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Minimum Technical Preanalytical, Patient, and Clinical Context Data Elements for Cerebrospinal Fluid Liquid Biopsy: Recommendations for Public Database Submissions Open

Stephen Bagley, Nike Beaubier, Leonora Balaj, Chetan Bettegowda, Erica L. Carpenter , et al. · 2025

Medicine Biology

PURPOSE Blood-based liquid biopsy has enabled minimally invasive molecular profiling in patients with solid tumors. For cancers of the CNS, however, the use of peripheral blood for cell-free DNA (cfDNA) detection and sequencing has proved …

Recommended Clinical Context and Patient Context Data Elements for Liquid Biopsy Data Submitted to Data Repositories and Data Commons Open

Robert L. Grossman, Jake Vinson, Elizabeth B. Bain, Karl Stessy Bisselou, Chandan Shivamallu , et al. · 2025

Medicine Computer science Political science

In 2020, BLOODPAC recommended 11 pre‐analytical minimal technical data elements for collection and submission of liquid biopsy data to public databases. This article expands on that work by recommending 22 clinical context and 10 patient c…

Table S6 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma Open

Julija Hmeljak, Francisco Sánchez-Vega, Katherine A. Hoadley, Juliann Shih, Chip Stewart , et al. · 2023

Biology Medicine Computer science

Table S6 contains results from the analysis of DNA methylation in SETD2 mutated and BAP1 inactivated samples.

Table S7 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma Open

Julija Hmeljak, Francisco Sánchez-Vega, Katherine A. Hoadley, Juliann Shih, Chip Stewart , et al. · 2023

Medicine Computer science Biology

Table S7 contains microbe screening results.

Supplementary Data from Integrative Molecular Characterization of Malignant Pleural Mesothelioma Open

Julija Hmeljak, Francisco Sánchez-Vega, Katherine A. Hoadley, Juliann Shih, Chip Stewart , et al. · 2023

Medicine Biology Materials science

Supplementary materials and methods, as well as supplementary figures S1-S7.

Table S1 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma Open

Julija Hmeljak, Francisco Sánchez-Vega, Katherine A. Hoadley, Juliann Shih, Chip Stewart , et al. · 2023

Medicine Computer science

Table S1 contains cohort description, Master Patient Table and MutSigCV results.

Table S4 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma Open

Julija Hmeljak, Francisco Sánchez-Vega, Katherine A. Hoadley, Juliann Shih, Chip Stewart , et al. · 2023

Medicine Computer science Biology

Table S4 includes immune signature and iCluster results.

Table S2 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma Open

Julija Hmeljak, Francisco Sánchez-Vega, Katherine A. Hoadley, Juliann Shih, Chip Stewart , et al. · 2023

Medicine Computer science Materials science

Table S2 contains BAP1 analysis results, as well as detailed lists of YY1 and IRF8 target genes.

Table S5 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma Open

Julija Hmeljak, Francisco Sánchez-Vega, Katherine A. Hoadley, Juliann Shih, Chip Stewart , et al. · 2023

Computer science Medicine Biology

Table S5 contains detailed miRs and lncRNAs results.

Table S3 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma Open

Julija Hmeljak, Francisco Sánchez-Vega, Katherine A. Hoadley, Juliann Shih, Chip Stewart , et al. · 2023

Medicine Biology Computer science

Table S3 contains the karyotypes of 16 genome-wide LOH MPM cases from the BWH cohort.

Table S3 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma Open

Julija Hmeljak, Francisco Sánchez-Vega, Katherine A. Hoadley, Juliann Shih, Chip Stewart , et al. · 2023

Medicine Biology Computer science

Table S3 contains the karyotypes of 16 genome-wide LOH MPM cases from the BWH cohort.

Table S4 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma Open

Julija Hmeljak, Francisco Sánchez-Vega, Katherine A. Hoadley, Juliann Shih, Chip Stewart , et al. · 2023

Medicine Biology Computer science

Table S4 includes immune signature and iCluster results.

Data from Integrative Molecular Characterization of Malignant Pleural Mesothelioma Open

Julija Hmeljak, Francisco Sánchez-Vega, Katherine A. Hoadley, Juliann Shih, Chip Stewart , et al. · 2023

Biology Medicine

Malignant pleural mesothelioma (MPM) is a highly lethal cancer of the lining of the chest cavity. To expand our understanding of MPM, we conducted a comprehensive integrated genomic study, including the most detailed analysis of BAP1 alter…

Supplementary Data from Integrative Molecular Characterization of Malignant Pleural Mesothelioma Open

Julija Hmeljak, Francisco Sánchez-Vega, Katherine A. Hoadley, Juliann Shih, Chip Stewart , et al. · 2023

Medicine Biology

Supplementary materials and methods, as well as supplementary figures S1-S7.

Table S5 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma Open

Julija Hmeljak, Francisco Sánchez-Vega, Katherine A. Hoadley, Juliann Shih, Chip Stewart , et al. · 2023

Medicine Computer science Biology

Table S5 contains detailed miRs and lncRNAs results.

Table S7 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma Open

Julija Hmeljak, Francisco Sánchez-Vega, Katherine A. Hoadley, Juliann Shih, Chip Stewart , et al. · 2023

Medicine Computer science Biology

Table S7 contains microbe screening results.

Data from Integrative Molecular Characterization of Malignant Pleural Mesothelioma Open

Julija Hmeljak, Francisco Sánchez-Vega, Katherine A. Hoadley, Juliann Shih, Chip Stewart , et al. · 2023

Medicine Biology Materials science

Malignant pleural mesothelioma (MPM) is a highly lethal cancer of the lining of the chest cavity. To expand our understanding of MPM, we conducted a comprehensive integrated genomic study, including the most detailed analysis of BAP1 alter…

Table S2 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma Open

Julija Hmeljak, Francisco Sánchez-Vega, Katherine A. Hoadley, Juliann Shih, Chip Stewart , et al. · 2023

Medicine Computer science Biology

Table S2 contains BAP1 analysis results, as well as detailed lists of YY1 and IRF8 target genes.

Table S6 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma Open

Julija Hmeljak, Francisco Sánchez-Vega, Katherine A. Hoadley, Juliann Shih, Chip Stewart , et al. · 2023

Biology Medicine Computer science

Table S6 contains results from the analysis of DNA methylation in SETD2 mutated and BAP1 inactivated samples.

Table S1 from Integrative Molecular Characterization of Malignant Pleural Mesothelioma Open

Julija Hmeljak, Francisco Sánchez-Vega, Katherine A. Hoadley, Juliann Shih, Chip Stewart , et al. · 2023

Medicine Biology Computer science

Table S1 contains cohort description, Master Patient Table and MutSigCV results.

Supplemental Figure 3 from Combining Anti-Mir-155 with Chemotherapy for the Treatment of Lung Cancers Open

Katrien Van Roosbroeck, Francesca Fanini, Tetsuro Setoyama, Cristina Ivan, Cristian Rodriguez-Aguayo , et al. · 2023

Medicine Biology

Clinical correlation of miR-155 expression with survival in leukemia. Kaplan-Meier survival analysis for patients expressing high levels of miR-155 vs. low levels of miR-155 in two CLL cohorts, CLL - NEJM (A) and CLL - Italy (B), and in on…

Supplemental Figure 2 from Combining Anti-Mir-155 with Chemotherapy for the Treatment of Lung Cancers Open

Katrien Van Roosbroeck, Francesca Fanini, Tetsuro Setoyama, Cristina Ivan, Cristian Rodriguez-Aguayo , et al. · 2023

Medicine Chemistry Biology

In vivo orthotopic lung cancer model for the role of miR-155 in chemoresistance. (A) Injection and treatment schedule for CDDP (green arrows) and anti-miR negative control (NC) or anti-miR-155 liposomal nanoparticles (red stars) for four d…

Supplemental Figure 4 from Combining Anti-Mir-155 with Chemotherapy for the Treatment of Lung Cancers Open

Katrien Van Roosbroeck, Francesca Fanini, Tetsuro Setoyama, Cristina Ivan, Cristian Rodriguez-Aguayo , et al. · 2023

Biology Medicine

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 h…

Data from Combining Anti-Mir-155 with Chemotherapy for the Treatment of Lung Cancers Open

Katrien Van Roosbroeck, Francesca Fanini, Tetsuro Setoyama, Cristina Ivan, Cristian Rodriguez-Aguayo , et al. · 2023

Medicine Biology

Purpose: The oncogenic miR-155 is upregulated in many human cancers, and its expression is increased in more aggressive and therapy-resistant tumors, but the molecular mechanisms underlying miR-155-induced therapy resistance are not fully …

Supplemental Figure 5 from Combining Anti-Mir-155 with Chemotherapy for the Treatment of Lung Cancers Open

Katrien Van Roosbroeck, Francesca Fanini, Tetsuro Setoyama, Cristina Ivan, Cristian Rodriguez-Aguayo , et al. · 2023

Medicine Computer science Mathematics

Supplementary Table S1 Clinical characteristics of two chronic lymphocytic leukemia patient datasets; Supplementary Table S2 Clinical characteristics of two lung cancer patient datasets; Supplementary Table S3 Clinical characteristics of t…

Supplemental Figure 1 from Combining Anti-Mir-155 with Chemotherapy for the Treatment of Lung Cancers Open

Katrien Van Roosbroeck, Francesca Fanini, Tetsuro Setoyama, Cristina Ivan, Cristian Rodriguez-Aguayo , et al. · 2023

Medicine

Dose-response curves for MEC1 and MEC2 cells treated with fludarabine.

Supplemental Figure 1 from Combining Anti-Mir-155 with Chemotherapy for the Treatment of Lung Cancers Open

Katrien Van Roosbroeck, Francesca Fanini, Tetsuro Setoyama, Cristina Ivan, Cristian Rodriguez-Aguayo , et al. · 2023

Medicine

Dose-response curves for MEC1 and MEC2 cells treated with fludarabine.

Supplemental Figure 4 from Combining Anti-Mir-155 with Chemotherapy for the Treatment of Lung Cancers Open

Katrien Van Roosbroeck, Francesca Fanini, Tetsuro Setoyama, Cristina Ivan, Cristian Rodriguez-Aguayo , et al. · 2023

Biology Medicine

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 h…

Supplemental Figure 3 from Combining Anti-Mir-155 with Chemotherapy for the Treatment of Lung Cancers Open

Katrien Van Roosbroeck, Francesca Fanini, Tetsuro Setoyama, Cristina Ivan, Cristian Rodriguez-Aguayo , et al. · 2023

Medicine Biology

Clinical correlation of miR-155 expression with survival in leukemia. Kaplan-Meier survival analysis for patients expressing high levels of miR-155 vs. low levels of miR-155 in two CLL cohorts, CLL - NEJM (A) and CLL - Italy (B), and in on…

Data from Combining Anti-Mir-155 with Chemotherapy for the Treatment of Lung Cancers Open

Katrien Van Roosbroeck, Francesca Fanini, Tetsuro Setoyama, Cristina Ivan, Cristian Rodriguez-Aguayo , et al. · 2023

Medicine Biology

Purpose: The oncogenic miR-155 is upregulated in many human cancers, and its expression is increased in more aggressive and therapy-resistant tumors, but the molecular mechanisms underlying miR-155-induced therapy resistance are not fully …

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