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Chen C, Lin CJ, Pei YC, Ma D, Liao L, Li SY, Fan L, Di GH, Wu SY, Liu XY, Wang YJ, Hong Q, Zhang GL, Xu LL, Li BB, Huang W, Shi JX, Jiang YZ, Hu X, Shao ZM. Comprehensive genomic profiling of breast cancers characterizes germline-somatic mutation interactions mediating therapeutic vulnerabilities. Cell Discov 2023; 9:125. [PMID: 38114467 PMCID: PMC10730692 DOI: 10.1038/s41421-023-00614-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/08/2023] [Indexed: 12/21/2023] Open
Abstract
Germline-somatic mutation interactions are universal and associated with tumorigenesis, but their role in breast cancer, especially in non-Caucasians, remains poorly characterized. We performed large-scale prospective targeted sequencing of matched tumor-blood samples from 4079 Chinese females, coupled with detailed clinical annotation, to map interactions between germline and somatic alterations. We discovered 368 pathogenic germline variants and identified 5 breast cancer DNA repair-associated genes (BCDGs; BRCA1/BRCA2/CHEK2/PALB2/TP53). BCDG mutation carriers, especially those with two-hit inactivation, demonstrated younger onset, higher tumor mutation burden, and greater clinical benefits from platinum drugs, PARP inhibitors, and immune checkpoint inhibitors. Furthermore, we leveraged a multiomics cohort to reveal that clinical benefits derived from two-hit events are associated with increased genome instability and an immune-activated tumor microenvironment. We also established an ethnicity-specific tool to predict BCDG mutation and two-hit status for genetic evaluation and therapeutic decisions. Overall, this study leveraged the large sequencing cohort of Chinese breast cancers, optimizing genomics-guided selection of DNA damaging-targeted therapy and immunotherapy within a broader population.
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Affiliation(s)
- Chao Chen
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cai-Jin Lin
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu-Chen Pei
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ding Ma
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Li Liao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Si-Yuan Li
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lei Fan
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Gen-Hong Di
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Song-Yang Wu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xi-Yu Liu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yun-Jin Wang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Qi Hong
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Guo-Liang Zhang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Lin-Lin Xu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Bei-Bei Li
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wei Huang
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Jin-Xiu Shi
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Xin Hu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China.
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China.
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An J, Oh JH, Oh B, Oh YJ, Ju JS, Kim W, Kang HJ, Sung CO, Shim JH. Clinicogenomic characteristics and synthetic lethal implications of germline homologous recombination-deficient hepatocellular carcinoma. Hepatology 2023; 78:452-467. [PMID: 36177702 DOI: 10.1002/hep.32812] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 09/20/2022] [Accepted: 09/24/2022] [Indexed: 12/08/2022]
Abstract
BACKGROUNDS AND AIMS We performed an in-depth examination of pathogenic germline variants (PGVs) and somatic variants in DNA damage response (DDR) genes in hepatocellular carcinoma (HCC) to explore their clinical and genomic impacts. APPROACH AND RESULTS We used a merged whole-exome or RNA sequencing data set derived from in-house ( n = 230) and The Cancer Genome Atlas ( n = 362) databases of multiethnic HCC samples. We also evaluated synthetic lethal approaches targeting mutations in homologous recombination (HR) genes using HCC cells selected from five genomic databases of cancer cell lines. A total of 110 PGVs in DDR pathways in 96 patients were selected. Of the PGV carriers, 44 were HR-altered and found to be independently associated with poorer disease-free survival after hepatectomy. The most frequently altered HR gene in both germline and somatic tissues was POLQ , and this variant was detected in 22.7% (10/44) and 23.8% (5/21) of all the corresponding carriers, respectively. PGVs in HR were significantly associated with upregulation of proliferation and replication-related genes and familial risk of HCC. Samples harboring PGVs in HR with loss of heterozygosity were most strongly correlated with the genomic footprints of deficient HR, such as mutation burden and denovoSig2 (analogous to Catalogue of Somatic Mutations in Cancer [COSMIC] 3), and poor outcome. Pharmacologic experiments with HCC cells defective in BRCA2 or POLQ suggested that tumors with this phenotype are synthetic lethal with poly(ADP-ribose) polymerase inhibitors. CONCLUSIONS Our findings suggest that germline HR defects in HCC tend to confer a poor prognosis and result in distinctive genomic scarring. Tests of the clinical benefits of HR-directed treatments in the affected patients are needed.
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Affiliation(s)
- Jihyun An
- Gastroenterology and Hepatology , Hanyang University College of Medicine , Guri , Republic of Korea
| | - Ji-Hye Oh
- Medical Science, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine , Seoul , Republic of Korea
| | - Bora Oh
- Asan Institute for Life Science, Asan Medical Center , Seoul , Republic of Korea
| | - Yoo-Jin Oh
- Asan Institute for Life Science, Asan Medical Center , Seoul , Republic of Korea
| | - Jin-Sung Ju
- Asan Institute for Life Science, Asan Medical Center , Seoul , Republic of Korea
| | - Wonkyung Kim
- Medical Science, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine , Seoul , Republic of Korea
| | - Hyo Jung Kang
- Pathology, Asan Medical Center , University of Ulsan College of Medicine , Seoul , Republic of Korea
- Asan Liver Center, Asan Medical Center , University of Ulsan College of Medicine , Seoul , South Korea
| | - Chang Ohk Sung
- Medical Science, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine , Seoul , Republic of Korea
- Pathology, Asan Medical Center , University of Ulsan College of Medicine , Seoul , Republic of Korea
- Center for Cancer Genome Discovery , Asan Institute for Life Science, University of Ulsan College of Medicine, Asan Medical Center , Seoul , Republic of Korea
| | - Ju Hyun Shim
- Asan Liver Center, Asan Medical Center , University of Ulsan College of Medicine , Seoul , South Korea
- Gastroenterology, Asan Medical Center , University of Ulsan College of Medicine , Seoul , Republic of Korea
- Digestive Diseases Research Center , University of Ulsan College of Medicine , Seoul , Republic of Korea
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3
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Cohen-Gogo S, Denburg AE, Villani A, Thacker N, Egan G, Simao Rafael M, Malkin D, Morgenstern DA. Precision oncology for children: A primer for paediatricians. Paediatr Child Health 2023; 28:278-284. [PMID: 37484033 PMCID: PMC10362955 DOI: 10.1093/pch/pxac123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 11/09/2022] [Indexed: 07/25/2023] Open
Abstract
Cancer is the leading cause of disease-related death in children, adolescents, and young adults beyond the newborn period in North America. Improving survival rates for patients with hard-to-cure cancer remains a challenge. One approach that has gained particular traction is 'precision oncology', whereby next-generation sequencing is used to identify genomic or transcriptomic changes that can help clarify the diagnosis, refine prognosis, define an underlying genetic cause, or identify a unique treatment target for a patient's cancer. In this primer, we provide a brief overview of the evolution of precision paediatric oncology, its current application to clinical oncology practice, and its future potential as a foundational approach to paediatric oncology care in Canada and around the world. We also address the many challenges and limitations inherent to the implementation of precision oncology as the standard of care, including ethical and economic considerations.
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Affiliation(s)
- Sarah Cohen-Gogo
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Avram E Denburg
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Anita Villani
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Nirav Thacker
- Division of Hematology/Oncology, Children’s Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Grace Egan
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Margarida Simao Rafael
- Department of Oncology, Solid Tumor Section, Hospital Sant Joan de Déu, Barcelona, Spain
| | - David Malkin
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Daniel A Morgenstern
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
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4
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Subasri V, Light N, Kanwar N, Brzezinski J, Luo P, Hansford JR, Cairney E, Portwine C, Elser C, Finlay JL, Nichols KE, Alon N, Brunga L, Anson J, Kohlmann W, de Andrade KC, Khincha PP, Savage SA, Schiffman JD, Weksberg R, Pugh TJ, Villani A, Shlien A, Goldenberg A, Malkin D. Multiple Germline Events Contribute to Cancer Development in Patients with Li-Fraumeni Syndrome. CANCER RESEARCH COMMUNICATIONS 2023; 3:738-754. [PMID: 37377903 PMCID: PMC10150777 DOI: 10.1158/2767-9764.crc-22-0402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/19/2023] [Accepted: 03/29/2023] [Indexed: 06/29/2023]
Abstract
Li-Fraumeni syndrome (LFS) is an autosomal dominant cancer-predisposition disorder. Approximately 70% of individuals who fit the clinical definition of LFS harbor a pathogenic germline variant in the TP53 tumor suppressor gene. However, the remaining 30% of patients lack a TP53 variant and even among variant TP53 carriers, approximately 20% remain cancer-free. Understanding the variable cancer penetrance and phenotypic variability in LFS is critical to developing rational approaches to accurate, early tumor detection and risk-reduction strategies. We leveraged family-based whole-genome sequencing and DNA methylation to evaluate the germline genomes of a large, multi-institutional cohort of patients with LFS (n = 396) with variant (n = 374) or wildtype TP53 (n = 22). We identified alternative cancer-associated genetic aberrations in 8/14 wildtype TP53 carriers who developed cancer. Among variant TP53 carriers, 19/49 who developed cancer harbored a pathogenic variant in another cancer gene. Modifier variants in the WNT signaling pathway were associated with decreased cancer incidence. Furthermore, we leveraged the noncoding genome and methylome to identify inherited epimutations in genes including ASXL1, ETV6, and LEF1 that confer increased cancer risk. Using these epimutations, we built a machine learning model that can predict cancer risk in patients with LFS with an area under the receiver operator characteristic curve (AUROC) of 0.725 (0.633-0.810). Significance Our study clarifies the genomic basis for the phenotypic variability in LFS and highlights the immense benefits of expanding genetic and epigenetic testing of patients with LFS beyond TP53. More broadly, it necessitates the dissociation of hereditary cancer syndromes as single gene disorders and emphasizes the importance of understanding these diseases in a holistic manner as opposed to through the lens of a single gene.
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Affiliation(s)
- Vallijah Subasri
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
| | - Nicholas Light
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Nisha Kanwar
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jack Brzezinski
- Division of Haematology/Oncology, The Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Ping Luo
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Jordan R. Hansford
- Children's Cancer Centre, Royal Children's Hospital, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Pediatrics, University of Melbourne, Melbourne, Australia
- Michael Rice Cancer Centre, Women's and Children's Hospital, North Adelaide, South Australia, Australia
- South Australia Health and Medical Research Institute, Adelaide, South Australia, Australia
- South Australia Immunogenomics Cancer Institute, University of Adelaide, Adelaide, Australia
| | - Elizabeth Cairney
- Department of Paediatrics, London Health Sciences Centre and Western University, London, Ontario, Canada
| | - Carol Portwine
- Department of Paediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Christine Elser
- Department of Medical Oncology, Princess Margaret Hospital and Mount Sinai Hospital, Toronto, Ontario, Canada
- Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan L. Finlay
- Neuro-Oncology Program, Nationwide Children's Hospital and The Ohio State University, Columbus, Ohio
| | - Kim E. Nichols
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Noa Alon
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ledia Brunga
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jo Anson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Wendy Kohlmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Kelvin C. de Andrade
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Payal P. Khincha
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Sharon A. Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Joshua D. Schiffman
- Department of Pediatrics, University of Utah, Salt Lake City, Utah
- PEEL Therapeutics, Inc., Salt Lake City, Utah
| | - Rosanna Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Trevor J. Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Anita Villani
- Division of Haematology/Oncology, The Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anna Goldenberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
- CIFAR: Child and Brain Development, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - David Malkin
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Haematology/Oncology, The Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
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Fu F, Tao X, Jiang Z, Gao Z, Zhao Y, Li Y, Hu H, Shen L, Sun Y, Zhang Y. Identification of Germline Mutations in East-Asian Young Never-Smokers with Lung Adenocarcinoma by Whole-Exome Sequencing. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:182-189. [PMID: 37197646 PMCID: PMC10110802 DOI: 10.1007/s43657-022-00062-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 05/19/2023]
Abstract
Recently, an increasing number of young never-smokers are diagnosed with lung cancer. The aim of this study is to investigate the genetic predisposition of lung cancer in these patients and discover candidate pathogenic variants for lung adenocarcinoma in young never-smokers. Peripheral blood was collected from 123 never-smoking east-Asian patients diagnosed with lung adenocarcinoma before the age of 40. Whole-exome sequencing (WES) was conducted on genomic DNA extracted from peripheral blood cells. As a result, 3,481 single nucleotide variants were identified. By bioinformatical tools and the published gene list associated with genetic predisposition of cancer, pathogenic variants were detected in ten germline genes: ATR, FANCD2, FANCE, GATA2, HFE, MSH2, PDGFRA, PMS2, SDHB, and WAS. Patients with pathogenic variants were more likely to occur in females (9/10, 90.0%) and have stage IV lung adenocarcinoma (4/10, 40%). Furthermore, germline mutations in 17 genes (ASB18, B3GALT5, CLEC4F, COL6A6, CYP4B1, C6orf132, EXO1, GATA4, HCK, KCP, NPHP4, PIGX, PPIL2, PPP1R3G, RRBP1, SALL4, and TTC28), which occurred in at least two patients, displayed potentially pathogenic effects. Gene ontology analysis further showed that these genes with germline mutations were mainly located in nucleoplasm and associated with DNA repair-related biological processes. The study provides spectrum of pathogenic variants and functional explanation for genetic predisposition of lung adenocarcinoma in young never-smokers, which sheds a light on prevention and early diagnosis of lung cancer. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-022-00062-1.
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Affiliation(s)
- Fangqiu Fu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032 China
- Institute of Thoracic Oncology, Fudan University, Shanghai, 200032 China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Xiaoting Tao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032 China
- Institute of Thoracic Oncology, Fudan University, Shanghai, 200032 China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Zhonglin Jiang
- Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031 China
| | - Zhendong Gao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032 China
- Institute of Thoracic Oncology, Fudan University, Shanghai, 200032 China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Yue Zhao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032 China
- Institute of Thoracic Oncology, Fudan University, Shanghai, 200032 China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Yuan Li
- Institute of Thoracic Oncology, Fudan University, Shanghai, 200032 China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032 China
| | - Hong Hu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032 China
- Institute of Thoracic Oncology, Fudan University, Shanghai, 200032 China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Libing Shen
- International Human Phenome Institutes (Shanghai), Shanghai, 200433 China
| | - Yihua Sun
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032 China
- Institute of Thoracic Oncology, Fudan University, Shanghai, 200032 China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Yang Zhang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032 China
- Institute of Thoracic Oncology, Fudan University, Shanghai, 200032 China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China
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Imyanitov EN, Kuligina ES, Sokolenko AP, Suspitsin EN, Yanus GA, Iyevleva AG, Ivantsov AO, Aleksakhina SN. Hereditary cancer syndromes. World J Clin Oncol 2023; 14:40-68. [PMID: 36908677 PMCID: PMC9993141 DOI: 10.5306/wjco.v14.i2.40] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/09/2022] [Accepted: 02/15/2023] [Indexed: 02/21/2023] Open
Abstract
Hereditary cancer syndromes (HCSs) are arguably the most frequent category of Mendelian genetic diseases, as at least 2% of presumably healthy subjects carry highly-penetrant tumor-predisposing pathogenic variants (PVs). Hereditary breast-ovarian cancer and Lynch syndrome make the highest contribution to cancer morbidity; in addition, there are several dozen less frequent types of familial tumors. The development of the majority albeit not all hereditary malignancies involves two-hit mechanism, i.e. the somatic inactivation of the remaining copy of the affected gene. Earlier studies on cancer families suggested nearly fatal penetrance for the majority of HCS genes; however, population-based investigations and especially large-scale next-generation sequencing data sets demonstrate that the presence of some highly-penetrant PVs is often compatible with healthy status. Hereditary cancer research initially focused mainly on cancer detection and prevention. Recent studies identified multiple HCS-specific drug vulnerabilities, which translated into the development of highly efficient therapeutic options.
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Affiliation(s)
- Evgeny N Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Ekaterina S Kuligina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Anna P Sokolenko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Evgeny N Suspitsin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Grigoriy A Yanus
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Aglaya G Iyevleva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Alexandr O Ivantsov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Svetlana N Aleksakhina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
- Department of Clinical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
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7
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Lampson BL, Gupta A, Tyekucheva S, Mashima K, Petráčková A, Wang Z, Wojciechowska N, Shaughnessy CJ, Baker PO, Fernandes SM, Shupe S, Machado JH, Fardoun R, Kim AS, Brown JR. Rare Germline ATM Variants Influence the Development of Chronic Lymphocytic Leukemia. J Clin Oncol 2023; 41:1116-1128. [PMID: 36315919 PMCID: PMC9928739 DOI: 10.1200/jco.22.00269] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/07/2022] Open
Abstract
PURPOSE Germline missense variants of unknown significance in cancer-related genes are increasingly being identified with the expanding use of next-generation sequencing. The ataxia telangiectasia-mutated (ATM) gene on chromosome 11 has more than 1,000 germline missense variants of unknown significance and is a tumor suppressor. We aimed to determine if rare germline ATM variants are more frequent in chronic lymphocytic leukemia (CLL) compared with other hematologic malignancies and if they influence the clinical characteristics of CLL. METHODS We identified 3,128 patients (including 825 patients with CLL) in our hematologic malignancy clinic who had received clinical-grade sequencing of the entire coding region of ATM. We ascertained the comparative frequencies of germline ATM variants in categories of hematologic neoplasms, and, in patients with CLL, we determined whether these variants affected CLL-associated characteristics such as somatic 11q deletion. RESULTS Rare germline ATM variants are present in 24% of patients with CLL, significantly greater than that in patients with other lymphoid malignancies (16% prevalence), myeloid disease (15%), or no hematologic neoplasm (14%). Patients with CLL with germline ATM variants are younger at diagnosis and twice as likely to have 11q deletion. The ATM variant p.L2307F is present in 3% of patients with CLL, is associated with a three-fold increase in rates of somatic 11q deletion, and is a hypomorph in cell-based assays. CONCLUSION Germline ATM variants cluster within CLL and affect the phenotype of CLL that develops, implying that some of these variants (such as ATM p.L2307F) have functional significance and should not be ignored. Further studies are needed to determine whether these variants affect the response to therapy or account for some of the inherited risk of CLL.
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Affiliation(s)
- Benjamin L. Lampson
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Aditi Gupta
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Kiyomi Mashima
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Anna Petráčková
- Department of Immunology, Palacký University, Olomouc, Czech Republic
| | - Zixu Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Natalia Wojciechowska
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Current Address: Wrocław Medical University, Wrocław, Poland
| | - Conner J. Shaughnessy
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Peter O. Baker
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Stacey M. Fernandes
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Samantha Shupe
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - John-Hanson Machado
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Rayan Fardoun
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Annette S. Kim
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Jennifer R. Brown
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
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8
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Villani A, Davidson S, Kanwar N, Lo WW, Li Y, Cohen-Gogo S, Fuligni F, Edward LM, Light N, Layeghifard M, Harripaul R, Waldman L, Gallinger B, Comitani F, Brunga L, Hayes R, Anderson ND, Ramani AK, Yuki KE, Blay S, Johnstone B, Inglese C, Hammad R, Goudie C, Shuen A, Wasserman JD, Venier RE, Eliou M, Lorenti M, Ryan CA, Braga M, Gloven-Brown M, Han J, Montero M, Spatare F, Whitlock JA, Scherer SW, Chun K, Somerville MJ, Hawkins C, Abdelhaleem M, Ramaswamy V, Somers GR, Kyriakopoulou L, Hitzler J, Shago M, Morgenstern DA, Tabori U, Meyn S, Irwin MS, Malkin D, Shlien A. The clinical utility of integrative genomics in childhood cancer extends beyond targetable mutations. NATURE CANCER 2023; 4:203-221. [PMID: 36585449 PMCID: PMC9970873 DOI: 10.1038/s43018-022-00474-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/02/2022] [Indexed: 12/31/2022]
Abstract
We conducted integrative somatic-germline analyses by deeply sequencing 864 cancer-associated genes, complete genomes and transcriptomes for 300 mostly previously treated children and adolescents/young adults with cancer of poor prognosis or with rare tumors enrolled in the SickKids Cancer Sequencing (KiCS) program. Clinically actionable variants were identified in 56% of patients. Improved diagnostic accuracy led to modified management in a subset. Therapeutically targetable variants (54% of patients) were of unanticipated timing and type, with over 20% derived from the germline. Corroborating mutational signatures (SBS3/BRCAness) in patients with germline homologous recombination defects demonstrates the potential utility of PARP inhibitors. Mutational burden was significantly elevated in 9% of patients. Sequential sampling identified changes in therapeutically targetable drivers in over one-third of patients, suggesting benefit from rebiopsy for genomic analysis at the time of relapse. Comprehensive cancer genomic profiling is useful at multiple points in the care trajectory for children and adolescents/young adults with cancer, supporting its integration into early clinical management.
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Affiliation(s)
- Anita Villani
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Scott Davidson
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada.,Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nisha Kanwar
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Winnie W Lo
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Yisu Li
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sarah Cohen-Gogo
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Fabio Fuligni
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Lisa-Monique Edward
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Nicholas Light
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Mehdi Layeghifard
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Ricardo Harripaul
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Larissa Waldman
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Cancer Genetics and High-Risk Program, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Bailey Gallinger
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Department of Genetic Counselling, University of Toronto, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Federico Comitani
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Ledia Brunga
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Reid Hayes
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Nathaniel D Anderson
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Arun K Ramani
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada.,Center for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kyoko E Yuki
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Sasha Blay
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Brittney Johnstone
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Cancer Genetics and High-Risk Program, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Cara Inglese
- Department of Genetic Counselling, University of Toronto, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rawan Hammad
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Division of Hematology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Catherine Goudie
- Division of Hematology-Oncology, McGill University Health Centre, Montreal, Quebec, Canada.,Department of Pediatrics, McGill University, Montreal, Quebec, Canada
| | - Andrew Shuen
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Jonathan D Wasserman
- Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada.,Division of Endocrinology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rosemarie E Venier
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Department of Genetic Counselling, University of Toronto, Toronto, Ontario, Canada
| | - Marianne Eliou
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Miranda Lorenti
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Carol Ann Ryan
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael Braga
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Meagan Gloven-Brown
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jianan Han
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maria Montero
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Famida Spatare
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - James A Whitlock
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada
| | - Kathy Chun
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Martin J Somerville
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Cynthia Hawkins
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Mohamed Abdelhaleem
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Vijay Ramaswamy
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Gino R Somers
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Lianna Kyriakopoulou
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Johann Hitzler
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada.,Developmental and Stem Cell Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Mary Shago
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Daniel A Morgenstern
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Uri Tabori
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Stephen Meyn
- Center for Human Genomics and Precision Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Meredith S Irwin
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - David Malkin
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada. .,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada. .,Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada.
| | - Adam Shlien
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada. .,Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.
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9
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Jobanputra V, Wrzeszczynski KO, Buttner R, Caldas C, Cuppen E, Grimmond S, Haferlach T, Mullighan C, Schuh A, Elemento O. Clinical interpretation of whole-genome and whole-transcriptome sequencing for precision oncology. Semin Cancer Biol 2022; 84:23-31. [PMID: 34256129 DOI: 10.1016/j.semcancer.2021.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 07/01/2021] [Accepted: 07/07/2021] [Indexed: 02/08/2023]
Abstract
Whole-genome sequencing either alone or in combination with whole-transcriptome sequencing has started to be used to analyze clinical tumor samples to improve diagnosis, provide risk stratification, and select patient-specific therapies. Compared with current genomic testing strategies, largely focused on small number of genes tested individually or targeted panels, whole-genome and transcriptome sequencing (WGTS) provides novel opportunities to identify and report a potentially much larger number of actionable alterations with diagnostic, prognostic, and/or predictive impact. Such alterations include point mutations, indels, copy- number aberrations and structural variants, but also germline variants, fusion genes, noncoding alterations and mutational signatures. Nevertheless, these comprehensive tests are accompanied by many challenges ranging from the extent and diversity of sequence alterations detected by these methods to the complexity and limited existing standardization in interpreting them. We describe the challenges of WGTS interpretation and the opportunities with comprehensive genomic testing.
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Affiliation(s)
- Vaidehi Jobanputra
- New York Genome Center, 101 Avenue of the Americas, New York, NY 100132, United States; Columbia University Medical Center, 650 W 168th St, New York, NY 10032, United States.
| | | | | | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of Oncology, University of Cambridge, United Kingdom
| | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, Netherlands; Center for Molecular Medicine and Oncode Institute, University Medical Center, Utrecht, Netherlands
| | - Sean Grimmond
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | | | - Charles Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, United States
| | - Anna Schuh
- NIHR Oxford Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, United States; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, United States.
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10
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Comprehensive cancer predisposition testing within the prospective MASTER trial identifies hereditary cancer patients and supports treatment decisions for rare cancers. Ann Oncol 2022; 33:1186-1199. [PMID: 35988656 DOI: 10.1016/j.annonc.2022.07.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 07/04/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Germline variant evaluation in precision oncology opens new paths towards the identification of patients with genetic tumor risk syndromes and the exploration of therapeutic relevance. Here, we present the results of germline variant analysis and their clinical implications in a precision oncology study for patients with predominantly rare cancers. PATIENTS AND METHODS Matched tumor and control genome/exome and RNA sequencing was performed for 1,485 patients with rare cancers (79%) and/or young adults (77% younger than 51 years) in the NCT/DKTK MASTER trial, a German multicenter, prospective observational precision oncology study. Clinical and therapeutic relevance of prospective pathogenic germline variant (PGV) evaluation was analyzed and compared to other precision oncology studies. RESULTS Ten percent of patients (n=157) harbored PGVs in 35 genes associated with autosomal dominant cancer predisposition, whereof up to 75% were unknown before study participation. Another five percent of patients (n=75) were heterozygous carriers for recessive genetic tumor risk syndromes. Particularly high PGV yields were found in patients with gastrointestinal stromal tumors (GISTs) (28%, 11/40), and more specific in wild-type GISTS (50%, n=10/20), leiomyosarcomas (21%, n=19/89), and hepatopancreaticobiliary cancers (16%, n=16/97). Forty-five percent of PGVs (n=100/221) supported treatment recommendations, and its implementation led to a clinical benefit in 40% of patients (n=10/25). A comparison of different precision oncology studies revealed variable PGV yields and considerable differences in germline variant analysis workflows. We therefore propose a detailed workflow for germline variant evaluation. CONCLUSIONS Genetic germline testing in patients with rare cancers can identify the very first patient in a hereditary cancer family and can lead to clinical benefit in a broad range of entities. Its routine implementation in precision oncology accompanied by the harmonization of germline variant evaluation workflows will increase clinical benefit and boost research.
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11
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Toss A, Quarello P, Mascarin M, Banna GL, Zecca M, Cinieri S, Peccatori FA, Ferrari A. Cancer Predisposition Genes in Adolescents and Young Adults (AYAs): a Review Paper from the Italian AYA Working Group. Curr Oncol Rep 2022; 24:843-860. [PMID: 35320498 PMCID: PMC9170630 DOI: 10.1007/s11912-022-01213-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2021] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW The present narrative systematic review summarizes current knowledge on germline gene mutations predisposing to solid tumors in adolescents and young adults (AYAs). RECENT FINDINGS AYAs with cancer represent a particular group of patients with specific challenging characteristics and yet unmet needs. A significant percentage of AYA patients carry pathogenic or likely pathogenic variants (PV/LPVs) in cancer predisposition genes. Nevertheless, knowledge on spectrum, frequency, and clinical implications of germline variants in AYAs with solid tumors is limited. The identification of PV/LPV in AYA is especially critical given the need for appropriate communicative strategies, risk of second primary cancers, need for personalized long-term surveillance, potential reproductive implications, and cascade testing of at-risk family members. Moreover, these gene alterations may potentially provide novel biomarkers and therapeutic targets that are lacking in AYA patients. Among young adults with early-onset phenotypes of malignancies typically presenting at later ages, the increased prevalence of germline PV/LPVs supports a role for genetic counseling and testing irrespective of tumor type.
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Affiliation(s)
- Angela Toss
- Department of Oncology and Hematology, Azienda Ospedaliero-Universitaria di Modena, Modena, Italy
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Paola Quarello
- Paediatric Onco-Haematology, Stem Cell Transplantation and Cellular Therapy Division, Regina Margherita Children's Hospital, Turin, Italy
- Department of Public Health and Paediatric Sciences, University of Torino, Turin, Italy
| | - Maurizio Mascarin
- AYA Oncology and Pediatric Radiotherapy Unit, Centro di Riferimento Oncologico IRCCS, Aviano, Italy
| | - Giuseppe Luigi Banna
- Candiolo Cancer Institute, FPO-IRCCS, SP142, km 3.95, 10060, Candiolo, Turin, Italy.
| | - Marco Zecca
- Department of Pediatric Hematology/Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Saverio Cinieri
- Medical Oncology Unit and Breast Unit Ospedale Perrino ASL, Brindisi, Italy
| | - Fedro Alessandro Peccatori
- Fertility and Procreation Unit, Gynecologic Oncology Program, European Institute of Oncology IRCCS, Milan, Italy
| | - Andrea Ferrari
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133, Milan, Italy
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12
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Reid S, Spalluto LB, Lang K, Weidner A, Pal T. An overview of genetic services delivery for hereditary breast cancer. Breast Cancer Res Treat 2022; 191:491-500. [PMID: 35079980 PMCID: PMC8789372 DOI: 10.1007/s10549-021-06478-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/02/2021] [Indexed: 02/06/2023]
Abstract
Breast cancer is the most common cancer diagnosed in women worldwide, with approximately 5-10% of cases attributed to high penetrance hereditary breast cancer (HBC) genes. The tremendous advances in precision oncology have broadened indications for germline genetic testing to guide both systemic and surgical treatment, with increasing demand for cancer genetic services. The HBC continuum of care includes (1) identification, access, and uptake of genetic counseling and testing; (2) the delivery of genetic counseling and testing services; and (3) initiation of guideline-adherent follow-up care and family communication of results. Challenges to delivering care on the HBC care continuum include factors such as access to services, cost, discrimination and bias, and lack of education and awareness, which can be mitigated through implementing a multi-level approach. This includes strategies such as increasing awareness and utilization of genetic counseling and testing, developing new methods to meet the growing demand for genetic services, and improving the uptake of follow-up care by increasing patient and provider awareness of the management recommendations.
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Affiliation(s)
- Sonya Reid
- Vanderbilt University Medical Center (VUMC)/Vanderbilt-Ingram Cancer Center (VICC), 2220 Pierce Ave. 777 PRB, Nashville, TN, 37232, USA.
| | - Lucy B Spalluto
- Vanderbilt University Medical Center (VUMC)/Vanderbilt-Ingram Cancer Center (VICC), 2220 Pierce Ave. 777 PRB, Nashville, TN, 37232, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine/Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Health Administration-Tennessee Valley Healthcare System Geriatric Research, Education and Clinical Center, Nashville, USA
| | - Katie Lang
- Department of Medicine/Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anne Weidner
- Department of Medicine/Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Tuya Pal
- Vanderbilt University Medical Center (VUMC)/Vanderbilt-Ingram Cancer Center (VICC), 2220 Pierce Ave. 777 PRB, Nashville, TN, 37232, USA.
- Department of Medicine/Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt University Medical Center (VUMC)/Vanderbilt-Ingram Cancer Center (VICC), 1500 21st Avenue South. Suite 2810, Nashville, TN, 37212, USA.
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13
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Grisanti S, Cosentini D, Sigala S, Berruti A. Molecular genotyping of adrenocortical carcinoma: a systematic analysis of published literature 2019-2021. Curr Opin Oncol 2022; 34:19-28. [PMID: 34669649 PMCID: PMC10863665 DOI: 10.1097/cco.0000000000000799] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE OF REVIEW comprehensive molecular characterization of adrenocortical carcinoma (ACC) through next-generation sequencing and bioinformatics analyses is expanding the number of targets with potential prognostic and therapeutic value. We performed a critical review of recent published literature on genotyping of ACC. RECENT FINDINGS 423 studies were published between 2019 and 2021. After manual curation we summarized selected evidence in two thematic areas: germline deoxyribonucleic acid (DNA) variations, genomic alterations and prognosis. SUMMARY the evolving genomic landscape of ACC requires target validation in terms of prognostic and predictive value within scientific consortia. Although the existing multiple driver genes are difficult targets in the perspective of precision oncology, alterations in DNA damage repair genes or in promoter hypermethylation could open new venues for repurposing of existing drugs in ACC.
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Affiliation(s)
- Salvatore Grisanti
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, ASST Spedali Civili
| | - Deborah Cosentini
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, ASST Spedali Civili
| | - Sandra Sigala
- Section of Pharmacology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Alfredo Berruti
- Medical Oncology Unit, Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, ASST Spedali Civili
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14
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Srinivasan P, Bandlamudi C, Jonsson P, Kemel Y, Chavan SS, Richards AL, Penson AV, Bielski CM, Fong C, Syed A, Jayakumaran G, Prasad M, Hwee J, Sumer SO, de Bruijn I, Li X, Gao J, Schultz N, Cambria R, Galle J, Mukherjee S, Vijai J, Cadoo KA, Carlo MI, Walsh MF, Mandelker D, Ceyhan-Birsoy O, Shia J, Zehir A, Ladanyi M, Hyman DM, Zhang L, Offit K, Robson ME, Solit DB, Stadler ZK, Berger MF, Taylor BS. The context-specific role of germline pathogenicity in tumorigenesis. Nat Genet 2021; 53:1577-1585. [PMID: 34741162 PMCID: PMC8957388 DOI: 10.1038/s41588-021-00949-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 09/09/2021] [Indexed: 11/08/2022]
Abstract
Human cancers arise from environmental, heritable and somatic factors, but how these mechanisms interact in tumorigenesis is poorly understood. Studying 17,152 prospectively sequenced patients with cancer, we identified pathogenic germline variants in cancer predisposition genes, and assessed their zygosity and co-occurring somatic alterations in the concomitant tumors. Two major routes to tumorigenesis were apparent. In carriers of pathogenic germline variants in high-penetrance genes (5.1% overall), lineage-dependent patterns of biallelic inactivation led to tumors exhibiting mechanism-specific somatic phenotypes and fewer additional somatic oncogenic drivers. Nevertheless, 27% of cancers in these patients, and most tumors in patients with pathogenic germline variants in lower-penetrance genes, lacked particular hallmarks of tumorigenesis associated with the germline allele. The dependence of tumors on pathogenic germline variants is variable and often dictated by both penetrance and lineage, a finding with implications for clinical management.
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Affiliation(s)
- Preethi Srinivasan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Stanford University School of Medicine, Palo Alto, CA, USA
| | - Chaitanya Bandlamudi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Philip Jonsson
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yelena Kemel
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shweta S Chavan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Allison L Richards
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander V Penson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Craig M Bielski
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher Fong
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aijazuddin Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meera Prasad
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jason Hwee
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Selcuk Onur Sumer
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ino de Bruijn
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiang Li
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - JianJiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roy Cambria
- Research and Technology Management, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jesse Galle
- Research and Technology Management, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Semanti Mukherjee
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph Vijai
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karen A Cadoo
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria I Carlo
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Walsh
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ozge Ceyhan-Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Loxo Oncology, Stamford, CT, USA
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kenneth Offit
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark E Robson
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zsofia K Stadler
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Barry S Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Loxo Oncology, Stamford, CT, USA
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15
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Schienda J, Church AJ, Corson LB, Decker B, Clinton CM, Manning DK, Imamovic-Tuco A, Reidy D, Strand GR, Applebaum MA, Bagatell R, DuBois SG, Glade-Bender JL, Kang W, Kim A, Laetsch TW, Macy ME, Maese L, Pinto N, Sabnis AJ, Schiffman JD, Colace SI, Volchenboum SL, Weiser DA, Nowak JA, Lindeman NI, Janeway KA, Crompton BD, Kamihara J. Germline Sequencing Improves Tumor-Only Sequencing Interpretation in a Precision Genomic Study of Patients With Pediatric Solid Tumor. JCO Precis Oncol 2021; 5:PO.21.00281. [PMID: 34964003 PMCID: PMC8710335 DOI: 10.1200/po.21.00281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/14/2021] [Accepted: 11/09/2021] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Molecular tumor profiling is becoming a routine part of clinical cancer care, typically involving tumor-only panel testing without matched germline. We hypothesized that integrated germline sequencing could improve clinical interpretation and enhance the identification of germline variants with significant hereditary risks. MATERIALS AND METHODS Tumors from pediatric patients with high-risk, extracranial solid malignancies were sequenced with a targeted panel of cancer-associated genes. Later, germline DNA was analyzed for a subset of these genes. We performed a post hoc analysis to identify how an integrated analysis of tumor and germline data would improve clinical interpretation. RESULTS One hundred sixty participants with both tumor-only and germline sequencing reports were eligible for this analysis. Germline sequencing identified 38 pathogenic or likely pathogenic variants among 35 (22%) patients. Twenty-five (66%) of these were included in the tumor sequencing report. The remaining germline pathogenic or likely pathogenic variants were single-nucleotide variants filtered out of tumor-only analysis because of population frequency or copy-number variation masked by additional copy-number changes in the tumor. In tumor-only sequencing, 308 of 434 (71%) single-nucleotide variants reported were present in the germline, including 31% with suggested clinical utility. Finally, we provide further evidence that the variant allele fraction from tumor-only sequencing is insufficient to differentiate somatic from germline events. CONCLUSION A paired approach to analyzing tumor and germline sequencing data would be expected to improve the efficiency and accuracy of distinguishing somatic mutations and germline variants, thereby facilitating the process of variant curation and therapeutic interpretation for somatic reports, as well as the identification of variants associated with germline cancer predisposition.
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Affiliation(s)
- Jaclyn Schienda
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | | | - Laura B. Corson
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Brennan Decker
- Department of Pathology, Boston Children's Hospital, Boston, MA
| | - Catherine M. Clinton
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | | | - Alma Imamovic-Tuco
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Deirdre Reidy
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Gianna R. Strand
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | | | - Rochelle Bagatell
- Department of Pediatrics, Children's Hospital of Philadelphia/University of Pennsylvania, Philadelphia, PA
| | - Steven G. DuBois
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | | | - Wenjun Kang
- Center for Research Informatics, University of Chicago, Chicago, IL
| | - AeRang Kim
- Center for Cancer and Blood Disorders, Children's National Hospital, Washington, DC
| | - Theodore W. Laetsch
- Department of Pediatrics, Children's Hospital of Philadelphia/University of Pennsylvania, Philadelphia, PA
| | - Margaret E. Macy
- Children's Hospital Colorado and University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Luke Maese
- Division of Pediatrics (Pediatric Hematology and Oncology University of Utah), Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Navin Pinto
- Division of Pediatric Hematology/Oncology, University of Washington, Seattle, WA
| | - Amit J. Sabnis
- Department of Pediatrics, University of California, San Francisco, CA, San Francisco, CA
| | - Joshua D. Schiffman
- Division of Pediatrics (Pediatric Hematology and Oncology University of Utah), Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Susan I. Colace
- Division of Pediatric Hematology, Oncology, and BMT, Nationwide Children's Hospital, Columbus, OH
| | | | - Daniel A. Weiser
- Division of Pediatric Hematology, Oncology, and Cellular Therapy, Children's Hospital at Montefiore, Bronx, NY
| | | | - Neal I. Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Katherine A. Janeway
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Brian D. Crompton
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
- Broad Institute of Harvard and MIT, Cambridge, MA
| | - Junne Kamihara
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
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16
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Thavaneswaran S, Ballinger M, Butow P, Meiser B, Goldstein D, Lin F, Napier C, Thomas D, Best M. The experiences and needs of Australian medical oncologists in integrating comprehensive genomic profiling into clinical care: a nation-wide survey. Oncotarget 2021; 12:2169-2176. [PMID: 34676049 PMCID: PMC8522847 DOI: 10.18632/oncotarget.28076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 09/04/2021] [Indexed: 11/26/2022] Open
Abstract
PURPOSE Comprehensive genomic profiling (CGP) is increasingly used to guide cancer therapy. This study aimed to characterise oncologists' experiences and needs when utilising genomic results. MATERIALS AND METHODS An electronic survey distributed nation-wide to practising medical oncologists in Australia explored oncologists' experiences with consenting, interpreting and communicating CGP results to patients. RESULTS The survey was completed by 108 of 333 oncologists (32%) and most respondents (n = 97, 90%) had referred patients for CGP. Using a 100-point visual analogue scale score [VAS], where higher values indicate greater confidence, most oncologists were confident consenting patients for referral [median 75 (Interquartile range, IQR: 53-85), discussing CGP results (median VAS: 70, IQR: 51-80), but significantly less confident discussing secondary germline findings (median VAS: 56, IQR 30-70, p < 0.001). Confidence with pursuing therapies based on CGP results increased with clinical experience (mean VAS increases by 4.8 per 5 years of experience, p < 0.001). Most oncologists (N = 68, 63%) reported wanting assistance with interpretation of CGP and patient-centric resources to aid communication with patients. CONCLUSIONS Oncologists are integrating genomics into clinical care, but only display moderate confidence in communication and changing management accordingly. The development of patient- and clinician- targeted resources may assist with routine utilisation of CGP results in cancer care.
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Affiliation(s)
- Subotheni Thavaneswaran
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- The Kinghorn Cancer Centre, St Vincent’s Hospital, Darlinghurst, NSW 2010, Australia
- St Vincent’s Clinical School, University of NSW, Darlinghurst, NSW 2010, Australia
| | - Mandy Ballinger
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- St Vincent’s Clinical School, University of NSW, Darlinghurst, NSW 2010, Australia
| | - Phyllis Butow
- School of Psychology, Psycho-Oncology Co-Operative Research Group (PoCoG), The University of Sydney, Sydney, NSW 2006, Australia
| | - Bettina Meiser
- Prince of Wales Clinical School, University of NSW, Sydney, NSW 2052, Australia
| | - David Goldstein
- Prince of Wales Clinical School, University of NSW, Sydney, NSW 2052, Australia
| | - Frank Lin
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- St Vincent’s Clinical School, University of NSW, Darlinghurst, NSW 2010, Australia
| | - Christine Napier
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - David Thomas
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- The Kinghorn Cancer Centre, St Vincent’s Hospital, Darlinghurst, NSW 2010, Australia
- St Vincent’s Clinical School, University of NSW, Darlinghurst, NSW 2010, Australia
| | - Megan Best
- Institute for Ethics and Society, University of Notre Dame Australia, Sydney, NSW 2007, Australia
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17
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Germline variants in DNA repair genes are associated with young-onset head and neck cancer. Oral Oncol 2021; 122:105545. [PMID: 34598035 DOI: 10.1016/j.oraloncology.2021.105545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/27/2021] [Accepted: 09/21/2021] [Indexed: 01/04/2023]
Abstract
The genetic predisposition to head and neck carcinomas (HNSCC) and how the known risk factors (papillomavirus infection, alcohol, and tobacco consumption) contribute to the early-onset disease are barely explored. Although HNSCC at early onset is rare, its frequency is increasing in recent years. Germline and somatic variants were assessed to build a comprehensive genetic influence pattern in HNSCC predisposition and patient outcome. Whole-exome sequencing was performed in 45 oral and oropharynx carcinomas paired with normal samples of young adults (≤49 years). We found FANCG, CDKN2A, and TPP germline variants previously associated with HNSCC risk. At least one germline variant in DNA repair pathway genes was detected in 67% of cases. Germline and somatic variants (including copy number variations) in FAT1 gene were identified in 9 patients (20%) and 12 tumors (30%), respectively. Somatic variants were found in HNSCC associated genes, such as TP53, CDKN2A, and PIK3CA. To date, 55 of 521 cases from the large cohort of TCGA presented < 49 years old. A comparison between the somatic alterations of TCGA-HNSCC at early onset and our dataset revealed strong similarities. Protein-protein interaction analysis between somatic and germline altered genes revealed a central role of TP53. Altogether, germline alterations in DNA repair genes potentially contribute to an increased risk of developing HNSCC at early-onset, while FAT1 could impact the prognosis.
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18
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Liu YL, Stadler ZK. The Future of Parallel Tumor and Germline Genetic Testing: Is There a Role for All Patients With Cancer? J Natl Compr Canc Netw 2021; 19:871-878. [PMID: 34340209 PMCID: PMC11123333 DOI: 10.6004/jnccn.2021.7044] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 04/09/2021] [Indexed: 11/17/2022]
Abstract
Under the traditional paradigm of genetic testing in cancer, the role of germline testing was to assess for the inherited risk of cancer, whereas the role of tumor testing was to determine therapeutic selection. Parallel tumor-normal genetic testing uses simultaneous genetic testing of the tumor and normal tissue to identify mutations and allows their classification as either germline or somatic. The increasing adoption of parallel testing has revealed a greater number of germline findings in patients who otherwise would not have met clinical criteria for testing. This result has widespread implications for the screening and further testing of at-risk relatives and for gene discovery. It has also revealed the importance of germline testing in therapeutic actionability. Herein, we describe the pros and cons of tumor-only versus parallel tumor-normal testing and summarize the data on the prevalence of incidental actionable germline findings. Because germline testing in patients with cancer continues to expand, it is imperative that systems be in place for the proper interpretation, dissemination, and counseling for patients and at-risk relatives. We also review new therapeutic approvals with germline indications and highlight the increasing importance of germline testing in selecting therapies. Because recommendations for universal genetic testing are increasing in multiple cancer types and the number of approved therapies with germline indications is also increasing, a gradual transition toward parallel tumor-normal genetic testing in all patients with cancer is foreseeable.
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Affiliation(s)
- Ying L. Liu
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zsofia K. Stadler
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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19
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Nakken S, Saveliev V, Hofmann O, Møller P, Myklebost O, Hovig E. Cancer Predisposition Sequencing Reporter (CPSR): A flexible variant report engine for high-throughput germline screening in cancer. Int J Cancer 2021; 149:1955-1960. [PMID: 34310709 DOI: 10.1002/ijc.33749] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 06/30/2021] [Accepted: 07/09/2021] [Indexed: 12/11/2022]
Abstract
The value of high-throughput germline genetic testing is increasingly recognized in clinical cancer care. Disease-associated germline variants in cancer patients are important for risk management and surveillance, surgical decisions and can also have major implications for treatment strategies since many are in DNA repair genes. With the increasing availability of high-throughput DNA sequencing in cancer clinics and research, there is thus a need to provide clinically oriented sequencing reports for germline variants and their potential therapeutic relevance on a per-patient basis. To meet this need, we have developed the Cancer Predisposition Sequencing Reporter (CPSR), an open-source computational workflow that generates a structured report of germline variants identified in known cancer predisposition genes, highlighting markers of therapeutic, prognostic and diagnostic relevance. A fully automated variant classification procedure based on more than 30 refined American College of Medical Genetics and Genomics (ACMG) criteria represents an integral part of the workflow. Importantly, the set of cancer predisposition genes profiled in the report can be flexibly chosen from more than 40 virtual gene panels established by scientific experts, enabling customization of the report for different screening purposes and clinical contexts. The report can be configured to also list actionable secondary variant findings, as recommended by ACMG. CPSR demonstrates comparable sensitivity and specificity for the detection of pathogenic variants when compared to other algorithms in the field. Technically, the tool is implemented in Python/R, and is freely available through Docker technology. Source code, documentation, example reports and installation instructions are accessible via the project GitHub page: https://github.com/sigven/cpsr.
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Affiliation(s)
- Sigve Nakken
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Vladislav Saveliev
- Centre for Cancer Research, University of Melbourne, Victoria, Australia
| | - Oliver Hofmann
- Centre for Cancer Research, University of Melbourne, Victoria, Australia
| | - Pål Møller
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Ola Myklebost
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway.,Western Norway Familial Cancer Center, Haukeland University Hospital, Bergen, Norway
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
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20
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Martin-Giacalone BA, Weinstein PA, Plon SE, Lupo PJ. Pediatric Rhabdomyosarcoma: Epidemiology and Genetic Susceptibility. J Clin Med 2021; 10:2028. [PMID: 34065162 PMCID: PMC8125975 DOI: 10.3390/jcm10092028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 12/18/2022] Open
Abstract
Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma in children, yet little is known about its etiology. Studies that examine either environmental exposures or germline genetic predisposition in RMS have begun to identify factors that contribute to this malignancy. Here, we summarize epidemiological reports of RMS incidence in terms of several factors, including age at diagnosis, biological sex, and geographic location. We then describe findings from association studies, which explore the role of parental exposures, birth and perinatal characteristics, and childhood exposures in RMS. Further, we discuss RMS predisposition syndromes and large-scale sequencing studies that have further identified RMS-associated genes. Finally, we propose future directions of study, which aim to advance our understanding of the origin of RMS and can provide knowledge for novel RMS therapies.
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Affiliation(s)
- Bailey A. Martin-Giacalone
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (B.A.M.-G.); (P.A.W.); (S.E.P.)
- Program in Translational Biology and Molecular Medicine, Graduate School of Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - P. Adam Weinstein
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (B.A.M.-G.); (P.A.W.); (S.E.P.)
- Genetics and Genomics Graduate Program, Graduate School of Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sharon E. Plon
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (B.A.M.-G.); (P.A.W.); (S.E.P.)
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Philip J. Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (B.A.M.-G.); (P.A.W.); (S.E.P.)
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21
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Ji X, Ning B, Liu J, Roberts R, Lesko L, Tong W, Liu Z, Shi T. Towards population-specific pharmacogenomics in the era of next-generation sequencing. Drug Discov Today 2021; 26:1776-1783. [PMID: 33892143 DOI: 10.1016/j.drudis.2021.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 01/22/2021] [Accepted: 04/12/2021] [Indexed: 11/27/2022]
Abstract
Pharmacogenomics (PGx) has essential roles in identifying optimal drug responders, optimizing dosage regimens and avoiding adverse events. Population-specific therapeutic interventions that tackle the genetic root causes of clinical outcomes are an important precision medicine strategy. In this perspective, we discuss next-generation sequencing genotyping and its significance for population-specific PGx applications. We emphasize the potential of NGS for preemptive pharmacogenotyping, which is crucial to population-specific clinical studies and patient care. We also provide examples that use publicly available population-based genomics data for population-specific PGx studies. Last, we discuss the remaining challenges and regulatory efforts towards improvements in this field.
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Affiliation(s)
- Xiangjun Ji
- The Center for Bioinformatics and Computational Biology, The Institute of Biomedical Sciences and School of Life Sciences, School of Statistics, East China Normal University, Shanghai 200241, China; Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Baitang Ning
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA
| | - Jinghua Liu
- Guangdong Provincial Key Laboratory of Proteomics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ruth Roberts
- ApconiX, BioHub at Alderley Park, Alderley Edge SK10 4TG, UK; University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Larry Lesko
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA; Department of Pharmaceutics, Center for Pharmacometrics and Systems Pharmacology, University of Florida at Lake Nona, Orlando, FL, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA.
| | - Zhichao Liu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA.
| | - Tieliu Shi
- The Center for Bioinformatics and Computational Biology, The Institute of Biomedical Sciences and School of Life Sciences, School of Statistics, East China Normal University, Shanghai 200241, China; Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA; National Center for International Research of Biological Targeting Diagnosis and Therapy, Guangxi Key Laboratory of Biological Targeting Diagnosis and Therapy Research, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, Guangxi 530021, China.
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22
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Ming H, Li B, Zhou L, Goel A, Huang C. Long non-coding RNAs and cancer metastasis: Molecular basis and therapeutic implications. Biochim Biophys Acta Rev Cancer 2021; 1875:188519. [PMID: 33548345 DOI: 10.1016/j.bbcan.2021.188519] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/29/2021] [Accepted: 01/29/2021] [Indexed: 02/08/2023]
Abstract
Cancer metastasis, defined by the epithelial to mesenchymal transition (EMT) of tumor cells, disseminates from the primary site to progressively colonize in distant tissues, and accounts for most cancer-associated deaths. However, studies on the molecular basis of cancer metastasis are still in their infancy. Besides genetic mutations, accumulating evidence indicates that epigenetic alterations also contribute in a major way to the refractory nature of cancer metastasis. Considered as one of the essential epigenetic regulators, long non-coding RNAs (lncRNAs) can act as signaling regulators, decoys, guides and scaffolds, modulating key molecules in every step of cancer metastasis including dissemination of carcinoma cells, intravascular transit, and metastatic colonization. Although still having limited clinical application, it is encouraging to witness that several lncRNAs, including CCAT1 and HOTAIR, are under clinical evaluation as potential biomarkers for cancer staging and assessment of metastatic potential. In this review, we focus on the molecular mechanisms underlying lncRNAs in the regulation of cancer metastasis and discuss their clinical potential as novel therapeutic targets as well as their diagnostic and prognostic significance for cancer treatment. Gaining clear insights into the detailed molecular basis underlying lncRNA-modulated cancer metastasis may provide previously unrecognized diagnostic and therapeutic strategies for metastatic patients.
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Affiliation(s)
- Hui Ming
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Bowen Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Li Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, 1218 S. Fifth Avenue, Suite 2226, Biomedical Research Center, Monrovia, CA 91016, USA.
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital and West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
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23
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Arbitrio M, Scionti F, Di Martino MT, Caracciolo D, Pensabene L, Tassone P, Tagliaferri P. Pharmacogenomics Biomarker Discovery and Validation for Translation in Clinical Practice. Clin Transl Sci 2021; 14:113-119. [PMID: 33089968 PMCID: PMC7877857 DOI: 10.1111/cts.12869] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/14/2020] [Indexed: 12/23/2022] Open
Abstract
Interindividual variability in drug efficacy and toxicity is a major challenge in clinical practice. Variations in drug pharmacokinetics (PKs) and pharmacodynamics (PDs) can be, in part, explained by polymorphic variants in genes encoding drug metabolizing enzymes and transporters (absorption, distribution, metabolism, and excretion) or in genes encoding drug receptors. Pharmacogenomics (PGx) has allowed the identification of predictive biomarkers of drug PKs and PDs and the current knowledge of genome-disease and genome-drug interactions offers the opportunity to optimize tailored drug therapy. High-throughput PGx genotyping, from targeted to more comprehensive strategies, allows the identification of PK/PD genotypes to be developed as clinical predictive biomarkers. However, a biomarker needs a robust process of validation followed by clinical-grade assay development and must comply to stringent regulatory guidelines. We here discuss the methodological challenges and the emerging technological tools in PGx biomarker discovery and validation, at the crossroad among molecular genetics, bioinformatics, and clinical medicine.
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Affiliation(s)
- Mariamena Arbitrio
- Institute of Research and Biomedical Innovation (IRIB), Italian National Council (CNR), Catanzaro, Italy
| | - Francesca Scionti
- Department of Clinical and Experimental Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Maria Teresa Di Martino
- Department of Clinical and Experimental Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Daniele Caracciolo
- Department of Clinical and Experimental Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Licia Pensabene
- Department of Medical and Surgical Science, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Pierfrancesco Tassone
- Department of Clinical and Experimental Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Pierosandro Tagliaferri
- Department of Clinical and Experimental Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
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24
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Li H, Sisoudiya SD, Martin-Giacalone BA, Khayat MM, Dugan-Perez S, Marquez-Do DA, Scheurer ME, Muzny D, Boerwinkle E, Gibbs RA, Chi YY, Barkauskas DA, Lo T, Hall D, Stewart DR, Schiffman JD, Skapek SX, Hawkins DS, Plon SE, Sabo A, Lupo PJ. Germline Cancer Predisposition Variants in Pediatric Rhabdomyosarcoma: A Report From the Children's Oncology Group. J Natl Cancer Inst 2020; 113:875-883. [PMID: 33372952 DOI: 10.1093/jnci/djaa204] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 10/15/2020] [Accepted: 12/09/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Several cancer-susceptibility syndromes are reported to underlie pediatric rhabdomyosarcoma (RMS); however, to our knowledge there have been no systematic efforts to characterize the heterogeneous genetic etiologies of this often-fatal malignancy. METHODS We performed exome-sequencing on germline DNA from 615 patients with newly diagnosed RMS consented through the Children's Oncology Group. We compared the prevalence of cancer predisposition variants in 63 autosomal-dominant cancer predisposition genes in these patients with population controls (n = 9963). All statistical tests were 2-sided. RESULTS We identified germline cancer predisposition variants in 45 RMS patients (7.3%; all FOXO1 fusion negative) across 15 autosomal dominant genes, which was statistically significantly enriched compared with controls (1.4%, P = 1.3 × 10-22). Specifically, 73.3% of the predisposition variants were found in predisposition syndrome genes previously associated with pediatric RMS risk, such as Li-Fraumeni syndrome (TP53) and neurofibromatosis type I (NF1). Notably, 5 patients had well-described oncogenic missense variants in HRAS (p.G12V and p.G12S) associated with Costello syndrome. Also, genetic etiology differed with histology, as germline variants were more frequent in embryonal vs alveolar RMS patients (10.0% vs 3.0%, P = .02). Although patients with a cancer predisposition variant tended to be younger at diagnosis (P = 9.9 × 10-4), 40.0% of germline variants were identified in those older than 3 years of age, which is in contrast to current genetic testing recommendations based on early age at diagnosis. CONCLUSIONS These findings demonstrate that genetic risk of RMS results from germline predisposition variants associated with a wide spectrum of cancer susceptibility syndromes. Germline genetic testing for children with RMS should be informed by RMS subtypes and not be limited to only young patients.
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Affiliation(s)
- He Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Saumya D Sisoudiya
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Bailey A Martin-Giacalone
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Michael M Khayat
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shannon Dugan-Perez
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Deborah A Marquez-Do
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Michael E Scheurer
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,School of Public Health, the University of Texas Health Science Center, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yueh-Yun Chi
- Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Donald A Barkauskas
- QuadW Childhood Sarcoma Biostatistics and Annotation Office at the Children's Oncology Group, Monrovia, CA, USA.,Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Tammy Lo
- QuadW Childhood Sarcoma Biostatistics and Annotation Office at the Children's Oncology Group, Monrovia, CA, USA
| | - David Hall
- QuadW Childhood Sarcoma Biostatistics and Annotation Office at the Children's Oncology Group, Monrovia, CA, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Joshua D Schiffman
- Departments of Pediatrics and Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Stephen X Skapek
- Department of Pediatrics, the University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Douglas S Hawkins
- Division of Hematology-Oncology, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - Sharon E Plon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Philip J Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
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25
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Juarez OA, Pencheva BB, Bellcross C, Schneider KW, Turner J, Porter CC. Cancer genetic counseling for childhood cancer predisposition is associated with improved levels of knowledge and high satisfaction in parents. J Genet Couns 2020; 30:710-719. [PMID: 33179831 DOI: 10.1002/jgc4.1357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/28/2022]
Abstract
Previous surveys of adults with cancer have revealed increased levels of genetic knowledge, varying levels of worry, and high satisfaction with cancer genetic counseling. We sought to determine the impact of cancer genetic counseling on parental levels of genetic knowledge, worry about cancer, and satisfaction in the context of suspected cancer predisposition in a child. We hypothesized that parents would be satisfied with cancer genetic counseling and that cancer genetic counseling would improve baseline parental genetic knowledge and decrease levels of worry. Parents were recruited from a pediatric cancer predisposition clinic in the United States. A survey was administered to two cohorts: One cohort had received cancer genetic counseling in the past and only completed one survey (post-only, n = 26), and another cohort completed the survey before and after cancer genetic counseling (pre/post, n = 23). The survey included questions on demographics, knowledge of genetics, worry levels, and satisfaction with the cancer genetic counseling service. The post-genetic counseling survey also contained a free-text section for parents to indicate what they took away from the sessions. Parental levels of genetics knowledge increased by an average of 1.9 points (p = .01), with 65.2% of parents demonstrating an increase in genetics knowledge score. Average worry levels did not change significantly (p = .37), with 52.2% of parents indicating decreased worry, and 34.8% indicating increased worry. Overall, 91.8% of parents reported high levels of satisfaction. Our results show that cancer genetic counseling in a pediatric cancer predisposition clinic improves parental levels of genetics knowledge. Satisfaction rates suggest that parents find this service beneficial. These results demonstrate the positive impacts of cancer genetic counseling on parents of children in which a hereditary cancer syndrome is known or suspected.
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Affiliation(s)
| | - Bojana B Pencheva
- Emory University School of Medicine, Atlanta, GA, USA.,Aflac Cancer and Blood Disorders Center at Children's Healthcare of Atlanta, Atlanta, GA, USA
| | | | - Kami W Schneider
- Children's Hospital Colorado, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Joyce Turner
- Children's National Health System Rare Disease Institute, Washington, DC, USA
| | - Christopher C Porter
- Emory University School of Medicine, Atlanta, GA, USA.,Aflac Cancer and Blood Disorders Center at Children's Healthcare of Atlanta, Atlanta, GA, USA
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26
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Manchanda R, Lieberman S, Gaba F, Lahad A, Levy-Lahad E. Population Screening for Inherited Predisposition to Breast and Ovarian Cancer. Annu Rev Genomics Hum Genet 2020; 21:373-412. [DOI: 10.1146/annurev-genom-083118-015253] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The discovery of genes underlying inherited predisposition to breast and ovarian cancer has revolutionized the ability to identify women at high risk for these diseases before they become affected. Women who are carriers of deleterious variants in these genes can undertake surveillance and prevention measures that have been shown to reduce morbidity and mortality. However, under current strategies, the vast majority of women carriers remain undetected until they become affected. In this review, we show that universal testing, particularly of the BRCA1 and BRCA2 genes, fulfills classical disease screening criteria. This is especially true for BRCA1 and BRCA2 in Ashkenazi Jews but is translatable to all populations and may include additional genes. Utilizing genetic information for large-scale precision prevention requires a paradigmatic shift in health-care delivery. To address this need, we propose a direct-to-patient model, which is increasingly pertinent for fulfilling the promise of utilizing personal genomic information for disease prevention.
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Affiliation(s)
- Ranjit Manchanda
- Wolfson Institute of Preventive Medicine, Queen Mary University of London, London EC1M 6BQ, United Kingdom;,
- Department of Gynaecological Oncology, Barts Health NHS Trust, London E1 1FR, United Kingdom
| | - Sari Lieberman
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 9103102, Israel;,
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Faiza Gaba
- Wolfson Institute of Preventive Medicine, Queen Mary University of London, London EC1M 6BQ, United Kingdom;,
- Department of Gynaecological Oncology, Barts Health NHS Trust, London E1 1FR, United Kingdom
| | - Amnon Lahad
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Clalit Health Services, Jerusalem 9548323, Israel
| | - Ephrat Levy-Lahad
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 9103102, Israel;,
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112102, Israel
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27
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Reid S, Pal T. Update on multi-gene panel testing and communication of genetic test results. Breast J 2020; 26:1513-1519. [PMID: 32639074 PMCID: PMC7484453 DOI: 10.1111/tbj.13971] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 11/14/2019] [Indexed: 12/20/2022]
Abstract
With technological advances, multi-gene panel testing has become increasingly used to identify patients at risk for hereditary breast cancer (HBC). There are currently evidence-based interventions and breast cancer screening strategies that exist for cancer prevention and early detection among patients with HBC. Moreover, in addition to the personal impact of identifying HBC, this information may be shared with at-risk family members to amplify the benefits of testing and subsequent care among those at high risk. Opportunities and challenges with the utilization of updated multi-gene panel testing for HBC, including: (a) tumor sequencing with germline consequences; (b) genetic counseling implications; and (c) strategies to improve the communication of genetic test results to family members will be reviewed. With the advances and expansion of genetic testing, all health care providers need to be updated on both the importance and complexities of HBC counseling and testing, in order to optimize patient care.
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Affiliation(s)
- Sonya Reid
- Vanderbilt University Medical Center, Nashville, Tennessee
| | - Tuya Pal
- Vanderbilt University Medical Center, Nashville, Tennessee
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28
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Peng Q, Zhou Y, Jin L, Cao C, Gao C, Zhou J, Yang D, Zhu J. Development and validation of an integrative methylation signature and nomogram for predicting survival in clear cell renal cell carcinoma. Transl Androl Urol 2020; 9:1082-1098. [PMID: 32676392 PMCID: PMC7354314 DOI: 10.21037/tau-19-853] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Growing evidence has shown that genetic or epigenetic alterations are highly involved in the initiation and progression of renal cell carcinoma (RCC). This study aimed to find prognostic methylation markers in clear cell RCC (ccRCC). Methods In this study, we developed and confirmed an integrated and comprehensive methylation signature by integrating DNA methylation, gene expression, and The Cancer Genome Atlas (TCGA) survival data. First, the methylation signature was found and checked based on data analysis of published datasets. Then, independent predictive factors were selected using the Cox proportional model and incorporated into the nomogram. Finally, the predictive nomogram was derived and validated using a concordance index and calibration plots. Results A series of differentially expressed and methylated genes were identified. After intersection analysis, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, protein-protein interaction (PPI) analysis, and correlation analysis, FCGR1A, F2, and NOD2 were established as a predictive signature. According to the Kaplan-Meier survival analysis, the risk score system based on the predictive signature was able to stratify the patients into high- and low-risk groups with significantly different overall survival. The receiver operating characteristic (ROC) analysis further showed that the predictive signature yielded high sensitivity and specificity in predicting the prognosis outcome of ccRCC patients. Moreover, univariate and multivariate Cox regression analysis confirmed that the three-gene methylation signature was an independent prognostic factor in ccRCC. Finally, a nomogram comprising the predictive signature and several independent variables were constructed and proved to effectively predict ccRCC patient survival. Conclusions The three-gene methylation signature was revealed to be a potential novel and independent adverse predictor of prognosis for ccRCC patients and may serve as a promising marker for treatment management and survival outcome improvement. However, substantial validation experiments are required to characterize the molecular background of the predictive signature.
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Affiliation(s)
- Qiliang Peng
- Department of Radiotherapy & Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Radiotherapy & Oncology, Soochow University, Suzhou, China
| | - Yibin Zhou
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Lu Jin
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Cheng Cao
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Cheng Gao
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Jianfang Zhou
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Dongrong Yang
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Jin Zhu
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, China
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29
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Comprehensive germline genomic profiles of children, adolescents and young adults with solid tumors. Nat Commun 2020; 11:2206. [PMID: 32371905 PMCID: PMC7200683 DOI: 10.1038/s41467-020-16067-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 04/08/2020] [Indexed: 02/07/2023] Open
Abstract
Compared to adult carcinomas, there is a paucity of targeted treatments for solid tumors in children, adolescents, and young adults (C-AYA). The impact of germline genomic signatures has implications for heritability, but its impact on targeted therapies has not been fully appreciated. Performing variant-prioritization analysis on germline DNA of 1,507 C-AYA patients with solid tumors, we show 12% of these patients carrying germline pathogenic and/or likely pathogenic variants (P/LP) in known cancer-predisposing genes (KCPG). An additional 61% have germline pathogenic variants in non-KCPG genes, including PRKN, SMARCAL1, SMAD7, which we refer to as candidate genes. Despite germline variants in a broad gene spectrum, pathway analysis leads to top networks centering around p53. Our drug-target analysis shows 1/3 of patients with germline P/LP variants have at least one druggable alteration, while more than half of them are from our candidate gene group, which would otherwise go unidentified in routine clinical care. Targeted therapies for solid tumors in children, adolescents, and young adults (C-AYA) lag behind that of adult carcinomas. Here, the authors study the germline genomic signatures of 1,507 C-AYA patients with solid tumors and find pathogenic/likely pathogenic germline variants in diverse genes of which 1/3 of these alterations are druggable.
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30
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Haddadi N, Travis G, Nassif NT, Simpson AM, Marsh DJ. Toward Systems Pathology for PTEN Diagnostics. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a037127. [PMID: 31615872 DOI: 10.1101/cshperspect.a037127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Germline alterations of the tumor suppressor PTEN have been extensively characterized in patients with PTEN hamartoma tumor syndromes, encompassing subsets of Cowden syndrome, Bannayan-Riley-Ruvalcaba syndrome, Proteus and Proteus-like syndromes, as well as autism spectrum disorder. Studies have shown an increase in the risk of developing specific cancer types in the presence of a germline PTEN mutation. Furthermore, outside of the familial setting, somatic variants of PTEN occur in numerous malignancies. Here we introduce and discuss the prospect of moving toward a systems pathology approach for PTEN diagnostics, incorporating clinical and molecular pathology data with the goal of improving the clinical management of patients with a PTEN mutation. Detection of a germline PTEN mutation can inform cancer surveillance and in the case of somatic mutation, have value in predicting disease course. Given that PTEN functions in the PI3K/AKT/mTOR pathway, identification of a PTEN mutation may highlight new therapeutic opportunities and/or inform therapeutic choices.
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Affiliation(s)
- Nahal Haddadi
- School of Life Sciences, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Glena Travis
- School of Life Sciences, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Najah T Nassif
- School of Life Sciences, University of Technology Sydney, Ultimo, New South Wales 2007, Australia.,Centre for Health Technologies, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Ann M Simpson
- School of Life Sciences, University of Technology Sydney, Ultimo, New South Wales 2007, Australia.,Centre for Health Technologies, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Deborah J Marsh
- School of Life Sciences, University of Technology Sydney, Ultimo, New South Wales 2007, Australia.,Centre for Health Technologies, University of Technology Sydney, Ultimo, New South Wales 2007, Australia.,Translational Oncology Group, School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, New South Wales 2007, Australia.,Northern Clinical School, Kolling Institute, Faculty of Medicine and Health, University of Sydney, New South Wales 2006, Australia
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31
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Amaral T, Schulze M, Sinnberg T, Nieser M, Martus P, Battke F, Garbe C, Biskup S, Forschner A. Are Pathogenic Germline Variants in Metastatic Melanoma Associated with Resistance to Combined Immunotherapy? Cancers (Basel) 2020; 12:cancers12051101. [PMID: 32354124 PMCID: PMC7281129 DOI: 10.3390/cancers12051101] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 01/10/2023] Open
Abstract
Background: Combined immunotherapy has significantly improved survival of patients with advanced melanoma, but there are still patients that do not benefit from it. Early biomarkers that indicate potential resistance would be highly relevant for these patients. Methods: We comprehensively analyzed tumor and blood samples from patients with advanced melanoma, treated with combined immunotherapy and performed descriptive and survival analysis. Results: Fifty-nine patients with a median follow-up of 13 months (inter quartile range (IQR) 11–15) were included. Interestingly, nine patients were found to have pathogenic or likely pathogenic (P/LP) germline variants in one of these genes: BRCA2, POLE, WRN, FANCI, CDKN2A, BAP1, PALB2 and RAD54B. Most of them are involved in DNA repair mechanisms. Patients with P/LP germline variants had a significantly shorter progression-free survival (PFS) and melanoma specific survival (MSS) compared to patients without P/LP germline variants (HR = 2.16; 95% CI: 1.01–4.64; p = 0.048 and HR = 3.21; 95% CI: 1.31–7.87; p = 0.011, respectively). None of the patients with a P/LP germline variant responded to combined immunotherapy. In the multivariate Cox-regression analysis, presence of a P/LP germline variant, S100B and lactate dehydrogenase (LDH) remained independently significant factors for MSS (p = 0.036; p = 0.044 and p = 0.001, respectively). Conclusions: The presence of P/LP germline variants was associated with resistance to combined immunotherapy in our cohort. As genes involved in DNA repair mechanisms are also involved in lymphocyte development and T-cell differentiation, a P/LP germline variant in these genes may preclude an antitumor immune response.
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Affiliation(s)
- Teresa Amaral
- Center for Dermatooncology, Department of Dermatology, University Hospital Tuebingen, Eberhard Karls University, 72076 Tuebingen, Germany; (T.A.); (T.S.); (C.G.)
- Portuguese Air Force, Health Care Direction, 1649-020 Lisbon, Portugal
| | - Martin Schulze
- Practice for Human Genetics, 72076 Tuebingen, Germany; (M.S.); (M.N.); (S.B.)
| | - Tobias Sinnberg
- Center for Dermatooncology, Department of Dermatology, University Hospital Tuebingen, Eberhard Karls University, 72076 Tuebingen, Germany; (T.A.); (T.S.); (C.G.)
| | - Maike Nieser
- Practice for Human Genetics, 72076 Tuebingen, Germany; (M.S.); (M.N.); (S.B.)
| | - Peter Martus
- Institute for Clinical Epidemiology and applied Biostatistics (IKEaB), Eberhard Karls University, 72076 Tuebingen, Germany;
| | - Florian Battke
- Center for Genomics and Transcriptomics (CeGaT) GmbH, 72076 Tuebingen, Germany;
| | - Claus Garbe
- Center for Dermatooncology, Department of Dermatology, University Hospital Tuebingen, Eberhard Karls University, 72076 Tuebingen, Germany; (T.A.); (T.S.); (C.G.)
| | - Saskia Biskup
- Practice for Human Genetics, 72076 Tuebingen, Germany; (M.S.); (M.N.); (S.B.)
- Center for Genomics and Transcriptomics (CeGaT) GmbH, 72076 Tuebingen, Germany;
| | - Andrea Forschner
- Center for Dermatooncology, Department of Dermatology, University Hospital Tuebingen, Eberhard Karls University, 72076 Tuebingen, Germany; (T.A.); (T.S.); (C.G.)
- Correspondence: ; Tel.: +49-(0)-7071-29 84555; Fax: +49-(0)-7071-29-4599
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32
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Bitzer M, Ostermann L, Horger M, Biskup S, Schulze M, Ruhm K, Hilke F, Öner Ö, Nikolaou K, Schroeder C, Riess O, Fend F, Zips D, Hinterleitner M, Zender L, Tabatabai G, Beha J, Malek NP. Next-Generation Sequencing of Advanced GI Tumors Reveals Individual Treatment Options. JCO Precis Oncol 2020; 4:PO.19.00359. [PMID: 32923905 PMCID: PMC7446530 DOI: 10.1200/po.19.00359] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2020] [Indexed: 12/17/2022] Open
Abstract
PURPOSE Precision oncology connects highly complex diagnostic procedures with patient histories to identify individualized treatment options in interdisciplinary molecular tumor boards (MTBs). Detailed data on MTB-guided treatments and outcome with a focus on advanced GI cancers have not been reported yet. PATIENTS AND METHODS Next-generation sequencing of tumor and normal tissue pairs was performed between April 2016 and February 2018. After identification of relevant molecular alterations, available clinical studies or in-label, off-label, or matched experimental treatment options were recommended. Follow-up data and a response assessment that was based on radiologic imaging were recorded. RESULTS Ninety-six patients were presented to the MTB of Tuebingen University Hospital. Sixteen (17%) showed "pathogenic" or "likely pathogenic" germline variants. Recommendations on the basis of molecular alterations or tumor mutational burden were given for 41 patients (43%). Twenty-five received the suggested drug, and 20 were evaluable for best response assessment. Three patients (15%) reached a partial response (PR), and 6 (30%), stable disease (SD), whereas 11 (55%) had tumor progression (progressive disease). Median progression-free survival (PFS) for all treated and evaluable patients was 2.8 months (range, 1.0-9.0 months), and median overall survival (OS) of all treated patients was 5.2 months (range, 0.1 months to not reached). Patients with SD for ≥ 3 months or PR compared with progressive disease showed both a statistically significant longer median PFS (7.8 months [95% CI, 4.2 to 11.4 months] v 2.2 months [95% CI, 1.5 to 2.8 months], P < .0001) and median OS (18.0 months [95% CI, 10.4 to 25.6 months] v 3.8 months [95% CI, 2.3 to 5.4 months], P < .0001). CONCLUSION Next-generation sequencing diagnostics of advanced GI cancers identified a substantial number of pathogenic or likely pathogenic germline variants and unique individual treatment options. Patients with PR or SD in the course of MTB-recommended treatments seemed to benefit with respect to PFS and OS.
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Affiliation(s)
- Michael Bitzer
- Department of Internal Medicine I, Eberhard-Karls University, Tuebingen, Germany
- Cluster of Excellence, Image Guided and Functionally Instructed Tumor Therapies, Eberhard-Karls University, Tuebingen, Germany
- Center for Personalized Medicine, Eberhard-Karls University, Tuebingen, Germany
| | - Leonie Ostermann
- Department of Internal Medicine I, Eberhard-Karls University, Tuebingen, Germany
| | - Marius Horger
- Department of Diagnostic and Interventional Radiology, Eberhard-Karls University, Tuebingen, Germany
| | - Saskia Biskup
- CeGaT GmbH and Praxis für Humangenetik, Tuebingen, Germany
| | - Martin Schulze
- CeGaT GmbH and Praxis für Humangenetik, Tuebingen, Germany
| | - Kristina Ruhm
- Center for Personalized Medicine, Eberhard-Karls University, Tuebingen, Germany
| | - Franz Hilke
- Institute of Medical Genetics and Applied Genomics, Eberhard-Karls University, Tuebingen, Germany
| | - Öznur Öner
- Center for Personalized Medicine, Eberhard-Karls University, Tuebingen, Germany
| | - Konstantin Nikolaou
- Cluster of Excellence, Image Guided and Functionally Instructed Tumor Therapies, Eberhard-Karls University, Tuebingen, Germany
- Department of Diagnostic and Interventional Radiology, Eberhard-Karls University, Tuebingen, Germany
| | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, Eberhard-Karls University, Tuebingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, Eberhard-Karls University, Tuebingen, Germany
| | - Falko Fend
- Institute of Pathology and Neuropathology, Eberhard-Karls University, Tuebingen, Germany
- German Cancer Research Consortium, German Cancer Research Center, Heidelberg, Germany
| | - Daniel Zips
- German Cancer Research Consortium, German Cancer Research Center, Heidelberg, Germany
- Department of Radiation Oncology, Eberhard-Karls University, Tuebingen, Germany
| | | | - Lars Zender
- Cluster of Excellence, Image Guided and Functionally Instructed Tumor Therapies, Eberhard-Karls University, Tuebingen, Germany
- German Cancer Research Consortium, German Cancer Research Center, Heidelberg, Germany
- Department of Internal Medicine VIII, Eberhard-Karls University, Tuebingen, Germany
| | - Ghazaleh Tabatabai
- Cluster of Excellence, Image Guided and Functionally Instructed Tumor Therapies, Eberhard-Karls University, Tuebingen, Germany
- German Cancer Research Consortium, German Cancer Research Center, Heidelberg, Germany
- Interdisciplinary Division of Neuro-Oncology, Eberhard-Karls University, Tuebingen, Germany
| | - Janina Beha
- Center for Personalized Medicine, Eberhard-Karls University, Tuebingen, Germany
| | - Nisar P. Malek
- Department of Internal Medicine I, Eberhard-Karls University, Tuebingen, Germany
- Cluster of Excellence, Image Guided and Functionally Instructed Tumor Therapies, Eberhard-Karls University, Tuebingen, Germany
- Center for Personalized Medicine, Eberhard-Karls University, Tuebingen, Germany
- German Cancer Research Consortium, German Cancer Research Center, Heidelberg, Germany
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Pharmacogenomics, biomarker network, and allele frequencies in colorectal cancer. THE PHARMACOGENOMICS JOURNAL 2019; 20:136-158. [PMID: 31616044 DOI: 10.1038/s41397-019-0102-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 09/09/2019] [Accepted: 10/02/2019] [Indexed: 02/06/2023]
Abstract
Colorectal cancer is one of the leading causes of cancer death worldwide. Over the last decades, several studies have shown that tumor-related genomic alterations predict tumor prognosis, drug response, and toxicity. These observations have led to the development of several therapies based on individual genomic profiles. As part of these approaches, pharmacogenomics analyses genomic alterations which may predict an efficient therapeutic response. Studying these mutations as biomarkers for predicting drug response is of a great interest to improve precision medicine. We conduct a comprehensive review of the main pharmacogenomics biomarkers and genomic alterations affecting enzyme activity, transporter capacity, channels, and receptors; and therefore the new advances in CRC precision medicine to select the best therapeutic strategy in populations worldwide, with a focus on Latin America.
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