Concordance Between Genomic Alterations Detected by Tumor and Germline Sequencing: Results from a Tertiary Care Academic Center Molecular Tumor Board.

Abstract

Objective

The majority of tumor sequencing currently performed on cancer patients does not include a matched normal control, and in cases where germline testing is performed, it is usually run independently of tumor testing. The rates of concordance between variants identified via germline and tumor testing in this context are poorly understood. We compared tumor and germline sequencing results in patients with breast, ovarian, pancreatic, and prostate cancer who were found to harbor alterations in genes associated with homologous recombination deficiency (HRD) and increased hereditary cancer risk. We then evaluated the potential for a computational somatic-germline-zygosity (SGZ) modeling algorithm to predict germline status based on tumor-only comprehensive genomic profiling (CGP) results.

Methods

A retrospective chart review was performed using an academic cancer center's databases of somatic and germline sequencing tests, and concordance between tumor and germline results was assessed. SGZ modeling from tumor-only CGP was compared to germline results to assess this method's accuracy in determining germline mutation status.

Results

A total of 115 patients with 146 total alterations were identified. Concordance rates between somatic and germline alterations ranged from 0% to 85.7% depending on the gene and variant classification. After correcting for differences in variant classification and filtering practices, SGZ modeling was found to have 97.2% sensitivity and 90.3% specificity for the prediction of somatic versus germline origin.

Conclusions

Mutations in HRD genes identified by tumor-only sequencing are frequently germline. Providers should be aware that technical differences related to assay design, variant filtering, and variant classification can contribute to discordance between tumor-only and germline sequencing test results. In addition, SGZ modeling had high predictive power to distinguish between mutations of somatic and germline origin without the need for a matched normal control, and could potentially be considered to inform clinical decision-making.

Department

Description

Provenance

Citation

Published Version (Please cite this version)

10.1093/oncolo/oyac164

Publication Info

Green, Michelle F, Catherine H Watson, Sarah Tait, Jie He, Dean C Pavlick, Garrett Frampton, Jinny Riedel, Jennifer K Plichta, et al. (2023). Concordance Between Genomic Alterations Detected by Tumor and Germline Sequencing: Results from a Tertiary Care Academic Center Molecular Tumor Board. The oncologist, 28(1). pp. 33–39. 10.1093/oncolo/oyac164 Retrieved from https://hdl.handle.net/10161/26552.

This is constructed from limited available data and may be imprecise. To cite this article, please review & use the official citation provided by the journal.

Scholars@Duke

Plichta

Jennifer K Plichta

Associate Professor of Surgery

Dr. Jennifer Plichta is an Associate Professor of Surgery & Population Health Sciences at Duke University. She serves as the Director of the Breast Risk Assessment Clinic in the Duke Cancer Institute, where she cares for patients with breast cancer, benign breast problems, and those with an increased risk of breast cancer. Her clinical interests include establishing routine breast cancer risk assessment for women and creating personalized management strategies for those found to be “high risk”.

 

Dr. Plichta’s research focuses of identifying and managing women with risk factors for breast cancer, including those with genetic mutations, such as BRCA, those with abnormal breast biopsies, and those with a family history of breast cancer. She is also studying metastatic breast cancer and how breast cancer staging can be used to improve patient care and education. 

 

However, her dedication to breast cancer extends beyond her clinical and research interests. She also enjoys educating the community about breast cancer and helping to raise money for breast cancer research and education. She is the creator and primary coordinator of Duke’s free, annual breast education day for the community, “What’s best for breasts?”.

Armstrong

Andrew John Armstrong

Professor of Medicine

I am a clinical and translational investigator focused on precision therapies and biomarkers in advanced prostate and other GU cancers.  I oversee a large research team of clinical and lab based investigators focused on improving patient outcomes, preventing metastatic disease, and understanding the biology of aggressive prostate cancer.  Some key themes:
1. Predictors of sensitivity and clinical efficacy of therapies in advanced prostate cancer
2. Novel designs of clinical trials and pharmacodynamic/translational studies in prostate, kidney, bladder cancer
3. Pre-operative models for drug development of novel agents in human testing in prostate cancer
4. Novel therapies and drug development for prostate, renal, bladder, and testicular cancer
5. Design of rational combination therapies in men with metastatic hormone-refractory prostate cancer
6. Developing prognostic and predictive models for progression and survival in metastatic prostate cancer
7. Examining surrogate markers of mortality in metastatic prostate cancer
8. Clear cell and non-clear cell renal cell carcinoma: natural history, sensitivity to novel agents including mTOR and VEGF inhibition

Strickler

John Strickler

Professor of Medicine

John Strickler, MD is a Professor of Medicine in the Division of Medical Oncology, where he is Co-Leader for the Precision Cancer Medicine and Investigational Therapeutics Program at the Duke Cancer Institute, Leader of the Molecular Tumor Board, and Associate Director of Clinical Research – GI Oncology. Dr. Strickler’s clinic specializes on the treatment of gastrointestinal malignancies, with a particular emphasis on gastroesophageal, pancreatic, and colorectal cancers. His research focuses on precision cancer medicine: identification of biomarkers that predict sensitivity or resistance to targeted therapies and immunotherapy. He has designed and executed clinical trials that test novel therapies and innovative therapeutic strategies. He was Principal Investigator on an investigator sponsored trial that led to the first FDA-approved therapy for HER2+ metastatic colorectal cancer. He has first-author publications in several high impact factor medical journals, including the New England Journal of Medicine, Clinical Cancer Research, Cancer Discovery, Journal of Clinical Oncology, and Lancet Oncology. Nationally, he has served as a member of the American Society of Clinical Oncology (ASCO) Treatment Guidelines Committee for Advanced Colon Cancer.

Datto

Michael Bradley Datto

Associate Professor of Pathology

Dr. Datto is an AP/CP/MGP board certified pathologist who specializes in molecular pathology. He is the Associate Vice President for Duke University Health System Clinical Laboratories, the Vice Chair for Clinical Pathology and Medical Director for Duke University Health System Clinical Laboratories.  

In these roles, he is responsible for maintaining the standards of the College of American Pathologists and CLIA/CMS within all Clinical Laboratories at Duke.  Specifically, Dr. Datto oversees clinical testing and reporting, develops quality management systems and proficiency testing programs, provides consultation with ordering physicians, ensures educational programs, develops strategic plans that are in line with the needs of our patient population, physicians and health system leadership, coordinates research and development, ensures adequate and appropriately trained personnel, and provides profession interpretation for molecular diagnostic testing including the wide range of PCR, quantitative PCR, sequencing and FISH based tests for inherited genetic diseases, hematologic malignancies, solid tumors and infectious diseases.

Dr. Datto also serves as the chair of the Accreditation Committee (AC) for the College of American Pathologists (CAP).  The CAP is the largest accreditor of hospital based laboratories in the US and serves as a ‘deemed entity’ by the Center for Medicare Services. In his role of chair of the AC, Dr. Datto oversees the committee that makes clinical accreditation decisions for approximately 7,000 clinical domestic and international laboratories.

Finally, Dr. Datto has an active academic program developing data system to aggregate, normalize and utilize high complexity and high volume laboratory data.  Dr. Datto and his team have developed the Molecular Registry of Tumors (Mr.T); a software solution that supports clinical trials matching, engagement with the AACR GENIE Project and the Molecular Tumor Board for Duke University Health System.  The ultimate goal of this work is to ensure that the vast amount of laboratory data generated on our Duke patients can be put to use, driving better patient care, research and education.

Berchuck

Andrew Berchuck

James M. Ingram Distinguished Professor of Gynecologic Oncology

Dr. Andrew Berchuck is Director of the Duke Division of Gynecologic Oncology and holds the James M. Ingram Distinguished Professorship. He is a practicing oncologist who is actively involved in the surgical and chemotherapy management of women with ovarian, endometrial and lower genital tract cancers. This includes minimally invasive laparoscopic surgical approaches. He also has developed a research program that focuses on the molecular-genetic alterations involved in malignant transformation of the ovarian and endometrial epithelium. He has published over 300 peer-reviewed papers in these areas. The objectives of his research include 1) identification of ovarian cancer susceptibility polymorphisms through a population-based case-control molecular epidemiologic study, and 2) use of genomic approaches  to elucidate the molecular heterogenetity of ovarian cancer. Thirty fellows and residents have worked in his lab, several of whom are now funded investigators. His research efforts have been recognized nationally and he has received awards for best oral presentation at the annual meetings of both the Society of Gynecologic Oncology and the International Gynecologic Cancer Society. Dr. Berchuck was awarded the Barbara Thomason Ovarian Cancer Research Professorship by the American Cancer Society in 2006. He has served as editor of several books in the field including Principles and Practice of Gynecologic Oncology. Dr. Berchuck also has a major commitment to national activities, and was President of the Society of Gynecologic Oncology in 2008. He served as chair of the scientific advisory committee of the Ovarian Cancer Research Fund (http://www.ocrf.org) in New York City. Finally, he is also head of the steering committee of the international Ovarian Cancer Association Consortium (OCAC), a group of 50 case-control studies that are working together to identify ovarian cancer susceptibility polymorphisms (www.srl.cam.ac.uk/consortia/ocac/index.html).

Menendez

Carolyn Sue Menendez

Assistant Professor of Surgery

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