Donald J. Johann
Federal Grant PI
High Impact
Professor
faculty
Biomedical Informatics, College of Medicine
23 h-index
117 pubs
2,475 cited
Research Areas
Biography and Research Information
OverviewAI-generated summary
Donald J. Johann's research focuses on the application of high-throughput sequencing and mass spectrometry techniques for the detection of cancer biomarkers, particularly circulating tumor DNA (ctDNA).
His work investigates the analytical validity and performance of next-generation sequencing (NGS) assays used in precision oncology. This includes developing and verifying genomic reference samples to assess the accuracy of cancer panels in detecting low-frequency genetic variants. Johann has published studies evaluating the sensitivity and accuracy of various oncopanels, noting that performance can depend on specific genomic regions and sample processing methods, such as the degradation of quality in formalin-fixed paraffin-embedded (FFPE) samples based on their position within the block.
He also contributes to the development of data commons for liquid biopsy research, such as the BloodPAC Data Commons. His research has received federal funding, including a $750,000 grant from the NIH/National Institute of General Medical Sciences for an advanced next-generation sequencer. Johann leads a research group and collaborates with researchers at the University of Arkansas for Medical Sciences and the National Center for Toxicological Research.
Metrics
- h-index: 23
- Publications: 117
- Citations: 2,475
Selected Publications
-
Generic Protocols for Analytical Validation of Tumor-Informed Circulating Tumor DNA Assays for Molecular Residual Disease: The Blood Profiling Atlas in Cancer's Molecular Residual Disease Analytical Validation Working Group Consensus Recommendation (2026)
-
Lexicon for Clonal Hematopoiesis in Liquid Biopsy (2025)
-
Harnessing Native-Resolution 2D Embeddings for Lung Cancer Classification: A Feasibility Study with the RAD-DINO Self-supervised Foundation Model (2025)
-
EET-Based Therapeutics Mitigate Sorafenib-Associated Glomerular Cell Damage (2025)
-
Augmenting precision medicine via targeted RNA-Seq detection of expressed mutations (2025)
-
Recommended Clinical Context and Patient Context Data Elements for Liquid Biopsy Data Submitted to Data Repositories and Data Commons (2025)
-
Towards Preanalytical Best Practices for Liquid Biopsy Studies: A BLOODPAC Landscape Analysis (2024)
-
Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing (2024)
-
A Microdissection Protocol for Proteogenomic Analysis of Histological Sections to Advance Drug Development (2024)
-
Advancing drug development by leveraging microdissection for proteogenomic analysis of histological sections. (2024)
-
Abstract PO5-02-05: Assessing Vaccine-Mediated Cellular Immune Responses in Patients Receiving Combined Vaccine and Chemotherapy Treatment (2024)
-
Assessments of tumor mutational burden estimation by targeted panel sequencing: A comprehensive simulation analysis (2023)
-
Liquid biopsy based on circulating tumor DNA for lung cancer: A step toward prevention (2023)
-
Contrived Materials and a Data Set for the Evaluation of Liquid Biopsy Tests (2023)
-
An advanced molecular medicine case report of a rare human tumor using genomics, pathomics, and radiomics (2023)
Federal Grants 1 $750,000 total
NIH/National Institute of General Medical Sciences
Contact PI
Jun 2024 - Jun 2025
Grants & Funding
- Scientific and methodological advancement in liquid biopsies to further the development of lung cancer-based precision medicine (Bio 3) U.S. Food and Drug Administration - Pass Through: Arkansas Research Alliance Principal Investigator
- Development and Validation of a Microdissection Method to Advance Precision Medicine in the Clinical Setting - Continuation - Continuation NIH/Nat. Cancer Institute Principal Investigator
- Financial Support for the Breast Cancer Intergroup Correlative Science Studies Breast Cancer Research Foundation - Pass Through: University of Michigan Principal Investigator
- NovaSeq X Plus, Advanced Next Generation Sequencer NIH/Office of the Director Principal Investigator
- NovaSeq X Plus, Advanced Next Generation Sequencer NIH/Office of the Director Principal Investigator
- Center for Studies of Host Response to Cancer Therapy NIH Co-Investigator
- Scientific and methodological advancement in liquid biopsies to further the development of lung cancer-based precision medicine U.S. Food and Drug Administration - Pass Through: Arkansas Research Alliance Principal Investigator
- Scientific and methodological advancement in liquid biopsies to further the development of lung cancer-based precision medicine U.S. Food and Drug Administration - Pass Through: Arkansas Research Alliance Principal Investigator
Collaboration Network
Top Collaborators
Rebecca Kusko
12 shared publications
- Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology
- A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency
- Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions
- Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA
- Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples
Showing 5 of 12 shared publications
Binsheng Gong
11 shared publications
In database
- Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology
- A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency
- Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions
- Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples
- Ultra-deep sequencing data from a liquid biopsy proficiency study demonstrating analytic validity
Showing 5 of 11 shared publications
Natalia Novoradovskaya
11 shared publications
- Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology
- A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency
- Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions
- Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA
- Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples
Showing 5 of 11 shared publications
Erich A. Peterson
University of Arkansas for Medical Sciences (US)
10 shared publications
- Exogenous phosphatidic acid reduces acetaminophen-induced liver injury in mice by activating hepatic interleukin-6 signaling through inter-organ crosstalk
- Expansion of Human Papillomavirus-Specific T Cells in Periphery and Cervix in a Therapeutic Vaccine Recipient Whose Cervical High-Grade Squamous Intraepithelial Lesion Regressed
- An advanced molecular medicine case report of a rare human tumor using genomics, pathomics, and radiomics
- NPARS—A Novel Approach to Address Accuracy and Reproducibility in Genomic Data Science
- Effect of Antigen Retrieval on Genomic DNA From Immunodissected Samples
Showing 5 of 10 shared publications
Jennifer S. LoCoco
9 shared publications
- Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology
- Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions
- Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA
- Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples
- Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing
Showing 5 of 9 shared publications
Ik Jae Shin
University of Arkansas for Medical Sciences (US)
8 shared publications
- An advanced molecular medicine case report of a rare human tumor using genomics, pathomics, and radiomics
- NPARS—A Novel Approach to Address Accuracy and Reproducibility in Genomic Data Science
- Effect of Antigen Retrieval on Genomic DNA From Immunodissected Samples
- Microdissection Methods Utilizing Single-Cell Subtype Analysis and the Impact on Precision Medicine
- Synergizing microdissection with ddPCR to advance precision oncology.
Showing 5 of 8 shared publications
Jason Muesse
Winthrop Rockefeller Foundation
8 shared publications
In database
- An advanced molecular medicine case report of a rare human tumor using genomics, pathomics, and radiomics
- NPARS—A Novel Approach to Address Accuracy and Reproducibility in Genomic Data Science
- Effect of Antigen Retrieval on Genomic DNA From Immunodissected Samples
- Microdissection Methods Utilizing Single-Cell Subtype Analysis and the Impact on Precision Medicine
- Synergizing microdissection with ddPCR to advance precision oncology.
Showing 5 of 8 shared publications
Fujun Qiu
7 shared publications
- Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology
- Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions
- Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples
- Deep oncopanel sequencing reveals fixation time- and within block position-dependent quality degradation in FFPE processed samples
- Additional file 3 of Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples
Showing 5 of 7 shared publications
Todd Richmond
7 shared publications
- Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology
- A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency
- Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions
- Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA
- Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing
Showing 5 of 7 shared publications
Guangchun Chen
7 shared publications
- Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology
- A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency
- Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions
- Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA
- Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing
Showing 5 of 7 shared publications
Wendell Jones
7 shared publications
- Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology
- A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency
- Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA
- Ultra-deep sequencing data from a liquid biopsy proficiency study demonstrating analytic validity
- Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing
Showing 5 of 7 shared publications
Michael R. Emmert‐Buck
Maryland Medical Research Institute (US)
7 shared publications
- Effect of Antigen Retrieval on Genomic DNA From Immunodissected Samples
- Microdissection Methods Utilizing Single-Cell Subtype Analysis and the Impact on Precision Medicine
- Synergizing microdissection with ddPCR to advance precision oncology.
- Abstract 373: Advancing precision oncology by synergizing ddPCR with microdissection
- Abstract 730: Leveraging microdissection for proteogenomic analysis of histological sections to advance drug development
Showing 5 of 7 shared publications
Michael A. Tangrea
Loyola University Maryland (US)
7 shared publications
- Effect of Antigen Retrieval on Genomic DNA From Immunodissected Samples
- Microdissection Methods Utilizing Single-Cell Subtype Analysis and the Impact on Precision Medicine
- Synergizing microdissection with ddPCR to advance precision oncology.
- Abstract 373: Advancing precision oncology by synergizing ddPCR with microdissection
- Abstract 730: Leveraging microdissection for proteogenomic analysis of histological sections to advance drug development
Showing 5 of 7 shared publications
Matthew A. Steliga
Winthrop Rockefeller Foundation
7 shared publications
In database
- An advanced molecular medicine case report of a rare human tumor using genomics, pathomics, and radiomics
- NPARS—A Novel Approach to Address Accuracy and Reproducibility in Genomic Data Science
- Effect of Antigen Retrieval on Genomic DNA From Immunodissected Samples
- Microdissection Methods Utilizing Single-Cell Subtype Analysis and the Impact on Precision Medicine
- Abstract 5038: Applying reproducible genomic data science methods for the analysis of a rare tumor type
Showing 5 of 7 shared publications
Daniel Stetson
6 shared publications
- Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology
- Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples
- Deep oncopanel sequencing reveals fixation time- and within block position-dependent quality degradation in FFPE processed samples
- Additional file 3 of Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples
- Additional file 2 of Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples
Showing 5 of 6 shared publications
Similar Researchers
Based on overlapping research topics
Dan Li
National Center for Toxicological Research
Cancer Genomics and Diagnostics
Genomics and Phylogenetic Studies
Molecular Biology Techniques and Applications
Binsheng Gong
National Center for Toxicological Research
Cancer Genomics and Diagnostics
Genomics and Phylogenetic Studies
Molecular Biology Techniques and Applications
Ikjae Shin
University of Arkansas for Medical Sciences
Cancer Genomics and Diagnostics
Genomics and Phylogenetic Studies
Molecular Biology Techniques and Applications
Ik Jae Shin
University of Arkansas for Medical Sciences
Cancer Genomics and Diagnostics
Genomics and Phylogenetic Studies
Molecular Biology Techniques and Applications
Meagan B. Myers
National Center for Toxicological Research
Cancer Genomics and Diagnostics
Genomics and Phylogenetic Studies
Molecular Biology Techniques and Applications
Penelope Duerken-Hughes
National Center for Toxicological Research
Cancer Genomics and Diagnostics
Genomics and Phylogenetic Studies
Molecular Biology Techniques and Applications