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Vuocolo B, German RJ, Lalani SR, Murali CN, Bacino CA, Baskin S, Littlejohn R, Odom JD, McLean S, Schmid C, Nutter M, Stuebben M, Magness E, Juarez O, El Achi D, Mitchell B, Glinton KE, Robak L, Nagamani SCS, Saba L, Ritenour A, Zhang L, Streff H, Chan K, Kemere KJ, Carter K, Owen N, Vossaert L, Liu P, Bellen H, Wangler MF. Improving access to exome sequencing in a medically underserved population through the Texome Project. Genet Med 2024; 26:101102. [PMID: 38431799 DOI: 10.1016/j.gim.2024.101102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/16/2024] [Accepted: 02/21/2024] [Indexed: 03/05/2024] Open
Abstract
PURPOSE Genomic medicine can end diagnostic odysseys for patients with complex phenotypes; however, limitations in insurance coverage and other systemic barriers preclude individuals from accessing comprehensive genetics evaluation and testing. METHODS The Texome Project is a 4-year study that reduces barriers to genomic testing for individuals from underserved and underrepresented populations. Participants with undiagnosed, rare diseases who have financial barriers to obtaining exome sequencing (ES) clinically are enrolled in the Texome Project. RESULTS We highlight the Texome Project process and describe the outcomes of the first 60 ES results for study participants. Participants received a genetic evaluation, ES, and return of results at no cost. We summarize the psychosocial or medical implications of these genetic diagnoses. Thus far, ES provided molecular diagnoses for 18 out of 60 (30%) of Texome participants. Plus, in 11 out of 60 (18%) participants, a partial or probable diagnosis was identified. Overall, 5 participants had a change in medical management. CONCLUSION To date, the Texome Project has recruited a racially, ethnically, and socioeconomically diverse cohort. The diagnostic rate and medical impact in this cohort support the need for expanded access to genetic testing and services. The Texome Project will continue reducing barriers to genomic care throughout the future study years.
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Affiliation(s)
- Blake Vuocolo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX
| | - Ryan J German
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Chaya N Murali
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Stephanie Baskin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | | | - John D Odom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Scott McLean
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Carrie Schmid
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Morgan Nutter
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Melissa Stuebben
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Emily Magness
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Olivia Juarez
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Dina El Achi
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Bailey Mitchell
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX
| | - Kevin E Glinton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Laurie Robak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Sandesh C S Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital Department of Pathology, Houston, TX
| | - Lisa Saba
- Texas Children's Hospital Department of Pathology, Houston, TX
| | - Adasia Ritenour
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Lilei Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital Department of Pathology, Houston, TX
| | - Katie Chan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - K Jordan Kemere
- Department of Internal Medicine, Section Transition Medicine, Baylor College of Medicine and Texas Children's Hospital, Houston, TX
| | - Kent Carter
- Department of Pediatrics, University of Texas Rio Grande Valley, Harlingen, TX
| | | | | | | | - Hugo Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX.
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German RJ, Vuocolo B, Vossaert L, Owen N, Lewis RA, Saba L, Wangler MF, Nagamani S. Novel hemizygous single-nucleotide duplication in RPGR in a patient with retinal dystrophy and sensorineural hearing loss. Mol Genet Genomic Med 2024; 12:e2404. [PMID: 38404254 PMCID: PMC10895382 DOI: 10.1002/mgg3.2404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/27/2024] Open
Abstract
BACKGROUND The RPGR gene has been associated with X-linked cone-rod dystrophy. This report describes a variant in RPGR detected with exome sequencing (ES). Genes like RPGR have not always been included in panel-based testing and thus genome-wide tests such as ES may be required for accurate diagnosis. METHODS The Texome Project is studying the impact of ES in medically underserved patients who are in need of genomic testing to guide diagnosis and medical management. The hypothesis is that ES could uncover diagnoses not made by standard medical care. RESULTS A 58-year-old male presented with retinitis pigmentosa, sensorineural hearing loss, and a family history of retinal diseases. A previous targeted gene panel for retinal disorders had not identified a molecular cause. ES through the Texome Project identified a novel, hemizygous variant in RPGR (NM_000328.3: c.1302dup, p.L435Sfs*18) that explained the ocular phenotype. CONCLUSIONS Continued genetics evaluation can help to end diagnostic odysseys of patients. Careful consideration of genes represented when utilizing gene panels is crucial to ensure an accurate diagnosis. Medically underserved populations are less likely to receive comprehensive genetic testing in their diagnostic workup. Our report is an example of the medical impact of genomic medicine implementation.
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Affiliation(s)
- Ryan J. German
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
- Jan and Dan Duncan Neurological Research InstituteTexas Children's HospitalHoustonTexasUSA
| | - Blake Vuocolo
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
- Jan and Dan Duncan Neurological Research InstituteTexas Children's HospitalHoustonTexasUSA
| | - Liesbeth Vossaert
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
- Baylor Genetics LaboratoriesHoustonTexasUSA
| | - Nichole Owen
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
- Baylor Genetics LaboratoriesHoustonTexasUSA
| | - Richard A. Lewis
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
- Department of MedicineBaylor College of MedicineHoustonTexasUSA
- Department of OphthalmologyBaylor College of MedicineHoustonTexasUSA
| | - Lisa Saba
- Department of PathologyTexas Children's HospitalHoustonTexasUSA
| | | | - Michael F. Wangler
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
- Jan and Dan Duncan Neurological Research InstituteTexas Children's HospitalHoustonTexasUSA
- Texas Children's HospitalHoustonTexasUSA
| | - Sandesh Nagamani
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
- Department of MedicineBaylor College of MedicineHoustonTexasUSA
- Texas Children's HospitalHoustonTexasUSA
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Vuocolo B, Gutierrez AM, Robinson JO, Recinos AM, Desrosiers LR, Majumder MA, Bernini JC, Gill J, Griffin T, Tomlinson GE, Vallance K, McGuire AL, Parsons DW, Plon SE, Scollon S. Families' experiences accessing care after genomic sequencing in the pediatric cancer context: "It's just been a big juggle". J Genet Couns 2024. [PMID: 38225886 DOI: 10.1002/jgc4.1858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 11/30/2023] [Accepted: 12/27/2023] [Indexed: 01/17/2024]
Abstract
Access to genomic sequencing (GS) and resulting recommendations have not been well described in pediatric oncology. GS results may provide a cancer predisposition syndrome (CPS) diagnosis that warrants screening and specialist visits beyond cancer treatment, including testing or surveillance for family members. The Texas KidsCanSeq (KCS) Study evaluated implementation of GS in a diverse pediatric oncology population. We conducted semi-structured interviews (n = 20) to explore experiences of KCS patients' families around learning about a CPS diagnosis and following up on recommended care. We used qualitative content analysis to develop themes and subthemes across families' descriptions of their experiences accessing care and to understand which factors presented barriers and/or facilitators. We found participants had difficulty differentiating which follow-up care recommendations were made for their child's current cancer treatment versus the CPS. In families' access to follow-up care for CPS, organizational factors were crucial: travel time and distance were common hardships, while coordination of care to streamline multiple appointments with different providers helped facilitate CPS care. Financial factors also impacted families' access to CPS-related follow-up care: having financial assistance and insurance were facilitators for families, while costs and lack of insurance posed as barriers for patients who lost coverage during transitions from pediatric to adult care, and for adult family members who had no coverage. Factors related to beliefs and perceptions, specifically perceiving the risk as less salient to them and feeling overwhelmed with the patient's cancer care, presented barriers to follow-up care primarily for family members. Regarding social factors, competing life priorities made it difficult for families to access follow-up care, though having community support alleviated these barriers. We suggest interventions to improve coordination of cancer treatment and CPS-related care and adherence to surveillance protocols for families as children age, such as care navigators and integrating longitudinal genetic counseling into hereditary cancer centers.
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Affiliation(s)
- Blake Vuocolo
- Department of Molecular and Human Genetics, School of Health Professions, Baylor College of Medicine, Houston, Texas, USA
| | - Amanda M Gutierrez
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Jill O Robinson
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Alva M Recinos
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas, USA
| | - Lauren R Desrosiers
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas, USA
| | - Mary A Majumder
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - Juan Carlos Bernini
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Cancer and Hematology Clinic, Vannie E. Cook Clinic, McAllen, Texas, USA
| | - Jonathan Gill
- UT MD Anderson Cancer Center, Children's Cancer Hospital, Houston, Texas, USA
| | - Timothy Griffin
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatric Hematology-Oncology, Children's Hospital of San Antonio, San Antonio, Texas, USA
| | - Gail E Tomlinson
- UT Health Science Center, Greehey Children's Cancer Research Institute and Division of Pediatric Hematology-Oncology, San Antonio, Texas, USA
| | - Kelly Vallance
- Cook Children's Hematology and Oncology, Cook Children's Hospital, Forth Worth, Texas, USA
| | - Amy L McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, Texas, USA
| | - D Williams Parsons
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas, USA
| | - Sharon E Plon
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas, USA
| | - Sarah Scollon
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas, USA
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Vuocolo B, Sierra R, Brooks D, Holder C, Urbanski L, Rodriguez K, Gamez JD, Mulukutla SN, Berry L, Hernandez A, Allegre A, Hidalgo H, Rodriguez S, Magallan S, Gibson J, Bernini JC, Watson M, Nelson R, Mellin-Sanchez L, Dai H, Soler-Alfonso C, Carter K, Lee B, Lalani SR. Reducing Time to Diagnosis of Rare Genetic Diseases in a Medically Underserved Hispanic Population- Lessons Learned for Meaningful Engagement. Res Sq 2023:rs.3.rs-3699740. [PMID: 38168160 PMCID: PMC10760238 DOI: 10.21203/rs.3.rs-3699740/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Background The utilization of genomic information to improve health outcomes is progressively becoming more common in clinical practice. Nonetheless, disparities persist in accessing genetic services among ethnic minorities, individuals with low socioeconomic status, and other vulnerable populations. The Rio Grande Valley at the Texas-Mexico border is predominantly Hispanic with a high poverty rate and an increased prevalence of birth defects, with very limited access to genetics services. The cost of a diagnosis is often times out of reach for these underserved families. Funded by the National Center for Advancing Translational Sciences (NCATS), Project GIVE (Genetic Inclusion by Virtual Evaluation) was launched in 2022 to shorten the time to diagnosis and alleviate healthcare inequities in this region, with the goal of improving pediatric health outcomes. Methods Utilizing Consultagene, an innovative electronic health record (EHR) agnostic virtual telehealth and educational platform, we designed the study to recruit 100 children with rare diseases over a period of two years from this region, through peer-to-peer consultation and referral. Conclusions Project GIVE study has allowed advanced genetic evaluation and delivery of genome sequencing through the virtual portal, effectively circumventing the recognized socioeconomic and other barriers within this population. This paper explores the successful community engagement process and implementation of an alternate genomics evaluation platform and testing approach, aiming to reduce the diagnostic journey for individuals with rare diseases residing in a medically underserved region.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Lori Berry
- The University of Texas Rio Grande Valley
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Ford CP, Littlejohn RO, German R, Vuocolo B, Aceves J, Vossaert L, Owen N, Wangler M, Schmid CA. Precision therapy for a medically actionable ATP1A3 variant from a genomic medicine program in an underserved population. Mol Genet Genomic Med 2023; 11:e2272. [PMID: 37614148 PMCID: PMC10724509 DOI: 10.1002/mgg3.2272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/21/2023] [Accepted: 08/08/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Genomic medicine is revolutionizing the diagnosis of rare diseases, but the implementation has not benefited underrepresented populations to the same degree. Here, we report the case of a 7-year-old boy with hypotonia, global developmental delay, strabismus, seizures, and previously suspected mitochondrial myopathy. This proband comes from an underrepresented minority and was denied exome sequencing by his public insurance. METHODS After informed consent was obtained, buccal cells from the proband were collected and whole exome sequencing was performed. Illumina Dragen and Emedgene software was used to analyze the data at Baylor Genetics. The variants were further intepreted according to ACMG guidelines and the patient's phenotype. RESULTS Through whole-exome sequencing (WES) under the Community Texome project, he was found to have a heterozygous de novo pathogenic variant in the ATP1A3 gene located on chromosome 19q13. CONCLUSION In retrospect, his symptomatology matches the known medical conditions associated with the ATP1A3 gene namely Alternating Hemiplegia of Childhood 2 (AHC), a rare autosomal dominant disorder with an incidence of 1 in one million. His single nucleotide variant, (c.2401G>A, p.D801N), is predicted to be damaging. The specific amino acid change p.D801N has been previously reported in ClinVar along with the allelic variant p.D801Y and both are considered pathogenic. The identification of this variant altered medical management for this patient as he was started on a calcium antagonist and has reported no further hemiplegic episodes. This case illustrates the value of implementing genomic medicine for precision therapy in underserved populations.
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Affiliation(s)
- Cara P. Ford
- School of MedicineMeharry Medical CollegeNashvilleTennesseeUSA
- Clinical Research Education Training Program at Baylor College of MedicineHoustonTexasUSA
| | - Rebecca O. Littlejohn
- Department of PediatricsBaylor College of MedicineSan AntonioTexasUSA
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Ryan German
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's HospitalHoustonTexasUSA
| | - Blake Vuocolo
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's HospitalHoustonTexasUSA
| | - Jose Aceves
- Department of PediatricsBaylor College of MedicineSan AntonioTexasUSA
| | - Liesbeth Vossaert
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
- Baylor GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Nichole Owen
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
- Baylor GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Michael Wangler
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's HospitalHoustonTexasUSA
| | - Carrie A. Schmid
- Department of PediatricsBaylor College of MedicineSan AntonioTexasUSA
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
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Vuocolo B, Holder JL. Unwind and Relax: DDX3X RNA Helicase as a Critical Mediator of Cortical Neurogenesis. Neuron 2020; 106:357-358. [PMID: 32380046 DOI: 10.1016/j.neuron.2020.03.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In this issue of Neuron, Lennox et al. (2020) report the largest cohort of patients to date with DDX3X syndrome, discovering unique genotype-phenotype relationships that inform molecular pathogenesis. They then uncover unique roles of DDX3X in cortical neuron development and ribonucleoprotein granule formation.
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Affiliation(s)
- Blake Vuocolo
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA; Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - J Lloyd Holder
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA; Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, USA.
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