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 Wins 3 Awards Worth $7.5k at Hack4NF

In late 2022, CGDS, in collaboration with Dr. Deeann Wallis lab, participated in a hackathon organized by the Children’s Tumor Foundation to tackle challenges with Neurofibromatosis disease. Here’s the presentation from the hackathon to learn more about the project.

In response to the ground-breaking work, Hack4NF organizers awarded three prestigious awards to our team.

  1. Winning team for Challenge-II: Devising in silico strategies to prioritize likely pathogenic NF1 germline variants.

2. Awarded Incubation award to work with the foundation to further develop methods for practical use in a clinical setting.

3. Third award for best overall use of the Hack4NF data platform.

CGDS at UAB Cancer Retreat

In October 2022, the O’Neal Comprehensive Cancer Center at the University of Alabama at Birmingham (UAB) held its highly anticipated annual Research Retreat at Regions Field. This event brought together researchers, medical professionals, and trainees to share the latest advancements in cancer research. Among the many projects presented was a groundbreaking study on Pediatric Thyroid Cancer, presented as a poster by Dr. Gurpreet Kaur, a post-doctoral trainee at the Center for Genomic Data Sciences (CGDS).

Dr. Kaur’s research project aimed to shed light on the molecular mechanisms underlying the disease. As a post-doctoral trainee at the CGDS, she utilized cutting-edge genomic technologies and bioinformatics tools to analyze tumor samples from pediatric patients with thyroid cancer. Her poster allowed her to visually convey the key aspects of her research, including the objectives, methodology, findings, and potential implications. Attendees had the opportunity to engage with Dr. Kaur, ask questions, and gain a deeper understanding of her work.

Dr. Gurpreet Kaur presenting her poster on Pediatric Thyroid cancer project

CGDS Trainees Attend the 2022 CCTS Translational Training Symposium

CGDS trainees Shaurita Hutchins, Brandon Wilik, and Tarun Mamidi attended and presented at the 2022 CCTS Translational Training Symposium in Mobile, Alabama. Both Mamidi and Hutchins received the CCTS Scientific Excellence Award to support travel to the symposium starting on September 14th.

Shaurita, Brandon, and Tarun (left to right) on the final day.
Shaurita presenting a poster on pulmonary arterial hypertension.
Tarun presenting his variant pathogenicity tool called DITTO.

All trainees presented posters at the conference and were able to gain valuable knowledge on networking, utilizing social media as scientists, navigating relationships with mentors, and writing aims for their researchers.

CGDS at ISMB 2022 Madison, WI

Dr. Manavalan Gajapathy, Dr. Liz Worthey, and Tarun Mamidi attended the Intelligent Systems for Molecular Biology (ISMB) conference in July 2022.

Manavalan Gajapathy, Elizabeth Worthey and Tarun Mamidi at ISMB 2022 (left to right)

Mana and Tarun both presented posters on their current projects.

Additionally, members of CDGS were able to network with others at the conference as well as spend time with collaborators in Dr. Brittany Lasseigne’s lab.

CGDS representing at ACMG 2022

From left to right – Donna Brown, Shaurita Hutchins, Tarun Mamidi, James Scherer, Angelina Uno-Antonison, Manavalan Gajapathy, Deeptha Srirangam

Several members of CGDS (Center for Computational Genomics and Data Science) attended annual ACMG (American College of Medical Genetics) conference held in Nashville, TN. This is the first in-person conference for people at CGDS since the pandemic.

Dr. Manavalan Gajapathy presented a poster titled “QuaC: Implementing Quality Control Best Practices for Genome Sequencing and Exome Sequencing Data”. Please use the below link to download the poster.

quac_acmgDownload

Hackin’ it at the Hackathon

Recently, members of CGDS participated in the UAB hosted AI Against Cancer Data Science Hackathon with not just one team, but two teams. Their aim was at “solving cancer-related research, prevention, and healthcare practice problems using Artificial Intelligence (AI) and data science.” Both teams were formed of a diverse range of skilled individuals bringing together capabilities and experience from areas of genetics, genomics, transcriptomics, bioinformatics, machine learning, molecular biology, developmental biology, and clinical genomics.

Team Ditto, comprised of the same members that’d placed third in the 2020 UAB COVID-19 Hackathon (https://sites.uab.edu/cgds/2020/08/04/rico/): Tarun Mamidi, doctoral trainee in Genetics, Genomics and Bioinformatics; Dr. Ryan Melvin, Data Scientist in Anesthesiology; Dr. Thi K. Tran-Nguyen, Postdoctoral Fellow in PMI; Dr. Liz Worthey formed a new collaboration with Dr. Rati Chkheidze from Neuropathology. They presented work on “AI Guided Multiomics Data Mapping on Pathology Whole Slide Images of Glioblastoma”. For more information on their project, please watch their presentation recording here.

The new team this year, entered as Team BirthSeq-AI, was comprised of: Dr. Gurpreet Kaur, Postdoctoral Fellow in CGDS; Shaurita Hutchins, doctoral trainee in Genetics, Genomics and Bioinformatics; Brandon Wilk, doctoral trainee in Genetics, Genomics and Bioinformatics; Kristen Coutinho, doctoral trainee in Genetics, Genomics and Bioinformatics & Cortes Brain Aging and Physiology Lab; and mentored by Dr. Liz Worthey. Their focus on was on “Development of an AI-based Approach to Better Understand Chorangiomas by Studying Placental Heterogeneity”. For more information on their project, please watch their presentation recording here.

Team Ditto winning Second prize and Team BirthSeq-AI winning Health Equity Award

Both teams had stellar presentations and work performed in their respective areas with Team Ditto taking Second Place and Team BirthSeq-AI taking the Health Equity Award. See more at https://twitter.com/cctsnetwork/status/1430263483904532488

My Gene Counsel Selected by Foundation for Prader-Willi Research to Enable Responsible Return of Results for Genome Sequencing Project


My Gene Counsel, a digital health company that provides innovative genetic counseling solutions, today announced it is partnering with the Foundation for Prader-Willi Research (FPWR) on the first Prader-Willi syndrome (PWS) Genome Project. Through this partnership, My Gene Counsel will support FPWR in the responsible return of select genetic test results to research participants with PWS who undergo whole genome sequencing.

The study, which began enrolling participants in May 2021, will use whole genome and RNA sequence analysis to identify how variations in patients’ DNA influence the range and severity of PWS symptoms and response to treatments.

“We are excited to take the first steps towards harnessing the knowledge of the genome to better understand and optimize individual outcomes for those with Prader-Willi syndrome,” said Theresa Strong, Director of Research Programs at the Foundation for Prader-Willi Research.

Analysis of the DNA sequences will be performed at the University of Alabama at Birmingham (UAB). Liz Worthey, who leads the Center for Computational Genomics and Data Science at the UAB School of Medicine stated, “PWS patients are burdened with a highly complex array of symptoms. By using both whole genome sequencing and RNAseq, we’ll be working to discover and understand the molecular mechanisms that underlie those symptoms, and potentially lead to new therapies. Aiding patient cohorts and individual patients with rare, undiagnosed, or misdiagnosed disease is the primary focus of our expert team. We’re honored that FPWR chose our team for this study.”

As part of the initiative, FPWR will return pathogenic variants in genes on the American College of Medical Genetics and Genomics Secondary Findings list (ACMG SF v3.0) to participants and has enlisted health technology company My Gene Counsel to help return these results in a safe and responsible way.

To that end, My Gene Counsel will ensure that patients who undergo whole genome testing as part of the PWS Genome Project have access to comprehensive genetic counseling information designed to enhance participant understanding. Each participant who chooses to have their results returned will receive an electronic Living Lab Report® from My Gene Counsel that is personalized to the individual’s genetic test results and covers topics related to disease risk, medical management options, relevance to family, emotional support, and available resources.

“Offering rare disease communities, like PWS, genetic testing will push research forward,” said Ellen Matloff, President and CEO of My Gene Counsel. “We are proud to enter the rare disease space by partnering with the Foundation for Prader-Willi Research to return genetic test results that are paired with updating genetic counseling information.”

The Living Lab Reports are written and continuously updated by a network of top certified genetic counselors and medical experts and are vetted by patient advocates. In addition to delivering complex genomic information in a patient-friendly format, the reports will update and notify participants automatically by text and/or email as new risk information, management guidelines, and variant reclassifications become available. Living Lab Reports can also be used to update participants on study progress and findings over time. The PWS Genome Project is currently enrolling participants, ages 10 to 65 and residing in the U.S., with a genetically confirmed diagnosis of Prader-Willi syndrome. Additional requirements can be found here. Those interested in joining the study should contact Caroline Vrana-Diaz, Research Project Coordinator for the Foundation for Prader-Willi Research, at caroline@fpwr.org.

About My Gene Counsel
My Gene Counsel was created to address the need for an automated, scalable solution to meet the growing demand for accurate and timely genetic counseling information. With its industry-leading database of proprietary genetics content organized by gene and variant, My Gene Counsel’s HIPAA-compliant SaaS solution delivers continuously updating genetic counseling information to patients and providers via Living Lab Reports® in many areas of genomics, including hereditary and somatic cancer testing, hereditary cardiovascular disease, noninvasive prenatal testing, and more. Founded by certified genetic counselors with 30+ years of clinical experience, My Gene Counsel helps partners save resources, retain patients, and efficiently deliver on the promise of precision medicine. For more information, visit https://www.mygenecounsel.com.

About Foundation for Prader-Willi Research
Prader-Willi syndrome is a genetic disorder that typically causes low muscle tone, short stature, incomplete sexual development, cognitive disabilities, behavior problems, and a chronic hunger that can lead to excessive eating and life-threatening obesity. The Foundation for Prader-Willi Research is a non-profit organization dedicated to eliminating the challenges of Prader-Willi syndrome through the advancement of research and therapeutic development. It was founded and is maintained by parents and other relatives of persons with the syndrome. For more information, visit https://www.fpwr.org.

Senior Bioinformatician

For application details, please contact Dr. Elizabeth Worthey (eworthey@peds.uab.edu) with your CV.

Come join a diverse and growing team of computational biologists working to develop and apply computational biology, bioinformatics, and data science methods to identify the molecular underpinnings of disease and to generate knowledge of the functional impact of molecular variation to better understand disease onset, progression, and outcome, response to therapeutics, and relationship to human health. This individual will have the opportunity to work with world class researchers and clinicians and to work on a variety of pediatric and adult diseases. Current projects are focused on gaining knowledge and understanding of disease mechanisms and outcomes for Mendelian disorders and more common complex diseases including cancer, neurodegenerative diseases, and immune disorders.

Mission, Vision & Values

UAB serves students, patients, the community and the global need for discovery, knowledge dissemination, education, creativity and the application of groundbreaking solutions. We are a leader among comprehensive public urban research universities with academic medical centers. We expect all employees to adhere to our shared values of Integrity, Respect, Diversity and inclusiveness, Collaboration, Excellence and achievement, Stewardship, and Accountability. UAB’s Vision, Mission & Shared Values can be found here: https://www.uab.edu/plan/the-plan/mission-vision-shared-values/

General Responsibilities

To participate in research activities involved in the analysis of Next Generation Sequencing such as data derived from genomics and transcriptomics (bulk and single-cell sequencing) to the UAB Biological Data Science institutional core. To support research services such as study design, data management, data analysis, pipeline development and to aid in the generation of training guides and documentation. To stay abreast of recent literature and other new developments, incorporating new techniques into existing data analysis protocols and pipelines in support of the institutional core’s mission of high quality, reproducible computational biology research.

Key Duties & Responsibilities

  1. Performs computational data analysis of transcriptomics and genomics studies.
  2. Designs, develops and implements software tools and analytical procedures supporting bioinformatics analysis.
  3. Participates in projects related to the core sustainability including but not limited to pipeline development, web application development, maintenance of documentation and training guides and other services to support the needs of UAB investigators.
  4. Provides computational support services such as study design, data management and data migration.
  5. Offers bioinformatics consultation services to UAB investigators.
  6. Evaluates and identifies new technologies for implementation.
  7. Performs other duties as assigned.

Minimum Requirements

Doctorate in a related field OR Master’s degree in a related field and two (2) years of related experience OR Bachelor’s degree in related field and four (4) years of related experience OR Associate’s degree in related field and six (6) years of related experience required. Work experience may NOT substitute for education requirements.

Knowledge / Skills / Abilities

  • Knowledge of the biological sciences
  • Experience in computational biology analysis
  • Experience in Linux and using a command-line environment
  • Knowledge of scripting languages such as, Python, shell scripts, and R
  • Knowledge of best practices of reproducible and scalable research such as version control (git) and environment managing systems (e.g.: conda, Docker, Singularity)
  • Proficiency in the visualization of omics data
  • Experience in High Performance Computing environment is preferable
  • Ability to work as part of a team
  • Knowledge of theoretical and applied statistics, and molecular biology, as demonstrated through previous work or academic experience
  • Problem-solving skills
  • Attentive to detail
  • Organizational skills
  • Excellent written and verbal communication skills

An ideal candidate will follow best practices described to ensure reproducible and scalable research and be proficient in the analysis of transcriptomics data (e.g.: differential expression analysis, enrichment analysis, single-cell or nuclei data visualization and analysis, gene set annotation and contribute to upstream data analysis through the development of pipelines). An ideal candidate should also be familiar with managing virtual computational environments and be familiar with high performance computing clusters.

Disclaimer

Please Note: The duties and responsibilities described are not a comprehensive list and additional tasks may be assigned to the employee as necessitated by business demands. This job description does not constitute a contract of employment or otherwise limit UAB’s employment-at-will rights at any time. Employees are expected to comply with all UAB policies and procedures during their employment.