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Texas Whole-Exome Sequencing Project Aims to Help Address Disparities in Genomic Medicine

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BALTIMORE – A team of clinicians, researchers, and genetic counselors from several biomedical institutions in Texas has created a program to help address disparities in genomic medicine between racial and ethnic groups.

Funded by the National Human Genome Research Institute (NHGRI), the initiative, named the Texome project, aims to deliver free whole-exome sequencing to about 400 patients with undiagnosed disorders in Texas over four years, while providing them with bioinformatic analysis and genetic counseling resources to help reach an answer for their unsolved cases. Additionally, the project hopes to identify barriers that hinder low-resource communities from accessing genomic medicine by conducting longitudinal follow-up studies with participants.

"A lot of communities and a lot of groups of people within the United States don't have the same kind of access to high-quality genomic medicine or genetic testing that some other groups have access to," said Ryan German, a research coordinator at Baylor College of Medicine who is part of the project. "The Texome project is in place to provide genomic medicine to [these] underserved communities."

Co-led by Baylor College of Medicine professors Michael Wangler and Hugo Bellen, the Texome project began enrollment in December 2021, German said. In addition to Baylor, Texas Children’s Hospital, Harris Health System, and Children’s Hospital of San Antonio are also contributing to the project.

To achieve inclusive enrollment, the Texome project only has two main recruitment criteria: a patient should have a rare condition of unknown cause that is suspected to be genetic, and the patient does not have the resources to receive genomic testing to reach a diagnosis or to further investigate the condition. Additionally, the project primarily enrolls patients currently living in Texas, German noted.

So far, Texome has received more than 90 applications, most of which are completed by clinicians on behalf of a patient. However, German said the application is also available online for patients who choose to self-refer.

Of these applicants, about 78 percent are English speakers and 22 percent Spanish speakers; approximately 34 percent are adults and 66 percent children; and around 60 percent are male while 40 percent are female, according to German.

The project accepted 68 of the applications and successfully enrolled 47 patients. There were many factors that may have contributed to the drop-off, German said, including applicants moving out of state or being unreachable for enrollment.

Based on voluntary survey responses from the enrolled participants, half of them self-identified as Hispanic or Latino and about 25 percent as white or European American. The remaining 25 percent included individuals from Black, Asian, or Native American communities.

In general, the Texome project comprises five visits over a two-year period for each participant. The first visit is at Texas Children's Hospital, where the patient receives pre-test genetic counseling from a clinician and is consented for the study.

Once the patient agrees to the study, a buccal swab is collected, and if possible, the team also tries to collect samples from both parents for trio sequencing, German noted.

The samples will then be sent to a clinical lab at Baylor, which will perform whole-exome sequencing. "Essentially, the participants are receiving the same quality of testing as they would if it was a clinical test," German said.

After the test is completed, the participant will return for a second visit and meet with a clinician to discuss the results. According to German, the current diagnostic rate for the project is about 43 percent, which he considers "quite high" for an exome study. "We believe that the main reason for that is … not because of us or because the technology is so new, it's more because this population just hasn’t had access to this kind of genomic medicine before," he said.

In a poster presentation at this year’s American Society of Human Genetics (ASHG) meeting in October, German showed that the project has helped identify mutations in over a dozen disease-causing genes associated with conditions ranging from intellectual developmental disorders to retinitis pigmentosa.

While the Texome project does not provide treatments for newly diagnosed patients, it will work with them to explore available resources and make sure they receive appropriate and necessary follow-up care, German said.

Meanwhile, for patients whose cases remain unsolved, the project team will continue to re-analyze their sequencing data and report any new findings back to them when necessary. Furthermore, German said there is the possibility of referring these patients to other undiagnosed disease networks that Baylor is part of.

After the initial visits, the project entails three additional follow-ups with the patient at the six-month, one-year, and two-year marks. During these visits, the patients will complete surveys to share their ongoing experience with genomic medicine and discuss any updates on their cases.

In addition to providing clinical diagnoses, the Texome project also aims to enhance genomic research for low-resource communities. "Since this is an underserved and understudied population, we are invested in increasing the discovery in a sensitive way that is not just beneficial for researchers, but beneficial for the patients themselves," German said.

One of the ways that the project is helping with research is through data sharing, he noted, adding that the project has been uploading data to the National Institutes of Health’s database of Genotypes and Phenotypes (dbGaP), which collects data and results from human genotype-phenotype interaction studies. In addition, the project will upload certain clinically important variants to ClinVar, another NIH-sponsored database that contains genomic variations important to human health.

Beyond these, the Texome project also contains a functional study arm, which taps the model organism lab at Baylor to further explore variants or genes of interest in model organisms.

As part of their longitudinal follow-up, the Texome investigators also try to identify and overcome barriers that patients from underserved communities face when participating in genomic studies.

German said the team has found, for example, that a study’s inflexible enrollment criteria can often turn these patients away. "For example, there's a good number of families who are enrolled in our study that might not be eligible for other studies simply because one of the parents is not available," he said.

Moreover, he noted that the ability to travel to a clinic can be another obstacle for these communities to participate in a study.

"We realized that for a lot of families travel is a barrier," he said. "So, we work with the families where they are to get the services they need."

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