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Carey-Smith SL, Kotecha RS, Cheung LC, Malinge S. Insights into the Clinical, Biological and Therapeutic Impact of Copy Number Alteration in Cancer. Int J Mol Sci 2024; 25:6815. [PMID: 38999925 PMCID: PMC11241182 DOI: 10.3390/ijms25136815] [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: 05/21/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 07/14/2024] Open
Abstract
Copy number alterations (CNAs), resulting from the gain or loss of genetic material from as little as 50 base pairs or as big as entire chromosome(s), have been associated with many congenital diseases, de novo syndromes and cancer. It is established that CNAs disturb the dosage of genomic regions including enhancers/promoters, long non-coding RNA and gene(s) among others, ultimately leading to an altered balance of key cellular functions. In cancer, CNAs have been associated with almost all steps of the disease: predisposition, initiation, development, maintenance, response to treatment, resistance, and relapse. Therefore, understanding how specific CNAs contribute to tumourigenesis may provide prognostic insight and ultimately lead to the development of new therapeutic approaches to improve patient outcomes. In this review, we provide a snapshot of what is currently known about CNAs and cancer, incorporating topics regarding their detection, clinical impact, origin, and nature, and discuss the integration of innovative genetic engineering strategies, to highlight the potential for targeting CNAs using novel, dosage-sensitive and less toxic therapies for CNA-driven cancer.
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Affiliation(s)
- Shannon L. Carey-Smith
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
| | - Rishi S. Kotecha
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
- Department of Clinical Haematology, Oncology, Blood and Marrow Transplantation, Perth Children’s Hospital, Perth, WA 6009, Australia
- UWA Medical School, University of Western Australia, Perth, WA 6009, Australia
| | - Laurence C. Cheung
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Sébastien Malinge
- Telethon Kids Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia; (S.L.C.-S.); (R.S.K.); (L.C.C.)
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
- UWA Medical School, University of Western Australia, Perth, WA 6009, Australia
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Han SH, Camp SY, Chu H, Collins R, Gillani R, Park J, Bakouny Z, Ricker CA, Reardon B, Moore N, Kofman E, Labaki C, Braun D, Choueiri TK, AlDubayan SH, Van Allen EM. Integrative Analysis of Germline Rare Variants in Clear and Non-clear Cell Renal Cell Carcinoma. EUR UROL SUPPL 2024; 62:107-122. [PMID: 38496821 PMCID: PMC10940785 DOI: 10.1016/j.euros.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2024] [Indexed: 03/19/2024] Open
Abstract
Background and objective Previous germline studies on renal cell carcinoma (RCC) have usually pooled clear and non-clear cell RCCs and have not adequately accounted for population stratification, which might have led to an inaccurate estimation of genetic risk. Here, we aim to analyze the major germline drivers of RCC risk and clinically relevant but underexplored germline variant types. Methods We first characterized germline pathogenic variants (PVs), cryptic splice variants, and copy number variants (CNVs) in 1436 unselected RCC patients. To evaluate the enrichment of PVs in RCC, we conducted a case-control study of 1356 RCC patients ancestry matched with 16 512 cancer-free controls using approaches accounting for population stratification and histological subtypes, followed by characterization of secondary somatic events. Key findings and limitations Clear cell RCC patients (n = 976) exhibited a significant burden of PVs in VHL compared with controls (odds ratio [OR]: 39.1, p = 4.95e-05). Non-clear cell RCC patients (n = 380) carried enrichment of PVs in FH (OR: 77.9, p = 1.55e-08) and MET (OR: 1.98e11, p = 2.07e-05). In a CHEK2-focused analysis with European participants, clear cell RCC (n = 906) harbored nominal enrichment of low-penetrance CHEK2 variants-p.Ile157Thr (OR: 1.84, p = 0.049) and p.Ser428Phe (OR: 5.20, p = 0.045), while non-clear cell RCC (n = 295) exhibited nominal enrichment of CHEK2 loss of function PVs (OR: 3.51, p = 0.033). Patients with germline PVs in FH, MET, and VHL exhibited significantly earlier age of cancer onset than patients without germline PVs (mean: 46.0 vs 60.2 yr, p < 0.0001), and more than half had secondary somatic events affecting the same gene (n = 10/15, 66.7%). Conversely, CHEK2 PV carriers exhibited a similar age of onset to patients without germline PVs (mean: 60.1 vs 60.2 yr, p = 0.99), and only 30.4% carried somatic events in CHEK2 (n = 7/23). Finally, pathogenic germline cryptic splice variants were identified in SDHA and TSC1, and pathogenic germline CNVs were found in 18 patients, including CNVs in FH, SDHA, and VHL. Conclusions and clinical implications This analysis supports the existing link between several RCC risk genes and RCC risk manifesting in earlier age of onset. It calls for caution when assessing the role of CHEK2 due to the burden of founder variants with varying population frequency. It also broadens the definition of the RCC germline landscape of pathogenicity to incorporate previously understudied types of germline variants. Patient summary In this study, we carefully compared the frequency of rare inherited mutations with a focus on patients' genetic ancestry. We discovered that subtle variations in genetic background may confound a case-control analysis, especially in evaluating the cancer risk associated with specific genes, such as CHEK2. We also identified previously less explored forms of rare inherited mutations, which could potentially increase the risk of kidney cancer.
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Affiliation(s)
- Seung Hun Han
- Ph.D. Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sabrina Y. Camp
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hoyin Chu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan Collins
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Riaz Gillani
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Jihye Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ziad Bakouny
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cora A. Ricker
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brendan Reardon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicholas Moore
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
| | - Eric Kofman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Chris Labaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - David Braun
- Center of Molecular and Cellular Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Toni K. Choueiri
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Brigham and Women’s Hospital, Boston, MA, USA
| | - Saud H. AlDubayan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA, USA
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Eliezer M. Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
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Oketch DJA, Giulietti M, Piva F. Copy Number Variations in Pancreatic Cancer: From Biological Significance to Clinical Utility. Int J Mol Sci 2023; 25:391. [PMID: 38203561 PMCID: PMC10779192 DOI: 10.3390/ijms25010391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/20/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer, characterized by high tumor heterogeneity and a poor prognosis. Inter- and intra-tumoral heterogeneity in PDAC is a major obstacle to effective PDAC treatment; therefore, it is highly desirable to explore the tumor heterogeneity and underlying mechanisms for the improvement of PDAC prognosis. Gene copy number variations (CNVs) are increasingly recognized as a common and heritable source of inter-individual variation in genomic sequence. In this review, we outline the origin, main characteristics, and pathological aspects of CNVs. We then describe the occurrence of CNVs in PDAC, including those that have been clearly shown to have a pathogenic role, and further highlight some key examples of their involvement in tumor development and progression. The ability to efficiently identify and analyze CNVs in tumor samples is important to support translational research and foster precision oncology, as copy number variants can be utilized to guide clinical decisions. We provide insights into understanding the CNV landscapes and the role of both somatic and germline CNVs in PDAC, which could lead to significant advances in diagnosis, prognosis, and treatment. Although there has been significant progress in this field, understanding the full contribution of CNVs to the genetic basis of PDAC will require further research, with more accurate CNV assays such as single-cell techniques and larger cohorts than have been performed to date.
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Affiliation(s)
| | - Matteo Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Francesco Piva
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
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Schmitz D, Li Z, Lo Faro V, Rask-Andersen M, Ameur A, Rafati N, Johansson Å. Copy number variations and their effect on the plasma proteome. Genetics 2023; 225:iyad179. [PMID: 37793096 PMCID: PMC10697815 DOI: 10.1093/genetics/iyad179] [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: 08/25/2023] [Revised: 08/25/2023] [Accepted: 09/15/2023] [Indexed: 10/06/2023] Open
Abstract
Structural variations, including copy number variations (CNVs), affect around 20 million bases in the human genome and are common causes of rare conditions. CNVs are rarely investigated in complex disease research because most CNVs are not targeted on the genotyping arrays or the reference panels for genetic imputation. In this study, we characterize CNVs in a Swedish cohort (N = 1,021) using short-read whole-genome sequencing (WGS) and use long-read WGS for validation in a subcohort (N = 15), and explore their effect on 438 plasma proteins. We detected 184,182 polymorphic CNVs and identified 15 CNVs to be associated with 16 proteins (P < 8.22×10-10). Of these, 5 CNVs could be perfectly validated using long-read sequencing, including a CNV which was associated with measurements of the osteoclast-associated immunoglobulin-like receptor (OSCAR) and located upstream of OSCAR, a gene important for bone health. Two other CNVs were identified to be clusters of many short repetitive elements and another represented a complex rearrangement including an inversion. Our findings provide insights into the structure of common CNVs and their effects on the plasma proteome, and highlights the importance of investigating common CNVs, also in relation to complex diseases.
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Affiliation(s)
- Daniel Schmitz
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, 751 08 Uppsala, Sweden
| | - Zhiwei Li
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, 751 08 Uppsala, Sweden
| | - Valeria Lo Faro
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, 751 08 Uppsala, Sweden
| | - Mathias Rask-Andersen
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, 751 08 Uppsala, Sweden
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, 751 08 Uppsala, Sweden
| | - Nima Rafati
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Box 582, 751 23 Uppsala, Sweden
| | - Åsa Johansson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, 751 08 Uppsala, Sweden
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Han S, Camp SY, Chu H, Collins R, Gillani R, Park J, Bakouny Z, Ricker CA, Reardon B, Moore N, Kofman E, Labaki C, Braun D, Choueiri TK, AlDubayan SH, Van Allen EM. Integrative Analysis of Germline Rare Variants in Clear and Non-Clear Cell Renal Cell Carcinoma. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.18.23284664. [PMID: 36712083 PMCID: PMC9882438 DOI: 10.1101/2023.01.18.23284664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
IMPORTANCE RCC encompasses a set of histologically distinct cancers with a high estimated genetic heritability, of which only a portion is currently explained. Previous rare germline variant studies in RCC have usually pooled clear and non-clear cell RCCs and have not adequately accounted for population stratification that may significantly impact the interpretation and discovery of certain candidate risk genes. OBJECTIVE To evaluate the enrichment of germline PVs in established cancer-predisposing genes (CPGs) in clear cell and non-clear cell RCC patients compared to cancer-free controls using approaches that account for population stratification and to identify unconventional types of germline RCC risk variants that confer an increased risk of developing RCC. DESIGN SETTING AND PARTICIPANTS In 1,436 unselected RCC patients with sufficient data quality, we systematically identified rare germline PVs, cryptic splice variants, and copy number variants (CNVs). From this unselected cohort, 1,356 patients were ancestry-matched with 16,512 cancer-free controls, and gene-level enrichment of rare germline PVs were assessed in 143 CPGs, followed by an investigation of somatic events in matching tumor samples. MAIN OUTCOMES AND MEASURES Gene-level burden of rare germline PVs, identification of secondary somatic events accompanying the germline PVs, and characterization of less-explored types of rare germline PVs in RCC patients. RESULTS In clear cell RCC (n = 976 patients), patients exhibited significantly higher prevalence of PVs in VHL compared to controls (OR: 39.1, 95% CI: 7.01-218.07, p-value:4.95e-05, q-value:0.00584). In non-clear cell RCC (n = 380 patients), patients carried enriched burden of PVs in FH (OR: 77.9, 95% CI: 18.68-324.97, p-value:1.55e-08, q-value: 1.83e-06) and MET (OR: 1.98e11, 95% CI: 0-inf, p-value: 2.07e-05, q-value: 3.50e-07). In a CHEK2-focused analysis with European cases and controls, clear cell RCC patients (n=906 European patients) harbored nominal enrichment of the previously reported low-penetrance CHEK2 variants, p.Ile157Thr (OR:1.84, 95% CI: 1.00-3.36, p-value:0.049) and p.Ser428Phe (OR:5.20, 95% CI: 1.00-26.40, p-value:0.045) while non-clear cell RCC patients (n=295 European patients) exhibited nominal enrichment of CHEK2 LOF germline PVs (OR: 3.51, 95% CI: 1.10-11.10, p-value: 0.033). RCC patients with germline PVs in FH, MET, and VHL exhibited significantly earlier age of cancer onset compared to patients without any germline PVs in CPGs (Mean: 46.0 vs 60.2 years old, Tukey adjusted p-value < 0.0001), and more than half had secondary somatic events affecting the same gene (n=10/15, 66.7%, 95% CI: 38.7-87.0%). Conversely, patients with rare germline PVs in CHEK2 exhibited a similar age of disease onset to patients without any identified germline PVs in CPGs (Mean: 60.1 vs 60.2 years old, Tukey adjusted p-value: 0.99), and only 30.4% of the patients carried secondary somatic events in CHEK2 (n=7/23, 95% CI: 14.1-53.0%). Finally, rare pathogenic germline cryptic splice variants underexplored in RCC were identified in SDHA and TSC1, and rare pathogenic germline CNVs were found in 18 patients, including CNVs in FH, SDHA, and VHL. CONCLUSIONS AND RELEVANCE This systematic analysis supports the existing link between several RCC risk genes and elevated RCC risk manifesting in earlier age of RCC onset. Our analysis calls for caution when assessing the role of germline PVs in CHEK2 due to the burden of founder variants with varying population frequency in different ancestry groups. It also broadens the definition of the RCC germline landscape of pathogenicity to incorporate previously understudied types of germline variants, such as cryptic splice variants and CNVs.
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Affiliation(s)
- Seunghun Han
- Ph.D. Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sabrina Y. Camp
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hoyin Chu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan Collins
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Riaz Gillani
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Jihye Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ziad Bakouny
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cora A. Ricker
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brendan Reardon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicholas Moore
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
| | - Eric Kofman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Chris Labaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - David Braun
- Center of Molecular and Cellular Oncology, Yale School of Medicine, New Haven, CT, USA
| | - Toni K. Choueiri
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Brigham and Women’s Hospital, Boston, MA, USA
| | - Saud H. AlDubayan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA, USA
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Eliezer M. Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Cancer Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
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Shallow Whole-Genome Sequencing of Cell-Free DNA (cfDNA) Detects Epithelial Ovarian Cancer and Predicts Patient Prognosis. Cancers (Basel) 2023; 15:cancers15020530. [PMID: 36672479 PMCID: PMC9857189 DOI: 10.3390/cancers15020530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Despite the progress in diagnostics and therapeutics, epithelial ovarian cancer (EOC) remains a fatal disease. Using shallow whole-genome sequencing of plasma cell-free DNA (cfDNA), we investigated biomarkers that could detect EOC and predict survival. Plasma cfDNA from 40 EOC patients and 20 healthy subjects were analyzed by shallow whole-genome sequencing (WGS) to identify copy number variations (CNVs) and determine the Z-scores of genes. In addition, we also calculated the genome-wide scores (Gi scores) to quantify chromosomal instability. We found that the Gi scores could distinguish EOC patients from healthy subjects and identify various EOC histological subtypes (e.g., high-grade serous carcinoma). In addition, we characterized EOC CNVs and demonstrated a relationship between RAB25 amplification (alone or with CA125), and disease-free survival and overall survival. This study identified RAB25 amplification as a predictor of EOC patient survival. Moreover, we showed that Gi scores could detect EOC. These data demonstrated that cfDNA, detected by shallow WGS, represented a potential tool for diagnosing EOC and predicting its prognosis.
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Bian J, Long J, Yang X, Yang X, Xu Y, Lu X, Guan M, Sang X, Zhao H. Construction and validation of a prognostic signature using CNV-driven genes for hepatocellular carcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:765. [PMID: 34268378 PMCID: PMC8246234 DOI: 10.21037/atm-20-7101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 03/10/2021] [Indexed: 12/24/2022]
Abstract
Background Hepatocellular carcinoma (HCC) is one of the major causes of cancer-related deaths worldwide. Copy number variations (CNVs) affect the expression of genes and play critical roles in carcinogenesis. We aimed to identify specific CNV-driven genes and establish a prognostic model for HCC. Methods Integrative analysis of CNVs difference data and differentially expressed genes (DEGs) data from The Cancer Genome Atlas (TCGA) were conducted to identify critical CNV-driven genes for HCC. A risk model was constructed based on univariate Cox regression analysis, Least Absolute Shrinkage and Selection Operator (LASSO), and multivariate Cox regression analyses. The associations between CNV-driven genes signature and infiltrating immune cells were explored. The International Cancer Genome Consortium (ICGC) dataset was utilized to validate this model. Results After integrative analysis of CNVs and corresponding mRNA expression profiles, 568 CNV-driven genes were identified. Sixty-three CNV-driven genes were found to be markedly associated with overall survival (OS) after univariate Cox regression analysis. Finally, eight CNV-driven genes were screened to generate a prognostic risk model. Compared with low-risk group, the OS of patients in the high-risk group was significantly shorter in both the TCGA [hazard ratio (HR) =6.14, 95% confidence interval (CI): 2.72-13.86, P<0.001] and ICGC (HR =3.23, 95% CI: 1.17-8.92, P<0.001) datasets. Further analysis revealed the infiltrating neutrophils were positively correlated with risk score. Meanwhile, the high-risk group was associated with higher expression of immune checkpoint genes. Conclusions A novel signature based on CNV-driven genes was built to predict the survival of HCC patients and showed good performance. The results of our study may improve understanding of the mechanism that drives HCC, and provide an immunological perspective for individualized therapies.
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Affiliation(s)
- Jin Bian
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Junyu Long
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Xu Yang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Xiaobo Yang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Yiyao Xu
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Xin Lu
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Mei Guan
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Xinting Sang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
| | - Haitao Zhao
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing, China
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Kim HAJ, Zeng PYF, Shaikh MH, Mundi N, Ghasemi F, Di Gravio E, Khan H, MacNeil D, Khan MI, Patel K, Mendez A, Yoo J, Fung K, Lang P, Palma DA, Mymryk JS, Barrett JW, Boutros PC, Nichols AC. All HPV-negative head and neck cancers are not the same: Analysis of the TCGA dataset reveals that anatomical sites have distinct mutation, transcriptome, hypoxia, and tumor microenvironment profiles. Oral Oncol 2021; 116:105260. [PMID: 33725617 DOI: 10.1016/j.oraloncology.2021.105260] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/04/2021] [Accepted: 02/28/2021] [Indexed: 12/14/2022]
Abstract
PURPOSE Head and neck squamous cell carcinoma (HNSCC) affects various anatomical sites, which often dictates whether the cancer is managed with primary surgery or radiation. This study aimed to assess differences in single nucleotide variation (SNV), copy number, mRNA abundance, methylation, and tumor microenvironment (TME) between HPV-negative oral cavity (OC), oropharyngeal (OPC), hypopharyngeal (HPC), and laryngeal (LC) cancers within The Cancer Genome Atlas (TCGA). METHODS We downloaded the clinical information and molecular data for the TCGA HNSCC cohort from the data portal and published literature. The TME was estimated using mRNA abundance data. We conducted our analyses within the Bioconductor statistical framework in the R environment. CNA and mRNA abundance results were correlated and grouped with SNV results for downstream pathway analysis. RESULTS LC had a higher mutational burden than OC and OPC (p <10-4). LC tumors were enriched in CSMD3, NSD1, DCHS2 and ANK2 SNVs, while OC tumors were enriched in CASP8 SNVs (FDR < 0.1). LCs were enriched for neuronal and glycosylation pathways, while OCs were enriched for extracellular matrix pathways. B cells and endothelial cells were more abundant in LC while monocytes were more abundant in OC (FDR < 0.1). OPC was the most hypoxic, followed by OC then LC (FDR < 0.05). OC had greater methylation of Hox genes than LC. Subsite analysis revealed that oral tongue cancers had fewer CASP8 and FBN2 mutations and higher dendritic cell abundance than other oral cavity cancers. CONCLUSIONS We identified significant genomic, transcriptional, and microenvironmental differences between HPV-negative HNSCC. Further study is warranted to determine if these findings portend differential response to specific treatment modalities.
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Affiliation(s)
- Hugh Andrew Jinwook Kim
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Peter Y F Zeng
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Mushfiq Hassan Shaikh
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Neil Mundi
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Farhad Ghasemi
- Department of General Surgery, University of Western Ontario, London, Ontario, Canada
| | - Eric Di Gravio
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Halema Khan
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Danielle MacNeil
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - Mohammed Imran Khan
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Krupal Patel
- Department of Otolaryngology, Moffitt Cancer Center, Tampa, FL, USA
| | - Adrian Mendez
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - John Yoo
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - Kevin Fung
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - Pencilla Lang
- Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - David A Palma
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - Joe S Mymryk
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada; Department of Microbiology & Immunology, University of Western Ontario, London, Ontario, Canada
| | - John W Barrett
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - Paul C Boutros
- Department of Human Genetics, University of California, Los Angeles, CA, USA; Department of Urology, University of California, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA; Institute for Precision Health, University of California, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, CA, USA
| | - Anthony C Nichols
- Department of Otolaryngology - Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada; Department of Oncology, University of Western Ontario, London, Ontario, Canada.
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9
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Uzilov AV, Taik P, Cheesman KC, Javanmard P, Ying K, Roehnelt A, Wang H, Fink MY, Lau CY, Moe AS, Villar J, Bederson JB, Stewart AF, Donovan MJ, Mahajan M, Sebra R, Post KD, Chen R, Geer EB. USP8 and TP53 Drivers are Associated with CNV in a Corticotroph Adenoma Cohort Enriched for Aggressive Tumors. J Clin Endocrinol Metab 2021; 106:826-842. [PMID: 33221858 DOI: 10.1210/clinem/dgaa853] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Indexed: 12/18/2022]
Abstract
CONTEXT Pituitary corticotroph adenomas are rare tumors that can be associated with excess adrenocorticotropin (ACTH) and adrenal cortisol production, resulting in the clinically debilitating endocrine condition Cushing disease. A subset of corticotroph tumors behave aggressively, and genomic drivers behind the development of these tumors are largely unknown. OBJECTIVE To investigate genomic drivers of corticotroph tumors at risk for aggressive behavior. DESIGN Whole-exome sequencing of patient-matched corticotroph tumor and normal deoxyribonucleic acid (DNA) from a patient cohort enriched for tumors at risk for aggressive behavior. SETTING Tertiary care center. PATIENTS Twenty-seven corticotroph tumors from 22 patients were analyzed. Twelve tumors were macroadenomas, of which 6 were silent ACTH tumors, 2 were Crooke's cell tumors, and 1 was a corticotroph carcinoma. INTERVENTION Whole-exome sequencing. MAIN OUTCOME MEASURE Somatic mutation genomic biomarkers. RESULTS We found recurrent somatic mutations in USP8 and TP53 genes, both with higher allelic fractions than other somatic mutations. These mutations were mutually exclusive, with TP53 mutations occurring only in USP8 wildtype (WT) tumors, indicating they may be independent driver genes. USP8-WT tumors were characterized by extensive somatic copy number variation compared with USP8-mutated tumors. Independent of molecular driver status, we found an association between invasiveness, macroadenomas, and aneuploidy. CONCLUSIONS Our data suggest that corticotroph tumors may be categorized into a USP8-mutated, genome-stable subtype versus a USP8-WT, genome-disrupted subtype, the latter of which has a TP53-mutated subtype with high level of chromosome instability. These findings could help identify high risk corticotroph tumors, namely those with widespread CNV, that may need closer monitoring and more aggressive treatment.
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Affiliation(s)
- Andrew V Uzilov
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
- Sema4, Stamford, Connecticut
| | | | - Khadeen C Cheesman
- Division of Endocrinology, Diabetes, and Bone Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Pedram Javanmard
- Division of Endocrinology, Diabetes, and Bone Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Alessia Roehnelt
- Division of Endocrinology, Diabetes, and Bone Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Marc Y Fink
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
- Sema4, Stamford, Connecticut
| | - Chun Yee Lau
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | | | - Joshua B Bederson
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Andrew F Stewart
- Diabetes, Obesity, and Metabolism Institute and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Michael J Donovan
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Milind Mahajan
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
- Sema4, Stamford, Connecticut
| | - Robert Sebra
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
- Sema4, Stamford, Connecticut
| | - Kalmon D Post
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Rong Chen
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
- Sema4, Stamford, Connecticut
| | - Eliza B Geer
- Multidisciplinary Pituitary and Skull Base Tumor Center, Departments of Medicine and Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, New York
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10
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Zhong Q, Fan J, Chu H, Pang M, Li J, Fan Y, Liu P, Wu C, Qiao J, Li R, Hang J. Integrative analysis of genomic and epigenetic regulation of endometrial cancer. Aging (Albany NY) 2020; 12:9260-9274. [PMID: 32412912 PMCID: PMC7288931 DOI: 10.18632/aging.103202] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/17/2020] [Indexed: 11/25/2022]
Abstract
Endometrial carcinomas (EC) are characterized by high DNA copy numbers and DNA methylation aberrations. In this study, we sought to comprehensively explore the effect of these two factors on development and progression of EC by analyzing integrated genomic and epigenetic analysis to. We found high DNA copy number and DNA methylation abnormalities in EC, with 6308 copy-number variation genes (CNV-G) and 4376 methylation genes (MET-G). We used these CNV-G and MET-G to subcategorize the samples for prognostic analysis, and identified three molecular subtypes (iC1, iC2, iC3). Moreover, the subtypes exhibited different tumor immune microenvironment characteristics. A further analysis of their molecular characteristics revealed three potential prognostic markers (KIAA1324, nonexpresser of pathogenesis-related genes1 (NPR1) and idiopathic hypogonadotropic hypogonadism (IHH)). Notably, all three markers showed distinct CNV, DNA methylation, and gene expression profiles. Analysis of mutations among the three subtypes revealed that iC2 had fewer mutations than the other subtypes. Conversely, iC2 showed significantly higher CNV levels than other subtypes. This comprehensive analysis of genomic and epigenetic profiles identified three prognostic markers, therefore, provides new insights into the multi-layered pathology of EC. These can be utilized for accurate treatment of EC patients.
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Affiliation(s)
- Qihang Zhong
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China.,Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing 100191, China
| | - Junpeng Fan
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Honglei Chu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Mujia Pang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Junsheng Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
| | - Yong Fan
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Ping Liu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
| | - Congying Wu
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing 100191, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Rong Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
| | - Jing Hang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China
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11
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Karim MR, Rahman A, Jares JB, Decker S, Beyan O. A snapshot neural ensemble method for cancer-type prediction based on copy number variations. Neural Comput Appl 2019. [DOI: 10.1007/s00521-019-04616-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
AbstractAn accurate diagnosis and prognosis for cancer are specific to patients with particular cancer types and molecular traits, which needs to address carefully. The discovery of important biomarkers is becoming an important step toward understanding the molecular mechanisms of carcinogenesis in which genomics data and clinical outcomes need to be analyzed before making any clinical decision. Copy number variations (CNVs) are found to be associated with the risk of individual cancers and hence can be used to reveal genetic predispositions before cancer develops. In this paper, we collect the CNVs data about 8000 cancer patients covering 14 different cancer types from The Cancer Genome Atlas. Then, two different sparse representations of CNVs based on 578 oncogenes and 20,308 protein-coding genes, including genomic deletions and duplication across the samples, are prepared. Then, we train Conv-LSTM and convolutional autoencoder (CAE) networks using both representations and create snapshot models. While the Conv-LSTM can capture locally and globally important features, CAE can utilize unsupervised pretraining to initialize the weights in the subsequent convolutional layers against the sparsity. Model averaging ensemble (MAE) is then applied to combine the snapshot models in order to make a single prediction. Finally, we identify most significant CNVs biomarkers using guided-gradient class activation map plus (GradCAM++) and rank top genes for different cancer types. Results covering several experiments show fairly high prediction accuracies for the majority of cancer types. In particular, using protein-coding genes, Conv-LSTM and CAE networks can predict cancer types correctly at least 72.96% and 76.77% of the cases, respectively. Contrarily, using oncogenes gives moderately higher accuracies of 74.25% and 78.32%, whereas the snapshot model based on MAE shows overall 2.5% of accuracy improvement.
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12
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Germline 16p11.2 Microdeletion Predisposes to Neuroblastoma. Am J Hum Genet 2019; 105:658-668. [PMID: 31474320 DOI: 10.1016/j.ajhg.2019.07.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/29/2019] [Indexed: 12/27/2022] Open
Abstract
Neuroblastoma is a cancer of the developing sympathetic nervous system. It is diagnosed in 600-700 children per year in the United States and accounts for 12% of pediatric cancer deaths. Despite recent advances in our understanding of this malignancy's complex genetic architecture, the contribution of rare germline variants remains undefined. Here, we conducted a genome-wide analysis of large (>500 kb), rare (<1%) germline copy number variants (CNVs) in two independent, multi-ethnic cohorts totaling 5,585 children with neuroblastoma and 23,505 cancer-free control children. We identified a 550-kb deletion on chromosome 16p11.2 significantly enriched in neuroblastoma cases (0.39% of cases and 0.03% of controls; p = 3.34 × 10-9). Notably, this CNV corresponds to a known microdeletion syndrome that affects approximately one in 3,000 children and confers risk for diverse developmental phenotypes including autism spectrum disorder and other neurodevelopmental disorders. The CNV had a substantial impact on neuroblastoma risk, with an odds ratio of 13.9 (95% confidence interval = 5.8-33.4). The association remained significant when we restricted our analysis to individuals of European ancestry in order to mitigate potential confounding by population stratification (0.42% of cases and 0.03% of controls; p = 4.10 × 10-8). We used whole-genome sequencing (WGS) to validate the deletion in paired germline and tumor DNA from 12 cases. Finally, WGS of four parent-child trios revealed that the deletion primarily arose de novo without maternal or paternal bias. This finding expands the clinical phenotypes associated with 16p11.2 microdeletion syndrome to include cancer, and it suggests that disruption of the 16p11.2 region may dysregulate neurodevelopmental pathways that influence both neurological phenotypes and neuroblastoma.
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13
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Bi H, Liu Y, Tian T, Xia T, Pu R, Zhang Y, Hu F, Zhao Y. A Propensity Score-adjusted Analysis of the Effects of Ubiquitin E3 Ligase Copy Number Variation in Peripheral Blood Leukocytes on Colorectal Cancer Risk. J Cancer 2019; 10:3291-3302. [PMID: 31289601 PMCID: PMC6603381 DOI: 10.7150/jca.29872] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 05/07/2019] [Indexed: 12/29/2022] Open
Abstract
Background: The ubiquitin ligases E3 (E3s) plays a key role in the specific protein degradation in many carcinogenic biological processes. Colorectal cancer (CRC) development may be affected by the copy number variation (CNV) of E3s. Prior studies may have underestimated the impact of potential confounding factors' effects on the association between gene CNV and CRC risk, and CRC risk predictive model integrating gene CNV patterns is lacking. Our research sought to assess the genes CNVs of MDM2, SKP2, FBXW7, β-TRCP, and NEDD4-1 and CRC risk by using propensity score (PS) adjustment and developing models that integrate CNV patterns for CRC risk predictions. Methods: This study comprising 1036 participants used traditional regression and different PS techniques to adjust the confounding factors to evaluate the relationships between five gene CNVs and CRC risk, and to establish a CRC risk predictive model. The AUC was applied to evaluate the effect of the model. The categorical net reclassification improvement (NRI) and the integrated discrimination improvement (IDI) were analyzed to evaluate the discriminatory accuracy improvement among the models. Results: Compared to variable adjustment, the odds ratios (ORs) tended to be conservative and accurate with narrow confidence intervals (CIs) after PS adjustment. After PS adjustment, MDM2 amplification was related to increased CRC risk (Amp-pattern: OR = 8.684, 95% CI: 1.213-62.155, P = 0.031), whereas SKP2 deletion and the (del+amp) genotype were associated with reduced CRC risk (Del-pattern: OR = 0.323, 95% CI: 0.106-0.979, P = 0.046; Var-pattern: OR = 0.339, 95% CI: 0.135-0.854, P = 0.024). The predictive model integrating the gene CNV pattern could correctly reclassify 1.7% of the subjects. Conclusions: MDM2 amplification and SKP2 CNVs are associated with increased and decreased CRC risk, respectively; abnormal CNV-integrated model is more precise for predicting CRC risk. Further studies are needed to verify these encouraging outcomes.
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Affiliation(s)
- Haoran Bi
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Harbin, Heilongjiang, People's Republic of China
| | - Yupeng Liu
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Harbin, Heilongjiang, People's Republic of China
| | - Tian Tian
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Harbin, Heilongjiang, People's Republic of China
| | - Tingting Xia
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Harbin, Heilongjiang, People's Republic of China
| | - Rui Pu
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Harbin, Heilongjiang, People's Republic of China
| | - Yiwei Zhang
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Harbin, Heilongjiang, People's Republic of China
| | - Fulan Hu
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Harbin, Heilongjiang, People's Republic of China
| | - Yashuang Zhao
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Harbin, Heilongjiang, People's Republic of China
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14
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MR imaging phenotype correlates with extent of genome-wide copy number abundance in IDH mutant gliomas. Neuroradiology 2019; 61:1023-1031. [PMID: 31134296 DOI: 10.1007/s00234-019-02219-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 04/29/2019] [Indexed: 12/15/2022]
Abstract
PURPOSE There is variability in survival within IDH mutant gliomas determined by chromosomal events. Copy number variation (CNV) abundance associated with survival in low-grade and IDH mutant astrocytoma has been reported. Our purpose was to correlate the extent of genome-wide CNV abundance in IDH mutant astrocytomas with MRI features. METHODS Presurgical MRI and CNV plots derived from Illumina 850k EPIC DNA methylation arrays of 18 cases of WHO grade II-IV IDH mutant astrocytomas were reviewed. IDH mutant astrocytomas were divided into CNV stable group (CNV-S) with ≤ 3 chromosomal gains or losses and lack of focal gene amplifications and CNV unstable group (CNV-U) with > 3 large chromosomal gains/losses and/or focal amplifications. The associations between MR features, relative cerebral blood volume (rCBV), CNV abundance, and time to progression were assessed. Tumor rCBV estimates were obtained using DSC T2* perfusion analysis. RESULTS There were nine (50%) CNV-S and nine (50%) CNV-U IDH mutant astrocytomas. CNV-U tumors showed larger mean tumor size (P = 0.004) and maximum diameter on FLAIR (P = 0.004) and also demonstrated significantly higher median rCBV than CNV-S tumors (2.62 vs 0.78, P = 0.019). CNV-U tumors tended to have shorter time to progression although without statistical significance (P = 0.393). CONCLUSIONS Larger size/diameter and higher rCBVs were seen associated CNV-U astrocytomas, suggesting a correlation of aggressive imaging phenotype with unstable and aggressive genotype in IDH mutant astrocytomas.
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15
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Tatsi C, Pankratz N, Lane J, Faucz FR, Hernández-Ramírez LC, Keil M, Trivellin G, Chittiboina P, Mills JL, Stratakis CA, Lodish MB. Large Genomic Aberrations in Corticotropinomas Are Associated With Greater Aggressiveness. J Clin Endocrinol Metab 2019; 104:1792-1801. [PMID: 30597087 PMCID: PMC6452317 DOI: 10.1210/jc.2018-02164] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/21/2018] [Indexed: 11/19/2022]
Abstract
CONTEXT Genomic losses/gains are associated with cancer progression and prognosis. In pituitary adenomas, analyses of copy number variations (CNVs) have shown that a subset of adenomas have higher genomic variability. However, whether CNVs are associated with tumor aggressiveness and prognosis has not been determined. OBJECTIVE We hypothesized that somatic CNVs of pituitary tumors may play a role in the progression and aggressiveness of pituitary corticotropinomas in children and adolescents. SAMPLES AND DESIGN Paired germline and tumor DNA samples from 27 pediatric patients with Cushing disease (CD), were subjected to whole exome sequencing. Somatic CNVs were identified using the ExomeDepth tool. Clinical, histological, and biochemical data from the patients were collected and correlated with the results of the CNV analysis. RESULTS Chromosomal instability, involving 23% to 59% of the tumor genome, was noted in 5 of the 27 samples (18.5%). The patients with tumors showing chromosomal instability had similar clinical and biochemical characteristics to the remaining patients, except for tumor size, which was larger (median size 18 mm vs 5.5 mm, P = 0.005). Tumors with chromosomal instability were also associated with a higher rate of invasion of the cavernous sinus (P = 0.029). There was insufficient information on persistence or recurrence of CD to determine whether the risk was higher in those with chromosomal instability. CONCLUSIONS A subgroup of corticotropinomas demonstrates chromosomal instability that is associated with markers of aggressiveness of these adenomas. It appears that more genomic gains/losses in a few, rare corticotropinomas may predict poorer prognosis for pediatric patients with CD.
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Affiliation(s)
- Christina Tatsi
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology University of Minnesota Medical School, Minneapolis, Minnesota
| | - John Lane
- Department of Laboratory Medicine and Pathology University of Minnesota Medical School, Minneapolis, Minnesota
| | - Fabio R Faucz
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Laura C Hernández-Ramírez
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Margaret Keil
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Giampaolo Trivellin
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Prashant Chittiboina
- Surgical Neurology Branch, National Institute of Neurologic Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - James L Mills
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institutes of Health, Bethesda, Maryland
| | - Constantine A Stratakis
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
- Correspondence and Reprint Requests: Constantine A. Stratakis, MD, National Institutes of Health, 10 Center Drive, Building 10, NIH-Clinical Research Center, Room 1-3330, MSC1103, Bethesda, Maryland 20892. E-mail:
| | - Maya B Lodish
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
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16
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Talukdar S, Hawkes L, Hanson H, Kulkarni A, Brady AF, McMullan DJ, Ahn JW, Woodward E, Turnbull C. Structural Aberrations with Secondary Implications (SASIs): consensus recommendations for reporting of cancer susceptibility genes identified during analysis of Copy Number Variants (CNVs). J Med Genet 2019; 56:718-726. [DOI: 10.1136/jmedgenet-2018-105820] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/19/2019] [Accepted: 03/02/2019] [Indexed: 11/04/2022]
Abstract
Clinical testing with chromosomal microarray (CMA) is most commonly undertaken for clinical indications such as intellectual disability, dysmorphic features and/or congenital abnormalities. Identification of a structural aberration (SA) involving a cancer susceptibility gene (CSG) constitutes a type of incidental or secondary finding. Laboratory reporting, risk communication and clinical management of these structural aberrations with secondary implications (SASIs) is currently inconsistent. We undertake meta-analysis of 18 622 instances of CMA performed for unrelated indications in which 106 SASIs are identified involving in total 40 different CSGs. Here we present the recommendations of a joint UK working group representing the British Society of Genomic Medicine, UK Cancer Genetics Group and UK Association for Clinical Genomic Science. SASIs are categorised into four groups, defined by the type of SA and the cancer risk. For each group, recommendations are provided regarding reflex parental testing and cancer risk management.
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17
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Cheng Y, Dai JY, Wang X, Kooperberg C. Identifying disease-associated copy number variations by a doubly penalized regression model. Biometrics 2018; 74:1341-1350. [PMID: 29894562 PMCID: PMC6663092 DOI: 10.1111/biom.12920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 05/01/2018] [Accepted: 05/01/2018] [Indexed: 11/27/2022]
Abstract
Copy number variation (CNV) of DNA plays an important role in the development of many diseases. However, due to the irregularity and sparsity of the CNVs, studying the association between CNVs and a disease outcome or a trait can be challenging. Up to now, not many methods have been proposed in the literature for this problem. Most of the current researchers reply on an ad hoc two-stage procedure by first identifying CNVs in each individual genome and then performing an association test using these identified CNVs. This potentially leads to information loss and as a result a lower power to identify disease associated CNVs. In this article, we describe a new method that combines the two steps into a single coherent model to identify the common CNV across patients that are associated with certain diseases. We use a double penalty model to capture CNVs' association with both the intensities and the disease trait. We validate its performance in simulated datasets and a data example on platinum resistance and CNV in ovarian cancer genome.
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Affiliation(s)
- Yichen Cheng
- Institute for Insight, Georgia State University, Atlanta, Georgia, USA
| | - James Y. Dai
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A
| | - Xiaoyu Wang
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A
| | - Charles Kooperberg
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A
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18
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Wu X, Yan Y, Li H, Ji N, Yu T, Huang Y, Shi W, Gao L, Ma L, Hu Y. DNA copy number gain-mediated lncRNA LINC01061 upregulation predicts poor prognosis and promotes papillary thyroid cancer progression. Biochem Biophys Res Commun 2018; 503:1247-1253. [PMID: 30029886 DOI: 10.1016/j.bbrc.2018.07.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 07/07/2018] [Indexed: 02/03/2023]
Abstract
Several DNA copy number amplifications (CNAs) have been reported in papillary thyroid cancer (PTC). However, the functional role of CNAs in PTC remains very unclear. And whether there is a correlation between long noncoding RNA (lncRNA) and CNA requires to be explored. Here, we identified a novel lncRNA LINC01061. The genomic copy number of LINC01061 is amplified, which leads to its elevated expression level in PTC tissues. Moreover, increased level of LINC01061 was correlated with aggressive clinicopathological characteristics. Functional study indicated that LINC01061 silence significantly inhibited the proliferation, cell-cycle and invasion of PTC cells in vitro and tumor growth in vivo. Mechanistically, we showed that LINC01061 interacted with miR-4316 to promote E2F6 expression. The expression of miR-4316 was downregulated in PTC tissues while that of E2F6 was upregulated. Through rescue assay, we demonstrated that LINC01061 promoted PTC cell proliferation, cell-cycle progression and invasion by regulating miR-4316/E2F6 signaling pathway. In conclusion, our research indicated that LINC01061 might be a target for PTC therapy.
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MESH Headings
- Animals
- Cell Proliferation
- Cells, Cultured
- DNA Copy Number Variations
- Disease Progression
- Female
- Humans
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Middle Aged
- Neoplasms, Experimental/diagnosis
- Neoplasms, Experimental/metabolism
- Neoplasms, Experimental/pathology
- Prognosis
- RNA, Long Noncoding/genetics
- Thyroid Cancer, Papillary/diagnosis
- Thyroid Cancer, Papillary/genetics
- Thyroid Cancer, Papillary/pathology
- Thyroid Neoplasms/diagnosis
- Thyroid Neoplasms/genetics
- Thyroid Neoplasms/pathology
- Up-Regulation
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Affiliation(s)
- Xinhua Wu
- Department of Endocrinology, Huaian Hospital of Huaian District, Huaian, 223200, Jiangsu province, China.
| | - Yan Yan
- Department of Endocrinology, Huaian Hospital of Huaian District, Huaian, 223200, Jiangsu province, China
| | - Hang Li
- Department of Endocrinology, Huaian Hospital of Huaian District, Huaian, 223200, Jiangsu province, China
| | - Ning Ji
- Department of Endocrinology, Huaian Hospital of Huaian District, Huaian, 223200, Jiangsu province, China
| | - Tao Yu
- Department of Endocrinology, Huaian Hospital of Huaian District, Huaian, 223200, Jiangsu province, China
| | - Yujie Huang
- Department of Endocrinology, Huaian Hospital of Huaian District, Huaian, 223200, Jiangsu province, China
| | - Wen Shi
- Department of Endocrinology, Huaian Hospital of Huaian District, Huaian, 223200, Jiangsu province, China
| | - Lingcheng Gao
- Department of Endocrinology, Huaian Hospital of Huaian District, Huaian, 223200, Jiangsu province, China
| | - Liming Ma
- Department of Endocrinology, Huaian Hospital of Huaian District, Huaian, 223200, Jiangsu province, China
| | - Yunshu Hu
- Department of Laboratory, Xin'an Hospital, Huaian, 223200, Jiangsu province, China
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19
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Ritenour LE, Randall MP, Bosse KR, Diskin SJ. Genetic susceptibility to neuroblastoma: current knowledge and future directions. Cell Tissue Res 2018; 372:287-307. [PMID: 29589100 DOI: 10.1007/s00441-018-2820-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 02/27/2018] [Indexed: 12/16/2022]
Abstract
Neuroblastoma, a malignancy of the developing peripheral nervous system that affects infants and young children, is a complex genetic disease. Over the past two decades, significant progress has been made toward understanding the genetic determinants that predispose to this often lethal childhood cancer. Approximately 1-2% of neuroblastomas are inherited in an autosomal dominant fashion and a combination of co-morbidity and linkage studies has led to the identification of germline mutations in PHOX2B and ALK as the major genetic contributors to this familial neuroblastoma subset. The genetic basis of "sporadic" neuroblastoma is being studied through a large genome-wide association study (GWAS). These efforts have led to the discovery of many common susceptibility alleles, each with modest effect size, associated with the development and progression of sporadic neuroblastoma. More recently, next-generation sequencing efforts have expanded the list of potential neuroblastoma-predisposing mutations to include rare germline variants with a predicted larger effect size. The evolving characterization of neuroblastoma's genetic basis has led to a deeper understanding of the molecular events driving tumorigenesis, more precise risk stratification and prognostics and novel therapeutic strategies. This review details the contemporary understanding of neuroblastoma's genetic predisposition, including recent advances and discusses ongoing efforts to address gaps in our knowledge regarding this malignancy's complex genetic underpinnings.
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Affiliation(s)
- Laura E Ritenour
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael P Randall
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristopher R Bosse
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sharon J Diskin
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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20
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Chen C, Zhou L, Wang H, Chen J, Li W, Liu W, Shen M, Liu H, Fu X. Long noncoding RNA CNALPTC1 promotes cell proliferation and migration of papillary thyroid cancer via sponging miR-30 family. Am J Cancer Res 2018; 8:192-206. [PMID: 29416932 PMCID: PMC5794733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 10/03/2017] [Indexed: 06/08/2023] Open
Abstract
Several somatic copy number variations (CNVs) have been identified in papillary thyroid cancer (PTC). However, the functional roles of CNVs and the genes responsible for the roles of CNVs are largely unknown. In this study, we identified a novel long noncoding RNA (lncRNA) CNALPTC1 (copy number amplified long noncoding RNA in papillary thyroid cancer 1). The genomic copy number of CNALPTC1 is amplified and CNALPTC1 expression level is up-regulated in PTC. Increased expression of CNALPTC1 is associated with aggressive clinicopathological characteristics. Gain-of-function and loss-of-function assays revealed that CNALPTC1 promotes proliferation and migration of PTC cells, and inhibits apoptosis of PTC cells. Mechanistically, we found that CNALPTC1 physically associates to miR-30 family and down-regulates miR-30 expression. Furthermore, CNALPTC1 up-regulates the expression of miR-30 targets, such as BCL9, SNAI1, and VIM. The mutation of miR-30 binding site on CNALPTC1 or overexpression of miR-30 abrogates the oncogenic roles of CNALPTC1 in PTC. Collectively, our results suggested that the copy number amplified lncRNA CNALPTC1 promotes PTC progression via sponging miR-30 family. Our data also implied that CNALPTC1 may be a novel therapeutic target for PTC.
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Affiliation(s)
- Cunrong Chen
- Department of ICU, Fujian Medical University Union HospitalFuzhou, Fujian, China
| | - Lili Zhou
- Department of ICU, Fujian Medical University Union HospitalFuzhou, Fujian, China
| | - Hui Wang
- Department of ICU, Fujian Medical University Union HospitalFuzhou, Fujian, China
| | - Junnian Chen
- Department of ICU, Fujian Medical University Union HospitalFuzhou, Fujian, China
| | - Wen Li
- Department of ICU, Fujian Medical University Union HospitalFuzhou, Fujian, China
| | - Wei Liu
- Department of ICU, Fujian Medical University Union HospitalFuzhou, Fujian, China
| | - Mingjie Shen
- Department of Gynecology and Obstetrics of Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese MedicineShanghai, China
| | - Hongzhou Liu
- Department of Geriatric Endocrinology, Chinese PLA General HospitalBeijing, China
| | - Xiaomin Fu
- Department of Geriatric Endocrinology, Chinese PLA General HospitalBeijing, China
- Pediatrics Department, Division of Metabolism and Endocrinology, Johns Hopkins UniversityBaltimore, MD, USA
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21
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Bokhari Y, Arodz T. QuaDMutEx: quadratic driver mutation explorer. BMC Bioinformatics 2017; 18:458. [PMID: 29065872 PMCID: PMC5655866 DOI: 10.1186/s12859-017-1869-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 10/16/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Somatic mutations accumulate in human cells throughout life. Some may have no adverse consequences, but some of them may lead to cancer. A cancer genome is typically unstable, and thus more mutations can accumulate in the DNA of cancer cells. An ongoing problem is to figure out which mutations are drivers - play a role in oncogenesis, and which are passengers - do not play a role. One way of addressing this question is through inspection of somatic mutations in DNA of cancer samples from a cohort of patients and detection of patterns that differentiate driver from passenger mutations. RESULTS We propose QuaDMutEx, a method that incorporates three novel elements: a new gene set penalty that includes non-linear penalization of multiple mutations in putative sets of driver genes, an ability to adjust the method to handle slow- and fast-evolving tumors, and a computationally efficient method for finding gene sets that minimize the penalty, through a combination of heuristic Monte Carlo optimization and exact binary quadratic programming. Compared to existing methods, the proposed algorithm finds sets of putative driver genes that show higher coverage and lower excess coverage in eight sets of cancer samples coming from brain, ovarian, lung, and breast tumors. CONCLUSIONS Superior ability to improve on both coverage and excess coverage on different types of cancer shows that QuaDMutEx is a tool that should be part of a state-of-the-art toolbox in the driver gene discovery pipeline. It can detect genes harboring rare driver mutations that may be missed by existing methods. QuaDMutEx is available for download from https://github.com/bokhariy/QuaDMutEx under the GNU GPLv3 license.
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Affiliation(s)
- Yahya Bokhari
- Department of Computer Science, School of Engineering, Virginia Commonwealth University, 401 W. Main St., Richmond, 23284, VA, USA
| | - Tomasz Arodz
- Department of Computer Science, School of Engineering, Virginia Commonwealth University, 401 W. Main St., Richmond, 23284, VA, USA. .,Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, 23284, VA, USA.
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22
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ExCNVSS: A Noise-Robust Method for Copy Number Variation Detection in Whole Exome Sequencing Data. BIOMED RESEARCH INTERNATIONAL 2017; 2017:9631282. [PMID: 28698882 PMCID: PMC5494116 DOI: 10.1155/2017/9631282] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/04/2017] [Accepted: 05/21/2017] [Indexed: 11/18/2022]
Abstract
Copy number variations (CNVs) are structural variants associated with human diseases. Recent studies verified that disease-related genes are based on the extraction of rare de novo and transmitted CNVs from exome sequencing data. The need for more efficient and accurate methods has increased, which still remains a challenging problem due to coverage biases, as well as the sparse, small-sized, and noncontinuous nature of exome sequencing. In this study, we developed a new CNV detection method, ExCNVSS, based on read coverage depth evaluation and scale-space filtering to resolve these problems. We also developed the method ExCNVSS_noRatio, which is a version of ExCNVSS, for applying to cases with an input of test data only without the need to consider the availability of a matched control. To evaluate the performance of our method, we tested it with 11 different simulated data sets and 10 real HapMap samples' data. The results demonstrated that ExCNVSS outperformed three other state-of-the-art methods and that our method corrected for coverage biases and detected all-sized CNVs even without matched control data.
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23
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Azimi V, Chang YH, Thibault G, Smith J, Tsujikawa T, Kukull B, Jensen B, Corless C, Margolin A, Gray JW. BREAST CANCER HISTOPATHOLOGY IMAGE ANALYSIS PIPELINE FOR TUMOR PURITY ESTIMATION. PROCEEDINGS. IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING 2017; 2017:1137-1140. [PMID: 30364881 PMCID: PMC6198647 DOI: 10.1109/isbi.2017.7950717] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The translation of genomic sequencing technology to the clinic has greatly advanced personalized medicine. However, the presence of normal cells in tumors is a confounding factor in genome sequence analysis. Tumor purity, or the percentage of cancerous cells in whole tissue section, is a correction factor that can be used to improve the clinical utility of genomic sequencing. Currently, tumor purity is estimated visually by expert pathologists; however, it has been shown that there exist vast inter-observer discrepancies in tumor purity scoring. In this paper, we propose a quantitative image analysis pipeline for tumor purity estimation and provide a systematic comparison between pathologists' scores and our image-based tumor purity estimation.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Joe W Gray
- Oregon Health and Science University (OHSU)
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24
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Page K, Guttery DS, Fernandez-Garcia D, Hills A, Hastings RK, Luo J, Goddard K, Shahin V, Woodley-Barker L, Rosales BM, Coombes RC, Stebbing J, Shaw JA. Next Generation Sequencing of Circulating Cell-Free DNA for Evaluating Mutations and Gene Amplification in Metastatic Breast Cancer. Clin Chem 2017; 63:532-541. [PMID: 27940449 PMCID: PMC6241835 DOI: 10.1373/clinchem.2016.261834] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/19/2016] [Indexed: 12/21/2022]
Abstract
BACKGROUND Breast cancer tissues are heterogeneous and show diverse somatic mutations and somatic copy number alterations (CNAs). We used a novel targeted next generation sequencing (NGS) panel to examine cell-free DNA (cfDNA) to detect somatic mutations and gene amplification in women with metastatic breast cancer (MBC). METHODS cfDNA from pretreated patients (n = 42) and 9 healthy controls were compared with matched lymphocyte DNA by NGS, using a custom 158 amplicon panel covering hot-spot mutations and CNAs in 16 genes, with further validation of results by droplet digital PCR. RESULTS No mutations were identified in cfDNA of healthy controls, whereas exactly half the patients with metastatic breast cancer had at least one mutation or amplification in cfDNA (mean 2, range 1-6) across a total of 13 genes. Longitudinal follow up showed dynamic changes to mutations and gene amplification in cfDNA indicating clonal and subclonal response to treatment that was more dynamic than cancer antigen 15-3 (CA15-3). Interestingly, at the time of blood sampling disease progression was occurring in 7 patients with erb-b2 receptor tyrosine kinase 2 (ERBB2) gene amplification in their cfDNA and 3 of these patients were human epidermal growth factor receptor 2 (HER2) negative at diagnosis, suggesting clonal evolution to a more aggressive phenotype. Lastly, 6 patients harbored estrogen receptor 1 (ESR1) mutations in cfDNA, suggesting resistance to endocrine therapy. Overall 9 of 42 patients (21%) had alterations in cfDNA that could herald a change in treatment. CONCLUSIONS Targeted NGS of cfDNA has potential for monitoring response to targeted therapies through both mutations and gene amplification, for analysis of dynamic tumor heterogeneity and stratification to targeted therapy.
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Affiliation(s)
- Karen Page
- Department of Cancer Studies and Cancer Research UK Leicester Centre, University of Leicester, Leicester, UK
| | - David S Guttery
- Department of Cancer Studies and Cancer Research UK Leicester Centre, University of Leicester, Leicester, UK
| | - Daniel Fernandez-Garcia
- Department of Cancer Studies and Cancer Research UK Leicester Centre, University of Leicester, Leicester, UK
| | - Allison Hills
- Department of Surgery and Cancer, Division of Cancer, and
| | - Robert K Hastings
- Department of Cancer Studies and Cancer Research UK Leicester Centre, University of Leicester, Leicester, UK
| | - Jinli Luo
- Department of Cancer Studies and Cancer Research UK Leicester Centre, University of Leicester, Leicester, UK
| | - Kate Goddard
- Department of Medical Oncology, Imperial College London, Charing Cross Hospital, London, UK
| | - Vedia Shahin
- Department of Medical Oncology, Imperial College London, Charing Cross Hospital, London, UK
| | - Laura Woodley-Barker
- Department of Medical Oncology, Imperial College London, Charing Cross Hospital, London, UK
| | | | | | | | - Jacqueline A Shaw
- Department of Cancer Studies and Cancer Research UK Leicester Centre, University of Leicester, Leicester, UK;
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25
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Sapkota Y, Narasimhan A, Kumaran M, Sehrawat BS, Damaraju S. A Genome-Wide Association Study to Identify Potential Germline Copy Number Variants for Sporadic Breast Cancer Susceptibility. Cytogenet Genome Res 2016; 149:156-164. [PMID: 27668787 DOI: 10.1159/000448558] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2016] [Indexed: 11/19/2022] Open
Abstract
Breast cancer (BC) predisposition in populations arises from both genetic and nongenetic risk factors. Structural variations such as copy number variations (CNVs) are heritable determinants for disease susceptibility. The primary objectives of this study are (1) to identify CNVs associated with sporadic BC using a genome-wide association study (GWAS) design; (2) to utilize 2 distinct CNV calling algorithms to identify concordant CNVs as a strategy to reduce false positive associations in the hypothesis-generating GWAS discovery phase, and (3) to identify potential candidate CNVs for follow-up replication studies. We used Affymetrix SNP Array 6.0 data profiled on Caucasian subjects (422 cases/348 controls) to call CNVs using algorithms implemented in Nexus Copy Number and Partek Genomics Suite software. Nexus algorithm identified CNVs associated with BC (731 autosomal CNVs with >5% frequency in the total sample and Q < 0.05). Thirteen CNVs were identified when Partek algorithm-called CNVs were overlapped with Nexus-identified CNVs; these CNVs showed concordances for frequency, effect size, and direction. Coding genes present within BC-associated CNVs were known to play a role in disease etiology and prognosis. Long noncoding RNAs identified within CNVs showed tissue-specific expression, indicating potential functional relevance of the findings. The identified candidate CNVs warrant independent replication.
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Affiliation(s)
- Yadav Sapkota
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tenn., USA
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26
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Singh RR, Mehrotra M, Chen H, Almohammedsalim AA, Sahin A, Bosamra A, Patel KP, Routbort MJ, Lu X, Ronald A, Mishra BM, Virani S, Medeiros LJ, Luthra R. Comprehensive Screening of Gene Copy Number Aberrations in Formalin-Fixed, Paraffin-Embedded Solid Tumors Using Molecular Inversion Probe-Based Single-Nucleotide Polymorphism Array. J Mol Diagn 2016; 18:676-687. [PMID: 27392636 DOI: 10.1016/j.jmoldx.2016.03.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/23/2016] [Accepted: 03/29/2016] [Indexed: 02/08/2023] Open
Abstract
Gene copy number aberrations (CNAs) represent a major class of cancer-related genomic alterations that drive solid tumors. Comprehensive and sensitive detection of CNAs is challenging because of often low quality and quantity of DNA isolated from the formalin-fixed, paraffin-embedded (FFPE) solid tumor samples. Here, in a clinical molecular diagnostic laboratory, we tested the utility and validated a molecular inversion probe-based (MIP) array to routinely screen for CNAs in solid tumors. Using low-input FFPE DNA, the array detects genome-wide CNAs with a special focus on 900 cancer-related genes. A cohort of 76 solid tumors of various types and tumor cellularity (20% to 100%), and four cancer cell lines were used. These harbored CNAs in clinically important genes (ERBB2, EGFR, FGFR1, KRAS, MYC) as detected by orthogonal techniques like next-generation sequencing or fluorescence in situ hybridization. Results of the MIP array were concordant with results from orthogonal techniques, and also provided additional information regarding the allelic nature of the CNAs. Limit-of-detection and assay reproducibility studies showed a high degree of sensitivity and reproducibility of detection, respectively. FFPE compatibility, ability to detect CNAs with high sensitivity, accuracy, and provide valuable information such as loss of heterozygosity along with relatively short turnaround times makes the MIP array a desirable clinical platform for routine screening of solid tumors in a clinical laboratory.
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Affiliation(s)
- Rajesh R Singh
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Meenakshi Mehrotra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hui Chen
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alaa A Almohammedsalim
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ayesagul Sahin
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alex Bosamra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Keyur P Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mark J Routbort
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xinyan Lu
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Abraham Ronald
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bal Mukund Mishra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shumaila Virani
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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27
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Zang ZS, Xu YM, Lau ATY. Molecular and pathophysiological aspects of metal ion uptake by the zinc transporter ZIP8 (SLC39A8). Toxicol Res (Camb) 2016; 5:987-1002. [PMID: 30090406 PMCID: PMC6062374 DOI: 10.1039/c5tx00424a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 02/16/2016] [Indexed: 02/05/2023] Open
Abstract
Zinc ion (Zn2+) is essential for life; its deficiency in the human body could cause stunted growth, anemia and susceptibility to infection. The Zn transporter ZIP8 (also known as SLC39A8) is an important Zn2+ importer; aberrant Zn2+ influx mediated by ZIP8 can lead to the pathogenesis of osteoarthritis and inflammatory diseases. ZIP8 also mediates the cellular uptake of divalent metal ions including iron, manganese, and the toxic heavy metal cadmium. Individuals with SLC39A8 mutations and transgenic mouse models are starting to reveal the critical role that this gene plays in embryonic development and the metabolism of essential metal ions. Here we summarize our current understanding of ZIP8's function and regulation, at both the molecular and biological levels. We also review the association of ZIP8 with various diseases and its linkage with complex disorders like obesity, hypertension, and schizophrenia as revealed by several large genome-wide association studies.
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Affiliation(s)
- Zhong-Sheng Zang
- Laboratory of Cancer Biology and Epigenetics , Department of Cell Biology and Genetics , Shantou University Medical College , 22 Xinling Road , Shantou , Guangdong 515041 , P. R. China . ; Tel: +86-754-8853-0052
| | - Yan-Ming Xu
- Laboratory of Cancer Biology and Epigenetics , Department of Cell Biology and Genetics , Shantou University Medical College , 22 Xinling Road , Shantou , Guangdong 515041 , P. R. China . ; Tel: +86-754-8853-0052
| | - Andy T Y Lau
- Laboratory of Cancer Biology and Epigenetics , Department of Cell Biology and Genetics , Shantou University Medical College , 22 Xinling Road , Shantou , Guangdong 515041 , P. R. China . ; Tel: +86-754-8853-0052
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da Silva JM, Giachetto PF, da Silva LO, Cintra LC, Paiva SR, Yamagishi MEB, Caetano AR. Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits. BMC Genomics 2016; 17:454. [PMID: 27297173 PMCID: PMC4907077 DOI: 10.1186/s12864-016-2752-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 05/19/2016] [Indexed: 11/10/2022] Open
Abstract
Background Copy number variations (CNVs) have been shown to account for substantial portions of observed genomic variation and have been associated with qualitative and quantitative traits and the onset of disease in a number of species. Information from high-resolution studies to detect, characterize and estimate population-specific variant frequencies will facilitate the incorporation of CNVs in genomic studies to identify genes affecting traits of importance. Results Genome-wide CNVs were detected in high-density single nucleotide polymorphism (SNP) genotyping data from 1,717 Nelore (Bos indicus) cattle, and in NGS data from eight key ancestral bulls. A total of 68,007 and 12,786 distinct CNVs were observed, respectively. Cross-comparisons of results obtained for the eight resequenced animals revealed that 92 % of the CNVs were observed in both datasets, while 62 % of all detected CNVs were observed to overlap with previously validated cattle copy number variant regions (CNVRs). Observed CNVs were used for obtaining breed-specific CNV frequencies and identification of CNVRs, which were subsequently used for gene annotation. A total of 688 of the detected CNVRs were observed to overlap with 286 non-redundant QTLs associated with important production traits in cattle. All of 34 CNVs previously reported to be associated with milk production traits in Holsteins were also observed in Nelore cattle. Comparisons of estimated frequencies of these CNVs in the two breeds revealed 14, 13, 6 and 14 regions in high (>20 %), low (<20 %) and divergent (NEL > HOL, NEL < HOL) frequencies, respectively. Conclusions Obtained results significantly enriched the bovine CNV map and enabled the identification of variants that are potentially associated with traits under selection in Nelore cattle, particularly in genome regions harboring QTLs affecting production traits. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2752-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joaquim Manoel da Silva
- Faculdade de Ciências Agrárias, Biológicas e Sociais Aplicadas, Universidade do Estado de Mato Grosso (UNEMAT), Av. Prof Dr. Renato Figueiro Varella, CEP 78.690-000, Nova Xavantina, Mato Grosso, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular-Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Poliana Fernanda Giachetto
- Embrapa Informática Agropecuária - Laboratório Multiusuário de Bioinformática (LMB), Campinas, São Paulo, Brazil
| | | | - Leandro Carrijo Cintra
- Embrapa Informática Agropecuária - Laboratório Multiusuário de Bioinformática (LMB), Campinas, São Paulo, Brazil
| | - Samuel Rezende Paiva
- Embrapa - Secretaria de Relações Internacionais, Brasília, Distrito Federal, Brazil.,Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil.,CNPq Fellow, ᅟ, ᅟ
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