Feiyu Du

Consolidation Therapy Based on Mutation Clearance in Acute Myeloid Leukemia

Meagan A. Jacoby, David H. Spencer, Feng Gao, Geoffrey L. Uy et autres

BACKGROUND: Optimal consolidation therapy for patients with intermediate-risk acute myeloid leukemia (AML) in first complete remission (CR1) is controversial. Retrospective studies have suggested that the clearance of leukemia-associated mutations (LAMs) in CR1 may predict lower relapse risk and better outcomes with high-dose …

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Automating neoantigen selection for personalized cancer vaccine design

Jennie X Yao, Kartik Singhal, Susanna Kiwala, Evelyn Schmidt et autres

Advancements in immunogenomics and immuno-oncology have enabled the development of personalized cancer vaccines (PCVs) that target cancer cell-specific somatic variants. A subset of these variants produce neoantigens that, when presented on tumor cells by MHC molecules, have the potential to elicit a …

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ImmunoNX: a robust bioinformatics workflow to support personalized neoantigen vaccine trials.

Kartik Singhal, E. E. Schmidt, Susanna Kiwala, S. Peter Goedegebuure et autres

Personalized neoantigen vaccines represent a promising immunotherapy approach that harnesses tumor-specific antigens to stimulate anti-tumor immune responses. However, the design of these vaccines requires sophisticated computational workflows to predict and prioritize neoantigen candidates from patient sequencing data, coupled with rigorous review to …

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Increased yield of recurrent structural variants (SVs) in Ph-like B-cell acute lymphoblastic leukemia (B-ALL) using a streamlined clinical whole-genome sequencing (WGS) assay

Andrew Hughes, Feiyu Du, Michele O’Laughlin, Mohamed Mahgoub et autres

Abstract Introduction Ph-like B-ALL is a poor-risk B-ALL subtype defined by gene expression signatures that resemble the BCR::ABL1-associated transcriptional program in the absence of the BCR-ABL1 oncoprotein. Recent studies have demonstrated that up to 80% of Ph-like B-ALLs have recurrent gene fusions …

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A fully next-generation sequencing-based method of classifying molecular sub-types of endometrial cancer retains prognostic value and expands biomarker targets

Mark C. Valentine, Amanda Wong, Ling Chen, Feiyu Du et autres

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Clearance of Leukemia Associated Mutations (LAMs) after Induction Therapy Is Associated with Favorable Outcomes in Intermediate Risk Acute Myeloid Leukemia: Interim Results of a Multicenter, Prospective Phase II Trial

Meagan A. Jacoby, David H. Spencer, Geoffrey L. Uy, Feng Gao et autres

Introduction: The optimal post-remission consolidation strategy for medically fit, intermediate-risk patients with AML in morphologic first complete remission (CR1) is controversial and can include high-dose cytarabine (HiDAC) or allogeneic hematopoietic cell transplant (alloHCT). We previously showed that patients in CR1 who cleared …

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A fully next-generation sequencing-based method of classifying molecular subtypes of endometrial cancer retains prognostic value and highlights racial disparities in disease-specific survival

Mark C. Valentine, Amanda Wong, Ling Chen, Feiyu Du et autres

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76. Automating immunogenomic tumor board decision-making for neoantigen cancer vaccine design

Jennie Yao, Kartik Singhal, Susanna Kiwala, Peter S. Goedegebuure et autres

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11. Developing a robust bioinformatics workflow to support personalized neoantigen vaccine clinical trials

Kartik Singhal, Susanna Kiwala, Peter S. Goedegebuure, Christopher A. Miller et autres

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Clonal Myeloid Heterogeneity in Older Autopsy Patients Determined By Multiple Bone Marrow Site Sequencing

Rohan Kodgule, Joshua Robinson, Sridhar Nonavinkere Srivatsan, Cara Lunn Shirai et autres

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Genome Sequencing as an Alternative to Cytogenetic Analysis in Myeloid Cancers

Eric J. Duncavage, Molly C. Schroeder, Michele O’Laughlin, Roxanne Wilson et autres

BACKGROUND: Genomic analysis is essential for risk stratification in patients with acute myeloid leukemia (AML) or myelodysplastic syndromes (MDS). Whole-genome sequencing is a potential replacement for conventional cytogenetic and sequencing approaches, but its accuracy, feasibility, and clinical utility have not been demonstrated. …

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Genome Modeling System: A Knowledge Management Platform for Genomics

Malachi Griffith, Obi L. Griffith, Scott M. Smith, Avinash Ramu et autres

In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis …

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