Tag: cgds

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.

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 Publishes Study on Genetic Factors Influencing Vitamin D Status in Cystic Fibrosis

CGDS researchers and collaborators have published new findings on the genetic basis of vitamin D variability in adults with cystic fibrosis (CF). The study analyzed 25-hydroxyvitamin D (25OHD) levels alongside whole genome sequencing data from 80 adults to investigate why some patients remain vitamin D insufficient despite consistent supplementation.

Results showed that 30% of participants had 25OHD concentrations below the 30 ng/mL threshold, despite normal vitamin E levels. Polygenic risk scores (PRS) were significantly correlated with 25OHD status, indicating that common genetic variants contribute to differences in response to vitamin D therapy. These findings align with prior results in children and support a more personalized approach to supplementation in CF care.

Read the full study in Journal of Cystic Fibrosis: Vitamin D status and variable responses to supplements depend in part on genetic factors in adults with cystic fibrosis.

CGDS Publishes on Caregiver Perspectives in Prader-Willi Syndrome Pharmacogenomics

Researchers at CGDS, in collaboration with FPWR, have published a study exploring caregiver interest in pharmacogenomic (PGx) testing for children with Prader-Willi syndrome (PWS). The study surveyed caregivers before returning PGx results, aiming to understand their expectations and planned use of this information in clinical care.

Among the 48 caregivers surveyed, 93.8% expressed strong interest in their child’s PGx results. Nearly all respondents (97.9%) intended to share the findings with medical providers, yet fewer than half (47.9%) felt confident that those providers would use the results. The findings highlight the enthusiasm among caregivers and the perceived gap in provider readiness to act on PGx data, signaling a need for increased education and support around clinical implementation.

Read the full study in Pharmacogenomics: Pharmacogenomics for Prader-Willi syndrome: caregiver interest and planned utilization.

CGDS Trainee Presents at the UAB Cystic Fibrosis Research Center Symposium

On October 4, 2023, Tarun Mamidi, a doctoral candidate in CGDS, showcased his research at the UAB Cystic Fibrosis Research Center Symposium, focusing on using neural networks to identify modifier variants in Cystic Fibrosis (CF).

His work aims to improve our understanding of how these variants can change how CF affects individuals and their response to treatments. By applying advanced neural network techniques, Tarun’s research offers potential pathways for more precise and effective therapeutic strategies.

Congratulations to Tarun!

CGDS Attends ACMG 2023 in Salt Lake City, UT

Left to right: Dr. Manavalan Gajapathy, Dr. Gurpreet Kaur, Tarun Mamidi, Dr. Liz Worthey

Tarun Mamidi gave a platform presentation on applying his thesis work to identify pathogenic variants causing Neurofibromatosis disease. Mana and Gurpreet also gave poster presentations on their projects. Here are the abstracts submitted to the conference –

  1. Presented by Mana – P464: ROH pipeline enables analysis of regions of homozygosity using next generation sequencing data
  2. Presented by Gurpreet – P492: Identification of molecular modifiers of disease in a group of systematically phenotyped patients with cystic fibrosis
  3. Presented by Tarun – O48: DITTO4NF: In silico classification and prioritization of likely pathogenic variants for NF1 using explainable machine learning

Gurpreet was awarded Office of Postdoctoral Education (OPE) Travel Award for ACMG2023 to present her work on Cystic Fibrosis

Tarun giving his platform presentation at ACMG on DITTO4NF.
Tarun Mamidi
Mana, Gurpreet and Tarun
Gurpreet presenting her poster on Cystic Fibrosis

CGDS ClinVar Submissions Update

The Center for Computational Genomics and Data Science (CGDS) at the University of Alabama recently submitted updates to ClinVar, highlighting its ongoing contributions to genomic research and variant interpretation.

GeneSubmissionsLast Updated
ENO31Jun 9, 2020
EPHX11Dec 18, 2019
HFE1Dec 18, 2019
LOC1087836451Dec 18, 2019
MBL21Dec 18, 2019
PLG1Dec 18, 2019
SERPINA11Dec 18, 2019

More details about the submission are here.