Customer Publications – September 2022

         September 30, 2022

Every month we compile customer publications that reference us, and every time I am excited to see the amazing work being done around the world. From pediatric heart conditions to rare diseases, or a Thai clinical study on dilated cardiomyopathy, it is always a pleasure to see the Golden Helix Software suite helping research and clinical genetics. Below are a few recent customer publications, or rather successes, that I would like to highlight.


Genomic findings of hypertrophic and dilated cardiomyopathy characterized in a Thai clinical genetics service

Hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM) are the most common referrals in the Inherited Cardiovascular Condition (ICC) Genetics Service. Several issues must be discussed with patients and their families during the genetic consultation session, including the options for genetic testing and cardiovascular surveillance in family members. We developed an ICC registry and performed next-generation-based DNA sequencing for all patients affected by non-syndromic HCM and idiopathic DCM in our joint specialist genetics service. The target gene sequencing panel relied on the Human Phenotype Ontology with 237 genes for HCM (HP:0001639) and 142 genes for DCM (HP:0001644). All subjects were asked to contact their asymptomatic first-degree relatives for genetic counseling regarding their risks and to initiate cardiovascular surveillance and cascade genetic testing. The study was performed from January 1, 2014, to December 31, 2020, and a total of 62 subjects (31-HCM and 31-DCM) were enrolled. The molecular detection frequency was 48.39% (32.26% pathogenic/likely pathogenic, 16.13% variant of uncertain significance or VUS for HCM, and 25.81% (16.13% pathogenic/likely pathogenic, 9.68% VUS) for DCM. The most prevalent gene associated with HCM was MYBPC3. The others identified in this study included ACTN2MYL2MYH7TNNI3TPM1, and VCL. Among the DCM subjects, variants were detected in two cases with the TTN nonsense variants, while the others were missense and identified in MYH7DRSP3MYBPC3, and SCN5A. Following the echocardiogram surveillance and cascade genetic testing in the asymptomatic first-degree relatives, the detection rate of new cases was 8.82% and 6.25% in relatives of HCM and DCM subjects, respectively. Additionally, a new pre-symptomatic relative belonging to an HCM family was identified, although the genomic finding in the affected case was absent. Thus, ICC service is promising for the national healthcare system, aiming to prevent morbidity and mortality in asymptomatic family members.

Trachoo O, Yingchoncharoen T, Ngernsritrakul T, Iemwimangsa N, Panthan B, Klumsathian S, et al. (2022) Genomic findings of hypertrophic and dilated cardiomyopathy characterized in a Thai clinical genetics service. PLoS ONE 17(9): e0267770. https://doi.org/10.1371/journal.pone.0267770

Clinical Implications of the Genetic Background in Pediatric Pulmonary Arterial Hypertension: Data from the Spanish REHIPED Registry

Pulmonary arterial hypertension (PAH) is a severe and rare disease with an important genetic background. The influence of genetic testing in the clinical classification of pediatric PAH is not well known and genetics could influence management and prognosis. Objectives: The aim of this work was to identify the molecular fingerprint of PH children in the REgistro de pacientes con HIpertensión Pulmonar PEDiátrica (REHIPED), and to investigate if genetics could have an impact in clinical reclassification and prognosis. Methods: We included pediatric patients with a genetic analysis from REHIPED. From 2011 onward, successive genetic techniques have been carried out. Before genetic diagnosis, patients were classified according to their clinical and hemodynamic data in five groups. After genetic analysis, the patients were reclassified. The impact of genetics in survival free of lung transplantation was estimated by Kaplan–Meier curves. Results: Ninety-eight patients were included for the analysis. Before the genetic diagnoses, there were idiopathic PAH forms in 53.1%, PAH associated with congenital heart disease in 30.6%, pulmonary veno-occlusive disease—PVOD—in 6.1%, familial PAH in 5.1%, and associated forms with multisystemic disorders—MSD—in 5.1% of the patients. Pathogenic or likely pathogenic variants were found in 44 patients (44.9%). After a genetic analysis, 28.6% of the cohort was “reclassified”, with the groups of heritable PAH, heritable PVOD, TBX4, and MSD increasing up to 18.4%, 8.2%, 4.1%, and 12.2%, respectively. The MSD forms had the worst survival rates, followed by PVOD. Conclusions: Genetic testing changed the clinical classification of a significant proportion of patients. This reclassification showed relevant prognostic implications.

Cruz-Utrilla, A.; Gallego-Zazo, N.; Tenorio-Castaño, J.A.; Guillén, I.; Torrent-Vernetta, A.; Moya-Bonora, A.; Labrandero, C.; Rodríguez-Monte, M.E.G.-L.; Rodríguez-Ogando, A.; Rey, M.d.M.R.V.D.; Espín, J.; Plata-Izquierdo, B.; Álvarez-Fuente, M.; Moreno-Gaudó, A.; Escribano-Subias, P.; Marín, M.J.D.C. Clinical Implications of the Genetic Background in Pediatric Pulmonary Arterial Hypertension: Data from the Spanish REHIPED Registry. Int. J. Mol. Sci. 2022, 23, 10433. https://doi.org/10.3390/ijms231810433

TBX3 and EFNA4 Variant in a Family with Ulnar-Mammary Syndrome and Sagittal Craniosynostosis

Ulnar-mammary syndrome (UMS) is a rare, autosomal dominant disorder characterized by anomalies affecting the limbs, apocrine glands, dentition, and genital development. This syndrome is caused by haploinsufficiency in the T-Box3 gene (TBX3), with considerable variability in the clinical phenotype being observed even within families. We describe a one-year-old female with unilateral, postaxial polydactyly, and bilateral fifth fingernail duplication. Next-generation sequencing revealed a novel, likely pathogenic, variant predicted to affect the canonical splice site in intron 3 of the TBX3 gene (c.804 + 1G > A, IVS3 + 1G > A). This variant was inherited from the proband’s father who was also diagnosed with UMS with the additional clinical finding of congenital, sagittal craniosynostosis. Subsequent whole genome analysis in the proband’s father detected a variant in the EFNA4 gene (c.178C > T, p.His60Tyr), which has only been reported to be associated with sagittal craniosynostosis in one patient prior to this report but reported in other cranial suture synostosis. The findings in this family extend the genotypic spectrum of UMS, as well as the phenotypic spectrum of EFNA4-related craniosynostosis.

Tung, M.L.; Chandra, B.; Kotlarek, J.; Melo, M.; Phillippi, E.; Justice, C.M.; Musolf, A.; Boyadijev, S.A.; Romitti, P.A.; Darbro, B.; et al. TBX3 and EFNA4 Variant in a Family with Ulnar-Mammary Syndrome and Sagittal Craniosynostosis. Genes 2022, 13, 1649. https://doi.org/10.3390/genes13091649


Golden Helix software provides simple, fast and repeatable variant analysis software for gene panels, exomes, and whole genomes. Our intuitive software is used for breakthroughs in cancer diagnostics, hereditary testing and diagnosis, trio analysis, and more. With integrated data visualization and unlimited support, Golden Helix’s VarSeq provides unparalleled genomic data analysis.

VarSeq

Leave a Reply

Your email address will not be published.