CGDS Team Publishes Study Supporting Distinct Molecular Mechanisms Underlying ME/CFS

We are excited to share a new paper from the lab and collaborators examining myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) using an individualized, n-of-1 genomic and transcriptomic framework. The study was led by Camille Birch, PhD, Brandon Wilk, Manavalan Gajapathy, Shaurita D. Hutchins, Gurpreet Kaur, Donna M. Brown, Tarun Mamidi, PhD, MS, Kathleen S. Hodgin, Alp Turgut, Jarred Younger, PhD, and Elizabeth A. Worthey.

ME/CFS is a disabling and heterogeneous condition with no validated biomarkers and limited therapeutic options. Clinical variability and unclear pathophysiology have constrained progress in diagnosis and treatment. In this work, we tested whether integrating individual-level genomic and transcriptomic data with deep, participant-informed phenotyping could uncover molecular signatures unique to each patient.

Our findings support the idea that a subset of ME/CFS cases may represent distinct molecular disorders that converge on shared physiological pathways. Importantly, the study suggests that simply increasing cohort size may not be sufficient to resolve causation in a disease defined by rarity, heterogeneity, and molecular complexity. Instead, progress will likely require experimental designs that prioritize individual-level molecular data, rare and common variant effects, and environmental modifiers.

This work motivates a precision medicine framework for ME/CFS that can enable biologically informed stratification, improved trial design, biomarker discovery, and targeted interventions.

We are actively seeking collaborators to extend this approach to much larger and more diverse cohorts. If you or your organization is interested in partnering on future studies, we would welcome the opportunity to connect.

Read the paper at https://link.springer.com/article/10.1186/s12967-025-07586-w.

UAB’s Center for Precision Animal Modeling Receives Continuing NIH Support

The UAB Center for Precision Animal Modeling (CPAM) has received renewed NIH funding (Grant No. 2U54OD030167-06) through 2030 to expand its efforts in modeling human genetic disease. This continuation supports the next phase of the Center’s work (CPAM2.0), enhancing its established framework for variant interpretation, disease modeling, and therapeutic discovery.

The Bioinformatics Section, led by Dr. Liz Worthey, will enhance CPAM’s computational framework through new applications of machine learning, generative AI, and cross-species analysis. This includes expanding Rosalution, which streamlines data integration, variant curation, and collaboration across CPAM teams. The renewed funding underscores CPAM’s role in translating genomic findings into actionable insights that accelerate diagnosis and treatment for rare diseases.

CGDS & U-BDS Co-Host July 2025 Software Carpentry Python Workshop at UAB

On July 9–10, 2025, CGDS and U-BDS co-hosted a Software Carpentry Python Workshop at the University of Alabama at Birmingham. The event welcomed over 40 students and staff from diverse disciplines to build core programming skills vital for computational and data-intensive research.

The two-day hands-on training covered the Unix shell, Python programming, and version control with Git. Participants worked through structured lessons designed to support reproducibility and best practices in scientific computing.

Instructors: Angelina Uno-Antonison, Austyn Trull, Brandon Wilk, Shaurita D. Hutchins

Helpers: James Scherer, Manavalan Gajapathy, Rabab Fatima

To learn more or review workshop materials, visit the full site at: https://u-bds.github.io/2025-07-09-uab/

CGDS granted continuing funding to extend our Patient-Centered WGS-Driven Pilot Study in Prader-Willi Syndrome

Launched in May 2021, this study applies whole genome and RNA sequencing to understand how genetic variation influences the severity of Prader-Willi Syndrome (PWS) symptoms and treatment response. Our team is dedicated to supporting individuals with rare, undiagnosed, or misdiagnosed conditions. We are proud to lead this work in partnership with the Foundation for Prader-Willi Research (FPWR).

Participants will receive findings on pathogenic variants from the ACMG Secondary Findings v3.0 gene list. FPWR has partnered with My Gene Counsel to ensure these results are delivered in a medically responsible and accessible way.

Congratulations to Dr. Tarun Mamidi!

We are thrilled to celebrate Dr. Tarun Mamidi, who graduated from UAB on Saturday, December 14th.

Dr. Mamidi defended his dissertation, “Improving Molecular Diagnosis Success Rates and Prognosis Prediction for Patients With Rare Diseases,” in June 2024.

He will begin his new role as a Bioinformatics Scientist at Children’s Mercy while continuing as a consultant in our lab.

We wish you continued success in your career, Tarun!

CGDS Team Publishes Largest Genomic Study to Date That Reveals RAS Pathway Involvement in JGCTs

Ten juxtaglomerular cell tumors (JGCTs) from nine institutions were analyzed using immunohistochemistry and whole exome sequencing. The study highlights significant morphologic variability, with tumors mimicking other renal neoplasms. Although three tumors exhibited concerning histologic features, patient outcomes were favorable, suggesting that morphology alone is not predictive of clinical behavior.

Genomic analysis identified activating variants in RAS GTPases without other recurrent alterations. These findings implicate the MAPK–RAS pathway in JGCT development and represent the largest JGCT series characterized by whole exome sequencing to date.

Read the full publication in Modern Pathology: Molecular Characterization of Juxtaglomerular Cell Tumors: Evidence of Alterations in MAPK-RAS Pathway.

CGDS Researchers Present Work at CSHL Biological Data Science Meeting

Two researchers from the Center for Computational Genomics and Data Science (CGDS) recently showcased their work at the prestigious Cold Spring Harbor Laboratory (CSHL) Biological Data Science Meeting, held November 13-16, 2024. This meeting, known as #CSHLData24, brings together experts from across the globe to discuss advances in computational biology and genomics.

Dr. Gurpreet Kaur, a Scientist III at CGDS, presented her project titled “Integrative Genomic Characterization of a Rare Pediatric Differentiated Thyroid Cancer.” This project is a collaborative effort to understand the genomic underpinnings of a rare thyroid cancer in pediatric patients.

Shaurita D. Hutchins, a PhD trainee at CGDS, presented a poster titled “Identification of Drug Targets in Pulmonary Arterial Hypertension Using Gene Expression Signature Reversal & Mechanism of Action.” Her attendance was supported by a scholarship from the JXTX Foundation, which “provides support for students to attend conferences in computational biology and data science.”

CGDS is proud to have its researchers contributing to discussions at leading scientific gatherings. The work presented at #CSHLData24 reflects the lab’s commitment to advancing computational biology.

Learn more about the CSHL Biological Data Science Meeting.

CGDS and Rosalution Featured in NIH Research Highlights

We’re excited to share that our lab’s work was featured in the NIH Research Highlights post on the University of Alabama at Birmingham’s (UAB) Center for Precision Animal Modeling (C-PAM). This recognition underscores our contributions to advancing precision disease modeling, a field at the forefront of personalized medicine.

C-PAM is one of three U54 centers established under the NIH Precision Disease Modeling Initiative, focused on creating advanced animal models for precision therapies targeting complex disorders like ciliopathies and Roberts syndrome. Our tool, Rosalution, plays a key role in these efforts, helping link unique human genomic variants to disease with high-throughput, cost-effective pipelines.

This recognition highlights our lab’s commitment to developing innovative tools that enhance our understanding of disease mechanisms and empower clinicians and researchers.

Read more about the initiative and C-PAM’s work here.