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Mohindroo C, Baydogan S, Agarwal P, Wright RD, Prakash LR, Mork ME, Klein AP, Laheru DA, Maxwell JE, Katz MHG, Dasari A, Kim MP, He J, McAllister F, De Jesus-Acosta A. Germline Testing Identifies Pathogenic/Likely Pathogenic Variants in Patients with Pancreatic Neuroendocrine Tumors. Cancer Prev Res (Phila) 2024; 17:335-342. [PMID: 38662083 DOI: 10.1158/1940-6207.capr-23-0483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/10/2024] [Accepted: 04/23/2024] [Indexed: 04/26/2024]
Abstract
Ten percent of pancreatic neuroendocrine tumors (pNET) are related to inherited syndromes (MEN1, MEN4, VHL, NF1, and TSC). Growing evidence suggests that clinically sporadic pNETs can also harbor germline pathogenic variants. In this study, we report the prevalence of pathologic/likely pathologic (P/LP) germline variants in a high-risk cohort and an unselected cohort. We collected clinical data of patients with pNETs seen at MD Anderson Cancer Center and Johns Hopkins Hospital. The high-risk cohort included (n = 132) patients seen at MD Anderson Cancer Center who underwent germline testing for high-risk criteria (early onset, personal or family history of cancer, and syndromic features) between 2013 and 2019. The unselected cohort included (n = 106) patients seen at Johns Hopkins Hospital who underwent germline testing following their diagnosis of pNETs between 2020 and 2022. In the high-risk cohort (n = 132), 33% (n = 44) had P/LP variants. The majority of the patients had P/LP variants in MEN1 56% (n = 25), followed by DNA repair pathways 18% (n = 8), and 7% (n = 3) in MSH2 (Lynch syndrome). Patients with P/LP were younger (45 vs. 50 years; P = 0.002). In the unselected cohort (n = 106), 21% (n = 22) had P/LP. The majority were noted in DNA repair pathways 40% (n = 9) and MEN1 36% (n = 8). Multifocal tumors correlated with the presence of P/LP (P = 0.0035). MEN1 germline P/LP variants correlated with younger age (40 vs. 56 years; P = 0.0012), presence of multifocal tumors (P < 0.0001), and World Health Organization grade 1 histology (P = 0.0078). P/LP variants are prevalent in patients with clinically sporadic pNET irrespective of high-risk features. The findings support upfront universal germline testing in all patients with pNET. Prevention Relevance: Here, we present germline data from the largest reported cohort of patients with pNET (n = 238), comprising both a high-risk cohort and an unselected cohort. In both cohorts, we identify a high number of P/LPs, including those in the DNA repair pathway. Our findings support universal germline testing in patients with pNET.
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Affiliation(s)
- Chirayu Mohindroo
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Seyda Baydogan
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Parul Agarwal
- Department of Oncology, Abramson Cancer Center at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Robin D Wright
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Laura R Prakash
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Maureen E Mork
- Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alison P Klein
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Daniel A Laheru
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jessica E Maxwell
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Matthew H G Katz
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Arvind Dasari
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael P Kim
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jin He
- Department of Surgical Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Florencia McAllister
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ana De Jesus-Acosta
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Zhou Y, Lauschke VM. Next-generation sequencing in pharmacogenomics - fit for clinical decision support? Expert Rev Clin Pharmacol 2024; 17:213-223. [PMID: 38247431 DOI: 10.1080/17512433.2024.2307418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/16/2024] [Indexed: 01/23/2024]
Abstract
INTRODUCTION The technological advances of sequencing methods during the past 20 years have fuelled the generation of large amounts of sequencing data that comprise common variations, as well as millions of rare and personal variants that would not be identified by conventional genotyping. While comprehensive sequencing is technically feasible, its clinical utility for guiding personalized treatment decisions remains controversial. AREAS COVERED We discuss the opportunities and challenges of comprehensive sequencing compared to targeted genotyping for pharmacogenomic applications. Current pharmacogenomic sequencing panels are heterogeneous and clinical actionability of the included genes is not a major focus. We provide a current overview and critical discussion of how current studies utilize sequencing data either retrospectively from biobanks, databases or repurposed diagnostic sequencing, or prospectively using pharmacogenomic sequencing. EXPERT OPINION While sequencing-based pharmacogenomics has provided important insights into genetic variations underlying the safety and efficacy of a multitude pharmacological treatments, important hurdles for the clinical implementation of pharmacogenomic sequencing remain. We identify gaps in the interpretation of pharmacogenetic variants, technical challenges pertaining to complex loci and variant phasing, as well as unclear cost-effectiveness and incomplete reimbursement. It is critical to address these challenges in order to realize the promising prospects of pharmacogenomic sequencing.
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Affiliation(s)
- Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
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Howard Sharp KM, Nichols KE. Insights into parent and adolescent patient understanding of genomic sequencing. Cancer 2023; 129:3519-3521. [PMID: 37698526 DOI: 10.1002/cncr.34996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
In a rapidly evolving genomics landscape, parents of children with cancer are asked to consider complex genetic concepts in order to make decisions about sequencing and comprehend the implications of results, all while facing a challenging diagnosis. To optimize parent and patient understanding, it is critical that the clinicians offering sequencing and disclosing results are aware of patient and family expectations and sufficiently educate them about the processes, procedures, and potential outcomes of paired tumor–germline sequencing.
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Affiliation(s)
- Katianne M Howard Sharp
- Department of Psychology and Biobehavioral Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kim E Nichols
- Division of Cancer Predisposition, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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Farinea G, Crespi V, Listì A, Righi L, Bironzo P, Merlini A, Malapelle U, Novello S, Scagliotti GV, Passiglia F. The Role of Germline Mutations in Thoracic Malignancies: Between Myth and Reality. J Thorac Oncol 2023; 18:1146-1164. [PMID: 37331604 DOI: 10.1016/j.jtho.2023.05.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/15/2023] [Accepted: 05/23/2023] [Indexed: 06/20/2023]
Abstract
Considering the established contribution of environmental factors to the development of thoracic malignancies, the inherited susceptibility of these tumors has rarely been explored. However, the recent introduction of next-generation sequencing-based tumor molecular profiling in the real-word setting enabled us to deeply characterize the genomic background of patients with lung cancer with or without smoking-related history, increasing the likelihood of detecting germline mutations with potential prevention and treatment implications. Pathogenic germline variants have been detected in 2% to 3% of patients with NSCLC undergoing next-generation sequencing analysis, whereas the proportion of germline mutations associated with the development of pleural mesothelioma widely varies across different studies, ranging between 5% and 10%. This review provides an updated summary of emerging evidence about germline mutations in thoracic malignancies, focusing on pathogenetic mechanisms, clinical features, therapeutic implications, and screening recommendations for high-risk individuals.
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Affiliation(s)
- Giovanni Farinea
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | - Veronica Crespi
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | - Angela Listì
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | - Luisella Righi
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | - Paolo Bironzo
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | - Alessandra Merlini
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | - Umberto Malapelle
- Department of Public Health, University Federico II of Naples, Naples, Italy
| | - Silvia Novello
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | | | - Francesco Passiglia
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
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Saldivar JS, Harris J, Ayash E, Hong M, Tandon P, Sinha S, Hebron PM, Houghton EE, Thorne K, Goodman LJ, Li C, Marfatia TR, Anderson J, Morra M, Lyle J, Bartha G, Chen R. Analytic validation of NeXT Dx™, a comprehensive genomic profiling assay. Oncotarget 2023; 14:789-806. [PMID: 37646774 PMCID: PMC10467627 DOI: 10.18632/oncotarget.28490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/19/2023] [Indexed: 09/01/2023] Open
Abstract
We describe the analytic validation of NeXT Dx, a comprehensive genomic profiling assay to aid therapy and clinical trial selection for patients diagnosed with solid tumor cancers. Proprietary methods were utilized to perform whole exome and whole transcriptome sequencing for detection of single nucleotide variants (SNVs), insertions/deletions (indels), copy number alterations (CNAs), and gene fusions, and determination of tumor mutation burden and microsatellite instability. Variant calling is enhanced by sequencing a patient-specific normal sample from, for example, a blood specimen. This provides highly accurate somatic variant calls as well as the incidental reporting of pathogenic and likely pathogenic germline alterations. Fusion detection via RNA sequencing provides more extensive and accurate fusion calling compared to DNA-based tests. NeXT Dx features the proprietary Accuracy and Content Enhanced technology, developed to optimize sequencing and provide more uniform coverage across the exome. The exome was validated at a median sequencing depth of >500x. While variants from 401 cancer-associated genes are currently reported from the assay, the exome/transcriptome assay is broadly validated to enable reporting of additional variants as they become clinically relevant. NeXT Dx demonstrated analytic sensitivities as follows: SNVs (99.4%), indels (98.2%), CNAs (98.0%), and fusions (95.8%). The overall analytic specificity was >99.0%.
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Affiliation(s)
| | - Jason Harris
- Personalis, Inc., Fremont, CA 94555, USA
- These authors contributed equally to this work
| | - Erin Ayash
- Personalis, Inc., Fremont, CA 94555, USA
| | | | | | | | | | | | | | | | - Conan Li
- Personalis, Inc., Fremont, CA 94555, USA
| | | | | | | | - John Lyle
- Personalis, Inc., Fremont, CA 94555, USA
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Subbiah V, Kurzrock R. Universal Germline and Tumor Genomic Testing Needed to Win the War Against Cancer: Genomics Is the Diagnosis. J Clin Oncol 2023; 41:3100-3103. [PMID: 36930859 PMCID: PMC10256401 DOI: 10.1200/jco.22.02833] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/08/2023] [Accepted: 02/13/2023] [Indexed: 03/19/2023] Open
Affiliation(s)
- Vivek Subbiah
- Department of Investigational Cancer Therapeutics, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Razelle Kurzrock
- Department of Medicine, Medical College of Wisconsin Cancer Center and Genome Sciences and Precision Medicine Center, Milwaukee, WI
- WIN Consortium, Paris, France
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