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  1. Article ; Online: Aligning Germline Cancer Predisposition With Tumor-Based Next-Generation Sequencing for Modern Oncology Diagnosis, Interception, and Therapeutic Development.

    Yap, Timothy A / Stadler, Zsofia K / Stout, Leigh Anne / Schneider, Bryan P

    American Society of Clinical Oncology educational book. American Society of Clinical Oncology. Annual Meeting

    2023  Volume 43, Page(s) e390738

    Abstract: In the era of precision medicine, genomic interrogation for identification of both germline and somatic genetic alterations has become increasingly important. While such germline testing was usually undertaken via a phenotype-driven single-gene approach, ...

    Abstract In the era of precision medicine, genomic interrogation for identification of both germline and somatic genetic alterations has become increasingly important. While such germline testing was usually undertaken via a phenotype-driven single-gene approach, with the advent of next-generation sequencing (NGS) technologies, the widespread utilization of multigene panels, often agnostic of cancer phenotype, has become a commonplace in many different cancer types. At the same time, somatic tumor testing in oncology performed for the purpose of guiding therapeutic decisions for targeted therapies has also rapidly expanded, recently starting to incorporate not just patients with recurrent or metastatic cancer but even patients with early-stage disease. An integrated approach may be the best approach for the optimal management of patients with different cancers. The lack of complete congruence between germline and somatic NGS tests does not minimize the power or importance of either, but highlights the need to understand their limitations so as not to overlook an important finding or omission. NGS tests built to more uniformly and comprehensively evaluate both the germline and tumor simultaneously are urgently required and are in development. In this article, we discuss approaches to somatic and germline analyses in patients with cancer and the knowledge gained from integration of tumor-normal sequencing. We also detail strategies for the incorporation of genomic analysis into oncology care delivery models and the important emergence of poly(ADP-ribose) polymerase and other DNA Damage Response inhibitors in the clinic for patients with cancer with germline and somatic
    MeSH term(s) Humans ; Neoplasms/diagnosis ; Neoplasms/genetics ; Neoplasms/therapy ; Medical Oncology ; High-Throughput Nucleotide Sequencing ; Neoplasms, Second Primary ; Disease Susceptibility ; Germ Cells
    Language English
    Publishing date 2023-07-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2431126-1
    ISSN 1548-8756 ; 1548-8748
    ISSN (online) 1548-8756
    ISSN 1548-8748
    DOI 10.1200/EDBK_390738
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Clinically significant germline pathogenic variants are missed by tumor genomic sequencing.

    Stout, Leigh Anne / Hunter, Cynthia / Schroeder, Courtney / Kassem, Nawal / Schneider, Bryan P

    NPJ genomic medicine

    2023  Volume 8, Issue 1, Page(s) 30

    Abstract: A germline pathogenic variant may be present even if the results of tumor genomic sequencing do not suggest one. There are key differences in the assay design and reporting of variants between germline and somatic laboratories. When appropriate, both ... ...

    Abstract A germline pathogenic variant may be present even if the results of tumor genomic sequencing do not suggest one. There are key differences in the assay design and reporting of variants between germline and somatic laboratories. When appropriate, both tests should be completed to aid in therapy decisions and determining optimal screening and risk-reduction interventions.
    Language English
    Publishing date 2023-10-13
    Publishing country England
    Document type Journal Article
    ZDB-ID 2813848-X
    ISSN 2056-7944 ; 2056-7944
    ISSN (online) 2056-7944
    ISSN 2056-7944
    DOI 10.1038/s41525-023-00374-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Precision Prevention: The Current State and Future of Genomically Guided Cancer Prevention.

    Kassem, Nawal / Stout, Leigh Anne / Hunter, Cynthia / Schneider, Bryan / Radovich, Milan

    JCO precision oncology

    2022  Volume 4, Page(s) 96–108

    Abstract: The identification of cancer-predisposing germline variants has potentially substantial clinical impact for patients and their families. Although management guidelines have been proposed for some genes, guidelines for other genes are lacking. This review ...

    Abstract The identification of cancer-predisposing germline variants has potentially substantial clinical impact for patients and their families. Although management guidelines have been proposed for some genes, guidelines for other genes are lacking. This review focuses on the current surveillance and management guidelines for the most common hereditary cancer syndromes and discusses some of the most pivotal studies supporting the available guidelines. We also highlight the gaps in the identification of germline carriers, the cascade testing of at-risk relatives, and the challenges impeding the proper follow-up and optimal management of pathogenic germline carriers. The anticipated surge in the number of identified germline carriers, deficient management guidelines, poor cascade testing uptake, and long-term follow-up necessitate the development of multidisciplinary clinics as an obligatory step toward the improvement of cancer prevention.
    Language English
    Publishing date 2022-01-20
    Publishing country United States
    Document type Journal Article
    ISSN 2473-4284
    ISSN (online) 2473-4284
    DOI 10.1200/PO.19.00278
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: CHEK2

    Brock, Pamela / Liynarachchi, Sandya / Nieminen, Taina T / Chan, Carlos / Kohlmann, Wendy / Stout, Leigh Anne / Yao, Song / La Greca, Amanda / Jensen, Kirk E / Kolesar, Jill M / Salhia, Bodour / Gulhati, Pat / Hicks, J Kevin / Ringel, Matthew D

    Thyroid : official journal of the American Thyroid Association

    2024  Volume 34, Issue 4, Page(s) 477–483

    Abstract: Background: ...

    Abstract Background:
    MeSH term(s) Humans ; Case-Control Studies ; Checkpoint Kinase 2/genetics ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Germ-Line Mutation ; Thyroid Cancer, Papillary ; Thyroid Neoplasms/genetics
    Chemical Substances Checkpoint Kinase 2 (EC 2.7.1.11) ; CHEK2 protein, human (EC 2.7.11.1)
    Language English
    Publishing date 2024-02-27
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1086044-7
    ISSN 1557-9077 ; 1050-7256
    ISSN (online) 1557-9077
    ISSN 1050-7256
    DOI 10.1089/thy.2023.0529
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Identification of germline cancer predisposition variants during clinical ctDNA testing.

    Stout, Leigh Anne / Kassem, Nawal / Hunter, Cynthia / Philips, Santosh / Radovich, Milan / Schneider, Bryan P

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 13624

    Abstract: Next-generation sequencing of circulating tumor DNA (ctDNA) is a non-invasive method to guide therapy selection for cancer patients. ctDNA variant allele frequency (VAF) is commonly reported and may aid in discerning whether a variant is germline or ... ...

    Abstract Next-generation sequencing of circulating tumor DNA (ctDNA) is a non-invasive method to guide therapy selection for cancer patients. ctDNA variant allele frequency (VAF) is commonly reported and may aid in discerning whether a variant is germline or somatic. We report on the fidelity of VAF in ctDNA as a predictor for germline variant carriage. Two patient cohorts were studied. Cohort 1 included patients with known germline variants. Cohort 2 included patients with any variant detected by the ctDNA assay with VAF of 40-60%. In cohort 1, 36 of 91 (40%) known germline variants were identified through ctDNA analysis with a VAF of 39-87.6%. In cohort 2, 111 of 160 (69%) variants identified by ctDNA analysis with a VAF between 40 and 60% were found to be germline. Therefore, variants with a VAF between 40 and 60% should induce suspicion for germline status but should not be used as a replacement for germline testing.
    MeSH term(s) Adult ; Aged ; Biomarkers, Tumor/genetics ; Circulating Tumor DNA/genetics ; Female ; Gene Frequency ; Genetic Testing ; Germ-Line Mutation ; Humans ; Male ; Middle Aged ; Neoplasms/genetics
    Chemical Substances Biomarkers, Tumor ; Circulating Tumor DNA
    Language English
    Publishing date 2021-07-01
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-93084-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Implications of Incidental Germline Findings Identified In the Context of Clinical Whole Exome Sequencing for Guiding Cancer Therapy.

    Schneider, Bryan P / Stout, Leigh Anne / Philips, Santosh / Schroeder, Courtney / Scott, Susanna F / Hunter, Cynthia / Kassem, Nawal / Kiel, Patrick J / Radovich, Milan

    JCO precision oncology

    2022  Volume 4, Page(s) 1109–1121

    Abstract: Purpose: Identification of incidental germline mutations in the context of next-generation sequencing is an unintended consequence of advancing technologies. These data are critical for family members to understand disease risks and take action.: ... ...

    Abstract Purpose: Identification of incidental germline mutations in the context of next-generation sequencing is an unintended consequence of advancing technologies. These data are critical for family members to understand disease risks and take action.
    Patients and methods: A retrospective cohort analysis was conducted of 1,028 adult patients with metastatic cancer who were sequenced with tumor and germline whole exome sequencing (WES). Germline variant call files were mined for pathogenic/likely pathogenic (P/LP) variants using the ClinVar database and narrowed to high-quality submitters.
    Results: Median age was 59 years, with 16% of patients ≤ 45 years old. The most common tumor types were breast cancer (12.5%), colorectal cancer (11.5%), sarcoma (9.3%), prostate cancer (8.4%), and lung cancer (6.6%). We identified 3,427 P/LP variants in 471 genes, and 84% of patients harbored one or more variant. One hundred thirty-two patients (12.8%) carried a P/LP variant in a cancer predisposition gene, with
    Conclusion: The majority of patients undergoing clinical cancer WES harbor a pathogenic germline variation. Identification of clinically actionable germline findings will create additional burden on oncology clinics as broader WES becomes common.
    Language English
    Publishing date 2022-01-20
    Publishing country United States
    Document type Journal Article
    ISSN 2473-4284
    ISSN (online) 2473-4284
    DOI 10.1200/PO.19.00354
    Database MEDical Literature Analysis and Retrieval System OnLINE

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