Advancing Precision Oncology in Hereditary Paraganglioma-Pheochromocytoma Syndromes: Integrated Interpretation and Data Sharing of the Germline and Tumor Genomes.
Huma Q RanaDiane R KoellerMcKenzie WalkerBusra UnalAlison Schwartz LevineAnu ChittendenRaymond A IsidroConnor P HayesMonica D ManamRyan M BuehlerDanielle K ManningJustine A BarlettaJason L HornickJudy E GarberArezou A Ghazaninull Int Grate Oncology ConsortiumPublished in: Cancers (2024)
Standard methods of variant assessment in hereditary cancer susceptibility genes are limited by the lack of availability of key supporting evidence. In cancer, information derived from tumors can serve as a useful source in delineating the tumor behavior and the role of germline variants in tumor progression. We have previously demonstrated the value of integrating tumor and germline findings to comprehensively assess germline variants in hereditary cancer syndromes. Building on this work, herein, we present the development and application of the INT 2 GRATE|HPPGL platform. INT 2 GRATE (INTegrated INTerpretation of GeRmline And Tumor gEnomes) is a multi-institution oncology consortium that aims to advance the integrated application of constitutional and tumor data and share the integrated variant information in publicly accessible repositories. The INT 2 GRATE|HPPGL platform enables automated parsing and integrated assessment of germline, tumor, and genetic findings in hereditary paraganglioma-pheochromocytoma syndromes (HPPGLs). Using INT 2 GRATE|HPPGL, we analyzed 8600 variants in succinate dehydrogenase (SDHx) genes and their associated clinical evidence. The integrated evidence includes germline variants in SDHx genes; clinical genetics evidence: personal and family history of HPPGL-related tumors; tumor-derived evidence: somatic inactivation of SDHx alleles, KIT and PDGFRA status in gastrointestinal stromal tumors (GISTs), multifocal or extra-adrenal tumors, and metastasis status; and immunohistochemistry staining status for SDHA and SDHB genes. After processing, 8600 variants were submitted programmatically from the INT 2 GRATE|HPPGL platform to ClinVar via a custom-made INT 2 GRATE|HPPGL variant submission schema and an application programming interface (API). This novel integrated variant assessment and data sharing in hereditary cancers aims to improve the clinical assessment of genomic variants and advance precision oncology.
Keyphrases
- copy number
- genome wide
- dna repair
- palliative care
- health information
- high throughput
- electronic health record
- healthcare
- machine learning
- squamous cell carcinoma
- dna methylation
- artificial intelligence
- oxidative stress
- deep learning
- dna damage
- genome wide identification
- long non coding rna
- data analysis
- genome wide analysis
- drug induced