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Spatial omics-based machine learning algorithms for the early detection of hepatocellular carcinoma Open

Mengjun Wang, Stéphane Elie Grauzam, Muhammed Bayram, James W. Dressman, Andrew DelaCourt , et al. · 2024

In conclusion, we present the development and application of a new biomarker platform, which can identify effective biomarkers for the early detection of HCC. This platform may also apply to other diseases, in which changes in N-linked gly…

The Spatial Extracellular Proteomic Tumor Microenvironment Distinguishes Molecular Subtypes of Hepatocellular Carcinoma Open

Jade K. Macdonald, Harrison Taylor, Mengjun Wang, Andrew DelaCourt, Christin Edge , et al. · 2024

Hepatocellular carcinoma (HCC) mortality rates continue to increase faster than those of other cancer types due to high heterogeneity, which limits diagnosis and treatment. Pathological and molecular subtyping have identified that HCC tumo…

Supplementary Table ST2 from Analysis of N-linked Glycan Alterations in Tissue and Serum Reveals Promising Biomarkers for Intrahepatic Cholangiocarcinoma Open

Shaaron Ochoa-Rios, Calvin R.K. Blaschke, Mengjun Wang, Kendell D. Peterson, Andrew DelaCourt , et al. · 2023

Lists individual N-glycans, ALT (Alanine transaminase), AST (aspartate aminotransferase), ALK (Alkaline phosphatase), and AFP (Alpha-fetoprotein) of analysis to differentiate patients with iCCA from PSC. 1Possible biomarkers 2n: number of …

Supplementary Figure SF4 from Analysis of N-linked Glycan Alterations in Tissue and Serum Reveals Promising Biomarkers for Intrahepatic Cholangiocarcinoma Open

Shaaron Ochoa-Rios, Calvin R.K. Blaschke, Mengjun Wang, Kendell D. Peterson, Andrew DelaCourt , et al. · 2023

A. Scatterplots and correlations between N-glycans of interest (1339, 1257, 2158) and clinical information available (ALT, AST, ALK, and AFP). B. Multivariate model-Multiple logistic regression in CCA and PSC serum samples (n=40). Model 1:…

Supplementary Table ST2 from Analysis of N-linked Glycan Alterations in Tissue and Serum Reveals Promising Biomarkers for Intrahepatic Cholangiocarcinoma Open

Shaaron Ochoa-Rios, Calvin R.K. Blaschke, Mengjun Wang, Kendell D. Peterson, Andrew DelaCourt , et al. · 2023

Lists individual N-glycans, ALT (Alanine transaminase), AST (aspartate aminotransferase), ALK (Alkaline phosphatase), and AFP (Alpha-fetoprotein) of analysis to differentiate patients with iCCA from PSC. 1Possible biomarkers 2n: number of …

Supplementary Table ST1 from Analysis of N-linked Glycan Alterations in Tissue and Serum Reveals Promising Biomarkers for Intrahepatic Cholangiocarcinoma Open

Shaaron Ochoa-Rios, Calvin R.K. Blaschke, Mengjun Wang, Kendell D. Peterson, Andrew DelaCourt , et al. · 2023

Peak list of N-glycans detected in tissue (TMA) and serum samples.

Supplementary Figure SF3 from Analysis of N-linked Glycan Alterations in Tissue and Serum Reveals Promising Biomarkers for Intrahepatic Cholangiocarcinoma Open

Shaaron Ochoa-Rios, Calvin R.K. Blaschke, Mengjun Wang, Kendell D. Peterson, Andrew DelaCourt , et al. · 2023

A. Relative contribution of each serum-glycan (left) and TMA-glycan (right) in the first and second principal components. The size and color of the circle represent a higher contribution of the glycan to the respective Dim. (Dimension). B.…

Supplementary Figure SF2 from Analysis of N-linked Glycan Alterations in Tissue and Serum Reveals Promising Biomarkers for Intrahepatic Cholangiocarcinoma Open

Shaaron Ochoa-Rios, Calvin R.K. Blaschke, Mengjun Wang, Kendell D. Peterson, Andrew DelaCourt , et al. · 2023

Patient demographics for A. TMA 1 and B. TMA 2. C. Patient demographics for serum cohort. ALT (Alanine transaminase), AST (aspartate aminotransferase), AFP (Alpha-fetoprotein), and ALP (Alkaline phosphatase). Other liver diseases include n…

Data from Analysis of N-linked Glycan Alterations in Tissue and Serum Reveals Promising Biomarkers for Intrahepatic Cholangiocarcinoma Open

Shaaron Ochoa-Rios, Calvin R.K. Blaschke, Mengjun Wang, Kendell D. Peterson, Andrew DelaCourt , et al. · 2023

There is an urgent need for the identification of reliable prognostic biomarkers for patients with intrahepatic cholangiocarcinoma (iCCA) and alterations in N-glycosylation have demonstrated an immense potential to be used as diagnostic st…

Supplementary Figure SF4 from Analysis of N-linked Glycan Alterations in Tissue and Serum Reveals Promising Biomarkers for Intrahepatic Cholangiocarcinoma Open

Shaaron Ochoa-Rios, Calvin R.K. Blaschke, Mengjun Wang, Kendell D. Peterson, Andrew DelaCourt , et al. · 2023

A. Scatterplots and correlations between N-glycans of interest (1339, 1257, 2158) and clinical information available (ALT, AST, ALK, and AFP). B. Multivariate model-Multiple logistic regression in CCA and PSC serum samples (n=40). Model 1:…

Supplementary Figure SF3 from Analysis of N-linked Glycan Alterations in Tissue and Serum Reveals Promising Biomarkers for Intrahepatic Cholangiocarcinoma Open

Shaaron Ochoa-Rios, Calvin R.K. Blaschke, Mengjun Wang, Kendell D. Peterson, Andrew DelaCourt , et al. · 2023

A. Relative contribution of each serum-glycan (left) and TMA-glycan (right) in the first and second principal components. The size and color of the circle represent a higher contribution of the glycan to the respective Dim. (Dimension). B.…

Supplementary Figure SF1 from Analysis of N-linked Glycan Alterations in Tissue and Serum Reveals Promising Biomarkers for Intrahepatic Cholangiocarcinoma Open

Shaaron Ochoa-Rios, Calvin R.K. Blaschke, Mengjun Wang, Kendell D. Peterson, Andrew DelaCourt , et al. · 2023

Hematoxylin & Eosin (H&E) staining of A. Intrahepatic Cholangiocarcinoma (iCCA) tissue, 10x (right) and 40x (left) magnification images from respective areas of the tissue, and B. Hepatocellular Carcinoma (HCC) tissue, 10x magnification im…

Supplementary Figure SF2 from Analysis of N-linked Glycan Alterations in Tissue and Serum Reveals Promising Biomarkers for Intrahepatic Cholangiocarcinoma Open

Shaaron Ochoa-Rios, Calvin R.K. Blaschke, Mengjun Wang, Kendell D. Peterson, Andrew DelaCourt , et al. · 2023

Patient demographics for A. TMA 1 and B. TMA 2. C. Patient demographics for serum cohort. ALT (Alanine transaminase), AST (aspartate aminotransferase), AFP (Alpha-fetoprotein), and ALP (Alkaline phosphatase). Other liver diseases include n…

Data from Analysis of N-linked Glycan Alterations in Tissue and Serum Reveals Promising Biomarkers for Intrahepatic Cholangiocarcinoma Open

Shaaron Ochoa-Rios, Calvin R.K. Blaschke, Mengjun Wang, Kendell D. Peterson, Andrew DelaCourt , et al. · 2023

There is an urgent need for the identification of reliable prognostic biomarkers for patients with intrahepatic cholangiocarcinoma (iCCA) and alterations in N-glycosylation have demonstrated an immense potential to be used as diagnostic st…

Supplementary Figure SF5 from Analysis of N-linked Glycan Alterations in Tissue and Serum Reveals Promising Biomarkers for Intrahepatic Cholangiocarcinoma Open

Shaaron Ochoa-Rios, Calvin R.K. Blaschke, Mengjun Wang, Kendell D. Peterson, Andrew DelaCourt , et al. · 2023

Relative intensity quantification of all N-glycans identified in serum (left row) and tissue (right row) analysis. Red font labeling for N-glycans follows the same trend between serum and tissue.

Supplementary Figure SF5 from Analysis of N-linked Glycan Alterations in Tissue and Serum Reveals Promising Biomarkers for Intrahepatic Cholangiocarcinoma Open

Shaaron Ochoa-Rios, Calvin R.K. Blaschke, Mengjun Wang, Kendell D. Peterson, Andrew DelaCourt , et al. · 2023

Relative intensity quantification of all N-glycans identified in serum (left row) and tissue (right row) analysis. Red font labeling for N-glycans follows the same trend between serum and tissue.

Supplementary Figure SF1 from Analysis of N-linked Glycan Alterations in Tissue and Serum Reveals Promising Biomarkers for Intrahepatic Cholangiocarcinoma Open

Shaaron Ochoa-Rios, Calvin R.K. Blaschke, Mengjun Wang, Kendell D. Peterson, Andrew DelaCourt , et al. · 2023

Hematoxylin & Eosin (H&E) staining of A. Intrahepatic Cholangiocarcinoma (iCCA) tissue, 10x (right) and 40x (left) magnification images from respective areas of the tissue, and B. Hepatocellular Carcinoma (HCC) tissue, 10x magnification im…

Supplementary Table ST1 from Analysis of N-linked Glycan Alterations in Tissue and Serum Reveals Promising Biomarkers for Intrahepatic Cholangiocarcinoma Open

Shaaron Ochoa-Rios, Calvin R.K. Blaschke, Mengjun Wang, Kendell D. Peterson, Andrew DelaCourt , et al. · 2023

Peak list of N-glycans detected in tissue (TMA) and serum samples.

Table S1 from N-Glycosylation Patterns Correlate with Hepatocellular Carcinoma Genetic Subtypes Open

Andrew DelaCourt, Alyson Black, Peggi M. Angel, Richard R. Drake, Yujin Hoshida , et al. · 2023

Patient Characteristics Table

Figure S2 from N-Glycosylation Patterns Correlate with Hepatocellular Carcinoma Genetic Subtypes Open

Andrew DelaCourt, Alyson Black, Peggi M. Angel, Richard R. Drake, Yujin Hoshida , et al. · 2023

An overview of how HCC samples are classified into one of three subtypes based upon a variety of histological, clinical, and genetic data. Genetic data is generated through RNA-seq of the HCC samples.

Table S4 from N-Glycosylation Patterns Correlate with Hepatocellular Carcinoma Genetic Subtypes Open

Andrew DelaCourt, Alyson Black, Peggi M. Angel, Richard R. Drake, Yujin Hoshida , et al. · 2023

N-glycan structures increased in non-tumor tissue cores compared to tumor tissue cores in the tissue micro-array

Table S2 from N-Glycosylation Patterns Correlate with Hepatocellular Carcinoma Genetic Subtypes Open

Andrew DelaCourt, Alyson Black, Peggi M. Angel, Richard R. Drake, Yujin Hoshida , et al. · 2023

Full list of glycans analyzed on the FT-ICR mass spectrometer.

Table S1 from N-Glycosylation Patterns Correlate with Hepatocellular Carcinoma Genetic Subtypes Open

Andrew DelaCourt, Alyson Black, Peggi M. Angel, Richard R. Drake, Yujin Hoshida , et al. · 2023

Patient Characteristics Table

Data from N-Glycosylation Patterns Correlate with Hepatocellular Carcinoma Genetic Subtypes Open

Andrew DelaCourt, Alyson Black, Peggi M. Angel, Richard R. Drake, Yujin Hoshida , et al. · 2023

Hepatocellular carcinoma (HCC) is the second leading cause of cancer deaths globally, and the incidence rate in the United States is increasing. Studies have identified inter- and intratumor heterogeneity as histologic and/or molecular sub…

Figure S2 from N-Glycosylation Patterns Correlate with Hepatocellular Carcinoma Genetic Subtypes Open

Andrew DelaCourt, Alyson Black, Peggi M. Angel, Richard R. Drake, Yujin Hoshida , et al. · 2023

An overview of how HCC samples are classified into one of three subtypes based upon a variety of histological, clinical, and genetic data. Genetic data is generated through RNA-seq of the HCC samples.

Data from N-Glycosylation Patterns Correlate with Hepatocellular Carcinoma Genetic Subtypes Open

Andrew DelaCourt, Alyson Black, Peggi M. Angel, Richard R. Drake, Yujin Hoshida , et al. · 2023

Hepatocellular carcinoma (HCC) is the second leading cause of cancer deaths globally, and the incidence rate in the United States is increasing. Studies have identified inter- and intratumor heterogeneity as histologic and/or molecular sub…

Table S2 from N-Glycosylation Patterns Correlate with Hepatocellular Carcinoma Genetic Subtypes Open

Andrew DelaCourt, Alyson Black, Peggi M. Angel, Richard R. Drake, Yujin Hoshida , et al. · 2023

Full list of glycans analyzed on the FT-ICR mass spectrometer.

Table S3 from N-Glycosylation Patterns Correlate with Hepatocellular Carcinoma Genetic Subtypes Open

Andrew DelaCourt, Alyson Black, Peggi M. Angel, Richard R. Drake, Yujin Hoshida , et al. · 2023

Full list of glycans analyzed on the MALDI-TOF mass spectrometer

Table S4 from N-Glycosylation Patterns Correlate with Hepatocellular Carcinoma Genetic Subtypes Open

Andrew DelaCourt, Alyson Black, Peggi M. Angel, Richard R. Drake, Yujin Hoshida , et al. · 2023

N-glycan structures increased in non-tumor tissue cores compared to tumor tissue cores in the tissue micro-array

Table S3 from N-Glycosylation Patterns Correlate with Hepatocellular Carcinoma Genetic Subtypes Open

Andrew DelaCourt, Alyson Black, Peggi M. Angel, Richard R. Drake, Yujin Hoshida , et al. · 2023

Full list of glycans analyzed on the MALDI-TOF mass spectrometer

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