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Linga BG, Mohammed SGAA, Farrell T, Rifai HA, Al-Dewik N, Qoronfleh MW. Genomic Newborn Screening for Pediatric Cancer Predisposition Syndromes: A Holistic Approach. Cancers (Basel) 2024; 16:2017. [PMID: 38893137 PMCID: PMC11171256 DOI: 10.3390/cancers16112017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
As next-generation sequencing (NGS) has become more widely used, germline and rare genetic variations responsible for inherited illnesses, including cancer predisposition syndromes (CPSs) that account for up to 10% of childhood malignancies, have been found. The CPSs are a group of germline genetic disorders that have been identified as risk factors for pediatric cancer development. Excluding a few "classic" CPSs, there is no agreement regarding when and how to conduct germline genetic diagnostic studies in children with cancer due to the constant evolution of knowledge in NGS technologies. Various clinical screening tools have been suggested to aid in the identification of individuals who are at greater risk, using diverse strategies and with varied outcomes. We present here an overview of the primary clinical and molecular characteristics of various CPSs and summarize the existing clinical genomics data on the prevalence of CPSs in pediatric cancer patients. Additionally, we discuss several ethical issues, challenges, limitations, cost-effectiveness, and integration of genomic newborn screening for CPSs into a healthcare system. Furthermore, we assess the effectiveness of commonly utilized decision-support tools in identifying patients who may benefit from genetic counseling and/or direct genetic testing. This investigation highlights a tailored and systematic approach utilizing medical newborn screening tools such as the genome sequencing of high-risk newborns for CPSs, which could be a practical and cost-effective strategy in pediatric cancer care.
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Affiliation(s)
- BalaSubramani Gattu Linga
- Department of Research, Women’s Wellness and Research Center, Hamad Medical Corporation (HMC), P.O. Box 3050, Doha 0974, Qatar
- Translational and Precision Medicine Research, Women’s Wellness and Research Center (WWRC), Hamad Medical Corporation (HMC), Doha 0974, Qatar
| | | | - Thomas Farrell
- Department of Research, Women’s Wellness and Research Center, Hamad Medical Corporation (HMC), P.O. Box 3050, Doha 0974, Qatar
| | - Hilal Al Rifai
- Neonatal Intensive Care Unit (NICU), Newborn Screening Unit, Department of Pediatrics and Neonatology, Women’s Wellness and Research Center (WWRC), Hamad Medical Corporation (HMC), Doha 0974, Qatar
| | - Nader Al-Dewik
- Department of Research, Women’s Wellness and Research Center, Hamad Medical Corporation (HMC), P.O. Box 3050, Doha 0974, Qatar
- Translational and Precision Medicine Research, Women’s Wellness and Research Center (WWRC), Hamad Medical Corporation (HMC), Doha 0974, Qatar
- Neonatal Intensive Care Unit (NICU), Newborn Screening Unit, Department of Pediatrics and Neonatology, Women’s Wellness and Research Center (WWRC), Hamad Medical Corporation (HMC), Doha 0974, Qatar
- Genomics and Precision Medicine (GPM), College of Health & Life Science (CHLS), Hamad Bin Khalifa University (HBKU), Doha 0974, Qatar
- Faculty of Health and Social Care Sciences, Kingston University and St George’s University of London, Kingston upon Thames, Surrey, London KT1 2EE, UK
| | - M. Walid Qoronfleh
- Healthcare Research & Policy Division, Q3 Research Institute (QRI), Ann Arbor, MI 48197, USA
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Mandiracioglu B, Ozden F, Kaynar G, Yilmaz MA, Alkan C, Cicek AE. ECOLE: Learning to call copy number variants on whole exome sequencing data. Nat Commun 2024; 15:132. [PMID: 38167256 PMCID: PMC10762021 DOI: 10.1038/s41467-023-44116-y] [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: 08/07/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Copy number variants (CNV) are shown to contribute to the etiology of several genetic disorders. Accurate detection of CNVs on whole exome sequencing (WES) data has been a long sought-after goal for use in clinics. This was not possible despite recent improvements in performance because algorithms mostly suffer from low precision and even lower recall on expert-curated gold standard call sets. Here, we present a deep learning-based somatic and germline CNV caller for WES data, named ECOLE. Based on a variant of the transformer architecture, the model learns to call CNVs per exon, using high-confidence calls made on matched WGS samples. We further train and fine-tune the model with a small set of expert calls via transfer learning. We show that ECOLE achieves high performance on human expert labelled data for the first time with 68.7% precision and 49.6% recall. This corresponds to precision and recall improvements of 18.7% and 30.8% over the next best-performing methods, respectively. We also show that the same fine-tuning strategy using tumor samples enables ECOLE to detect RT-qPCR-validated variations in bladder cancer samples without the need for a control sample. ECOLE is available at https://github.com/ciceklab/ECOLE .
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Affiliation(s)
- Berk Mandiracioglu
- Department of Computer and Communication Sciences, EPFL, Lausanne, Switzerland
| | - Furkan Ozden
- Department of Computer Science, Oxford University, Oxford, UK
| | - Gun Kaynar
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | | | - Can Alkan
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - A Ercument Cicek
- Department of Computer Engineering, Bilkent University, Ankara, Turkey.
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, US.
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Zhou Z, Wu J, Ma W, Dong F, Wang J. Pan-Cancer analyses of Necroptosis-Related genes as a potential target to predict immunotherapeutic outcome. J Cell Mol Med 2022; 27:204-221. [PMID: 36583248 PMCID: PMC9843528 DOI: 10.1111/jcmm.17634] [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: 09/14/2022] [Revised: 11/14/2022] [Accepted: 11/22/2022] [Indexed: 12/31/2022] Open
Abstract
Necroptosis is a unique programmed death mechanism of necrotic cells. However, its role and specific mechanism in cancer remain unclear, and a systematic pan-cancer analysis of necroptosis is yet to be conducted. Thus, we performed a specific pan-cancer analysis using The Cancer Genome Atlas and Genotype-Tissue Expression databases to analyse necroptosis expression in terms of cancer prognosis, DNA methylation status, tumour mutative burden, microsatellite instability, immune cell infiltration in different types of cancer and molecular mechanisms. For the first time, we explored the correlation between necroptosis and immunotherapy prognosis. Thus, our study provides a relatively comprehensive understanding of the carcinogenicity of necroptosis in different types of cancer. It is suggested that necroptosis can be used to evaluate the sensitivity of different patients to immunotherapy and may become a potential target for tumour immunotherapy.
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Affiliation(s)
- Zheng Zhou
- Bengbu Medical College Graduate SchoolBengbuChina,Department of Head and Neck Surgery, Centre of Otolaryngology‐Head and Neck Surgery, Zhejiang Provincial People's HospitalPeople's Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Jiajun Wu
- Bengbu Medical College Graduate SchoolBengbuChina,Department of Head and Neck Surgery, Centre of Otolaryngology‐Head and Neck Surgery, Zhejiang Provincial People's HospitalPeople's Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Wenli Ma
- Bengbu Medical College Graduate SchoolBengbuChina,Department of Head and Neck Surgery, Centre of Otolaryngology‐Head and Neck Surgery, Zhejiang Provincial People's HospitalPeople's Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Feilin Dong
- Zhejiang Provincial Key Laboratory of Diagnosis and Treatment of Endocrine Gland DiseasesHangzhouChina
| | - Jiafeng Wang
- Department of Head and Neck Surgery, Centre of Otolaryngology‐Head and Neck Surgery, Zhejiang Provincial People's HospitalPeople's Hospital of Hangzhou Medical CollegeHangzhouChina,Zhejiang Provincial Key Laboratory of Diagnosis and Treatment of Endocrine Gland DiseasesHangzhouChina
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4
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Shen MH, Huang CJ, Ho TF, Liu CY, Shih YY, Huang CS, Huang CC. Colorectal cancer concurrent gene signature based on coherent patterns between genomic and transcriptional alterations. BMC Cancer 2022; 22:590. [PMID: 35637462 PMCID: PMC9150289 DOI: 10.1186/s12885-022-09627-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 05/03/2022] [Indexed: 11/10/2022] Open
Abstract
Background The aim of the study was to enhance colorectal cancer prognostication by integrating single nucleotide polymorphism (SNP) and gene expression (GE) microarrays for genomic and transcriptional alteration detection; genes with concurrent gains and losses were used to develop a prognostic signature. Methods The discovery dataset comprised 32 Taiwanese colorectal cancer patients, of which 31 were assayed for GE and copy number variations (CNVs) with Illumina Human HT-12 BeadChip v4.0 and Omni 25 BeadChip v1.1. Concurrent gains and losses were declared if coherent manners were observed between GE and SNP arrays. Concurrent genes were also identified in The Cancer Genome Atlas Project (TCGA) as the secondary discovery dataset (n = 345). Results The “universal” concurrent genes, which were the combination of z-transformed correlation coefficients, contained 4022 genes. Candidate genes were evaluated within each of the 10 public domain microarray datasets, and 1655 (2000 probe sets) were prognostic in at least one study. Consensus across all datasets was used to build a risk predictive model, while distinct relapse-free/overall survival patterns between defined risk groups were observed among four out of five training datasets. The predictive accuracy of recurrence, metastasis, or death was between 61 and 86% (cross-validation area under the receiver operating characteristic (ROC) curve: 0.548-0.833) from five independent validation studies. Conclusion The colorectal cancer concurrent gene signature is prognostic in terms of recurrence, metastasis, or mortality among 1746 patients. Genes with coherent patterns between genomic and transcriptional contexts are more likely to provide prognostication for colorectal cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09627-9.
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Affiliation(s)
- Ming-Hung Shen
- Department of Surgery, Fu-Jen Catholic University Hospital, No. 69, Guizi Road, Taishan District, New Taipei City, 243, Taiwan.,Ph. D Program in Nutrition and Food Science, College of Human Ecology, Fu-Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang Dist., New Taipei City, 242062, Taiwan.,School of Medicine, College of Medicine, Fu-Jen Catholic University, No. 510, Zhongzheng Rd., Xinzhuang Dist., New Taipei City, 242062, Taiwan
| | - Chi-Jung Huang
- Department of Biochemistry, National Defense Medical Center, No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City, 11490, Taiwan.,Department of Medical Research, Cathay General Hospital, No.280, Sec. 4, Renai Rd., Daan Dist., Taipei City, 106, Taiwan
| | - Thien-Fiew Ho
- Division of General Surgery, Cathay General Hospital Sijhih, No. 2, Ln. 59, Jiancheng Rd., Xizhi Dist., New Taipei City, 221, Taiwan
| | - Chih-Yi Liu
- Division of Pathology, Cathay General Hospital Sijhih, No. 2, Ln. 59, Jiancheng Rd., Xizhi Dist., New Taipei City, 221, Taiwan
| | - Ying-Yih Shih
- Division of Hematology and Oncology, Cathay General Hospital Sijhih, No. 2, Ln. 59, Jiancheng Rd., Xizhi Dist., New Taipei City, 221, Taiwan
| | - Ching-Shui Huang
- Department of Surgery, Cathay General Hospital, No.280, Sec. 4, Renai Rd., Daan Dist., Taipei City, 106, Taiwan. .,School of Medicine, College of Medicine, Taipei Medical University, 250 Wu-Hsing Street, Taipei City, 110, Taiwan.
| | - Chi-Cheng Huang
- Department of Surgery, Taipei Veterans General Hospital, No.201, Sec. 2, Shipai Rd., Beitou District, Taipei City, 11217, Taiwan. .,Comprehensive Breast Health Center, Taipei Veterans General Hospital, No.201, Sec. 2, Shipai Rd., Beitou District, Taipei City, Taiwan, 11217. .,Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, No.17, Xuzhou Rd., Taipei City, 100, Taiwan.
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5
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Yang B, Zhou M, Wu Y, Ma Y, Tan Q, Yuan W, Ma J. The Impact of Immune Microenvironment on the Prognosis of Pancreatic Ductal Adenocarcinoma Based on Multi-Omics Analysis. Front Immunol 2021; 12:769047. [PMID: 34777388 PMCID: PMC8580856 DOI: 10.3389/fimmu.2021.769047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/07/2021] [Indexed: 01/02/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a malignant tumor characterized by rapid progression, early metastasis, high recurrence, and limited responsiveness to conventional therapies. The 5-year survival rate of PDAC is extremely low (<8%), which lacks effective prognostic evaluation indicators. In this study, we used xCell to analyze infiltrating immune cells in a tumor and through the univariate and multivariate Cox analyses screened out two prognosis-related immune cells, CD4+TN and common lymphoid progenitor (CLP), which were used to construct a Cox model and figure out the risk-score. It was found that the constructed model could greatly improve the sensitivity of prognostic evaluation, that the higher the risk-score, the worse the prognosis. In addition, the risk-score could also identify molecular subtypes with poor prognosis and immunotherapy sensitivity. Through transcriptome and whole-exome sequencing analysis of PDAC dataset from The Cancer Genome Atlas (TCGA), it was found that copy number deletion and low expression of CCL19 might be crucial factors to affect the risk-score. Lastly, validation of the above findings was confirmed not only in Gene Expression Omnibus (GEO) datasets but also in our PDAC patient samples, Peking2020 cohort.
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Affiliation(s)
- Bing Yang
- Center of Biotherapy, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China.,Peking University Fifth School of Clinical Medicine, Beijing, China
| | - Mingyao Zhou
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yunzi Wu
- Department of Pancreatic and Gastric Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuanyuan Ma
- Center of Biotherapy, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Qin Tan
- Center of Biotherapy, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Yuan
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Ma
- Center of Biotherapy, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
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A Comprehensive Multiomics Analysis Identified Ubiquilin 4 as a Promising Prognostic Biomarker of Immune-Related Therapy in Pan-Cancer. JOURNAL OF ONCOLOGY 2021; 2021:7404927. [PMID: 34539785 PMCID: PMC8443395 DOI: 10.1155/2021/7404927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/28/2021] [Indexed: 01/02/2023]
Abstract
Recently, it was reported that ubiquilin 4 (UBQLN4) alteration was associated with genomic instability in some cancers. However, whether UBQLN4 is a valuable biomarker for the prognosis of immunotherapy in pan-cancer was not identified. We evaluated the biologic and oncologic significance of UBQLN4 in pan-cancer at multiomics level, such as expression, mutation, copy number variation (CNV), methylation, and N6-methyladenosine (m6A) methylation. These omics data were obtained from several public databases, including Oncomine, The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), the Genotype-Tissue Expression (GTEx), the Human Protein Atlas (HPA), Gene Set Cancer Analysis (GSCA), m6A-Atlas, CancerSEA, and RNAactDrug. We found that UBQLN4 mRNA and protein were overexpressed in most cancer types, and the expression, mutation, CNV, and methylation of UBQLN4 were associated with the prognosis of some cancers. Mechanistically, UBQLN4 was involved in angiogenesis, DNA damage, apoptosis, and the pathway of PI3K/AKT and TSC/mTOR. Moreover, UBQLN4 mRNA was significantly correlated with immune checkpoints, tumor mutational burden (TMB), microsatellite instability (MSI), and mismatch repair (MMR). And, the correlation among UBQLN4 mRNA, CNV, and methylation and immune microenvironment was also identified. Furthermore, UBQLN4 was associated with the sensitivity of chemotherapy and targeted drugs at multiomics level. In conclusion, UBQLN4 was a promising prognostic biomarker of immune-related therapy in pan-cancer.
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7
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Hu W, Li M, Zhang Q, Liu C, Wang X, Li J, Qiu S, Li L. Establishment of a novel CNV-related prognostic signature predicting prognosis in patients with breast cancer. J Ovarian Res 2021; 14:103. [PMID: 34364397 PMCID: PMC8349487 DOI: 10.1186/s13048-021-00823-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/10/2021] [Indexed: 01/17/2023] Open
Abstract
Background Copy number variation (CNVs) is a key factor in breast cancer development. This study determined prognostic molecular characteristics to predict breast cancer through performing a comprehensive analysis of copy number and gene expression data. Methods Breast cancer expression profiles, CNV and complete information from The Cancer Genome Atlas (TCGA) dataset were collected. Gene Expression Omnibus (GEO) chip data sets (GSE20685 and GSE31448) containing breast cancer samples were used as external validation sets. Univariate survival COX analysis, multivariate survival COX analysis, least absolute shrinkage and selection operator (LASSO), Chi square, Kaplan-Meier (KM) survival curve and receiver operating characteristic (ROC) analysis were applied to build a gene signature model and assess its performance. Results A total of 649 CNV related-differentially expressed gene obtained from TCGA-breast cancer dataset were related to several cancer pathways and functions. A prognostic gene sets with 9 genes were developed to stratify patients into high-risk and low-risk groups, and its prognostic performance was verified in two independent patient cohorts (n = 327, 246). The result uncovered that 9-gene signature could independently predict breast cancer prognosis. Lower mutation of PIK3CA and higher mutation of TP53 and CDH1 were found in samples with high-risk score compared with samples with low-risk score. Patients in the high-risk group showed higher immune score, malignant clinical features than those in the low-risk group. The 9-gene signature developed in this study achieved a higher AUC. Conclusion The current research established a 5-CNV gene signature to evaluate prognosis of breast cancer patients, which may innovate clinical application of prognostic assessment. Supplementary Information The online version contains supplementary material available at 10.1186/s13048-021-00823-y.
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Affiliation(s)
- Wei Hu
- Department of Thyroid and Breast Surgery, Zibo Central Hospital, Zibo, 255036, China
| | - Mingyue Li
- Department of Rehabilitation Medicine, The Third Affilated Hospital, Sun Yat-sen University, Guangzhou, 510000, China
| | - Qi Zhang
- Blood Transfusion Department, Zibo Central Hospital, Zibo, 255036, China
| | - Chuan Liu
- Department of Thyroid and Breast Surgery, Zibo Central Hospital, Zibo, 255036, China
| | - Xinmei Wang
- Department of Pathology, ZiBo Central Hospital, Zibo, 255036, China
| | - Jing Li
- Department of Pathology, ZiBo Central Hospital, Zibo, 255036, China.
| | - Shusheng Qiu
- Department of Thyroid and Breast Surgery, Zibo Central Hospital, Zibo, 255036, China.
| | - Liang Li
- Department of Thyroid and Breast Surgery, Zibo Central Hospital, Zibo, 255036, China.
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Chandramohan R, Kakkar N, Roy A, Parsons DW. reconCNV: interactive visualization of copy number data from high-throughput sequencing. Bioinformatics 2021; 37:1164-1167. [PMID: 32821910 DOI: 10.1093/bioinformatics/btaa746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 07/21/2020] [Accepted: 08/17/2020] [Indexed: 12/30/2022] Open
Abstract
SUMMARY Copy number variation (CNV) is an important category of unbalanced structural rearrangement. While methods for detecting CNV in high-throughput targeted sequencing have become increasingly sophisticated, dedicated tools for interactive and dynamic visualization of CNV from these data are still lacking. We describe reconCNV, a tool that produces an interactive and annotated web-based dashboard for viewing and summarizing CNVs detected in next-generation sequencing (NGS) data. reconCNV is designed to work with delimited result files from most NGS CNV callers with minor adjustments to the configuration file. The reconCNV output is an HTML file that is viewable on any modern web browser, requires no backend server, and can be readily appended to existing analysis pipelines. In addition to a standard CNV track for visualizing relative fold change and absolute copy number, the tool includes an auxiliary variant allele fraction track for visualizing underlying allelic imbalance and loss of heterozygosity. A feature to mask assay-specific technical artifacts and a direct HTML link out to the UCSC Genome Browser are also included to augment the reviewer experience. By providing a light-weight plugin for interactive visualization to existing NGS CNV pipelines, reconCNV can facilitate efficient NGS CNV visualization and interpretation in both research and clinical settings. AVAILABILITY AND IMPLEMENTATION The source code and documentation including a tutorial can be accessed at https://github.com/rghu/reconCNV as well as a Docker image at https://hub.docker.com/repository/docker/raghuc1990/reconcnv. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Nipun Kakkar
- Department of Pediatrics, Texas Children's Cancer Center, Houston, TX 77030, USA
| | - Angshumoy Roy
- Department of Pediatrics, Texas Children's Cancer Center, Houston, TX 77030, USA
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - D Williams Parsons
- Department of Molecular and Human Genetics, Houston, TX 77030, USA
- Department of Pediatrics, Texas Children's Cancer Center, Houston, TX 77030, USA
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
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Zhou Y, Cheng X, Zhang F, Chen Q, Chen X, Shen Y, Lai C, Kota VG, Sun W, Huang Q, Yuan Y, Wang J, Lai M, Zhang D. Integrated multi-omics data analyses for exploring the co-occurring and mutually exclusive gene alteration events in colorectal cancer. Hum Mutat 2020; 41:1588-1599. [PMID: 32485022 DOI: 10.1002/humu.24059] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 03/04/2020] [Accepted: 05/29/2020] [Indexed: 12/19/2022]
Abstract
Co-occurring and mutually exclusive gene alteration events are helpful for understanding carcinogenesis but systematic screening for such events is quite limited. We conducted pairwise screening tests to identify "hit pairs" in colorectal cancer (CRC) by utilizing the cross-omics data from The Cancer Genome Atlas (TCGA). Numerous hit pairs involving somatic mutations, copy number variations, and DNA methylation were found to occur nonrandomly in CRC, such as KRAS and HOXB6, SMAD4 and PMEPA1. Based on these hit pairs, we identified 32 synthetic lethal pairs and 7,527 co-occurring pairs relating to drug response. Our further biological experiments showed that the co-occurrence of mutant FCGBP and NUDT12 silencing (or mutant TMC3 and RPS6KA6 silencing) with small interfering RNA reduced cell viability. Moreover, novel hit pairs could influence prognosis. The patients who carried concurrent mutations of IRF5 and NEFH, SYNE1 and TTN, or MUC16 and NEFH had worse survival outcomes. Particularly, the presence of mutant SYNE1 and TTN pair not only affects prognosis, but also is related to CRC patients' response to drug treatment. Our "hit pair" genes may provide insights into colorectal carcinogenesis and help open new avenues for CRC therapy.
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Affiliation(s)
- Yuan Zhou
- Department of Pathology, and Department of Medical Oncology of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoqing Cheng
- Department of Pathology, and Department of Medical Oncology of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fenglan Zhang
- Department of Pathology, and Department of Medical Oncology of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qingqing Chen
- Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xinyu Chen
- Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yaojia Shen
- Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Chong Lai
- Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Vishnu G Kota
- Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Wenjie Sun
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qiong Huang
- The Core Facilities, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Yuan
- Department of Medical Oncology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Chinese National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jin Wang
- Department of Pathology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Maode Lai
- Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Dandan Zhang
- Department of Pathology, and Department of Medical Oncology of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Department of Pathology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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10
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Lage LB, Freitas-Junior R, Corrêa RDS, dos Santos EE, Ferreira NC, Silva NC, Soares LR. Evaluation of ionizing radiation as a risk factor for the incidence of breast cancer: long-term analysis after the cesium-137 accident in Goiânia, Brazil. An ecological study. SAO PAULO MED J 2020; 138:297-304. [PMID: 32813846 PMCID: PMC9673839 DOI: 10.1590/1516-3180.2020.0041.r1.04052020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/04/2020] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The largest radiological accident to occur in any urban area happened in Goiânia, Brazil, in 1987. OBJECTIVE To evaluate the association between breast cancer incidence and ionizing radiation levels. DESIGN AND SETTING Ecological study among residents of the city of Goiânia, Brazil. METHODS The central region of Goiânia, with seven major sources of contamination from cesium-137, was defined as the study area. The addresses of women diagnosed with breast cancer were identified between 2001 and 2010. The data were geographically referenced and, using census data, the annual averages of crude incidence rates were estimated. The existence of clusters of new cases was ascertained by means of the Moran index. Correlations of radiometric measurements with the incidence were assessed using unconditional linear regression. RESULTS A total of 4,105 new cases were identified, of which 2,233 were in the study area, and of these, 1,286 (57.59%) were georeferenced. The gross rates of total and referenced cases were 102.91 and 71.86/100,000 women, respectively. These were close to the average for Brazilian state capitals, which is 79.37/100,000 women. The cluster analysis showed slight correlations in three small sets of census tracts, but these were far from the sources of contamination. The scatter plot of points and the R2 value close to zero indicated that there was no association between the variables. CONCLUSION This study reinforces the hypothesis that the ionizing radiation levels to which women living in Goiânia are now exposed to are not associated with the onset of new cases of breast cancer.
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Affiliation(s)
- Leonardo Bastos Lage
- MSc. Systems Analyst, Central-Western Regional Center for Nuclear Sciences, Comissão Nacional de Energia Nuclear (CNEN), Abadia de Goiás (GO), Brazil.
| | - Ruffo Freitas-Junior
- MD, PhD. Professor, Mastology Program, Universidade Federal de Goiás (UFG), Goiânia (GO), Brazil.
| | - Rosangela da Silveira Corrêa
- PhD. Senior Technologist, Central-Western Regional Center for Nuclear Sciences, Comissão Nacional de Energia Nuclear (CNEN), Abadia de Goiás (GO), Brazil.
| | - Eliane Eugênia dos Santos
- PhD. Senior Researcher, Central-Western Regional Center for Nuclear Sciences, Comissão Nacional de Energia Nuclear (CNEN), Abadia de Goiás (GO), Brazil.
| | - Nilson Clementino Ferreira
- PhD. Professor, School of Civil and Environmental Engineering, Universidade Federal de Goiás (UFG), Goiânia (GO), Brazil.
| | - Nivaldo Carlos Silva
- PhD. Physicist, Laboratório de Poços de Caldas (LAPOC), Comissão Nacional de Energia Nuclear (CNEN), Poços de Caldas (MG), Brazil.
| | - Leonardo Ribeiro Soares
- MD, PhD. Physician, Mastology Program, Universidade Federal de Goiás (UFG), Goiânia (GO), Brazil.
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11
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Zhang Y, Li W, Wang Y, Wang N. The PLCE1 rs2274223 variant is associated with the risk of laryngeal squamous cell carcinoma. Int J Med Sci 2020; 17:2826-2830. [PMID: 33162810 PMCID: PMC7645332 DOI: 10.7150/ijms.49012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/16/2020] [Indexed: 12/22/2022] Open
Abstract
Background: Laryngeal squamous cell carcinoma (LSCC) ranks second in the mortality rate in respiratory malignant tumors and has potential similarity in genomic alterations with the esophageal squamous cell carcinoma (ESCC). The PLCE1 rs2274223 variant is the most significant susceptibility loci identified in ESCC. Whether it is also associated with LSCC susceptibility is still unclear. Materials and Methods: A total of 331 LSCC patients and 349 healthy controls were recruited in this study. The PLCE1 rs2274223 variant was genotyped by using the Taqman SNP Genotyping Assay. Association between PLCE1 rs2274223 variant and LSCC risk was estimated by logistic regression analysis, which was performed using SAS software. Results: The PLCE1 rs2274223 variant was identified to be significantly associated with the susceptibility of LSCC in the additive model (OR = 1.40, 95% CI: 1.06-1.86, P=0.019). Compared with the wild-type (AA) carriers, the risk genotype (GG) carriers had a 2.8-fold risk of LSCC (95% CI: 1.13-7.06, P=0.026). Stratified analysis showed that the association between rs2274223 and LSCC risk was with higher significance in individuals above 60 (P = 0.027) males (P = 0.030) or non-smokers (P = 0.026). Conclusion: The PLCE1 rs2274223 variant was significantly associated with risk of LSCC, which may be a potential biomarker and therapeutic target for the LSCC.
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Affiliation(s)
- Yi Zhang
- Department of Otolaryngology-Head and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Wei Li
- The Department of Head and Neck surgery, Hubei Cancer Hospital, Wuhan, Hubei, China
| | - Ying Wang
- Department of Pathology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Ningyu Wang
- Department of Otolaryngology-Head and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
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12
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Brusselaers N, Ekwall K, Durand-Dubief M. Copy number of 8q24.3 drives HSF1 expression and patient outcome in cancer: an individual patient data meta-analysis. Hum Genomics 2019; 13:54. [PMID: 31699156 PMCID: PMC6836670 DOI: 10.1186/s40246-019-0241-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/01/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The heat-shock transcription factor 1 (HSF1) has been linked to cell proliferation and survival in cancer and has been proposed as a biomarker for poor prognosis. Here, we assessed the role of HSF1 expression in relation to copy number alteration (CNA) and cancer prognosis. METHODS Using 10,287 cancer genomes from The Cancer Genome Atlas and Cbioportal databases, we assessed the association of HSF1 expression with CNA and cancer prognosis. CNA of 8q24.3 was categorized as diploid (reference), deletion (fewer copies), gain (+ 1 copy) and amplification (≥ + 2 copies). Multivariate logistic regression modeling was used to assess 5-year survival among those with a first cancer diagnosis and complete follow-up data (N = 9568), categorized per anatomical location and histology, assessing interaction with tumor stage, and expressed as odds ratios and 95% confidence intervals. RESULTS We found that only 54.1% of all tumors have a normal predicted 8q24.3 copy number and that 8q24.3 located genes including HSF1 are mainly overexpressed due to increased copies number of 8q24.3 in different cancers. The tumor of patients having respectively gain (+ 1 copy) and amplification (≥ + 2 copies) of 8q24.3 display a global increase of 5-year mortality (odds ratio = 1.98, 95% CI 1.22-3.21) and (OR = 2.19, 1.13-4.26) after full adjustment. For separate cancer types, tumor patients with 8q24.3 deletion showed a marked increase of 5-year mortality in uterine (OR = 4.84, [2.75-8.51]), colorectal (OR = 4.12, [1.15-14.82]), and ovarian (OR = 1.83, [1.39-2.41]) cancers; and decreased mortality in kidney cancer (OR = 0.41, [0.21-0.82]). Gain of 8q24.3 resulted in significant mortality changes in 5-year mortality for cancer of the uterus (OR = 3.67, [2.03-6.66]), lung (OR = 1.76, [1.24-2.51]), colorectal (OR = 1.75, [1.32-2.31]) cancers; and amplification for uterine (OR = 4.58, [1.43-14.65]), prostate (OR = 4.41 [3.41-5.71]), head and neck (OR = 2.68, [2.17-3.30]), and stomach (OR = 0.56, [0.36-0.87]) cancers. CONCLUSIONS Here, we show that CNAs of 8q24.3 genes, including HSF1, are tightly linked to 8q24.3 copy number in tumor patients and can affect patient outcome. Our results indicate that the integration of 8q24.3 CNA detection may be a useful predictor for cancer prognosis.
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Affiliation(s)
- Nele Brusselaers
- Centre for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Karolinska Hospital, SE-17176, Stockholm, Sweden
- Science for Life Laboratory (SciLifeLab), SE-17165, Stockholm, Sweden
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo building, Blickagången 16, S-141 52, Huddinge, Sweden
| | - Mickael Durand-Dubief
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo building, Blickagången 16, S-141 52, Huddinge, Sweden.
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13
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Jin Y, Chen G, Xiao W, Hong H, Xu J, Guo Y, Xiao W, Shi T, Shi L, Tong W, Ning B. Sequencing XMET genes to promote genotype-guided risk assessment and precision medicine. SCIENCE CHINA-LIFE SCIENCES 2019; 62:895-904. [PMID: 31114935 DOI: 10.1007/s11427-018-9479-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/06/2018] [Indexed: 12/26/2022]
Abstract
High-throughput next generation sequencing (NGS) is a shotgun approach applied in a parallel fashion by which the genome is fragmented and sequenced through small pieces and then analyzed either by aligning to a known reference genome or by de novo assembly without reference genome. This technology has led researchers to conduct an explosion of sequencing related projects in multidisciplinary fields of science. However, due to the limitations of sequencing-based chemistry, length of sequencing reads and the complexity of genes, it is difficult to determine the sequences of some portions of the human genome, leaving gaps in genomic data that frustrate further analysis. Particularly, some complex genes are difficult to be accurately sequenced or mapped because they contain high GC-content and/or low complexity regions, and complicated pseudogenes, such as the genes encoding xenobiotic metabolizing enzymes and transporters (XMETs). The genetic variants in XMET genes are critical to predicate inter-individual variability in drug efficacy, drug safety and susceptibility to environmental toxicity. We summarized and discussed challenges, wet-lab methods, and bioinformatics algorithms in sequencing "complex" XMET genes, which may provide insightful information in the application of NGS technology for implementation in toxicogenomics and pharmacogenomics.
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Affiliation(s)
- Yaqiong Jin
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Geng Chen
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Wenming Xiao
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Huixiao Hong
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Joshua Xu
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Yongli Guo
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Wenzhong Xiao
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Cancer Center; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, 200433, China
| | - Weida Tong
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Baitang Ning
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.
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14
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Highly Multiplexed Fluorescence in Situ Hybridization for in Situ Genomics. J Mol Diagn 2019; 21:390-407. [PMID: 30862547 DOI: 10.1016/j.jmoldx.2019.01.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 12/16/2018] [Accepted: 01/30/2019] [Indexed: 12/31/2022] Open
Abstract
The quantification of changes in gene copy number is critical to our understanding of tumor biology and for the clinical management of cancer patients. DNA fluorescence in situ hybridization is the gold standard method to detect copy number alterations, but it is limited by the number of genes one can quantify simultaneously. To increase the throughput of this informative technique, a fluorescent bar-code system for the unique labeling of dozens of genes and an automated image analysis algorithm that enabled their simultaneous hybridization for the quantification of gene copy numbers were devised. We demonstrate the reliability of this multiplex approach on normal human lymphocytes, metaphase spreads of transformed cell lines, and cultured circulating tumor cells. It also opens the door to the development of gene panels for more comprehensive analysis of copy number changes in tissue, including the study of heterogeneity and of high-throughput clinical assays that could provide rapid quantification of gene copy numbers in samples with limited cellularity, such as circulating tumor cells.
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15
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Soni S, Anand P, Padwad YS. MAPKAPK2: the master regulator of RNA-binding proteins modulates transcript stability and tumor progression. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:121. [PMID: 30850014 PMCID: PMC6408796 DOI: 10.1186/s13046-019-1115-1] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/21/2019] [Indexed: 01/09/2023]
Abstract
The p38 mitogen-activated protein kinase (p38MAPK) pathway has been implicated in a variety of pathological conditions including inflammation and metastasis. Post-transcriptional regulation of genes harboring adenine/uridine-rich elements (AREs) in their 3'-untranslated region (3'-UTR) is controlled by MAPK-activated protein kinase 2 (MAPKAPK2 or MK2), a downstream substrate of the p38MAPK. In response to diverse extracellular stimuli, MK2 influences crucial signaling events, regulates inflammatory cytokines, transcript stability and critical cellular processes. Expression of genes involved in these vital cellular cascades is controlled by subtle interactions in underlying molecular networks and post-transcriptional gene regulation that determines transcript fate in association with RNA-binding proteins (RBPs). Several RBPs associate with the 3'-UTRs of the target transcripts and regulate their expression via modulation of transcript stability. Although MK2 regulates important cellular phenomenon, yet its biological significance in tumor progression has not been well elucidated till date. In this review, we have highlighted in detail the importance of MK2 as the master regulator of RBPs and its role in the regulation of transcript stability, tumor progression, as well as the possibility of use of MK2 as a therapeutic target in tumor management.
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Affiliation(s)
- Sourabh Soni
- Pharmacology and Toxicology Laboratory, Food and Nutraceuticals Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, India.,Academy of Scientific and Innovative Research, Chennai, Tamil Nadu, India
| | - Prince Anand
- Pharmacology and Toxicology Laboratory, Food and Nutraceuticals Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, India.,Academy of Scientific and Innovative Research, Chennai, Tamil Nadu, India
| | - Yogendra S Padwad
- Pharmacology and Toxicology Laboratory, Food and Nutraceuticals Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, India. .,Academy of Scientific and Innovative Research, Chennai, Tamil Nadu, India.
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16
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Mu W, Li B, Wu S, Chen J, Sain D, Xu D, Black MH, Karam R, Gillespie K, Farwell Hagman KD, Guidugli L, Pronold M, Elliott A, Lu HM. Detection of structural variation using target captured next-generation sequencing data for genetic diagnostic testing. Genet Med 2018; 21:1603-1610. [PMID: 30563988 PMCID: PMC6752280 DOI: 10.1038/s41436-018-0397-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 11/28/2018] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Structural variation (SV) is associated with inherited diseases. Next-generation sequencing (NGS) is an efficient method for SV detection because of its high-throughput, low cost, and base-pair resolution. However, due to lack of standard NGS protocols and a limited number of clinical samples with pathogenic SVs, comprehensive standards for SV detection, interpretation, and reporting are to be established. METHODS We performed SV assessment on 60,000 clinical samples tested with hereditary cancer NGS panels spanning 48 genes. To evaluate NGS results, NGS and orthogonal methods were used separately in a blinded fashion for SV detection in all samples. RESULTS A total of 1,037 SVs in coding sequence (CDS) or untranslated regions (UTRs) and 30,847 SVs in introns were detected and validated. Across all variant types, NGS shows 100% sensitivity and 99.9% specificity. Overall, 64% of CDS/UTR SVs were classified as pathogenic/likely pathogenic, and five deletions/duplications were reclassified as pathogenic using breakpoint information from NGS. CONCLUSION The SVs presented here can be used as a valuable resource for clinical research and diagnostics. The data illustrate NGS as a powerful tool for SV detection. Application of NGS and confirmation technologies in genetic testing ensures delivering accurate and reliable results for diagnosis and patient care.
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Affiliation(s)
- Wenbo Mu
- Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Bing Li
- Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Sitao Wu
- Ambry Genetics, Aliso Viejo, CA 92656, USA
| | | | - Divya Sain
- Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Dong Xu
- Ambry Genetics, Aliso Viejo, CA 92656, USA
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17
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Pang Y, Guan Y, Jin X, Shen H, Liu L, Jia Q, Meng F, Zhang X. Association of TSHR Gene Copy Number Variation with TSH Abnormalities. Biol Trace Elem Res 2018; 186:85-90. [PMID: 29546542 DOI: 10.1007/s12011-018-1300-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/06/2018] [Indexed: 12/09/2022]
Abstract
Thyroid-stimulating hormone (TSH) is secreted by the pituitary gland and promotes thyroid growth and function, with increased TSH levels typically associated with hypothyroidism. By consulting the literature, we found that the TSHR, PAX8, and PDE4B genes are associated with thyroid function. Recently, copy number variations (CNVs) have been used as genetic markers to investigate inter-individual variation. Therefore, we investigated the relationship between the TSHR, PAX8, and PDE4B gene CNVs and TSH abnormalities, by calculating variations in gene copy number. Four hundred and eighty-one participants, 232 healthy controls and 249 patients with TSH abnormalities, were selected from three distinct areas in China with different iodine statuses. RT-PCR was used to detect CNVs. Urinary iodine concentrations (UIC) were measured by As3+-Ce4+ catalytic spectrophotometry. There was an association between a CNV at the TSHR gene and TSH abnormalities (p = 0.002). The distribution of PAX8 and PDE4B gene CNVs between patients with TSH abnormalities and healthy controls was not significantly different. UIC > 200 μg/l (OR = 1.49, 95% CI = 1.01-2.22) and the TSHR gene (OR = 6.01, 95% CI = 1.96-18.41) were found to be risk factors for TSH abnormalities. PAX8 and PDE4B gene CNVs were not significantly associated with TSH abnormalities. There was no significant interaction between UIC and any of the examined CNVs. In conclusion, the TSHR gene CNV was associated with the development of TSH abnormalities. No significant associations were revealed between urinary iodine levels and candidate gene CNVs.
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Affiliation(s)
- Yi Pang
- Key Laboratory of Etiology and Epidemiology, National Health and Family Planning Commission, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yunfeng Guan
- Key Laboratory of Etiology and Epidemiology, National Health and Family Planning Commission, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xing Jin
- Key Laboratory of Etiology and Epidemiology, National Health and Family Planning Commission, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Hongmei Shen
- Key Laboratory of Etiology and Epidemiology, National Health and Family Planning Commission, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China.
| | - Lixiang Liu
- Key Laboratory of Etiology and Epidemiology, National Health and Family Planning Commission, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Qingzhen Jia
- Institute for Endemic Disease Prevention and Treatment of Shanxi Province, Linfen, Shanxi, China
| | - Fangang Meng
- Key Laboratory of Etiology and Epidemiology, National Health and Family Planning Commission, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiaoye Zhang
- Key Laboratory of Etiology and Epidemiology, National Health and Family Planning Commission, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
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18
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Zhao K, Zhao Y, Zhu JY, Dong H, Cong WM, Yu Y, Wang H, Zhu ZZ, Xu Q. A Panel of Genes Identified as Targets for 8q24.13-24.3 Gain Contributing to Unfavorable Overall Survival in Patients with Hepatocellular Carcinoma. Curr Med Sci 2018; 38:590-596. [PMID: 30128866 DOI: 10.1007/s11596-018-1918-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/17/2018] [Indexed: 12/12/2022]
Abstract
Copy number aberrations (CNAs) in chromosome arm 8q have been associated with unfavorable clinical outcomes of several cancers and progressive tumor characteristics of hepatocellular carcinoma (HCC). This study was to identify correlation of CNAs in 8q with clinical outcomes of HCC patients, and further screen for differentially expressed genes in outcome-related CNAs. Array comparative genomic hybridization and expression arrays were performed to detect CNAs and expression levels, respectively. The correlations between CNAs in 8q and outcomes were analyzed in 66 patients, with a median follow-up time of 45.0 months (range, 2.6-108.6 months). One hundred and nine cases were further evaluated to identify differentially expressed genes in the potential outcome-related CNAs. Copy number gain in 8q was observed in 22 (33.3%) of the 66 HCC cases. The most recurrent gains (with frequencies >20%) were 8q13.3-21.3,8q21.3-23.3,8q23.3-24.13,8q24.13-24.3, and 8q24.3. Survival analysis showed that 8q24.13-24.3 gain was significantly associated with reduced overall survival (jP=0.010). Multivariate Cox analysis identified 8q24.13-24.3 gain as an independent prognostic factor for poor overall survival (HR=2.47; 95% CI=1.16-5.26; Р=0.019). Apanel of 17 genes within the 8q24.13-24.3 region, including ATAD2,SQLE,PVT1,ASAP1, and NDRG1 were significantly upregulated in HCCs with 8q24.13-24.3 gain compared to those without. These results suggest that copy number gain at 8q24.13-24.3 is an unfavorable prognostic marker for HCC patients, and the potential oncogenes ATAD2,SQLE, PVT1, ASAP1,and NDRG1 within the regional gain, may contribute coordinately to the 8q24.13-24.3 gain-related poor prognosis.
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Affiliation(s)
- Kun Zhao
- Department of Oncology, Shanghai Tenth People' s Hospital, Tongji University School of Medicine, Shanghai, 200072, China.,Shanghai Clinical College of Anhui Medical University, Shanghai, 200072, China
| | - Yu Zhao
- Department of Oncology, Shanghai Tenth People' s Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Jia-Yi Zhu
- Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hui Dong
- Department of Pathology, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, China
| | - Wen-Ming Cong
- Department of Pathology, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, 200438, China
| | - Yi Yu
- Department of Oncology, Shanghai Tenth People' s Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Hui Wang
- Department of Oncology, Shanghai Tenth People' s Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Zhong-Zheng Zhu
- Department of Oncology, Shanghai Tenth People' s Hospital, Tongji University School of Medicine, Shanghai, 200072, China.
| | - Qing Xu
- Department of Oncology, Shanghai Tenth People' s Hospital, Tongji University School of Medicine, Shanghai, 200072, China.
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19
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Overwater E, Marsili L, Baars MJH, Baas AF, van de Beek I, Dulfer E, van Hagen JM, Hilhorst-Hofstee Y, Kempers M, Krapels IP, Menke LA, Verhagen JMA, Yeung KK, Zwijnenburg PJG, Groenink M, van Rijn P, Weiss MM, Voorhoeve E, van Tintelen JP, Houweling AC, Maugeri A. Results of next-generation sequencing gene panel diagnostics including copy-number variation analysis in 810 patients suspected of heritable thoracic aortic disorders. Hum Mutat 2018; 39:1173-1192. [PMID: 29907982 PMCID: PMC6175145 DOI: 10.1002/humu.23565] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 05/23/2018] [Accepted: 05/30/2018] [Indexed: 01/02/2023]
Abstract
Simultaneous analysis of multiple genes using next-generation sequencing (NGS) technology has become widely available. Copy-number variations (CNVs) in disease-associated genes have emerged as a cause for several hereditary disorders. CNVs are, however, not routinely detected using NGS analysis. The aim of this study was to assess the diagnostic yield and the prevalence of CNVs using our panel of Hereditary Thoracic Aortic Disease (H-TAD)-associated genes. Eight hundred ten patients suspected of H-TAD were analyzed by targeted NGS analysis of 21 H-TAD associated genes. In addition, the eXome hidden Markov model (XHMM; an algorithm to identify CNVs in targeted NGS data) was used to detect CNVs in these genes. A pathogenic or likely pathogenic variant was found in 66 of 810 patients (8.1%). Of these 66 pathogenic or likely pathogenic variants, six (9.1%) were CNVs not detectable by routine NGS analysis. These CNVs were four intragenic (multi-)exon deletions in MYLK, TGFB2, SMAD3, and PRKG1, respectively. In addition, a large duplication including NOTCH1 and a large deletion encompassing SCARF2 were detected. As confirmed by additional analyses, both CNVs indicated larger chromosomal abnormalities, which could explain the phenotype in both patients. Given the clinical relevance of the identification of a genetic cause, CNV analysis using a method such as XHMM should be incorporated into the clinical diagnostic care for H-TAD patients.
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Affiliation(s)
- Eline Overwater
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands.,Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Luisa Marsili
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands.,Medical Genetics Unit, Tor Vergata University Hospital, Rome, Italy
| | - Marieke J H Baars
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Annette F Baas
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Irma van de Beek
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands.,Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Eelco Dulfer
- Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands
| | - Johanna M van Hagen
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | | | - Marlies Kempers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ingrid P Krapels
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Leonie A Menke
- Department of Pediatrics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Judith M A Verhagen
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Kak K Yeung
- Department of Surgery, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam, the Netherlands.,Department of Physiology, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam, the Netherlands
| | - Petra J G Zwijnenburg
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - Maarten Groenink
- Department of Cardiology and Radiology, Academic Medical Center Amsterdam, University of Amsterdam, Amsterdam, the Netherlands
| | - Peter van Rijn
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - Marjan M Weiss
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - Els Voorhoeve
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - J Peter van Tintelen
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands.,Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Arjan C Houweling
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - Alessandra Maugeri
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
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20
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Chi C, Ajwad R, Kuang Q, Hu P. A Novel Graph-based Algorithm to Infer Recurrent Copy Number Variations in Cancer. Cancer Inform 2016; 15:43-50. [PMID: 27773988 PMCID: PMC5063805 DOI: 10.4137/cin.s39368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 12/17/2022] Open
Abstract
Many cancers have been linked to copy number variations (CNVs) in the genomic DNA. Although there are existing methods to analyze CNVs from individual samples, cancer-causing genes are more frequently discovered in regions where CNVs are common among tumor samples, also known as recurrent CNVs. Integrating multiple samples and locating recurrent CNV regions remain a challenge, both computationally and conceptually. We propose a new graph-based algorithm for identifying recurrent CNVs using the maximal clique detection technique. The algorithm has an optimal solution, which means all maximal cliques can be identified, and guarantees that the identified CNV regions are the most frequent and that the minimal regions have been delineated among tumor samples. The algorithm has successfully been applied to analyze a large cohort of breast cancer samples and identified some breast cancer-associated genes and pathways.
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Affiliation(s)
- Chen Chi
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada; Centre for Healthcare Innovation, Winnipeg Regional Health Authority/University of Manitoba, Winnipeg, Canada
| | - Rasif Ajwad
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada; Department of Computer Science, University of Manitoba, Winnipeg, Canada
| | - Qin Kuang
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada
| | - Pingzhao Hu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada; Centre for Healthcare Innovation, Winnipeg Regional Health Authority/University of Manitoba, Winnipeg, Canada; Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, Canada
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21
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Copy number variations and cancer susceptibility: Retraction. Curr Opin Oncol 2016; 28:453. [PMID: 27495794 DOI: 10.1097/01.cco.0000491182.00738.ba] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Jin DH, Lee J, Kim KM, Kim S, Kim DH, Park J. Overexpression of MAPK15 in gastric cancer is associated with copy number gain and contributes to the stability of c-Jun. Oncotarget 2016; 6:20190-203. [PMID: 26035356 PMCID: PMC4652997 DOI: 10.18632/oncotarget.4171] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 05/02/2015] [Indexed: 12/23/2022] Open
Abstract
This study was aimed at understanding the functional and clinicopathological significance of MAPK15 alteration in gastric cancer. Genome-wide copy number alterations (CNAs) were first investigated in 40 gastric cancers using Agilent aCGH-244K or aCGH-400K, and copy number gains of MAPK15 found in aCGH were validated in another set of 48 gastric cancer tissues. The expression of MAPK15 was analyzed using immunohistochemistry in concurrent lesions of normal, adenoma, and carcinoma from additional 45 gastric cancer patients. The effects of MAPK15 on cell cycle, c-Jun phosphorylation, and mRNA stability were analyzed in gastric cancer cells. Copy number gains of MAPK15 were found in 15 (17%) of 88 tumor tissues. The mRNA levels of MAPK15 were relatively high in the gastric cancer tissues and gastric cancer cells with higher copy number gains than those without. Knockdown of MAPK15 using siRNA in gastric cancer cells significantly suppressed cell proliferation and resulted in cell cycle arrest at G1-S phase. Reduced c-Jun phosphorylation and c-Jun half-life were observed in MAPK15-knockdowned cells. In addition, transient transfection of MAPK15 into AGS gastric cancer cells with low copy number resulted in an increase of c-Jun phosphorylation and stability. The overexpression of MAPK15 occurred at a high frequency in carcinomas (37%) compared to concurrent normal tissues (2%) and adenomas (21%). In conclusion, the present study suggests that MAPK15 overexpression may contribute to the malignant transformation of gastric mucosa by prolonging the stability of c-Jun. And, patients with copy number gain of MAPK15 in normal or premalignant tissues of stomach may have a chance to progress to invasive cancer.
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Affiliation(s)
- Dong-Hao Jin
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Jeeyun Lee
- Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyoung Mee Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sung Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Duk-Hwan Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Joobae Park
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Korea
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23
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Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression. PLoS Comput Biol 2016; 12:e1004871. [PMID: 27177143 PMCID: PMC4866742 DOI: 10.1371/journal.pcbi.1004871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/14/2016] [Indexed: 11/22/2022] Open
Abstract
By integrating Haar wavelets with Hidden Markov Models, we achieve drastically reduced running times for Bayesian inference using Forward-Backward Gibbs sampling. We show that this improves detection of genomic copy number variants (CNV) in array CGH experiments compared to the state-of-the-art, including standard Gibbs sampling. The method concentrates computational effort on chromosomal segments which are difficult to call, by dynamically and adaptively recomputing consecutive blocks of observations likely to share a copy number. This makes routine diagnostic use and re-analysis of legacy data collections feasible; to this end, we also propose an effective automatic prior. An open source software implementation of our method is available at http://schlieplab.org/Software/HaMMLET/ (DOI: 10.5281/zenodo.46262). This paper was selected for oral presentation at RECOMB 2016, and an abstract is published in the conference proceedings.
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24
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Copy number variants associated with 18p11.32, DCC and the promoter 1B region of APC in colorectal polyposis patients. Meta Gene 2015; 7:95-104. [PMID: 26909336 PMCID: PMC4733217 DOI: 10.1016/j.mgene.2015.12.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 12/16/2015] [Accepted: 12/21/2015] [Indexed: 01/05/2023] Open
Abstract
Familial Adenomatous Polyposis (FAP) is the second most common inherited predisposition to colorectal cancer (CRC) associated with the development of hundreds to thousands of adenomas in the colon and rectum. Mutations in APC are found in ~ 80% polyposis patients with FAP. In the remaining 20% no genetic diagnosis can be provided suggesting other genes or mechanisms that render APC inactive may be responsible. Copy number variants (CNVs) remain to be investigated in FAP and may account for disease in a proportion of polyposis patients. A cohort of 56 polyposis patients and 40 controls were screened for CNVs using the 2.7M microarray (Affymetrix) with data analysed using ChAS (Affymetrix). A total of 142 CNVs were identified unique to the polyposis cohort suggesting their involvement in CRC risk. We specifically identified CNVs in four unrelated polyposis patients among CRC susceptibility genes APC, DCC, MLH1 and CTNNB1 which are likely to have contributed to disease development in these patients. A recurrent deletion was observed at position 18p11.32 in 9% of the patients screened that was of particular interest. Further investigation is necessary to fully understand the role of these variants in CRC risk given the high prevalence among the patients screened.
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Key Words
- ALL, acute lymphoblastic leukaemia
- BH, Bengamini and Hochberg
- CHAS, Chromosome Analysis Suite
- CN, copy number
- CNV
- CNV, copy number variation
- COSMIC, Catalogue of Somatic Mutations in Cancer
- CRC, colorectal cancer
- Cancer
- DGV, Database of genomic variants
- DNA, deoxyribose nucleic acid
- FAP, familial adenomatous polyposis
- HMDD, human microRNA disease database
- KEGG, Kyoto Encyclopaedia of Genes and Genomes
- Kb, kilobase
- LOH, loss of heterozygosity
- MLPA, multiplex ligation-dependant probe amplification
- MMR, mismatch repair
- NTC, no template control
- QC, quality control
- RNA, ribose nucleic acid
- SNP, single nucleotide polymorphism
- TAM, Tool for the annotation of microRNAs
- TCGA, The Cancer Genome Atlas
- UCSC, University of California, Santa Cruz
- diagnostic testing
- lncRNA, link RNA
- long non-coding RNAs
- mapd, median absolute pairwise difference
- miR, microRNA
- ng, nanogram
- polyposis
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Chen L, Yang J, Huang T, Kong X, Lu L, Cai YD. Mining for novel tumor suppressor genes using a shortest path approach. J Biomol Struct Dyn 2015. [PMID: 26209080 DOI: 10.1080/07391102.2015.1042915] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cancer, being among the most serious diseases, causes many deaths every year. Many investigators have devoted themselves to designing effective treatments for this disease. Cancer always involves abnormal cell growth with the potential to invade or spread to other parts of the body. In contrast, tumor suppressor genes (TSGs) act as guardians to prevent a disordered cell cycle and genomic instability in normal cells. Studies on TSGs can assist in the design of effective treatments against cancer. In this study, we propose a computational method to discover potential TSGs. Based on the known TSGs, a number of candidate genes were selected by applying the shortest path approach in a weighted graph that was constructed using protein-protein interaction network. The analysis of selected genes shows that some of them are new TSGs recently reported in the literature, while others may be novel TSGs.
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Affiliation(s)
- Lei Chen
- a College of Life Science , Shanghai University , Shanghai 200444 , P.R. China.,b College of Information Engineering , Shanghai Maritime University , Shanghai 201306 , P.R. China
| | - Jing Yang
- c The Key Laboratory of Stem Cell Biology , Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine (SJTUSM) and Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS) , Shanghai 200025 , P.R. China
| | - Tao Huang
- c The Key Laboratory of Stem Cell Biology , Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine (SJTUSM) and Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS) , Shanghai 200025 , P.R. China
| | - Xiangyin Kong
- c The Key Laboratory of Stem Cell Biology , Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine (SJTUSM) and Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS) , Shanghai 200025 , P.R. China
| | - Lin Lu
- d Department of Radiology , Columbia University Medical Center , New York , NY 10032 , USA
| | - Yu-Dong Cai
- a College of Life Science , Shanghai University , Shanghai 200444 , P.R. China
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26
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Jin DH, Park SE, Lee J, Kim KM, Kim S, Kim DH, Park J. Copy Number Gains at 8q24 and 20q11-q13 in Gastric Cancer Are More Common in Intestinal-Type than Diffuse-Type. PLoS One 2015; 10:e0137657. [PMID: 26360582 PMCID: PMC4567330 DOI: 10.1371/journal.pone.0137657] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 08/19/2015] [Indexed: 12/21/2022] Open
Abstract
The present study was aimed at discovering DNA copy number alterations (CNAs) involved in the carcinogenesis of stomach and at understanding their clinicopathological significances in the Korean population. DNA copy numbers were analyzed using Agilent 244K or 400K array comparative genomic hybridization (aCGH) in fresh-frozen tumor and matched normal tissues from 40 gastric cancer patients. Some of the detected CNA regions were validated using multiplex ligation-dependent probe amplification (MLPA) in six of the 40 patients and customized Agilent 60K aCGH in an independent set of 48 gastric cancers. The mRNA levels of genes at common CNA regions were analyzed using quantitative real-time PCR. Copy number gains were more common than losses across the entire genome in tumor tissues compared to matched normal tissues. The mean number of alterations per case was 64 for gains and 40 for losses, and the median aberration length was 44016 bp for gains and 4732 bp for losses. Copy number gains were frequently detected at 7p22.1 (20%), 8q24.21 (27%-30%), 8q24.3 (22%-48%), 13q34 (20%-31%), and 20q11-q13 (25%-30%), and losses at 3p14.2 (43%), 4q35.2 (27%), 6q26 (23%), and 17p13.3 (20%-23%). CNAs at 7p22.1, 13q34, and 17p13.3 have not been reported in other populations. Most of the copy number losses were associated with down-regulation of mRNA levels, but the correlation between copy number gains and mRNA expression levels varied in a gene-dependent manner. In addition, copy number gains tended to occur more commonly in intestinal-type cancers than in diffuse-type cancers. In conclusion, the present study suggests that copy number gains at 8q24 and 20q11-q13 and losses at 3p14.2 may be common events in gastric cancer but CNAs at 7p22.1, 13q34, and 17p13.3 may be Korean-specific.
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Affiliation(s)
- Dong-Hao Jin
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 135–710, Korea
| | - Seong-Eun Park
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 135–710, Korea
| | - Jeeyun Lee
- Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135–710, Korea
| | - Kyung-Mi Kim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 135–710, Seoul, Korea
| | - Sung Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135–710, Korea
| | - Duk-Hwan Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 135–710, Korea
| | - Joobae Park
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 135–710, Korea
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27
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Zhang ZZ, Huang J, Wang YP, Cai B, Han ZG. NOXIN as a cofactor of DNA polymerase-primase complex could promote hepatocellular carcinoma. Int J Cancer 2015; 137:765-75. [PMID: 25612832 DOI: 10.1002/ijc.29451] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 12/23/2014] [Indexed: 12/17/2022]
Affiliation(s)
- Zhuang-Zhuang Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine of Rui-Jin Hospital; Shanghai Jiao Tong University School of Medicine; Shanghai China
- Shanghai-MOST Key Laboratory for Disease and Health Genomics; Chinese National Human Genome Center at Shanghai; Shanghai China
| | - Jian Huang
- Shanghai-MOST Key Laboratory for Disease and Health Genomics; Chinese National Human Genome Center at Shanghai; Shanghai China
| | - Yu-Ping Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine of Rui-Jin Hospital; Shanghai Jiao Tong University School of Medicine; Shanghai China
- Shanghai-MOST Key Laboratory for Disease and Health Genomics; Chinese National Human Genome Center at Shanghai; Shanghai China
| | - Bing Cai
- Department of Hepatobiliary Surgery; Wuxi People's Hospital of Nanjing Medical University; Jiangsu China
| | - Ze-Guang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine of Rui-Jin Hospital; Shanghai Jiao Tong University School of Medicine; Shanghai China
- Shanghai-MOST Key Laboratory for Disease and Health Genomics; Chinese National Human Genome Center at Shanghai; Shanghai China
- Shanghai Center for Systems Biomedicine; Shanghai Jiao Tong University; Shanghai China
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28
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Sapkota Y. Germline DNA variations in breast cancer predisposition and prognosis: a systematic review of the literature. Cytogenet Genome Res 2014; 144:77-91. [PMID: 25401968 DOI: 10.1159/000369045] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2014] [Indexed: 11/19/2022] Open
Abstract
Breast cancer is the most common cancer and the second leading cause of death in women worldwide. The disease is caused by a combination of genetic, environmental, lifestyle, and reproductive risk factors. Linkage and family-based studies have identified many pathological germline mutations, which account for around 20% of the genetic risk of familial breast cancer. In recent years, single nucleotide polymorphism-based genetic association studies, especially genome-wide association studies (GWASs), have been very successful in uncovering low-penetrance common variants associated with breast cancer risk. These common variants alone may explain up to an additional 30% of the familial risk of breast cancer. With the advent of available genetic resources and growing collaborations among researchers across the globe, the much needed large sample size to capture variants with small effect sizes and low population frequencies is being addressed, and hence many more common variants are expected to be discovered in the coming days. Here, major GWASs conducted for breast cancer predisposition and prognosis until 2013 are summarized. Few studies investigating other forms of genetic variations contributing to breast cancer predisposition and disease outcomes are also discussed. Finally, the potential utility of the GWAS-identified variants in disease risk models and some future perspectives are presented.
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Affiliation(s)
- Yadav Sapkota
- The Neurogenetics Laboratory, Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Qld., Australia
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29
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Park CH, Rha SY, Ahn JB, Shin SJ, Kwon WS, Kim TS, An S, Kim NK, Yang WI, Chung HC. PINCH-2 presents functional copy number variation and suppresses migration of colon cancer cells by paracrine activity. Int J Cancer 2014; 136:2273-83. [PMID: 25346044 DOI: 10.1002/ijc.29273] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 09/30/2014] [Indexed: 01/15/2023]
Abstract
In recent years, characterization of cancer and its environment has become necessary. However, studies of the cancer microenvironment remain insufficient. Copy number variations (CNVs) occur in 40% of cancer-related genes, but few studies have reported the correlation between CNVs in morphologically normal tissues adjacent to cancer and cancer progression. In this study, we evaluated cancer cell migration and invasion according to the genetic differences between cancer tissues and their surrounding normal tissues. To study the field cancerization effect, we screened 89 systemic metastasis-related CNVs from morphologically normal tissues adjacent to colon cancers. Among these CNVs, LIM and senescent cell antigen-like domain 2 (PINCH-2) showed copy number amplification and upregulation of mRNA in the nonrelapsed group compared to the systemic relapse group. PINCH-2 expression in colon cancer cells was lower than that in normal epithelial colon cells at both the protein and mRNA levels. Suppression of PINCH-2 resulted in decreased formation of the PINCH-2-IPP (PINCH-2, integrin-linked kinase and α-parvin) complex and reciprocally increased formation of the PINCH-1-IPP complex. Although PINCH-2 expression of survival pathway-related proteins (Akt and phospho-Akt) did not change upon suppression of PINCH-2 expression, cell migration-related proteins [matrix-metalloproteinase (MMP)-9 and -11] were upregulated through autocrine and paracrine activation. Thus, PINCH-2 participates in decreased systemic recurrence by competitively regulating IPP complex formation with PINCH-1, thereby suppressing autocrine and paracrine effects on motility in colon cancer. This genetic change in morphologically normal tissue suggests a field cancerization effect of the tumor microenvironment in cancer progression.
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Affiliation(s)
- Chan Hee Park
- National Biochip Research Center, Yonsei University College of Medicine, Yonsei University Health System, Seoul, Korea; Cancer Metastasis Research Center, Yonsei University College of Medicine, Yonsei University Health System, Seoul, Korea; Yonsei Cancer Research Institute, Yonsei University College of Medicine, Yonsei University Health System, Seoul, Korea
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30
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Horpaopan S, Spier I, Zink AM, Altmüller J, Holzapfel S, Laner A, Vogt S, Uhlhaas S, Heilmann S, Stienen D, Pasternack SM, Keppler K, Adam R, Kayser K, Moebus S, Draaken M, Degenhardt F, Engels H, Hofmann A, Nöthen MM, Steinke V, Perez-Bouza A, Herms S, Holinski-Feder E, Fröhlich H, Thiele H, Hoffmann P, Aretz S. Genome-wide CNV analysis in 221 unrelated patients and targeted high-throughput sequencing reveal novel causative candidate genes for colorectal adenomatous polyposis. Int J Cancer 2014; 136:E578-89. [PMID: 25219767 DOI: 10.1002/ijc.29215] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 08/04/2014] [Accepted: 09/03/2014] [Indexed: 12/27/2022]
Abstract
To uncover novel causative genes in patients with unexplained adenomatous polyposis, a model disease for colorectal cancer, we performed a genome-wide analysis of germline copy number variants (CNV) in a large, well characterized APC and MUTYH mutation negative patient cohort followed by a targeted next generation sequencing (NGS) approach. Genomic DNA from 221 unrelated German patients was genotyped on high-resolution SNP arrays. Putative CNVs were filtered according to stringent criteria, compared with those of 531 population-based German controls, and validated by qPCR. Candidate genes were prioritized using in silico, expression, and segregation analyses, data mining and enrichment analyses of genes and pathways. In 27% of the 221 unrelated patients, a total of 77 protein coding genes displayed rare, nonrecurrent, germline CNVs. The set included 26 candidates with molecular and cellular functions related to tumorigenesis. Targeted high-throughput sequencing found truncating point mutations in 12% (10/77) of the prioritized genes. No clear evidence was found for autosomal recessive subtypes. Six patients had potentially causative mutations in more than one of the 26 genes. Combined with data from recent studies of early-onset colorectal and breast cancer, recurrent potential loss-of-function alterations were detected in CNTN6, FOCAD (KIAA1797), HSPH1, KIF26B, MCM3AP, YBEY and in three genes from the ARHGAP family. In the canonical Wnt pathway oncogene CTNNB1 (β-catenin), two potential gain-of-function mutations were found. In conclusion, the present study identified a group of rarely affected genes which are likely to predispose to colorectal adenoma formation and confirmed previously published candidates for tumor predisposition as etiologically relevant.
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31
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Yang J, Chen L, Kong X, Huang T, Cai YD. Analysis of tumor suppressor genes based on gene ontology and the KEGG pathway. PLoS One 2014; 9:e107202. [PMID: 25207935 PMCID: PMC4160198 DOI: 10.1371/journal.pone.0107202] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2014] [Accepted: 08/07/2014] [Indexed: 12/31/2022] Open
Abstract
Cancer is a serious disease that causes many deaths every year. We urgently need to design effective treatments to cure this disease. Tumor suppressor genes (TSGs) are a type of gene that can protect cells from becoming cancerous. In view of this, correct identification of TSGs is an alternative method for identifying effective cancer therapies. In this study, we performed gene ontology (GO) and pathway enrichment analysis of the TSGs and non-TSGs. Some popular feature selection methods, including minimum redundancy maximum relevance (mRMR) and incremental feature selection (IFS), were employed to analyze the enrichment features. Accordingly, some GO terms and KEGG pathways, such as biological adhesion, cell cycle control, genomic stability maintenance and cell death regulation, were extracted, which are important factors for identifying TSGs. We hope these findings can help in building effective prediction methods for identifying TSGs and thereby, promoting the discovery of effective cancer treatments.
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Affiliation(s)
- Jing Yang
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine (SJTUSM) and Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, People’s Republic of China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, People’s Republic of China
| | - Xiangyin Kong
- The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine (SJTUSM) and Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, People’s Republic of China
| | - Tao Huang
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Yu-Dong Cai
- Institute of Systems Biology, Shanghai University, Shanghai, People’s Republic of China
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32
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Ambros IM, Brunner C, Abbasi R, Frech C, Ambros PF. Ultra-High Density SNParray in Neuroblastoma Molecular Diagnostics. Front Oncol 2014; 4:202. [PMID: 25161957 PMCID: PMC4129917 DOI: 10.3389/fonc.2014.00202] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 07/15/2014] [Indexed: 12/27/2022] Open
Abstract
Neuroblastoma serves as a paradigm for applying tumor genomic data for determining patient prognosis and thus for treatment allocation. MYCN status, i.e., amplified vs. non-amplified, was one of the very first biomarkers in oncology to discriminate aggressive from less aggressive or even favorable clinical courses of neuroblastoma. However, MYCN amplification is by far not the only genetic change associated with unfavorable clinical courses. So called “segmental chromosomal aberrations,” (SCAs) i.e., gains or losses of chromosomal fragments, can also indicate tumor aggressiveness. The clinical use of these genomic aberrations has, however, been hampered for many years by methodical and interpretational problems. Only after reaching worldwide consensus on markers, methodology, and data interpretation, information on SCAs has recently been implemented in clinical studies. Now, a number of collaborative studies within COG, GPOH, and SIOPEN use genomic information to stratify therapy for patients with localized and metastatic disease. Recently, new types of DNA based aberrations influencing the clinical behavior of neuroblastomas have been described. Deletions or mutations of genes like ATRX and a phenomenon referred to as “chromothripsis” are all assumed to correlate with an unfavorable clinical behavior. However, these genomic aberrations need to be scrutinized in larger studies applying the most appropriate techniques. Single nucleotide polymorphism arrays have proven successful in deciphering genomic aberrations of cancer cells; these techniques, however, are usually not applied in the daily routine. Here, we present an ultra-high density (UHD) SNParray technique which is, because of its high specificity and sensitivity and the combined copy number and allele information, highly appropriate for the genomic diagnosis of neuroblastoma and other malignancies.
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Affiliation(s)
- Inge M Ambros
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung , Vienna , Austria
| | - Clemens Brunner
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung , Vienna , Austria
| | - Reza Abbasi
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung , Vienna , Austria
| | - Christian Frech
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung , Vienna , Austria
| | - Peter F Ambros
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung , Vienna , Austria ; Department of Pediatrics, Medical University of Vienna , Vienna , Austria
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Krepischi ACV, Capelli LP, Silva AG, de Araújo ÉSS, Pearson PL, Heck B, da Costa CML, de Camargo B, Rosenberg C. Large germline copy number variations as predisposing factor in childhood neoplasms. Future Oncol 2014; 10:1627-33. [DOI: 10.2217/fon.14.41] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
ABSTRACT: Aims: Constitutive genetic factors are believed to predispose to cancer in children. This study investigated the role of rare germline copy number variations (CNVs) in pediatric cancer predisposition. Patients & methods: A total of 54 patients who developed cancer in infancy were screened by array-CGH for germline CNVs. Results: In total, 12 rare CNVs were detected, including a Xq27.2 triplication, and two >1.8 Mb deletions: one of them at 13q31, containing only RNA genes, and another at 3q26.33–q27.1, in a patient with congenital malformations. Detected rare CNVs are significantly larger than those identified in controls, and encompass genes never implicated in cancer predisposition. Conclusion: Our results suggest that constitutive CNVs contribute to the etiology of pediatric neoplasms, revealing new candidate genes for tumorigenesis.
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Affiliation(s)
- Ana Cristina Victorino Krepischi
- International Research Center, A C Camargo Cancer Center, São Paulo, São Paulo, Brazil
- Department of Genetics & Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | | | - Amanda Gonçalves Silva
- International Research Center, A C Camargo Cancer Center, São Paulo, São Paulo, Brazil
- Department of Genetics & Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | | | - Peter Lees Pearson
- Department of Genetics & Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | - Benjamin Heck
- Department of Pediatrics, A C Camargo Cancer Center, São Paulo, Brazil
- EmbrioConsult, São Paulo, Brazil
| | | | - Beatriz de Camargo
- Department of Pediatrics, A C Camargo Cancer Center, São Paulo, Brazil
- Pediatric Oncology Department, National Institute of Cancer, Rio de Janeiro, Brazil
| | - Carla Rosenberg
- Department of Genetics & Evolutionary Biology, University of São Paulo, São Paulo, Brazil
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Mascelli S, Severino M, Raso A, Nozza P, Tassano E, Morana G, De Marco P, Merello E, Milanaccio C, Pavanello M, Rossi A, Cama A, Garrè ML, Capra V. Constitutional chromosomal events at 22q11 and 15q26 in a child with a pilocytic astrocytoma of the spinal cord. Mol Cytogenet 2014; 7:31. [PMID: 24860619 PMCID: PMC4032172 DOI: 10.1186/1755-8166-7-31] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/28/2014] [Indexed: 12/28/2022] Open
Abstract
We report on a 9-years-old patient with mild intellectual disability, facial dimorphisms, bilateral semicircular canal dysplasia, periventricular nodular heterotopias, bilateral hippocampal malrotation and abnormal cerebellar foliation, who developed mild motor impairment and gait disorder due to a pilocytic astrocytoma of the spinal cord. Array-CGH analysis revealed two paternal inherited chromosomal events: a 484.3 Kb duplication on chromosome 15q26.3 and a 247 Kb deletion on 22q11.23. Further, a second de novo 1.5 Mb deletion on 22q11.21 occurred. Chromosome 22 at q11.2 and chromosome 15 at q24q26 are considered unstable regions subjected to copy number variations, i.e. structural alterations of genome, mediated by low copy repeat sequences or segmental duplications. The link between some structural CNVs, which compromise fundamental processes controlling DNA stability, and genomic disorders suggest a plausible scenario for cancer predisposition. Evaluation of the genes at the breakpoints cannot account simultaneously for the phenotype and tumour development in this patient. The two paternal inherited CNVs arguably are not pathogenic and do not contribute to the clinical manifestations. Similarly, although the de novo large deletion at 22q11.21 overlaps with the Di George (DGS) critical region and results in haploinsufficiency of genes compromising critical processes for DNA stability, this case lacks several hallmarks of DGS.
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Affiliation(s)
| | | | - Alessandro Raso
- Istituto Giannina Gaslini, via G. Gaslini 5, 16147 Genoa, Italy
| | - Paolo Nozza
- Istituto Giannina Gaslini, via G. Gaslini 5, 16147 Genoa, Italy
| | - Elisa Tassano
- Istituto Giannina Gaslini, via G. Gaslini 5, 16147 Genoa, Italy
| | - Giovanni Morana
- Istituto Giannina Gaslini, via G. Gaslini 5, 16147 Genoa, Italy
| | | | - Elisa Merello
- Istituto Giannina Gaslini, via G. Gaslini 5, 16147 Genoa, Italy
| | | | - Marco Pavanello
- Istituto Giannina Gaslini, via G. Gaslini 5, 16147 Genoa, Italy
| | - Andrea Rossi
- Istituto Giannina Gaslini, via G. Gaslini 5, 16147 Genoa, Italy
| | - Armando Cama
- Istituto Giannina Gaslini, via G. Gaslini 5, 16147 Genoa, Italy
| | | | - Valeria Capra
- Istituto Giannina Gaslini, via G. Gaslini 5, 16147 Genoa, Italy
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Fromer M, Purcell SM. Using XHMM Software to Detect Copy Number Variation in Whole-Exome Sequencing Data. CURRENT PROTOCOLS IN HUMAN GENETICS 2014; 81:7.23.1-7.23.21. [PMID: 24763994 PMCID: PMC4065038 DOI: 10.1002/0471142905.hg0723s81] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Copy number variation (CNV) has emerged as an important genetic component in human diseases, which are increasingly being studied for large numbers of samples by sequencing the coding regions of the genome, i.e., exome sequencing. Nonetheless, detecting this variation from such targeted sequencing data is a difficult task, involving sorting out signal from noise, for which we have recently developed a set of statistical and computational tools called XHMM. In this unit, we give detailed instructions on how to run XHMM and how to use the resulting CNV calls in biological analyses.
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Affiliation(s)
- Menachem Fromer
- Division of Psychiatric Genomics and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA,Stanley Center for Psychiatric Research and Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA,Analytic and Translational Genetics Unit, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Shaun M. Purcell
- Division of Psychiatric Genomics and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA,Stanley Center for Psychiatric Research and Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA,Analytic and Translational Genetics Unit, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
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Genomic profiling reveals extensive heterogeneity in somatic DNA copy number aberrations of canine hemangiosarcoma. Chromosome Res 2014; 22:305-19. [PMID: 24599718 DOI: 10.1007/s10577-014-9406-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 01/08/2023]
Abstract
Canine hemangiosarcoma is a highly aggressive vascular neoplasm associated with extensive clinical and anatomical heterogeneity and a grave prognosis. Comprehensive molecular characterization of hemangiosarcoma may identify novel therapeutic targets and advanced clinical management strategies, but there are no published reports of tumor-associated genome instability and disrupted gene dosage in this cancer. We performed genome-wide microarray-based somatic DNA copy number profiling of 75 primary intra-abdominal hemangiosarcomas from five popular dog breeds that are highly predisposed to this disease. The cohort exhibited limited global genomic instability, compared to other canine sarcomas studied to date, and DNA copy number aberrations (CNAs) were predominantly of low amplitude. Recurrent imbalances of several key cancer-associated genes were evident; however, the global penetrance of any single CNA was low and no distinct hallmark aberrations were evident. Copy number gains of dog chromosomes 13, 24, and 31, and loss of chromosome 16, were the most recurrent CNAs involving large chromosome regions, but their relative distribution within and between cases suggests they most likely represent passenger aberrations. CNAs involving CDKN2A, VEGFA, and the SKI oncogene were identified as potential driver aberrations of hemangiosarcoma development, highlighting potential targets for therapeutic modulation. CNA profiles were broadly conserved between the five breeds, although subregional variation was evident, including a near twofold lower incidence of VEGFA gain in Golden Retrievers versus other breeds (22 versus 40 %). These observations support prior transcriptional studies suggesting that the clinical heterogeneity of this cancer may reflect the existence of multiple, molecularly distinct subtypes of canine hemangiosarcoma.
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Liao WL, Wan L, Wang TY, Chen CC, Tse SS, Lu CH, Tsai FJ. Association of TLR7 and TSHR copy number variation with Graves' disease and Graves' ophthalmopathy in Chinese population in Taiwan. BMC Ophthalmol 2014; 14:15. [PMID: 24517461 PMCID: PMC3929160 DOI: 10.1186/1471-2415-14-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 01/27/2014] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Graves' disease (GD) and Graves' ophthalmopathy (GO) are autoimmune disorders, which might be influenced by genetic factors. Copy number variation (CNV) is an important source of genomic diversity in humans, and influences disease susceptibility. This study investigated the association between CNV in the TSHR and TLR7 genes and the development of GD and GO in a Chinese population in Taiwan. METHODS For this case-control study, sample from 196 healthy controls and 484 GD patients, including 203 patients with GO were studied. CNV was detected by real-time polymerase chain reaction (PCR) using TaqMan™ probes and the relative copy number (CN) was estimated by using the comparative Ct method. RESULTS The differences in the distribution of TSHR CNV in healthy controls and GD patients were statistically significant (p value = 0.01). However, the difference in the distribution of TSHR CNV in the control group and the GO group was not statistically significant (p value = 0.06). For TLR7 CNV, the results were not significantly different when we compared the distribution in healthy controls and GD patients and in healthy controls and GO patients (p values for Fisher's exact test were 0.13 and 0.09, respectively). However, a lower than normal CNV for TLR7 (CNV < 2 for female and CNV < 1 for male) was found to have a protective effect against the development of GD (odds ratio (OR) = 0.24; 95% confidence interval (CI), 0.07-0.75) after adjusting for age and gender. CONCLUSIONS These results suggested that TSHR and TLR7 CNV might be associated with susceptibility to GD.
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Affiliation(s)
| | | | | | | | | | | | - Fuu-Jen Tsai
- Department of Medical Genetics and Medical Research, China Medical University Hospital, No,2 Yuh-Der Road, 404 Taichung City, Taiwan.
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Jia D, Jing Y, Zhang Z, Liu L, Ding J, Zhao F, Ge C, Wang Q, Chen T, Yao M, Li J, Gu J, He X. Amplification of MPZL1/PZR promotes tumor cell migration through Src-mediated phosphorylation of cortactin in hepatocellular carcinoma. Cell Res 2013; 24:204-17. [PMID: 24296779 DOI: 10.1038/cr.2013.158] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 09/10/2013] [Accepted: 09/25/2013] [Indexed: 12/15/2022] Open
Abstract
We have previously identified 1 241 regions of somatic copy number alterations (CNAs) in hepatocellular carcinoma (HCC). In the present study, we found that a novel recurrent focal amplicon, 1q24.1-24.2, targets the MPZL1 gene in HCC. Notably, there is a positive correlation between the expression levels of MPZL1 and intrahepatic metastasis of the HCC specimens. MPZL1 can significantly enhance the migratory and metastatic potential of the HCC cells. Moreover, we found that one of the mechanisms by which MPZL1 promotes HCC cell migration is by inducing the phosphorylation and activation of the pro-metastatic protein, cortactin. Additionally, we found that Src kinase mediates the phosphorylation and activation of cortactin induced by MPZL1 overexpression. Taken together, these findings suggest that MPZL1 is a novel pro-metastatic gene targeted by a recurrent region of copy number amplification at 1q24.1-24.2 in HCC.
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Affiliation(s)
- Deshui Jia
- 1] State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China [2] Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ying Jing
- 1] State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China [2] Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Zhenfeng Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Li Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Jie Ding
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Fangyu Zhao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Chao Ge
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Qifeng Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Taoyang Chen
- Qidong Liver Cancer Institute, Qidong, Jiangsu 226200, China
| | - Ming Yao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Jinjun Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Jianren Gu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
| | - Xianghuo He
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200032, China
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Hopman S, Merks J, Eussen H, Douben H, Snijder S, Hennekam R, de Klein A, Caron H. Structural genome variations in individuals with childhood cancer and tumour predisposition syndromes. Eur J Cancer 2013; 49:2170-8. [DOI: 10.1016/j.ejca.2013.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 01/02/2013] [Accepted: 02/03/2013] [Indexed: 11/15/2022]
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de Clare M, Oliver SG. Copy-number variation of cancer-gene orthologs is sufficient to induce cancer-like symptoms in Saccharomyces cerevisiae. BMC Biol 2013; 11:24. [PMID: 23531409 PMCID: PMC3635878 DOI: 10.1186/1741-7007-11-24] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 03/19/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copy-number variation (CNV), rather than complete loss of gene function, is increasingly implicated in human disease. Moreover, gene dosage is recognised as important in tumourigenesis, and there is an increasing realisation that CNVs may not be just symptomatic of the cancerous state but may, in fact, be causative. However, the identification of CNV-related phenotypes for mammalian genes is a slow process, due to the technical difficulty of constructing deletion mutants. Using the genome-wide deletion library for the model eukaryote, Saccharomyces cerevisiae, we have identified genes (termed haploproficient, HP) which, when one copy is deleted from a diploid cell, result in an increased rate of proliferation. Since haploproficiency under nutrient-sufficient conditions is a novel phenotype, we sought here to characterise a subset of the yeast haploproficient genes which seem particularly relevant to human cancers. RESULTS We show that, for a subset of HP genes, heterozygous deletion is sufficient to cause aberrant cell cycling and altered rates of apoptosis, phenotypes associated with cancer in mammalian cells. A majority of these yeast genes are the orthologs of mammalian cancer genes, and hence our studies suggest that CNV of these oncogenic orthologs may be sufficient to lead to tumourigenesis in human cells. Moreover, where not already implicated, this cluster of cancer-like phenotypes in this model eukaryote may be predictive of the involvement in cancer of the mammalian orthologs of these yeast HP genes. Using the yeast set as a model, we show that the response to a range of anti-cancer drugs is strongly dependent on gene dosage, such that intermediate concentrations of the drugs can actually increase a mutant's growth rate. CONCLUSIONS The exploitation of data on the phenotypic impact of heterozygosis in Saccharomyces cerevisiae has permitted the prediction of CNVs affecting tumourigenesis in humans. Our yeast data also suggest that the identification of CNVs in tumour cells may assist both the selection of anti-cancer drugs and the dosages at which they should be administered if they are to be a beneficial, rather than a deleterious, therapy.
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Affiliation(s)
- Michaela de Clare
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
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41
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Sapkota Y, Ghosh S, Lai R, Coe BP, Cass CE, Yasui Y, Mackey JR, Damaraju S. Germline DNA copy number aberrations identified as potential prognostic factors for breast cancer recurrence. PLoS One 2013; 8:e53850. [PMID: 23342018 PMCID: PMC3547038 DOI: 10.1371/journal.pone.0053850] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 12/05/2012] [Indexed: 11/30/2022] Open
Abstract
Breast cancer recurrence (BCR) is a common treatment outcome despite curative-intent primary treatment of non-metastatic breast cancer. Currently used prognostic and predictive factors utilize tumor-based markers, and are not optimal determinants of risk of BCR. Germline-based copy number aberrations (CNAs) have not been evaluated as determinants of predisposition to experience BCR. In this study, we accessed germline DNA from 369 female breast cancer subjects who received curative-intent primary treatment following diagnosis. Of these, 155 experienced BCR and 214 did not, after a median duration of follow up after breast cancer diagnosis of 6.35 years (range = 0.60–21.78) and 8.60 years (range = 3.08–13.57), respectively. Whole genome CNA genotyping was performed on the Affymetrix SNP array 6.0 platform. CNAs were identified using the SNP-Fast Adaptive States Segmentation Technique 2 algorithm implemented in Nexus Copy Number 6.0. Six samples were removed due to poor quality scores, leaving 363 samples for further analysis. We identified 18,561 CNAs with ≥1 kb as a predefined cut-off for observed aberrations. Univariate survival analyses (log-rank tests) identified seven CNAs (two copy number gains and five copy neutral-loss of heterozygosities, CN-LOHs) showing significant differences (P<2.01×10−5) in recurrence-free survival (RFS) probabilities with and without CNAs.We also observed three additional but distinct CN-LOHs showing significant differences in RFS probabilities (P<2.86×10−5) when analyses were restricted to stratified cases (luminal A, n = 208) only. After adjusting for tumor stage and grade in multivariate analyses (Cox proportional hazards models), all the CNAs remained strongly associated with the phenotype of BCR. Of these, we confirmed three CNAs at 17q11.2, 11q13.1 and 6q24.1 in representative samples using independent genotyping platforms. Our results suggest further investigations on the potential use of germline DNA variations as prognostic markers in cancer-associated phenotypes.
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Affiliation(s)
- Yadav Sapkota
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Sunita Ghosh
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Raymond Lai
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Bradley P. Coe
- Department of Genome Sciences, University of Washington, School of Medicine, Seattle, Washington, United States of America
| | - Carol E. Cass
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Yutaka Yasui
- Department of Public Health Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - John R. Mackey
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Sambasivarao Damaraju
- Cross Cancer Institute, Alberta Health Services, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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Bødker J, Gyrup C, Johansen P, Schmitz A, Madsen J, Johnsen H, Bøgsted M, Dybkær K, Nyegaard M. Performance Comparison of Affymetrix SNP6.0 and Cytogenetic 2.7M Whole-Genome Microarrays in Complex Cancer Samples. Cytogenet Genome Res 2012. [DOI: 10.1159/000345125] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Charoentong P, Angelova M, Efremova M, Gallasch R, Hackl H, Galon J, Trajanoski Z. Bioinformatics for cancer immunology and immunotherapy. Cancer Immunol Immunother 2012; 61:1885-903. [PMID: 22986455 PMCID: PMC3493665 DOI: 10.1007/s00262-012-1354-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 09/04/2012] [Indexed: 01/24/2023]
Abstract
Recent mechanistic insights obtained from preclinical studies and the approval of the first immunotherapies has motivated increasing number of academic investigators and pharmaceutical/biotech companies to further elucidate the role of immunity in tumor pathogenesis and to reconsider the role of immunotherapy. Additionally, technological advances (e.g., next-generation sequencing) are providing unprecedented opportunities to draw a comprehensive picture of the tumor genomics landscape and ultimately enable individualized treatment. However, the increasing complexity of the generated data and the plethora of bioinformatics methods and tools pose considerable challenges to both tumor immunologists and clinical oncologists. In this review, we describe current concepts and future challenges for the management and analysis of data for cancer immunology and immunotherapy. We first highlight publicly available databases with specific focus on cancer immunology including databases for somatic mutations and epitope databases. We then give an overview of the bioinformatics methods for the analysis of next-generation sequencing data (whole-genome and exome sequencing), epitope prediction tools as well as methods for integrative data analysis and network modeling. Mathematical models are powerful tools that can predict and explain important patterns in the genetic and clinical progression of cancer. Therefore, a survey of mathematical models for tumor evolution and tumor-immune cell interaction is included. Finally, we discuss future challenges for individualized immunotherapy and suggest how a combined computational/experimental approaches can lead to new insights into the molecular mechanisms of cancer, improved diagnosis, and prognosis of the disease and pinpoint novel therapeutic targets.
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Affiliation(s)
- Pornpimol Charoentong
- Biocenter, Division of Bioinformatics, Innsbruck Medical University, Innrain 80, 6020 Innsbruck, Austria
| | - Mihaela Angelova
- Biocenter, Division of Bioinformatics, Innsbruck Medical University, Innrain 80, 6020 Innsbruck, Austria
| | - Mirjana Efremova
- Biocenter, Division of Bioinformatics, Innsbruck Medical University, Innrain 80, 6020 Innsbruck, Austria
| | - Ralf Gallasch
- Biocenter, Division of Bioinformatics, Innsbruck Medical University, Innrain 80, 6020 Innsbruck, Austria
| | - Hubert Hackl
- Biocenter, Division of Bioinformatics, Innsbruck Medical University, Innrain 80, 6020 Innsbruck, Austria
| | - Jerome Galon
- INSERM U872, Integrative Cancer Immunology Laboratory, Paris, France
| | - Zlatko Trajanoski
- Biocenter, Division of Bioinformatics, Innsbruck Medical University, Innrain 80, 6020 Innsbruck, Austria
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Abstract
Tumor suppressor genes (TSGs) are guardian genes that play important roles in controlling cell proliferation processes such as cell-cycle checkpoints and inducing apoptosis. Identification of these genes and understanding their functions are critical for further investigation of tumorigenesis. So far, many studies have identified numerous TSGs and illustrated their functions in various types of tumors or normal samples. Furthermore, accumulating evidence has shown that non-coding RNAs can act as TSGs to prevent the tumorigenesis processes. Therefore, there is a growing demand to integrate TSGs with large-scale experimental evidence (e.g. gene expression and epigenetic signatures) to provide a comprehensive resource for further investigation of TSGs and their molecular mechanisms in cancer. To achieve this goal, we first developed a comprehensive literature-based database called TSGene (tumor suppressor gene database), freely available at http://bioinfo.mc.vanderbilt.edu/TSGene/. In the current release, TSGene contains 716 human (637 protein-coding and 79 non-coding genes), 628 mouse and 567 rat TSGs curated from UniProtKB, the Tumor Associated Gene database and 5795 PubMed abstracts. Additionally, the TSGene provides detailed annotations for each TSG, such as cancer mutations, gene expressions, methylation sites, TF regulations and protein–protein interactions.
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Affiliation(s)
- Min Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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Fromer M, Moran J, Chambert K, Banks E, Bergen S, Ruderfer D, Handsaker R, McCarroll S, O’Donovan M, Owen M, Kirov G, Sullivan P, Hultman C, Sklar P, Purcell S. Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth. Am J Hum Genet 2012; 91:597-607. [PMID: 23040492 DOI: 10.1016/j.ajhg.2012.08.005] [Citation(s) in RCA: 437] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 06/23/2012] [Accepted: 08/09/2012] [Indexed: 12/20/2022] Open
Abstract
Sequencing of gene-coding regions (the exome) is increasingly used for studying human disease, for which copy-number variants (CNVs) are a critical genetic component. However, detecting copy number from exome sequencing is challenging because of the noncontiguous nature of the captured exons. This is compounded by the complex relationship between read depth and copy number; this results from biases in targeted genomic hybridization, sequence factors such as GC content, and batching of samples during collection and sequencing. We present a statistical tool (exome hidden Markov model [XHMM]) that uses principal-component analysis (PCA) to normalize exome read depth and a hidden Markov model (HMM) to discover exon-resolution CNV and genotype variation across samples. We evaluate performance on 90 schizophrenia trios and 1,017 case-control samples. XHMM detects a median of two rare (<1%) CNVs per individual (one deletion and one duplication) and has 79% sensitivity to similarly rare CNVs overlapping three or more exons discovered with microarrays. With sensitivity similar to state-of-the-art methods, XHMM achieves higher specificity by assigning quality metrics to the CNV calls to filter out bad ones, as well as to statistically genotype the discovered CNV in all individuals, yielding a trio call set with Mendelian-inheritance properties highly consistent with expectation. We also show that XHMM breakpoint quality scores enable researchers to explicitly search for novel classes of structural variation. For example, we apply XHMM to extract those CNVs that are highly likely to disrupt (delete or duplicate) only a portion of a gene.
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Pernot E, Hall J, Baatout S, Benotmane MA, Blanchardon E, Bouffler S, El Saghire H, Gomolka M, Guertler A, Harms-Ringdahl M, Jeggo P, Kreuzer M, Laurier D, Lindholm C, Mkacher R, Quintens R, Rothkamm K, Sabatier L, Tapio S, de Vathaire F, Cardis E. Ionizing radiation biomarkers for potential use in epidemiological studies. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2012; 751:258-286. [DOI: 10.1016/j.mrrev.2012.05.003] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 05/04/2012] [Accepted: 05/28/2012] [Indexed: 02/07/2023]
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Krepischi ACV, Pearson PL, Rosenberg C. Germline copy number variations and cancer predisposition. Future Oncol 2012; 8:441-50. [PMID: 22515447 DOI: 10.2217/fon.12.34] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We present an overview of the role of germline copy number variations (CNVs) in cancer predisposition. CNVs represent a significant source of genetic diversity, although the mechanisms by which they influence cancer susceptibility still remain largely unknown. Approximately 100 highly penetrant germline mutant genes are now known to cause cancer predisposition inherited in a Mendelian fashion; in this review, we show that nearly half of these genes have also been observed as rare CNVs associated with cancer. However, these highly penetrant alleles seem to account for less than 5% of all familial cancers. We surmise that most of the genetic risk of cancer in the general population must largely involve genes of low or moderate penetrance. In the last 5 years, studies have demonstrated that although common low penetrant CNVs are modest contributors to cancer individually, their combined impact on cancer predisposition must be taken into account in estimating cancer risk.
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A functional copy-number variation in MAPKAPK2 predicts risk and prognosis of lung cancer. Am J Hum Genet 2012; 91:384-90. [PMID: 22883146 DOI: 10.1016/j.ajhg.2012.07.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2012] [Revised: 05/22/2012] [Accepted: 07/02/2012] [Indexed: 02/06/2023] Open
Abstract
Mitogen-activated protein kinase-activated protein kinase 2 (MAPKAPK2) may promote cancer development and progression by inducing tumorigenesis and drug resistance. To assess whether the copy-number variation g.CNV-30450 located in the MAPKAPK2 promoter has any effect on lung cancer risk or prognosis, we investigated the association between g.CNV-30450 and cancer risk in three independent case-control studies of 2,332 individuals with lung cancer and 2,457 controls and the effects of g.CNV-30450 on cancer prognosis in 1,137 individuals with lung cancer with survival data in southern and eastern Chinese populations. We found that those subjects who had four copies of g.CNV-30450 had an increased cancer risk (odds ratio = 1.94, 95% confidence interval [CI] = 1.61-2.35) and a worse prognosis for individuals with lung cancer (with a median survival time of only 9 months) (hazard ratio = 1.47, 95% CI = 1.22-1.78) compared with those with two or three copies (with a median survival time of 14 months). Meanwhile, four copies of g.CNV-30450 significantly increased MAPKAPK2 expression, both in vitro and in vivo, compared with two or three copies. Our study establishes a robust association between the functional g.CNV-30450 in MAPKAPK2 and risk as well as prognosis of lung cancer, and it presents this functional copy-number variation as a potential biomarker for susceptibility to and prognosis for lung cancer.
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Sundström E, Imsland F, Mikko S, Wade C, Sigurdsson S, Pielberg GR, Golovko A, Curik I, Seltenhammer MH, Sölkner J, Lindblad-Toh K, Andersson L. Copy number expansion of the STX17 duplication in melanoma tissue from Grey horses. BMC Genomics 2012; 13:365. [PMID: 22857264 PMCID: PMC3443021 DOI: 10.1186/1471-2164-13-365] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 07/18/2012] [Indexed: 01/11/2023] Open
Abstract
Background Greying with age in horses is an autosomal dominant trait, associated with loss of hair pigmentation, melanoma and vitiligo-like depigmentation. We recently identified a 4.6 kb duplication in STX17 to be associated with the phenotype. The aims of this study were to investigate if the duplication in Grey horses shows copy number variation and to exclude that any other polymorphism is uniquely associated with the Grey mutation. Results We found little evidence for copy number expansion of the duplicated sequence in blood DNA from Grey horses. In contrast, clear evidence for copy number expansions was indicated in five out of eight tested melanoma tissues or melanoma cell lines. A tendency of a higher copy number in aggressive tumours was also found. Massively parallel resequencing of the ~350 kb Grey haplotype did not reveal any additional mutations perfectly associated with the phenotype, confirming the duplication as the true causative mutation. We identified three SNP alleles that were present in a subset of Grey haplotypes within the 350 kb region that shows complete linkage disequilibrium with the causative mutation. Thus, these three nucleotide substitutions must have occurred subsequent to the duplication, consistent with our interpretation that the Grey mutation arose more than 2,000 years before present. Conclusions These results suggest that the mutation acts as a melanoma-driving regulatory element. The elucidation of the mechanistic features of the duplication will be of considerable interest for the characterization of these horse melanomas as well as for the field of human melanoma research.
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Affiliation(s)
- Elisabeth Sundström
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Whale AS, Huggett JF, Cowen S, Speirs V, Shaw J, Ellison S, Foy CA, Scott DJ. Comparison of microfluidic digital PCR and conventional quantitative PCR for measuring copy number variation. Nucleic Acids Res 2012; 40:e82. [PMID: 22373922 PMCID: PMC3367212 DOI: 10.1093/nar/gks203] [Citation(s) in RCA: 305] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 02/14/2012] [Accepted: 02/14/2012] [Indexed: 12/28/2022] Open
Abstract
One of the benefits of Digital PCR (dPCR) is the potential for unparalleled precision enabling smaller fold change measurements. An example of an assessment that could benefit from such improved precision is the measurement of tumour-associated copy number variation (CNV) in the cell free DNA (cfDNA) fraction of patient blood plasma. To investigate the potential precision of dPCR and compare it with the established technique of quantitative PCR (qPCR), we used breast cancer cell lines to investigate HER2 gene amplification and modelled a range of different CNVs. We showed that, with equal experimental replication, dPCR could measure a smaller CNV than qPCR. As dPCR precision is directly dependent upon both the number of replicate measurements and the template concentration, we also developed a method to assist the design of dPCR experiments for measuring CNV. Using an existing model (based on Poisson and binomial distributions) to derive an expression for the variance inherent in dPCR, we produced a power calculation to define the experimental size required to reliably detect a given fold change at a given template concentration. This work will facilitate any future translation of dPCR to key diagnostic applications, such as cancer diagnostics and analysis of cfDNA.
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Affiliation(s)
- Alexandra S. Whale
- LGC Limited, Queens Road, Teddington, Middlesex TW11 0LY, Leeds Institute of Molecular Medicine, University of Leeds, St. James’s University Hospital, Leeds LS9 7TF and Cancer Studies & Molecular Medicine, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester LE2 7LX, UK
| | - Jim F. Huggett
- LGC Limited, Queens Road, Teddington, Middlesex TW11 0LY, Leeds Institute of Molecular Medicine, University of Leeds, St. James’s University Hospital, Leeds LS9 7TF and Cancer Studies & Molecular Medicine, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester LE2 7LX, UK
| | - Simon Cowen
- LGC Limited, Queens Road, Teddington, Middlesex TW11 0LY, Leeds Institute of Molecular Medicine, University of Leeds, St. James’s University Hospital, Leeds LS9 7TF and Cancer Studies & Molecular Medicine, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester LE2 7LX, UK
| | - Valerie Speirs
- LGC Limited, Queens Road, Teddington, Middlesex TW11 0LY, Leeds Institute of Molecular Medicine, University of Leeds, St. James’s University Hospital, Leeds LS9 7TF and Cancer Studies & Molecular Medicine, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester LE2 7LX, UK
| | - Jacqui Shaw
- LGC Limited, Queens Road, Teddington, Middlesex TW11 0LY, Leeds Institute of Molecular Medicine, University of Leeds, St. James’s University Hospital, Leeds LS9 7TF and Cancer Studies & Molecular Medicine, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester LE2 7LX, UK
| | - Stephen Ellison
- LGC Limited, Queens Road, Teddington, Middlesex TW11 0LY, Leeds Institute of Molecular Medicine, University of Leeds, St. James’s University Hospital, Leeds LS9 7TF and Cancer Studies & Molecular Medicine, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester LE2 7LX, UK
| | - Carole A. Foy
- LGC Limited, Queens Road, Teddington, Middlesex TW11 0LY, Leeds Institute of Molecular Medicine, University of Leeds, St. James’s University Hospital, Leeds LS9 7TF and Cancer Studies & Molecular Medicine, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester LE2 7LX, UK
| | - Daniel J. Scott
- LGC Limited, Queens Road, Teddington, Middlesex TW11 0LY, Leeds Institute of Molecular Medicine, University of Leeds, St. James’s University Hospital, Leeds LS9 7TF and Cancer Studies & Molecular Medicine, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester LE2 7LX, UK
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