , Gabra Hani , Wisman G. Bea A. , Trillsch Fabian , Heinze Georg , Horvat Reinhard , Polterauer Stephan , Berns Els , Theillet Charles , Cacsire Castillo-Tong Dan
Published: April 2023

Clinical and pathological parameters of the patients
Supplementary Figure S3 from A Complex Network of Tumor Microenvironment in Human High-Grade Serous Ovarian Cancer
Authors: Kreuzinger Caroline , Geroldinger Angelika , Smeets Dominiek , Braicu Elena Ioana , Sehouli Jalid , Koller Julia , Wolf Andrea , Darb-Esfahani Silvia , Joehrens Korinna , Vergote Ignace , Vanderstichele Adriaan , Boeckx Bram , Lambrechts Diether , Gabra Hani , Wisman G. Bea A. , Trillsch Fabian , Heinze Georg , Horvat Reinhard , Polterauer Stephan , Berns Els , Theillet Charles , Cacsire Castillo-Tong Dan
Published: April 2023

Supervised clustering of primary HGSOC (n=421) from the TCGA data using 59/126 immune related genes
Supplementary Figure S2 from A Complex Network of Tumor Microenvironment in Human High-Grade Serous Ovarian Cancer
Authors: Kreuzinger Caroline , Geroldinger Angelika , Smeets Dominiek , Braicu Elena Ioana , Sehouli Jalid , Koller Julia , Wolf Andrea , Darb-Esfahani Silvia , Joehrens Korinna , Vergote Ignace , Vanderstichele Adriaan , Boeckx Bram , Lambrechts Diether , Gabra Hani , Wisman G. Bea A. , Trillsch Fabian , Heinze Georg , Horvat Reinhard , Polterauer Stephan , Berns Els , Theillet Charles , Cacsire Castillo-Tong Dan
Published: April 2023

IHC staining of CD8 and CD20 in 4 active and 6 silent tissues
Supplementary Figures S1-S8 from Selected Alkylating Agents Can Overcome Drug Tolerance of G0-like Tumor Cells and Eradicate BRCA1-Deficient Mammary Tumors in Mice
Authors: Pajic Marina , Blatter Sohvi , Guyader Charlotte , Gonggrijp Maaike , Kersbergen Ariena , Küçükosmanoğlu Aslι , Sol Wendy , Drost Rinske , Jonkers Jos , Borst Piet , Rottenberg Sven
Published: April 2023

Figure S1: Treatment response to cisplatin spread over several days. Figure S2: Cisplatin adducts in tumor remants; GFP-marker in the BRCA1-deficient mouse model. Figure S3: EdU incorporation assay. Figure S4: Genomic profile and clonogenic assays of BRCA1-deficient cell lines. Figure S5: Determination of IC50 in KB1P-B11 and -G3; Cell cycle dependent cell death of KB1P-B11-FUCCI. Figure S6: Drug response to nimustine, melphalan, bendamustine or temozolomide. Figure S7: High dose treatment of mice with carboplatin or thiotepa. Figure S8: Combination or single treatment with cyclophosphamide, carboplatin or thiotepa.
Supplementary Figure S2 from Potential Predictive Value of TP53 and KRAS Mutation Status for Response to PD-1 Blockade Immunotherapy in Lung Adenocarcinoma
Authors: Dong Zhong-Yi , Zhong Wen-Zhao , Zhang Xu-Chao , Su Jian , Xie Zhi , Liu Si-Yang , Tu Hai-Yan , Chen Hua-Jun , Sun Yue-Li , Zhou Qing , Yang Jin-Ji , Yang Xue-Ning , Lin Jia-Xin , Yan Hong-Hong , Zhai Hao-Ran , Yan Li-Xu , Liao Ri-Qiang , Wu Si-Pei , Wu Yi-Long
Published: April 2023

Analysis of GC>TA transversion in four groups compared common mutations (TP53/KRAS/EGFR/STK11) with corresponding wild type.
Supplementary Tables 1-2 from The Novel KLF4/MSI2 Signaling Pathway Regulates Growth and Metastasis of Pancreatic Cancer
Authors: Guo Kun , Cui Jiujie , Quan Ming , Xie Dacheng , Jia Zhiliang , Wei Daoyan , Wang Liang , Gao Yong , Ma Qingyong , Xie Keping
Published: April 2023

Supplementary Table S1. Clinicopathologic characteristics of TMA Supplementary Table S2. MSI2 expression in the TMA PDAC specimens and clinicopathologic characteristics of the patients from whom the specimens were obtained
Supplementary Figures 1-3 from The Novel KLF4/MSI2 Signaling Pathway Regulates Growth and Metastasis of Pancreatic Cancer
Authors: Guo Kun , Cui Jiujie , Quan Ming , Xie Dacheng , Jia Zhiliang , Wei Daoyan , Wang Liang , Gao Yong , Ma Qingyong , Xie Keping
Published: April 2023

Supplementary Figure S1. Expression of MSI2 in PDAC specimens. Supplementary Figure S2. Localization of MSI2 in PDAC cells. Supplementary Figure S3. Co-expression of MSI2 and KLF4 in colon and gastric cancer cells.
Supplementary Figure S4 from Analytic Validation of RNA In Situ Hybridization (RISH) for AR and AR-V7 Expression in Human Prostate Cancer
Authors: Guedes Liana B. , Morais Carlos L. , Almutairi Fawaz , Haffner Michael C. , Zheng Qizhi , Isaacs John T. , Antonarakis Emmanuel S. , Lu Changxue , Tsai Harrison , Luo Jun , De Marzo Angelo M. , Lotan Tamara L.
Published: April 2023

AR-E1 and AR-CE3 RISH assay digital image quantification shows minimal inter-observer variability. To examine inter-observer variability in scoring, a second, independent operator (Observer 2) circled tumor areas and performed the scoring for AR-E1 and AR-CE3 in Frida across a subset of the autopsy samples and compared with the original values created by Observer 1 for Supplementary Figure S3C. In one experiment, the second operator made their own thresholds for brown and blue intensity scoring and in another experiment, the second operator used the intensity thresholds set by the first operator. In both cases there was negligible variability between operators, with highly correlated values across all specimens.
Supplemental Table S1 from GTL001, A Therapeutic Vaccine for Women Infected with Human Papillomavirus 16 or 18 and Normal Cervical Cytology: Results of a Phase I Clinical Trial
Authors: Van Damme Pierre , Bouillette-Marussig Myriam , Hens Annick , De Coster Ilse , Depuydt Christophe , Goubier Anne , Van Tendeloo Viggo , Cools Nathalie , Goossens Herman , Hercend Thierry , Timmerman Benedikt , Bissery Marie-Christine
Published: April 2023

Most common treatment-related TEAEs
Supplementary table 2. from Molecular Screening for Cancer Treatment Optimization (MOSCATO-01) in Pediatric Patients: A Single-Institutional Prospective Molecular Stratification Trial
Authors: Harttrampf Anne C. , Lacroix Ludovic , Deloger Marc , Deschamps Frederic , Puget Stephanie , Auger Nathalie , Vielh Philippe , Varlet Pascale , Balogh Zsofia , Abbou Samuel , Allorant Adrien , Valteau-Couanet Dominique , Sarnacki Sabine , Gamiche-Rolland Louise , Meurice Guillaume , Minard-Colin Veronique , Grill Jacques , Brugieres Laurence , Dufour Christelle , Gaspar Nathalie , Michiels Stefan , Vassal Gilles , Soria Jean-Charles , Geoerger Birgit
Published: April 2023

Clinical and genomics data on all patients included
Supplementary table 1. from Molecular Screening for Cancer Treatment Optimization (MOSCATO-01) in Pediatric Patients: A Single-Institutional Prospective Molecular Stratification Trial
Authors: Harttrampf Anne C. , Lacroix Ludovic , Deloger Marc , Deschamps Frederic , Puget Stephanie , Auger Nathalie , Vielh Philippe , Varlet Pascale , Balogh Zsofia , Abbou Samuel , Allorant Adrien , Valteau-Couanet Dominique , Sarnacki Sabine , Gamiche-Rolland Louise , Meurice Guillaume , Minard-Colin Veronique , Grill Jacques , Brugieres Laurence , Dufour Christelle , Gaspar Nathalie , Michiels Stefan , Vassal Gilles , Soria Jean-Charles , Geoerger Birgit
Published: April 2023

Quality data of the WES and RNAseq analyzes
Legends Supplementary Material from Molecular Screening for Cancer Treatment Optimization (MOSCATO-01) in Pediatric Patients: A Single-Institutional Prospective Molecular Stratification Trial
Authors: Harttrampf Anne C. , Lacroix Ludovic , Deloger Marc , Deschamps Frederic , Puget Stephanie , Auger Nathalie , Vielh Philippe , Varlet Pascale , Balogh Zsofia , Abbou Samuel , Allorant Adrien , Valteau-Couanet Dominique , Sarnacki Sabine , Gamiche-Rolland Louise , Meurice Guillaume , Minard-Colin Veronique , Grill Jacques , Brugieres Laurence , Dufour Christelle , Gaspar Nathalie , Michiels Stefan , Vassal Gilles , Soria Jean-Charles , Geoerger Birgit
Published: April 2023

Legends Supplementary Material
Table S2. from Subtypes of HPV-Positive Head and Neck Cancers Are Associated with HPV Characteristics, Copy Number Alterations, PIK3CA Mutation, and Pathway Signatures
Authors: Zhang Yanxiao , Koneva Lada A. , Virani Shama , Arthur Anna E. , Virani Alisha , Hall Pelle B. , Warden Charles D. , Carey Thomas E. , Chepeha Douglas B. , Prince Mark E. , McHugh Jonathan B. , Wolf Gregory T. , Rozek Laura S. , Sartor Maureen A.
Published: April 2023

Enriched GO terms for genes differentially expressed between HPV(+) and HPV(-) HNC tumors in the UM cohort.
Supplemental Table 1 from Genomic Copy Number Profiling Using Circulating Free Tumor DNA Highlights Heterogeneity in Neuroblastoma
Authors: Chicard Mathieu , Boyault Sandrine , Colmet Daage Leo , Richer Wilfrid , Gentien David , Pierron Gaelle , Lapouble Eve , Bellini Angela , Clement Nathalie , Iacono Isabelle , Bréjon Stéphanie , Carrere Marjorie , Reyes Cécile , Hocking Toby , Bernard Virginie , Peuchmaur Michel , Corradini Nadège , Faure-Conter Cécile , Coze Carole , Plantaz Dominique , Defachelles Anne Sophie , Thebaud Estelle , Gambart Marion , Millot Frédéric , Valteau-Couanet Dominique , Michon Jean , Puisieux Alain , Delattre Olivier , Combaret Valérie , Schleiermacher Gudrun
Published: April 2023

Patient Information
Supplemental Figures 1, 2, 3 and 4 from Malignant Astrocytic Tumor Progression Potentiated by JAK-mediated Recruitment of Myeloid Cells
Authors: Rajappa Prajwal , Cobb William S. , Vartanian Emma , Huang Yujie , Daly Laura , Hoffman Caitlin , Zhang Jane , Shen Beiyi , Yanowitch Rachel , Garg Kunal , Cisse Babacar , Haddock Sara , Huse Jason , Pisapia David J. , Chan Timothy A. , Lyden David C. , Bromberg Jacqueline F. , Greenfield Jeffrey P.
Published: April 2023

Supplemental Figure 1. CD11b+ myeloid cells in glioma correlate to tumor grade. Supplemental Figure 2. Schematic depicted for bone marrow transplant of RCAS tumor bearing animals. Supplemental Figure 3. Analysis of tumor sections for necrosis and microvascular proliferation. Supplemental Figure 4. AZD1480 impairs phosphorylation of Stat3 but has no effect in vitro and IDH status
Supplementary Table S2 from A Panel of Novel Detection and Prognostic Methylated DNA Markers in Primary Non–Small Cell Lung Cancer and Serum DNA
Authors: Ooki Akira , Maleki Zahra , Tsay Jun-Chieh J. , Goparaju Chandra , Brait Mariana , Turaga Nitesh , Nam Hae-Seong , Rom William N. , Pass Harvey I. , Sidransky David , Guerrero-Preston Rafael , Hoque Mohammad Obaidul
Published: April 2023

Supplementary Table S2.Thirty genes for further analyses selected from LUAD TCGA dataset.
Figure S4 from In Vivo Detection of EGFRvIII in Glioblastoma via Perfusion Magnetic Resonance Imaging Signature Consistent with Deep Peritumoral Infiltration: The ϕ-Index
Authors: Bakas Spyridon , Akbari Hamed , Pisapia Jared , Martinez-Lage Maria , Rozycki Martin , Rathore Saima , Dahmane Nadia , O'Rourke Donald M. , Davatzikos Christos
Published: April 2023

Leakage corrected rCBV distributions for each ROI of each subgroup (EGFRvIII+ and EGFRvIII-). We note although these rCBV results are consistent with those obtained via PHI, the separation between EGFRvIII+ and EGFRvIII- is notably weaker.
Suppl Figures from MAPK Pathway and TERT Promoter Gene Mutation Pattern and Its Prognostic Value in Melanoma Patients: A Retrospective Study of 2,793 Cases
Authors: Bai Xue , Kong Yan , Chi Zhihong , Sheng Xinan , Cui Chuanliang , Wang Xuan , Mao Lili , Tang Bixia , Li Siming , Lian Bin , Yan Xieqiao , Zhou Li , Dai Jie , Guo Jun , Si Lu
Published: April 2023

Fig S1-S5
Supplementary Legends from The Effect of Hepatic Impairment on Outcomes in Phase I Clinical Trials in Cancer Subjects
Authors: Mansfield Aaron S. , Rudek Michelle A. , Vulih Diana , Smith Gary L. , Harris Pamela Jo , Ivy S. Percy
Published: April 2023

Legends for supplementary tables and figures.
Supplementary Table 1 from Interleukin-17–Producing Neutrophils Link Inflammatory Stimuli to Disease Progression by Promoting Angiogenesis in Gastric Cancer
Authors: Li Tuan-Jie , Jiang Yu-Ming , Hu Yan-Feng , Huang Lei , Yu Jiang , Zhao Li-Ying , Deng Hai-Jun , Mou Ting-Yu , Liu Hao , Yang Yang , Zhang Qi , Li Guo-Xin
Published: April 2023

Clinical characteristics of the 573 gastric cancer patients
Supplementary Figures 1-8 from Epithelial-to-Mesenchymal Transition Antagonizes Response to Targeted Therapies in Lung Cancer by Suppressing BIM
Authors: Song Kyung-A , Niederst Matthew J. , Lochmann Timothy L. , Hata Aaron N. , Kitai Hidenori , Ham Jungoh , Floros Konstantinos V. , Hicks Mark A. , Hu Haichuan , Mulvey Hillary E. , Drier Yotam , Heisey Daniel A.R. , Hughes Mark T. , Patel Neha U. , Lockerman Elizabeth L. , Garcia Angel , Gillepsie Shawn , Archibald Hannah L. , Gomez-Caraballo Maria , Nulton Tara J. , Windle Brad E. , Piotrowska Zofia , Sahingur Sinem E. , Taylor Shirley M. , Dozmorov Mikhail , Sequist Lecia V. , Bernstein Bradley , Ebi Hiromichi , Engelman Jeffrey A. , Faber Anthony C.
Published: April 2023

We have developed several models of EMT-mediated resistance to EGFR inhibitors in EGFR mutant lung cancers. Figure S1. Expression of EMT-related genes are inversely correlated with BCL2L11 expression; Figure S2. EMT induced by TGF-ÃŽÂ² results in depressed BIM and apoptotic resistance to EGFR inhibitors in EGFR mutant lung cancer. Figure S3. EGFRi resistant models that underwent an EMT have suppressed BIM levels. Figure S4. ZEB1 binding site located within the BCL2L11 (BIM) promoter. Figure S5. ZEB1 is an EMT marker associated with resistance to EGFRi in lung cancer and its depletion leads to BIM de-repression. Figure S6. BIM can be liberated with BCL-xL inhibition in mesenchymal EGFR mutant lung cancers to restore EGFRi-induced apoptosis. Figure S7. ABT-263 + EGFRi treatment is effective in EGFRi resistant cancers that have undergone an EMT. Figure S8. ER-TWIST phenotype in vivo and mesenchymal KRAS mutant lung cancers downregulate BIM upon EMT induction.
Supplementary Methods from PI3K Inhibition Reduces Mammary Tumor Growth and Facilitates Antitumor Immunity and Anti-PD1 Responses
Authors: Sai Jiqing , Owens Philip , Novitskiy Sergey V. , Hawkins Oriana E. , Vilgelm Anna E. , Yang Jinming , Sobolik Tammy , Lavender Nicole , Johnson Andrew C. , McClain Colt , Ayers Gregory D. , Kelley Mark C. , Sanders Melinda , Mayer Ingrid A. , Moses Harold L. , Boothby Mark , Richmond Ann
Published: April 2023

This file describes additional methodology
Supplementary Methods from Genomic Profiling of Large-Cell Neuroendocrine Carcinoma of the Lung
Authors: Miyoshi Tomohiro , Umemura Shigeki , Matsumura Yuki , Mimaki Sachiyo , Tada Satoshi , Makinoshima Hideki , Ishii Genichiro , Udagawa Hibiki , Matsumoto Shingo , Yoh Kiyotaka , Niho Seiji , Ohmatsu Hironobu , Aokage Keiju , Hishida Tomoyuki , Yoshida Junji , Nagai Kanji , Goto Koichi , Tsuboi Masahiro , Tsuchihara Katsuya
Published: April 2023

Supplementary methods for Sanger sequencing, copy number analysis with quantitative PCR, and Immunohistochemical staining
Supplementary Figure 3 from Phase III HEAT Study Adding Lyso-Thermosensitive Liposomal Doxorubicin to Radiofrequency Ablation in Patients with Unresectable Hepatocellular Carcinoma Lesions
Authors: Tak Won Young , Lin Shi-Ming , Wang Yijun , Zheng Jiasheng , Vecchione Aldo , Park Soo Young , Chen Min Hua , Wong Stephen , Xu Ruocai , Peng Cheng-Yuan , Chiou Yi-You , Huang Guan-Tarn , Cai Jianqiang , Abdullah Basri Johan Jeet , Lee June Sung , Lee Jae Young , Choi Jong-Young , Gopez-Cervantes Julieta , Sherman Morris , Finn Richard S. , Omata Masao , O'Neal Michael , Makris Lukas , Borys Nicholas , Poon Ronnie , Lencioni Riccardo
Published: April 2023

Supplementary Figure 3: Forest Plot of Hazard Ratio of Treatment Effect on Progression-Free Survival, According to Baseline Prognostic Factors. (A) Intent-to-treat population, n=701; (B) Subset: Solitary lesion (BCLC A) and RFA dwell time {greater than or equal to}45 min, n=285.
Supplementary Figure 2B from Phase III HEAT Study Adding Lyso-Thermosensitive Liposomal Doxorubicin to Radiofrequency Ablation in Patients with Unresectable Hepatocellular Carcinoma Lesions
Authors: Tak Won Young , Lin Shi-Ming , Wang Yijun , Zheng Jiasheng , Vecchione Aldo , Park Soo Young , Chen Min Hua , Wong Stephen , Xu Ruocai , Peng Cheng-Yuan , Chiou Yi-You , Huang Guan-Tarn , Cai Jianqiang , Abdullah Basri Johan Jeet , Lee June Sung , Lee Jae Young , Choi Jong-Young , Gopez-Cervantes Julieta , Sherman Morris , Finn Richard S. , Omata Masao , O'Neal Michael , Makris Lukas , Borys Nicholas , Poon Ronnie , Lencioni Riccardo
Published: April 2023

Supplementary Figure 2b: Kaplan-Meier Survival Estimates:(B) Subset: Solitary lesion and RFA dwell time {greater than or equal to}45 min, n=285.
Supplementary Figure 1 - Quantification of EGFR Mutant and Wild-Type DNA Blends by PCR-NGS from Monitoring Daily Dynamics of Early Tumor Response to Targeted Therapy by Detecting Circulating Tumor DNA in Urine
Authors: Husain Hatim , Melnikova Vladislava O. , Kosco Karena , Woodward Brian , More Soham , Pingle Sandeep C. , Weihe Elizabeth , Park Ben Ho , Tewari Muneesh , Erlander Mark G. , Cohen Ezra , Lippman Scott M. , Kurzrock Razelle
Published: April 2023

A: Analysis of dilution series of indicated mutant EGFR variants spiked into 60 ng (â‰^18,180 genome equivalents) of WT DNA. Each data point represents one preparative within 6 independent dilutions series prepared and analyzed by two operators on two different instruments on three non-consecutive days for a total of 18 samples per dilution point. An analysis algorithm was applied to transform the mutant EGFR sequencing reads into the absolute mutant copies detected. The box-and-whisker plots show the median (center line), 25th and 75th percentiles (box) with the connecting "whiskers" extending from the first quartile minus 1.5 of the interquartile range (IQR, the third quartile less the first quartile) and the third quartile plus 1.5 of the IQR. A positive Spearman's correlation close to 1 indicates a strong, positive relationship between the absolute mutant EGFR copies detected and the absolute mutant EGFR copies per input. B: Inter-run reproducibility of the EGFR exon 19 deletions, L858R and T790M enrichment PCR-NGS assays for the dilution series shown in panel A. The Coefficient of Variation Percent (CV%) was calculated as the ratio of the standard deviation to the mean of the absolute EGFR copies detected within each absolute copy per input level and is reported as a percentage.
Supplementary Figure 2A from Phase III HEAT Study Adding Lyso-Thermosensitive Liposomal Doxorubicin to Radiofrequency Ablation in Patients with Unresectable Hepatocellular Carcinoma Lesions
Authors: Tak Won Young , Lin Shi-Ming , Wang Yijun , Zheng Jiasheng , Vecchione Aldo , Park Soo Young , Chen Min Hua , Wong Stephen , Xu Ruocai , Peng Cheng-Yuan , Chiou Yi-You , Huang Guan-Tarn , Cai Jianqiang , Abdullah Basri Johan Jeet , Lee June Sung , Lee Jae Young , Choi Jong-Young , Gopez-Cervantes Julieta , Sherman Morris , Finn Richard S. , Omata Masao , O'Neal Michael , Makris Lukas , Borys Nicholas , Poon Ronnie , Lencioni Riccardo
Published: April 2023

Supplementary Figure 2a: Kaplan-Meier Survival Estimates: Interim Overall Survival. (A) Intent-to-treat population, n=701.
Supplementary Table 7 from Next-Generation Sequencing of Pulmonary Large Cell Neuroendocrine Carcinoma Reveals Small Cell Carcinoma–like and Non–Small Cell Carcinoma–like Subsets
Authors: Rekhtman Natasha , Pietanza Maria C. , Hellmann Matthew D. , Naidoo Jarushka , Arora Arshi , Won Helen , Halpenny Darragh F. , Wang Hangjun , Tian Shaozhou K. , Litvak Anya M. , Paik Paul K. , Drilon Alexander E. , Socci Nicholas , Poirier John T. , Shen Ronglai , Berger Michael F. , Moreira Andre L. , Travis William D. , Rudin Charles M. , Ladanyi Marc
Published: April 2023

Supplementary Table 7: Detailed chemosensitivity data
Supoemental Figure 1 Patiens do not carry T790M mutation prior to MET-TKI are more likely to have longer PFS from Acquired MET Y1248H and D1246N Mutations Mediate Resistance to MET Inhibitors in Non–Small Cell Lung Cancer
Authors: Li Anna , Yang Jin-ji , Zhang Xu-chao , Zhang Zhou , Su Jian , Gou Lan-ying , Bai Yu , Zhou Qing , Yang Zhenfan , Han-Zhang Han , Zhong Wen-Zhao , Chuai Shannon , Zhang Qi , Xie Zhi , Gao Hongfei , Chen Huajun , Wang Zhen , Wang Zheng , Yang Xue-ning , Wang Bin-chao , Gan Bin , Chen Zhi-hong , Jiang Ben-yuan , Wu Si-pei , Liu Si-yang , Xu Chong-rui , Wu Yi-long
Published: April 2023

Kaplan-Meire plot of progression-free survival of patients with T790M mutation prior to MET-TKI treatment (blue) or without (red). Statistical significance was assessed using student's t-test (p=0.15)
Supplemental Figure 4 from Combining Anti-Mir-155 with Chemotherapy for the Treatment of Lung Cancers
Authors: Van Roosbroeck Katrien , Fanini Francesca , Setoyama Tetsuro , Ivan Cristina , Rodriguez-Aguayo Cristian , Fuentes-Mattei Enrique , Xiao Lianchun , Vannini Ivan , Redis Roxana S. , D'Abundo Lucilla , Zhang Xinna , Nicoloso Milena S. , Rossi Simona , Gonzalez-Villasana Vianey , Rupaimoole Rajesha , Ferracin Manuela , Morabito Fortunato , Neri Antonino , Ruvolo Peter P. , Ruvolo Vivian R. , Pecot Chad V. , Amadori Dino , Abruzzo Lynne , Calin Steliana , Wang Xuemei , You M. James , Ferrajoli Alessandra , Orlowski Robert , Plunkett William , Lichtenberg Tara M. , Davuluri Ramana V. , Berindan-Neagoe Ioana , Negrini Massimo , Wistuba Ignacio I. , Kantarjian Hagop M. , Sood Anil K. , Lopez-Berestein Gabriel , Keating Michael J. , Fabbri Muller , Calin George A.
Published: April 2023

Clinical correlation of miR-155 and TP53 expression with survival in the lung adenocarcinoma - TCGA dataset when distinguishing between TP53 wild-type and TP53 mutated samples. (A-B) Kaplan-Meier survival analysis for patients expressing high levels of miR-155 vs. low levels of miR-155 in samples that express wild-typeTP53 or harbor TP53 mutations that do not affect TP53 function (A), and in samples expressing mutated TP53 that affects TP53 function (B). (C-D) Kaplan-Meier survival analysis for patients expressing high levels of miR-155 and low levels of TP53 vs. low levels of miR-155 and high levels of TP53 in samples that express wild-type TP53 or harbor TP53 mutations that do not affect TP53 function (C), and in samples expressing mutated TP53 that affects TP53 function (D).
Supplemental Figure legends from Expression of CD14, IL10, and Tolerogenic Signature in Dendritic Cells Inversely Correlate with Clinical and Immunologic Response to TARP Vaccination in Prostate Cancer Patients
Authors: Castiello Luciano , Sabatino Marianna , Ren Jiaqiang , Terabe Masaki , Khuu Hanh , Wood Lauren V. , Berzofsky Jay A. , Stroncek David F.
Published: April 2023

Legends of supplemental figure 1, 2, 3
Table S6 from The Driver Mutational Landscape of Ovarian Squamous Cell Carcinomas Arising in Mature Cystic Teratoma
Authors: Cooke Susanna L. , Ennis Darren , Evers Lisa , Dowson Suzanne , Chan Mei Yen , Paul James , Hirschowitz Lynn , Glasspool Rosalind M. , Singh Naveena , Bell Sarah , Day Elizabeth , Kochman Agata , Wilkinson Nafisa , Beer Philip , Martin Sancha , Millan David , Biankin Andrew V. , McNeish Iain A.
Published: April 2023

Copy Number Alterations identified in SCC and MCT samples
Table S3 from The Driver Mutational Landscape of Ovarian Squamous Cell Carcinomas Arising in Mature Cystic Teratoma
Authors: Cooke Susanna L. , Ennis Darren , Evers Lisa , Dowson Suzanne , Chan Mei Yen , Paul James , Hirschowitz Lynn , Glasspool Rosalind M. , Singh Naveena , Bell Sarah , Day Elizabeth , Kochman Agata , Wilkinson Nafisa , Beer Philip , Martin Sancha , Millan David , Biankin Andrew V. , McNeish Iain A.
Published: April 2023

Quality Control parameters on all sequenced samples
Table S2 from The Driver Mutational Landscape of Ovarian Squamous Cell Carcinomas Arising in Mature Cystic Teratoma
Authors: Cooke Susanna L. , Ennis Darren , Evers Lisa , Dowson Suzanne , Chan Mei Yen , Paul James , Hirschowitz Lynn , Glasspool Rosalind M. , Singh Naveena , Bell Sarah , Day Elizabeth , Kochman Agata , Wilkinson Nafisa , Beer Philip , Martin Sancha , Millan David , Biankin Andrew V. , McNeish Iain A.
Published: April 2023

A list of genes analysed for copy number state
Table S1 from The Driver Mutational Landscape of Ovarian Squamous Cell Carcinomas Arising in Mature Cystic Teratoma
Authors: Cooke Susanna L. , Ennis Darren , Evers Lisa , Dowson Suzanne , Chan Mei Yen , Paul James , Hirschowitz Lynn , Glasspool Rosalind M. , Singh Naveena , Bell Sarah , Day Elizabeth , Kochman Agata , Wilkinson Nafisa , Beer Philip , Martin Sancha , Millan David , Biankin Andrew V. , McNeish Iain A.
Published: April 2023

A list of the 151 genes included in the Agilent Comprehensive Cancer Panel
Supplementary Figure 7 from Tumor-Specific Uptake of Fluorescent Bevacizumab–IRDye800CW Microdosing in Patients with Primary Breast Cancer: A Phase I Feasibility Study
Authors: Lamberts Laetitia E. , Koch Maximillian , de Jong Johannes S. , Adams Arthur L.L. , Glatz Jürgen , Kranendonk Mariëtte E.G. , Terwisscha van Scheltinga Anton G.T. , Jansen Liesbeth , de Vries Jakob , Lub-de Hooge Marjolijn N. , Schröder Carolien P. , Jorritsma-Smit Annelies , Linssen Matthijs D. , de Boer Esther , van der Vegt Bert , Nagengast Wouter B. , Elias Sjoerd G. , Oliveira Sabrina , Witkamp Arjen J. , Mali Willem P.Th.M. , Van der Wall Elsken , van Diest Paul J. , de Vries Elisabeth G.E. , Ntziachristos Vasilis , van Dam Gooitzen M.
Published: April 2023

Co-localization of Hematoxylin / Eosin (H/E), VEGF-A, and Bevacizumab-IRDye800CW in Tumor-negative Lymph Nodes.
Figure S1 from The Driver Mutational Landscape of Ovarian Squamous Cell Carcinomas Arising in Mature Cystic Teratoma
Authors: Cooke Susanna L. , Ennis Darren , Evers Lisa , Dowson Suzanne , Chan Mei Yen , Paul James , Hirschowitz Lynn , Glasspool Rosalind M. , Singh Naveena , Bell Sarah , Day Elizabeth , Kochman Agata , Wilkinson Nafisa , Beer Philip , Martin Sancha , Millan David , Biankin Andrew V. , McNeish Iain A.
Published: April 2023

Copy number profiles of MCT samples.
Supplemental Movie S1. Explanatory Movie of Multiplex Advanced Pathology Imaging (MAPI). from Tumor-Specific Uptake of Fluorescent Bevacizumab–IRDye800CW Microdosing in Patients with Primary Breast Cancer: A Phase I Feasibility Study
Authors: Lamberts Laetitia E. , Koch Maximillian , de Jong Johannes S. , Adams Arthur L.L. , Glatz Jürgen , Kranendonk Mariëtte E.G. , Terwisscha van Scheltinga Anton G.T. , Jansen Liesbeth , de Vries Jakob , Lub-de Hooge Marjolijn N. , Schröder Carolien P. , Jorritsma-Smit Annelies , Linssen Matthijs D. , de Boer Esther , van der Vegt Bert , Nagengast Wouter B. , Elias Sjoerd G. , Oliveira Sabrina , Witkamp Arjen J. , Mali Willem P.Th.M. , Van der Wall Elsken , van Diest Paul J. , de Vries Elisabeth G.E. , Ntziachristos Vasilis , van Dam Gooitzen M.
Published: April 2023

Multiplex pathology imaging of white-light microscopy, bevacizumab-IRDye800CW fluorescence imaging (green pseudocolor), VEGF-A (red pseudocolor), collagen (red pseudocolor) and CD34 (blue pseudocolor) in breast cancer, including overlay images is shown in a stepwise manner for reasons of clarity.
Supplementary Figures from Genomic Heterogeneity and Exceptional Response to Dual Pathway Inhibition in Anaplastic Thyroid Cancer
Authors: Gibson William J. , Ruan Daniel T. , Paulson Vera A. , Barletta Justine A. , Hanna Glenn J. , Kraft Stefan , Calles Antonio , Nehs Matthew A. , Moore Francis D. , Taylor-Weiner Amaro , Wala Jeremiah A. , Zack Travis I. , Lee Thomas C. , Fennessy Fiona M. , Alexander Erik K. , Thomas Tom , Janne Pasi A. , Garraway Levi A. , Carter Scott L. , Beroukhim Rameen , Lorch Jochen H. , Van Allen Eliezer M.
Published: April 2023

Supplementary Figure 1 The most frequent phylogenetic tree based on sampling mutations according to their detection power (276/1000 samples). Supplementary Figure 2 Allelic copy number profiles generated by ABSOLUTE (see Methods).
Supplementary Table 4 from Immune and Stromal Classification of Colorectal Cancer Is Associated with Molecular Subtypes and Relevant for Precision Immunotherapy
Authors: Becht Etienne , de Reyniès Aurélien , Giraldo Nicolas A. , Pilati Camilla , Buttard Bénédicte , Lacroix Laetitia , Selves Janick , Sautès-Fridman Catherine , Laurent-Puig Pierre , Fridman Wolf Herman
Published: April 2023

Antibodies used for immunohistochemical analyses
Supplementary methods from A Therapeutic Her2/neu Vaccine Targeting Dendritic Cells Preferentially Inhibits the Growth of Low Her2/neu–Expressing Tumor in HLA-A2 Transgenic Mice
Authors: Tran Thi , Diniz Mariana O. , Dransart Estelle , Gey Alain , Merillon Nathalie , Lone Yu Chun , Godefroy Sylvie , Sibley Craig , Ferreira Luis CS , Medioni Jacques , Oudard Stephane , Johannes Ludger , Tartour Eric
Published: April 2023

Description of supplementary methods
Supplementary Table 2 from Immune and Stromal Classification of Colorectal Cancer Is Associated with Molecular Subtypes and Relevant for Precision Immunotherapy
Authors: Becht Etienne , de Reyniès Aurélien , Giraldo Nicolas A. , Pilati Camilla , Buttard Bénédicte , Lacroix Laetitia , Selves Janick , Sautès-Fridman Catherine , Laurent-Puig Pierre , Fridman Wolf Herman
Published: April 2023

Colorectal cancer samples constituting the 3 cohorts analyzed, along with their molecular subgroups