1
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Lynch A, Bradford S, Burkard ME. The reckoning of chromosomal instability: past, present, future. Chromosome Res 2024; 32:2. [PMID: 38367036 DOI: 10.1007/s10577-024-09746-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 01/11/2024] [Accepted: 01/27/2024] [Indexed: 02/19/2024]
Abstract
Quantitative measures of CIN are crucial to our understanding of its role in cancer. Technological advances have changed the way CIN is quantified, offering increased accuracy and insight. Here, we review measures of CIN through its rise as a field, discuss considerations for its measurement, and look forward to future quantification of CIN.
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Affiliation(s)
- Andrew Lynch
- UW Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI, USA
- Division of Hematology/Oncology, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Shermineh Bradford
- UW Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI, USA
- Division of Hematology/Oncology, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Mark E Burkard
- UW Carbone Cancer Center, University of Wisconsin, Madison, WI, USA.
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI, USA.
- Division of Hematology/Oncology, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA.
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2
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Te Groen M, Derikx LAAP, van Lierop L, Ylstra B, Hoentjen F, Nagtegaal ID, Simmer F. Clonal Patterns Between Pouch Neoplasia and Prior Colorectal Neoplasia in Inflammatory Bowel Disease Patients: An Exploratory Cohort Study. Inflamm Bowel Dis 2023:izad112. [PMID: 37327081 PMCID: PMC10393204 DOI: 10.1093/ibd/izad112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Indexed: 06/18/2023]
Abstract
Lay Summary
Prior colorectal neoplasia is the strongest predictor of pouch neoplasia in inflammatory bowel disease, but the underlying mechanism is unknown. We observed clonality between colorectal and pouch neoplasia in 30% of patients, indicating that most pouch neoplasia develops clonally independent from prior colorectal lesions.
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Affiliation(s)
- Maarten Te Groen
- Department of Gastroenterology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lauranne A A P Derikx
- Department of Gastroenterology, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Gastroenterology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Lisa van Lierop
- Department of Gastroenterology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Bauke Ylstra
- Department of Pathology, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Frank Hoentjen
- Department of Gastroenterology, Radboud University Medical Center, Nijmegen, the Netherlands
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Femke Simmer
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
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3
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Ter Brugge P, Moser SC, Bièche I, Kristel P, Ibadioune S, Eeckhoutte A, de Bruijn R, van der Burg E, Lutz C, Annunziato S, de Ruiter J, Masliah Planchon J, Vacher S, Courtois L, El-Botty R, Dahmani A, Montaudon E, Morisset L, Sourd L, Huguet L, Derrien H, Nemati F, Chateau-Joubert S, Larcher T, Salomon A, Decaudin D, Reyal F, Coussy F, Popova T, Wesseling J, Stern MH, Jonkers J, Marangoni E. Homologous recombination deficiency derived from whole-genome sequencing predicts platinum response in triple-negative breast cancers. Nat Commun 2023; 14:1958. [PMID: 37029129 PMCID: PMC10082194 DOI: 10.1038/s41467-023-37537-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 03/22/2023] [Indexed: 04/09/2023] Open
Abstract
The high frequency of homologous recombination deficiency (HRD) is the main rationale of testing platinum-based chemotherapy in triple-negative breast cancer (TNBC), however, the existing methods to identify HRD are controversial and there is a medical need for predictive biomarkers. We assess the in vivo response to platinum agents in 55 patient-derived xenografts (PDX) of TNBC to identify determinants of response. The HRD status, determined from whole genome sequencing, is highly predictive of platinum response. BRCA1 promoter methylation is not associated with response, in part due to residual BRCA1 gene expression and homologous recombination proficiency in different tumours showing mono-allelic methylation. Finally, in 2 cisplatin sensitive tumours we identify mutations in XRCC3 and ORC1 genes that are functionally validated in vitro. In conclusion, our results demonstrate that the genomic HRD is predictive of platinum response in a large cohort of TNBC PDX and identify alterations in XRCC3 and ORC1 genes driving cisplatin response.
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Affiliation(s)
- Petra Ter Brugge
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Sarah C Moser
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ivan Bièche
- Genetics Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Petra Kristel
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Sabrina Ibadioune
- Genetics Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Alexandre Eeckhoutte
- INSERM U830, Institut Curie, PSL University, 75005, Paris, France
- Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Roebi de Bruijn
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Eline van der Burg
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Catrin Lutz
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Stefano Annunziato
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Julian de Ruiter
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Sophie Vacher
- Genetics Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Laura Courtois
- Genetics Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Rania El-Botty
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Ahmed Dahmani
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Elodie Montaudon
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Ludivine Morisset
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Laura Sourd
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Léa Huguet
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Heloise Derrien
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Fariba Nemati
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | | | | | - Anne Salomon
- Department of Pathology, Institut Curie, PSL University, 75005, Paris, France
| | - Didier Decaudin
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Fabien Reyal
- Department of Surgery, Institut Curie, PSL University, 75005, Paris, France
| | - Florence Coussy
- Department of Medical Oncology, Institut Curie, PSL University, 75005, Paris, France
| | - Tatiana Popova
- INSERM U830, Institut Curie, PSL University, 75005, Paris, France
- Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Jelle Wesseling
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Marc-Henri Stern
- Genetics Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
- INSERM U830, Institut Curie, PSL University, 75005, Paris, France
- Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands.
| | - Elisabetta Marangoni
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL University, 26 Rue d'Ulm, 75005, Paris, France.
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4
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Frigola J, Carbonell C, Iranzo P, Pardo N, Callejo A, Cedres S, Martinez-Marti A, Navarro A, Soleda M, Jimenez J, Hernandez-Losa J, Vivancos A, Felip E, Amat R. High levels of chromosomal aberrations negatively associate with benefit to checkpoint inhibition in NSCLC. J Immunother Cancer 2022; 10:jitc-2021-004197. [PMID: 35477861 PMCID: PMC9047699 DOI: 10.1136/jitc-2021-004197] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Immune checkpoint inhibitors (ICIs) targeting the programmed cell death 1/programmed death-ligand 1 axis have transformed the management of advanced non-small cell lung cancer (NSCLC). However, many patients do not benefit from this type of treatment, and thus several molecular biomarkers of benefit have been explored. The value of somatic copy number alterations (SCNAs) burden remains elusive. PATIENTS AND METHODS We assembled a cohort of 109 patients with NSCLC treated with ICIs and available tumor samples. We performed shallow whole-genome sequencing on 89 patients to determine genome-wide SCNAs and targeted gene expression analysis on 63 patients to study immune infiltration. We analyzed SCNAs burden in different ways (ie, the fraction of the genome altered or number of events) and studied their association with ICIs benefit based on survival analysis. We correlated SCNAs burden and immune infiltration on 35 patients of our cohort and on patients with lung adenocarcinoma from The Cancer Genome Atlas (TCGA). RESULTS High SCNAs burden, computed in diverse ways, is negatively associated with ICIs progression-free survival (PFS), with the fraction of the genome altered (FGA) by arm and chromosome events showing the strongest association with PFS (p=0.002) (n=77). Nevertheless, we found differences in SCNAs across some clinicopathological features (sample site origin). A multivariate analysis adjusted for relevant characteristics showed that the FGA of arm and chromosome alterations was strongly associated with PFS (HR=2.21, p=3.3 x 10-5). Finally, we confirmed that SCNAs burden negatively correlates with tumor immune infiltration (n=35), although this correlation was not found for the males studied. Similar results were observed in the TCGA cohort. CONCLUSIONS SCNAs burden is a potential biomarker of benefit to ICIs in patients with NSCLC, although there appear to be some nuances worth consideration. Further studies will be needed to establish its role as a biomarker of benefit to ICIs.
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Affiliation(s)
- Joan Frigola
- Thoracic Cancers Translational Genomics Unit, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Caterina Carbonell
- Thoracic Cancers Translational Genomics Unit, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Patricia Iranzo
- Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Nuria Pardo
- Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Ana Callejo
- Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Susana Cedres
- Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Alex Martinez-Marti
- Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Alejandro Navarro
- Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Mireia Soleda
- Thoracic Cancers Translational Genomics Unit, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Jose Jimenez
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Ana Vivancos
- Cancer Genomics Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Enriqueta Felip
- Thoracic Cancers Translational Genomics Unit, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Ramon Amat
- Thoracic Cancers Translational Genomics Unit, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain,Clinical Research Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
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5
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Chalumeau C, Carton M, Eeckhoutte A, Ballet S, Vincent-Salomon A, Vuagnat P, Bellesoeur A, Pierga JY, Stern MH, Bidard FC, Lerebours F. Oral Etoposide and Trastuzumab Use for HER2-Positive Metastatic Breast Cancer: A Retrospective Study from the Institut Curie Hospitals. Cancers (Basel) 2022; 14:2114. [PMID: 35565244 PMCID: PMC9101021 DOI: 10.3390/cancers14092114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/13/2022] [Accepted: 04/21/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The TOP2A and ERBB2 genes are co-amplified in about 40% of HER2 positive (HER2+) breast cancers. Oral etoposide (VP16), an inhibitor of topoisomerase-II (encoded by TOP2A), has demonstrated clinical activity in metastatic breast cancer (MBC). The benefit of oral VP16 combined with trastuzumab (VP16-T) in HER2+ MBC has not yet been evaluated. METHODS Patients treated at the Institut Curie Hospitals with VP16-T for HER2+ MBC were retrieved by an in silico search. Progression-free survival (PFS), overall survival (OS), response rate, prolonged PFS (defined as at least 6 months), clinical benefit, and toxicity were assessed. The co-amplification of ERBB2 and TOP2A was assessed by shallow whole genome sequencing on tumor tissue whenever available. RESULTS Forty-three patients received VP16-T after a median number of six prior treatment lines for HER2+ MBC. Median PFS and OS were 2.9 months (95% CI [2.4-4.7]) and 11.3 months (95% CI [8.3-25.0]), respectively. Three patients had a complete response, while 12/40 (30%) experienced clinical benefit. Only three patients stopped treatment for toxicity. Seven (35%) patients displayed a TOP2A/ERBB2 co-amplification. No statistically significant correlation was found between outcome and TOP2A/ERBB2 co-amplification. CONCLUSION Our analysis suggests a favorable efficacy and toxicity profile for VP16-T in patients with heavily pretreated HER2+ MBC.
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Affiliation(s)
- Clelia Chalumeau
- Department of Medical Oncology, Institut Curie, 92210 St Cloud, France; (P.V.); (F.-C.B.); (F.L.)
| | | | - Alexandre Eeckhoutte
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Institut Curie, 75248 Paris, France; (A.E.); (M.-H.S.)
- Institut Curie, PSL Research University, 75005 Paris, France
| | - Stelly Ballet
- Department of Diagnostic and Theranostic Medicine, Institut Curie, 75005 Paris, France; (S.B.); (A.V.-S.)
| | - Anne Vincent-Salomon
- Department of Diagnostic and Theranostic Medicine, Institut Curie, 75005 Paris, France; (S.B.); (A.V.-S.)
| | - Perrine Vuagnat
- Department of Medical Oncology, Institut Curie, 92210 St Cloud, France; (P.V.); (F.-C.B.); (F.L.)
| | - Audrey Bellesoeur
- Department of Medical Oncology, Institut Curie, 75005 Paris, France; (A.B.); (J.-Y.P.)
| | - Jean-Yves Pierga
- Department of Medical Oncology, Institut Curie, 75005 Paris, France; (A.B.); (J.-Y.P.)
- Health Faculty, University of Paris, 75005 Paris, France
| | - Marc-Henri Stern
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Institut Curie, 75248 Paris, France; (A.E.); (M.-H.S.)
- Institut Curie, PSL Research University, 75005 Paris, France
| | - Francois-Clement Bidard
- Department of Medical Oncology, Institut Curie, 92210 St Cloud, France; (P.V.); (F.-C.B.); (F.L.)
- UVSQ/Paris Saclay University, 78000 Versailles, France
| | - Florence Lerebours
- Department of Medical Oncology, Institut Curie, 92210 St Cloud, France; (P.V.); (F.-C.B.); (F.L.)
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6
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Shi Q, Shao K, Jia H, Cao B, Li W, Dong S, Liu J, Wu K, Liu M, Liu F, Zhou H, Lv J, Gu F, Li L, Zhu S, Li S, Li G, Fu L. Genomic alterations and evolution of cell clusters in metastatic invasive micropapillary carcinoma of the breast. Nat Commun 2022; 13:111. [PMID: 35013309 PMCID: PMC8748639 DOI: 10.1038/s41467-021-27794-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 10/25/2021] [Indexed: 11/09/2022] Open
Abstract
Invasive micropapillary carcinoma (IMPC) has very high rates of lymphovascular invasion and lymph node metastasis and has been reported in several organs. However, the genomic mechanisms underlying its metastasis are unclear. Here, we perform whole-genome sequencing of tumor cell clusters from primary IMPC and paired axillary lymph node metastases. Cell clusters in multiple lymph node foci arise from a single subclone of the primary tumor. We find evidence that the monoclonal metastatic ancestor in primary IMPC shares high frequency copy-number loss of PRDM16 and IGSF9 and the copy number gain of ALDH2. Immunohistochemistry analysis further shows that low expression of IGSF9 and PRDM16 and high expression of ALDH2 are associated with lymph node metastasis and poor survival of patients with IMPC. We expect these genomic and evolutionary profiles to contribute to the accurate diagnosis of IMPC.
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Affiliation(s)
- Qianqian Shi
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China
| | - Kang Shao
- BGI-Shenzhen, 518120, Shenzhen, China.,BGl College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, 450000, Zhengzhou, China
| | - Hongqin Jia
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China.,National Clinical Research Center for Cancer, 300060, Tianjin, China
| | - Boyang Cao
- BGI-Shenzhen, 518120, Shenzhen, China.,BGl College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, 450000, Zhengzhou, China
| | - Weidong Li
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China.,National Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, 300060, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, 300060, Tianjin, China
| | - Shichen Dong
- BGI-Shenzhen, 518120, Shenzhen, China.,BGl College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, 450000, Zhengzhou, China
| | - Jian Liu
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China.,National Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, 300060, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, 300060, Tianjin, China
| | - Kailiang Wu
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China.,National Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, 300060, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, 300060, Tianjin, China
| | - Meng Liu
- BGI-Shenzhen, 518120, Shenzhen, China.,BGl College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, 450000, Zhengzhou, China
| | - Fangfang Liu
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China.,National Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, 300060, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, 300060, Tianjin, China
| | - Hanlin Zhou
- BGI-Shenzhen, 518120, Shenzhen, China.,BGl College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, 450000, Zhengzhou, China
| | - Jianke Lv
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China.,National Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, 300060, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, 300060, Tianjin, China
| | - Feng Gu
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China.,National Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, 300060, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, 300060, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, 300060, Tianjin, China
| | - Luyuan Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, 300071, Tianjin, China
| | - Shida Zhu
- BGI-Shenzhen, 518120, Shenzhen, China.,BGl College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, 450000, Zhengzhou, China
| | - Shuai Li
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China. .,National Clinical Research Center for Cancer, 300060, Tianjin, China. .,Key Laboratory of Cancer Prevention and Therapy, 300060, Tianjin, China. .,Tianjin's Clinical Research Center for Cancer, 300060, Tianjin, China. .,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, 300060, Tianjin, China.
| | - Guibo Li
- BGI-Shenzhen, 518120, Shenzhen, China. .,BGl College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, 450000, Zhengzhou, China. .,Shenzhen Key Laboratory of Single-Cell Omics, 518120, Shenzhen, China.
| | - Li Fu
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China. .,National Clinical Research Center for Cancer, 300060, Tianjin, China. .,Key Laboratory of Cancer Prevention and Therapy, 300060, Tianjin, China. .,Tianjin's Clinical Research Center for Cancer, 300060, Tianjin, China. .,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, 300060, Tianjin, China.
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7
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Honoré N, Galot R, van Marcke C, Limaye N, Machiels JP. Liquid Biopsy to Detect Minimal Residual Disease: Methodology and Impact. Cancers (Basel) 2021; 13:5364. [PMID: 34771526 PMCID: PMC8582541 DOI: 10.3390/cancers13215364] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 12/15/2022] Open
Abstract
One reason why some patients experience recurrent disease after a curative-intent treatment might be the persistence of residual tumor cells, called minimal residual disease (MRD). MRD cannot be identified by standard radiological exams or clinical evaluation. Tumor-specific alterations found in the blood indirectly diagnose the presence of MRD. Liquid biopsies thus have the potential to detect MRD, allowing, among other things, the detection of circulating tumor DNA (ctDNA), circulating tumor cells (CTC), or tumor-specific microRNA. Although liquid biopsy is increasingly studied, several technical issues still limit its clinical applicability: low sensitivity, poor standardization or reproducibility, and lack of randomized trials demonstrating its clinical benefit. Being able to detect MRD could give clinicians a more comprehensive view of the risk of relapse of their patients and could select patients requiring treatment escalation with the goal of improving cancer survival. In this review, we are discussing the different methodologies used and investigated to detect MRD in solid cancers, their respective potentials and issues, and the clinical impacts that MRD detection will have on the management of cancer patients.
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Affiliation(s)
- Natasha Honoré
- Institute for Experimental and Clinical Research (IREC, Pôle MIRO), Université Catholique de Louvain (UCLouvain) ,1200 Brussels, Belgium; (R.G.); (C.v.M.)
| | - Rachel Galot
- Institute for Experimental and Clinical Research (IREC, Pôle MIRO), Université Catholique de Louvain (UCLouvain) ,1200 Brussels, Belgium; (R.G.); (C.v.M.)
- Department of Medical Oncology, Institut Roi Albert II, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
| | - Cédric van Marcke
- Institute for Experimental and Clinical Research (IREC, Pôle MIRO), Université Catholique de Louvain (UCLouvain) ,1200 Brussels, Belgium; (R.G.); (C.v.M.)
- Department of Medical Oncology, Institut Roi Albert II, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
| | - Nisha Limaye
- Genetics of Autoimmune Diseases and Cancer, de Duve Institute, Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium;
| | - Jean-Pascal Machiels
- Institute for Experimental and Clinical Research (IREC, Pôle MIRO), Université Catholique de Louvain (UCLouvain) ,1200 Brussels, Belgium; (R.G.); (C.v.M.)
- Department of Medical Oncology, Institut Roi Albert II, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
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8
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Lehmann U, Stenzinger A. [The molecular pathology breviary: read depth and coverage in NGS analysis]. DER PATHOLOGE 2021; 43:65-66. [PMID: 34643752 DOI: 10.1007/s00292-021-01009-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/02/2021] [Indexed: 11/24/2022]
Affiliation(s)
- Ulrich Lehmann
- Molekularpathologie, Institut für Pathologie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, OE5110, 30625, Hannover, Deutschland.
| | - Albrecht Stenzinger
- Molekularpathologisches Zentrum, Pathologisches Institut, Universität Heidelberg, Im Neuenheimer Feld 224, 69120, Heidelberg, Deutschland
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9
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Guan B, Liang Y, Lu H, Xu Z, Shi Y, Li J, Kong W, Tian C, Tan Y, Gong Y, Liu J, Fang D, Shen Q, He S, Shakeel M, Zhang Z, He Q, Li X, Ci W, Zhou L. Copy Number Signatures and Clinical Outcomes in Upper Tract Urothelial Carcinoma. Front Cell Dev Biol 2021; 9:713499. [PMID: 34513842 PMCID: PMC8427613 DOI: 10.3389/fcell.2021.713499] [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: 05/23/2021] [Accepted: 08/02/2021] [Indexed: 11/15/2022] Open
Abstract
Tumor staging of upper tract urothelial carcinomas (UTUCs) is relatively difficult to assert accurately before surgery. Here, we used copy number (CN) signatures as a tool to explore their clinical significance of molecular stratification in UTUC. CN signatures were extracted by non-negative matrix factorization from the whole-genome sequencing (WGS) data of 90 Chinese UTUC primary tumor samples. A validation UTUC cohort (n = 56) and a cohort from urinary cell-free DNA (cfDNA) of urothelial cancer patients (n = 94) and matched primary tumors were also examined. Survival analyses were measured using the Kaplan–Meier, and Cox regression was used for multivariate analysis. Here, we identified six CN signatures (Sig1–6). Patients with a high contribution of Sig6 (Sig6high) were associated with higher microsatellite instability level and papillary architecture and had a favorable outcome. Patients with a low weighted genome integrity index were associated with positive lymph node and showed the worst outcome. Sig6high was identified to be an independently prognostic factor. The predictive significance of CN signature was identified by a validation UTUC cohort. CN signatures retained great concordance between primary tumor and urinary cfDNA. In conclusion, our results reveal that CN signature assessment for risk stratification is feasible and provides a basis for clinical studies that evaluate therapeutic interventions and prognosis.
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Affiliation(s)
- Bao Guan
- Department of Urology, Peking University First Hospital, Beijing, China.,Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing, China
| | - Yuan Liang
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Huan Lu
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhengzheng Xu
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yue Shi
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Juan Li
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenwen Kong
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chuanyu Tian
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yezhen Tan
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing, China
| | - Jin Liu
- Department of Urology, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Dong Fang
- Department of Urology, Peking University First Hospital, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing, China
| | - Qi Shen
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing, China
| | - Shiming He
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing, China
| | - Muhammad Shakeel
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Jamil-ur-Rahman Center for Genome Research, PCMD, ICCBS, University of Karachi, Karachi, Pakistan
| | - Zhongyuan Zhang
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing, China
| | - Qun He
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing, China
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing, China
| | - Weimin Ci
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute of Stem cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing, China.,Institute of Urology, Peking University, Beijing, China.,Beijing Key Laboratory of Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, National Urological Cancer Center, Beijing, China
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10
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Lakatos E, Hockings H, Mossner M, Huang W, Lockley M, Graham TA. LiquidCNA: Tracking subclonal evolution from longitudinal liquid biopsies using somatic copy number alterations. iScience 2021; 24:102889. [PMID: 34401670 PMCID: PMC8350516 DOI: 10.1016/j.isci.2021.102889] [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: 04/20/2021] [Revised: 06/10/2021] [Accepted: 07/15/2021] [Indexed: 12/23/2022] Open
Abstract
Cell-free DNA (cfDNA) measured via liquid biopsies provides a way for minimally invasive monitoring of tumor evolutionary dynamics during therapy. Here we present liquidCNA, a method to track subclonal evolution from longitudinally collected cfDNA samples sequenced through cost-effective low-pass whole-genome sequencing. LiquidCNA utilizes somatic copy number alteration (SCNA) to simultaneously genotype and quantify the size of the dominant subclone without requiring B-allele frequency information, matched-normal samples, or prior knowledge on the genetic identity of the emerging clone. We demonstrate the accuracy of liquidCNA in synthetically generated sample sets and in vitro mixtures of cancer cell lines. In vivo application in patients with metastatic lung cancer reveals the progressive emergence of a novel tumor subpopulation. LiquidCNA is straightforward to use, is computationally inexpensive, and enables continuous monitoring of subclonal evolution to understand and control-therapy-induced resistance.
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Affiliation(s)
- Eszter Lakatos
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Helen Hockings
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Barts Health NHS Trust, St Bartholomew's Hospital, West Smithfield, London, UK
| | - Maximilian Mossner
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Weini Huang
- School of Mathematical Sciences, Queen Mary University of London, London, UK
| | - Michelle Lockley
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Department of Gynaecological Oncology, Cancer Services, University College London Hospital, London, UK
| | - Trevor A. Graham
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
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11
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Smolander J, Khan S, Singaravelu K, Kauko L, Lund RJ, Laiho A, Elo LL. Evaluation of tools for identifying large copy number variations from ultra-low-coverage whole-genome sequencing data. BMC Genomics 2021; 22:357. [PMID: 34000988 PMCID: PMC8130438 DOI: 10.1186/s12864-021-07686-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 05/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Detection of copy number variations (CNVs) from high-throughput next-generation whole-genome sequencing (WGS) data has become a widely used research method during the recent years. However, only a little is known about the applicability of the developed algorithms to ultra-low-coverage (0.0005-0.8×) data that is used in various research and clinical applications, such as digital karyotyping and single-cell CNV detection. RESULT Here, the performance of six popular read-depth based CNV detection algorithms (BIC-seq2, Canvas, CNVnator, FREEC, HMMcopy, and QDNAseq) was studied using ultra-low-coverage WGS data. Real-world array- and karyotyping kit-based validation were used as a benchmark in the evaluation. Additionally, ultra-low-coverage WGS data was simulated to investigate the ability of the algorithms to identify CNVs in the sex chromosomes and the theoretical minimum coverage at which these tools can accurately function. Our results suggest that while all the methods were able to detect large CNVs, many methods were susceptible to producing false positives when smaller CNVs (< 2 Mbp) were detected. There was also significant variability in their ability to identify CNVs in the sex chromosomes. Overall, BIC-seq2 was found to be the best method in terms of statistical performance. However, its significant drawback was by far the slowest runtime among the methods (> 3 h) compared with FREEC (~ 3 min), which we considered the second-best method. CONCLUSIONS Our comparative analysis demonstrates that CNV detection from ultra-low-coverage WGS data can be a highly accurate method for the detection of large copy number variations when their length is in millions of base pairs. These findings facilitate applications that utilize ultra-low-coverage CNV detection.
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Affiliation(s)
- Johannes Smolander
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Sofia Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Kalaimathy Singaravelu
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Leni Kauko
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Riikka J Lund
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland.
- Institute of Biomedicine, University of Turku, 20520, Turku, Finland.
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12
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Tarabichi M, Salcedo A, Deshwar AG, Leathlobhair MN, Wintersinger J, Wedge DC, Loo PV, Morris QD, Boutros PC. A practical guide to cancer subclonal reconstruction from DNA sequencing. Nat Methods 2021; 18:144-155. [PMID: 33398189 PMCID: PMC7867630 DOI: 10.1038/s41592-020-01013-2] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 11/09/2020] [Indexed: 01/28/2023]
Abstract
Subclonal reconstruction from bulk tumor DNA sequencing has become a pillar of cancer evolution studies, providing insight into the clonality and relative ordering of mutations and mutational processes. We provide an outline of the complex computational approaches used for subclonal reconstruction from single and multiple tumor samples. We identify the underlying assumptions and uncertainties in each step and suggest best practices for analysis and quality assessment. This guide provides a pragmatic resource for the growing user community of subclonal reconstruction methods.
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Affiliation(s)
- Maxime Tarabichi
- The Francis Crick Institute, London, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Adriana Salcedo
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Department of Human Genetics, University of California, Los Angeles
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles
- Institute for Precision Health, University of California, Los Angeles
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Amit G. Deshwar
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering, University of Toronto, Toronto, Canada
| | - Máire Ni Leathlobhair
- Big Data Institute, University of Oxford, Oxford, United Kingdom
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Jeff Wintersinger
- Department of Computer Science, University of Toronto, Toronto, Canada
| | - David C. Wedge
- Big Data Institute, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, Oxford, United Kingdom
- Manchester Cancer Research Centre, University of Manchester, Manchester, United Kingdom
| | | | - Quaid D. Morris
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
- Vector Institute, Toronto, Canada
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York
- Donnelly Centre, University of Toronto, Toronto, Canada
| | - Paul C. Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Department of Human Genetics, University of California, Los Angeles
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles
- Institute for Precision Health, University of California, Los Angeles
- Vector Institute, Toronto, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada
- Department of Urology, David Geffen School of Medicine, University of California, Los Angeles
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13
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Hänsel-Hertsch R, Simeone A, Shea A, Hui WWI, Zyner KG, Marsico G, Rueda OM, Bruna A, Martin A, Zhang X, Adhikari S, Tannahill D, Caldas C, Balasubramanian S. Landscape of G-quadruplex DNA structural regions in breast cancer. Nat Genet 2020; 52:878-883. [PMID: 32747825 DOI: 10.1038/s41588-020-0672-8] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 06/25/2020] [Indexed: 12/25/2022]
Abstract
Response and resistance to anticancer therapies vary due to intertumor and intratumor heterogeneity1. Here, we map differentially enriched G-quadruplex (G4) DNA structure-forming regions (∆G4Rs) in 22 breast cancer patient-derived tumor xenograft (PDTX) models. ∆G4Rs are associated with the promoters of highly amplified genes showing high expression, and with somatic single-nucleotide variants. Differences in ΔG4R landscapes reveal seven transcription factor programs across PDTXs. ∆G4R abundance and locations stratify PDTXs into at least three G4-based subtypes. ∆G4Rs in most PDTXs (14 of 22) were found to associate with more than one breast cancer subtype, which we also call an integrative cluster (IC)2. This suggests the frequent coexistence of multiple breast cancer states within a PDTX model, the majority of which display aggressive triple-negative IC10 gene activity. Short-term cultures of PDTX models with increased ∆G4R levels are more sensitive to small molecules targeting G4 DNA. Thus, G4 landscapes reveal additional IC-related intratumor heterogeneity in PDTX biopsies, improving breast cancer stratification and potentially identifying new treatment strategies.
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Affiliation(s)
- Robert Hänsel-Hertsch
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital Cologne, Cologne, Germany
- Institute of Human Genetics, University Hospital Cologne, Cologne, Germany
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Angela Simeone
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Abigail Shea
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Winnie W I Hui
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Katherine G Zyner
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Giovanni Marsico
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Inivata, Babraham Research Campus, Cambridge, UK
| | - Oscar M Rueda
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Alejandra Bruna
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- The Institute of Cancer Research, London, UK
| | - Alistair Martin
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Xiaoyun Zhang
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - David Tannahill
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Cambridge Breast Cancer Research Unit, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
- Cancer Research UK Cambridge Centre, NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK.
- Department of Chemistry, University of Cambridge, Cambridge, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, UK.
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14
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Dlamini Z, Francies FZ, Hull R, Marima R. Artificial intelligence (AI) and big data in cancer and precision oncology. Comput Struct Biotechnol J 2020; 18:2300-2311. [PMID: 32994889 PMCID: PMC7490765 DOI: 10.1016/j.csbj.2020.08.019] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/21/2020] [Accepted: 08/21/2020] [Indexed: 02/07/2023] Open
Abstract
Artificial intelligence (AI) and machine learning have significantly influenced many facets of the healthcare sector. Advancement in technology has paved the way for analysis of big datasets in a cost- and time-effective manner. Clinical oncology and research are reaping the benefits of AI. The burden of cancer is a global phenomenon. Efforts to reduce mortality rates requires early diagnosis for effective therapeutic interventions. However, metastatic and recurrent cancers evolve and acquire drug resistance. It is imperative to detect novel biomarkers that induce drug resistance and identify therapeutic targets to enhance treatment regimes. The introduction of the next generation sequencing (NGS) platforms address these demands, has revolutionised the future of precision oncology. NGS offers several clinical applications that are important for risk predictor, early detection of disease, diagnosis by sequencing and medical imaging, accurate prognosis, biomarker identification and identification of therapeutic targets for novel drug discovery. NGS generates large datasets that demand specialised bioinformatics resources to analyse the data that is relevant and clinically significant. Through these applications of AI, cancer diagnostics and prognostic prediction are enhanced with NGS and medical imaging that delivers high resolution images. Regardless of the improvements in technology, AI has some challenges and limitations, and the clinical application of NGS remains to be validated. By continuing to enhance the progression of innovation and technology, the future of AI and precision oncology show great promise.
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Affiliation(s)
- Zodwa Dlamini
- SAMRC/UP Precision Prevention & Novel Drug Targets for HIV-Associated Cancers (PPNDTHAC) Extramural Unit, Pan African Cancer Research Institute (PACRI), University of Pretoria, Faculty of Health Sciences, Hatfield 0028, South Africa
| | - Flavia Zita Francies
- SAMRC/UP Precision Prevention & Novel Drug Targets for HIV-Associated Cancers (PPNDTHAC) Extramural Unit, Pan African Cancer Research Institute (PACRI), University of Pretoria, Faculty of Health Sciences, Hatfield 0028, South Africa
| | - Rodney Hull
- SAMRC/UP Precision Prevention & Novel Drug Targets for HIV-Associated Cancers (PPNDTHAC) Extramural Unit, Pan African Cancer Research Institute (PACRI), University of Pretoria, Faculty of Health Sciences, Hatfield 0028, South Africa
| | - Rahaba Marima
- SAMRC/UP Precision Prevention & Novel Drug Targets for HIV-Associated Cancers (PPNDTHAC) Extramural Unit, Pan African Cancer Research Institute (PACRI), University of Pretoria, Faculty of Health Sciences, Hatfield 0028, South Africa
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15
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A Novel Approach for the Genetic Analysis of Biliary Tract Cancer Specimens Obtained Through Endoscopic Ultrasound-Guided Fine Needle Aspiration Using Targeted Amplicon Sequencing. Clin Transl Gastroenterol 2020; 10:e00022. [PMID: 30908307 PMCID: PMC6445609 DOI: 10.14309/ctg.0000000000000022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Biliary tract cancer (BTC) is an aggressive malignant tumor, and biomarker-based clinical trials for this cancer are currently ongoing. Endoscopic ultrasound–guided fine needle aspiration (EUS-FNA) is a safe procedure and enables pathological diagnoses; however, it is uncertain whether a tiny tumor sample of BTC obtained through EUS-FNA can be analyzed for diverse genetic alterations in the development and tolerance of BTC. Thus, we aimed to verify the feasibility of genetic analyses with EUS-FNA samples of BTC.
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16
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Buedts L, Smits S, Ameye G, Lehnert S, Ding J, Delforge M, Vermeesch J, Boeckx N, Tousseyn T, Michaux L, Vandenberghe P, Dewaele B. Ultra-low depth sequencing of plasma cell DNA for the detection of copy number aberrations in multiple myeloma. Genes Chromosomes Cancer 2020; 59:465-471. [PMID: 32259320 DOI: 10.1002/gcc.22848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 03/22/2020] [Accepted: 04/01/2020] [Indexed: 12/31/2022] Open
Abstract
Cytogenetic abnormalities are powerful prognostic factors in multiple myeloma (MM) and are routinely analyzed by FISH on bone marrow (BM) plasma cells (PC). Although considered the gold standard, FISH experiments can be laborious and expensive. Therefore, array-CGH (aCGH) has been introduced as an alternative approach for detecting copy number aberrations (CNA), reducing the number of FISH experiments per case and yielding genome-wide information. Currently, next generation sequencing (NGS) technologies offer new perspectives for the diagnostic workup of malignant disorders. In this study, we examined ultra-low depth whole genome sequencing (LDS) as a valid alternative for aCGH for the detection of CNA in BM PC in MM. To this end, BM aspirates obtained in a diagnostic setting from 20 MM cases were analyzed. CD138+ cell-sorted samples were subjected to FISH analysis. DNA was extracted for subsequent aCGH and LDS analysis. CNA were detected by aCGH and LDS in all but one case. Importantly, all CNA identified by parallel first generation aCGH analysis were also detected by LDS, along with six additional CNA in five cases. One of these additional aberrations was in a region of prognostic importance in MM and was confirmed using FISH. However, risk stratification in these particular cases was unaffected. Thus, a perfectly concordant prognostication between array-CGH and LDS was observed. This validates LDS as a novel and cost-efficient tool for the detection of CNA in MM.
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Affiliation(s)
| | - Sanne Smits
- Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Geneviève Ameye
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | | - Jia Ding
- Genomics Core, KU Leuven, Leuven, Belgium
| | - Michel Delforge
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Joris Vermeesch
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium.,Genomics Core, KU Leuven, Leuven, Belgium
| | - Nancy Boeckx
- Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium.,Department of Oncology, KU Leuven, Leuven, Belgium
| | - Thomas Tousseyn
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Lucienne Michaux
- Center for Human Genetics, KU Leuven, Leuven, Belgium.,Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Peter Vandenberghe
- Center for Human Genetics, KU Leuven, Leuven, Belgium.,Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Barbara Dewaele
- Center for Human Genetics, KU Leuven, Leuven, Belgium.,Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
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17
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Van der Linden M, Raman L, Vander Trappen A, Dheedene A, De Smet M, Sante T, Creytens D, Lievens Y, Menten B, Van Dorpe J, Van Roy N. Detection of Copy Number Alterations by Shallow Whole-Genome Sequencing of Formalin-Fixed, Paraffin-Embedded Tumor Tissue. Arch Pathol Lab Med 2019; 144:974-981. [PMID: 31846367 DOI: 10.5858/arpa.2019-0010-oa] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— In routine clinical practice, tumor tissue is stored in formalin-fixed, paraffin-embedded blocks. However, the use of formalin-fixed, paraffin-embedded tissue for genome analysis is challenged by poorer DNA quality and quantity. Although several studies have reported genome-wide massive parallel sequencing applied on formalin-fixed, paraffin-embedded samples for mutation analysis, copy number analysis is not yet commonly performed. OBJECTIVE.— To evaluate the use of formalin-fixed, paraffin-embedded tissue for copy number alteration detection using shallow whole-genome sequencing, more generally referred to as copy number variation sequencing. DESIGN.— We selected samples from 21 patients, covering a range of different tumor entities. The performance of copy number detection was compared across 3 setups: array comparative genomic hybridization in combination with fresh material; copy number variation sequencing on fresh material; and copy number variation sequencing on formalin-fixed, paraffin-embedded material. RESULTS.— Very similar copy number profiles between paired samples were obtained. Although formalin-fixed, paraffin-embedded profiles often displayed more noise, detected copy numbers seemed equally reliable if the tumor fraction was at least 20%. CONCLUSIONS.— Copy number variation sequencing of formalin-fixed, paraffin-embedded material represents a trustworthy method. It is very likely that copy number variation sequencing of routinely obtained biopsy material will become important for individual patient care and research. Moreover, the basic technology needed for copy number variation sequencing is present in most molecular diagnostics laboratories.
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Affiliation(s)
- Malaïka Van der Linden
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Lennart Raman
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Ansel Vander Trappen
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Annelies Dheedene
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Matthias De Smet
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Tom Sante
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - David Creytens
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Yolande Lievens
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Björn Menten
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Jo Van Dorpe
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
| | - Nadine Van Roy
- From the Department of Pathology (Ms Van der Linden, Mr Raman, and Drs Creytens and Van Dorpe), the Center for Medical Genetics Ghent (Messrs Vander Trappen and De Smet and Drs Dheedene, Sante, Menten and Van Roy), and the Department of Radiation Oncology (Dr Lievens), Ghent University Hospital, Ghent, Belgium; and Cancer Research Institute Ghent, Ghent, Belgium (Ms Van der Linden and Drs Creytens, Lievens, Menten, Van Dorpe, and Van Roy)
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Raman L, Dheedene A, De Smet M, Van Dorpe J, Menten B. WisecondorX: improved copy number detection for routine shallow whole-genome sequencing. Nucleic Acids Res 2019; 47:1605-1614. [PMID: 30566647 PMCID: PMC6393301 DOI: 10.1093/nar/gky1263] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/09/2018] [Accepted: 12/06/2018] [Indexed: 12/16/2022] Open
Abstract
Shallow whole-genome sequencing to infer copy number alterations (CNAs) in the human genome is rapidly becoming the method par excellence for routine diagnostic use. Numerous tools exist to deduce aberrations from massive parallel sequencing data, yet most are optimized for research and often fail to redeem paramount needs in a clinical setting. Optimally, a read depth-based analytical software should be able to deal with single-end and low-coverage data-this to make sequencing costs feasible. Other important factors include runtime, applicability to a variety of analyses and overall performance. We compared the most important aspect, being normalization, across six different CNA tools, selected for their assumed ability to satisfy the latter needs. In conclusion, WISECONDOR, which uses a within-sample normalization technique, undoubtedly produced the best results concerning variance, distributional assumptions and basic ability to detect true variations. Nonetheless, as is the case with every tool, WISECONDOR has limitations, which arise through its exclusiveness for non-invasive prenatal testing. Therefore, this work presents WisecondorX in addition, an improved WISECONDOR that enables its use for varying types of applications. WisecondorX is freely available at https://github.com/CenterForMedicalGeneticsGhent/WisecondorX.
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Affiliation(s)
- Lennart Raman
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium
- Center for Medical Genetics Ghent, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Annelies Dheedene
- Center for Medical Genetics Ghent, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Matthias De Smet
- Center for Medical Genetics Ghent, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University, Ghent University Hospital, Ghent, Belgium
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Stewart CM, Tsui DWY. Circulating cell-free DNA for non-invasive cancer management. Cancer Genet 2018; 228-229:169-179. [PMID: 29625863 PMCID: PMC6598437 DOI: 10.1016/j.cancergen.2018.02.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/19/2018] [Accepted: 02/23/2018] [Indexed: 01/06/2023]
Abstract
Cell-free DNA (cfDNA) was first identified in human plasma in 1948 and is thought to be released from cells throughout the body into the circulatory system. In cancer, a portion of the cfDNA originates from tumour cells, referred to as circulating-tumour DNA (ctDNA), and can contain mutations corresponding to the patient's tumour, for instance specific TP53 alleles. Profiling of cfDNA has recently become an area of increasing clinical relevance in oncology, in particular due to advances in the sensitivity of molecular biology techniques and development of next generation sequencing technologies, as this allows tumour mutations to be identified and tracked non-invasively. This has opened up new possibilities for monitoring tumour evolution and acquisition of resistance, as well as for guiding treatment decisions when tumour biopsy tissue is insufficient or unavailable. In this review, we will discuss the biology of cell-free nucleic acids, methods of analysis, and the potential clinical uses of these techniques, as well as the on-going clinical development of ctDNA assays.
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Affiliation(s)
- Caitlin M Stewart
- Marie-José and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 20, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana W Y Tsui
- Marie-José and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 20, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Lopez JV, Kamel B, Medina M, Collins T, Baums IB. Multiple Facets of Marine Invertebrate Conservation Genomics. Annu Rev Anim Biosci 2018; 7:473-497. [PMID: 30485758 DOI: 10.1146/annurev-animal-020518-115034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Conservation genomics aims to preserve the viability of populations and the biodiversity of living organisms. Invertebrate organisms represent 95% of animal biodiversity; however, few genomic resources currently exist for the group. The subset of marine invertebrates includes the most ancient metazoan lineages and possesses codes for unique gene products and possible keys to adaptation. The benefits of supporting invertebrate conservation genomics research (e.g., likely discovery of novel genes, protein regulatory mechanisms, genomic innovations, and transposable elements) outweigh the various hurdles (rare, small, or polymorphic starting materials). Here we review best conservation genomics practices in the laboratory and in silico when applied to marine invertebrates and also showcase unique features in several case studies of acroporid corals, crown-of-thorns starfish, apple snails, and abalone. Marine conservation genomics should also address how diversity can lead to unique marine innovations, the impact of deleterious variation, and how genomic monitoring and profiling could positively affect broader conservation goals (e.g., value of baseline data for in situ/ex situ genomic stocks).
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Affiliation(s)
- Jose V Lopez
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, Florida 33004, USA;
| | - Bishoy Kamel
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, New Mexico 87131, USA;
| | - Mónica Medina
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; ,
| | - Timothy Collins
- Department of Biological Sciences, Florida International University, Miami, Florida 33199, USA;
| | - Iliana B Baums
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; ,
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