Clinical Applications of Integrative Analysis of Validated Somatic and Germline Genomic Results in Oncology

A special issue of Cancers (ISSN 2072-6694). This special issue belongs to the section "Molecular Cancer Biology".

Deadline for manuscript submissions: 25 April 2025 | Viewed by 1111

Special Issue Editor


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Guest Editor
Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
Interests: precision oncology; clinical genomics

Special Issue Information

Dear Colleagues,

The aim of this Special Issue is to give a platform to studies that utilize and demonstrate the value of an integrated approach combining validated somatic (tumor) and germline (constitutional) genomic data for clinical management of cancer and precision oncology. Somatic and germline analysis has been reported to be beneficial in personalized therapeutic practice, tumorigenesis and cancer progression, inference on germline allele penetrance, and gene discovery. However, clinical applications of the integration of somatic and germline data are not routinely published. Signature somatic genomic profiles such as loss of heterozygosity (LOH), mismatch repair (MMR) status (i.e., MMR deficient or proficient), microsatellite instability (MSI), and tumor-derived information such as immunohistochemistry (IHC) of target proteins have unique values that can shed light on the role of germline genetic variants in disease. The understanding of genome findings from the somatic workflow can be much enhanced when performed in the context of patients’ constitutional genetic data. Conversely, the full extent of the consequence of germline findings, both in cancer susceptibility and therapy, can be elucidated when examined with somatic genetic data in unison.

Please note: manuscripts consisting solely of bioinformatics or computational analysis of public genomic or transcriptomic databases which are not accompanied by validation (independent cohort or biological validation in vitro or in vivo) are out of scope for this section and will not be accepted as part of this Special Issue.

Dr. Arezou A. Ghazani
Guest Editor

Manuscript Submission Information

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Keywords

  • tumor and constitutional genome integration
  • clinical application of somatic and germline findings
  • precision oncology

Published Papers (1 paper)

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Research

28 pages, 959 KiB  
Article
Advancing Precision Oncology in Hereditary Paraganglioma-Pheochromocytoma Syndromes: Integrated Interpretation and Data Sharing of the Germline and Tumor Genomes
by Huma Q. Rana, Diane R. Koeller, McKenzie Walker, Busra Unal, Alison Schwartz Levine, Anu Chittenden, Raymond A. Isidro, Connor P. Hayes, Monica D. Manam, Ryan M. Buehler, Danielle K. Manning, Justine A. Barletta, Jason L. Hornick, Judy E. Garber, Arezou A. Ghazani and INT2GRATE Oncology Consortium
Cancers 2024, 16(5), 947; https://doi.org/10.3390/cancers16050947 - 26 Feb 2024
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Abstract
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 [...] Read more.
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 INT2GRATE|HPPGL platform. INT2GRATE (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 INT2GRATE|HPPGL platform enables automated parsing and integrated assessment of germline, tumor, and genetic findings in hereditary paraganglioma–pheochromocytoma syndromes (HPPGLs). Using INT2GRATE|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 INT2GRATE|HPPGL platform to ClinVar via a custom-made INT2GRATE|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. Full article
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