The specification of the list of genes to be analyzed is of high importance in the NGS data analysis pipeline, as it determines the scope of the analysis. This is especially significant in the case of WES and WGS data, where multiple variants within the analyzed sample are expected to differ from the reference genome. Therefore it is crucial to adequately identify genes of interest, in particular, the genes that may be associated with the patient’s specific condition.
One valuable source that can be utilized to create a personalized gene panel is the HPO (Human Phenotype Ontology) database. The HPO database provides standardized terms for phenotypic abnormalities associated with human diseases, along with a comprehensive list of genes known to be associated with a given condition. In fact, generating a gene panel based on HPO terms is one of the options available in our automated workflows on the IntelliseqFlow platform.
Below, we present a practical example from a case report by Skoczen et. al. 2019 of the use of a gene panel generated solely on the basis of HPO terms. The publication describes a very rare coexistence of two independent primary tumors in a child – neuroblastoma (NBL) and hepatoblastoma (HBL). Two Intelliseq scientists, Michal Korostystynksi and Marcin Piechota, were involved in this research, contributing via i.a. the analysis of whole exome sequencing (WES) data and interpretation of the results.
Diagnosis of the patient’s conditions, HBL and NBL, was established through imaging techniques and histopathological examination. To explore potential disease-related germline mutations, the researchers performed Next-Generation Sequencing (NGS) of the whole exome (WES).
A personalized gene panel was generated using the Human Phenotype Ontology (HPO) database. A total of 646 genes were included based on the following HPO terms “HP:0003006 Neuroblastoma”; “HP:0002884 Hepatoblastoma” and “HP:0002664 Neoplasm”. The analysis included screening for both SNVs and INDELs (short INsertions and DELetions).
A few rare mutations with autosomal dominant mode of inheritance and a potential pathogenic impact on patient phenotype were identified:
– NF1 gene (p.Val2511Ile) – ultra-rare germline heterozygous missense mutation in a highly conserved region, associated with tumor predisposition.
– RAF1 gene (p.Leu445Arg) – potentially pathogenic non-synonymous variant, not yet associated with cancer.
– TWIST1 gene (p.Gly86dup) – a novel germline insertion variant, the impact of TWIST1 gene mutation on NBL development remains unclear
– WHSC1 gene (p.Ser4Asn) – variant associated with Wolf-Hirschhorn syndrome, with high SIFT deleteriousness score (SIFT score predicts whether an amino acid substitution affects protein function) and high evolutionary conservation.
– MYOC gene (p.Gln368*) – known pathogenic variant associated with glaucoma
The use of personalized gene panels, generated based on Human Phenotype Ontology (HPO) terms, is a powerful approach to identify disease-associated gene variants. In the presented case report, the utilization of the HPO database enabled targeted screening for variants potentially associated with a patient’s condition, i.e. the coexistence of two independent primary tumors (NBL and HBL). Several rare germline mutations with potential pathogenic impacts were identified.
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The research was lead by prof. Szymon n’s Hospital in Krakow (Department of Oncology and Hematology, Department of Pediatric Oncology and Hematology, Department of Radiology, Department of Pathology), Institute of Pharmacology of Polish Academy of Sciences in Krakow and Jagiellonian UnSkoczeń, and the publication is a result of a collaboration between University Childreiversity Medical College in Krakow.
Skoczen S, Stepien K, Krzysztofik M, Luszawska T, Hnatko-Kolacz M, Korostynski M, Piechota M., Kolanek K., Wyrobek L., Wysocka K., Gorecki W., Balwierz W., Genetic profile and clinical implications of Hepatoblastoma and neuroblastoma coexistence in a child. Front Oncol. 2019;9:230. https://doi.org/10.3389/fonc.2019.00230.