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Tremmel R, Zhou Y, Schwab M, Lauschke VM. Structural variation of the coding and non-coding human pharmacogenome. NPJ Genom Med 2023; 8:24. [PMID: 37684227 PMCID: PMC10491600 DOI: 10.1038/s41525-023-00371-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Genetic variants in drug targets and genes encoding factors involved in drug absorption, distribution, metabolism and excretion (ADME) can have pronounced impacts on drug pharmacokinetics, response, and toxicity. While the landscape of genetic variability at the level of single nucleotide variants (SNVs) has been extensively studied in these pharmacogenetic loci, their structural variation is only poorly understood. Thus, we systematically analyzed the genetic structural variability across 908 pharmacogenes (344 ADME genes and 564 drug targets) based on publicly available whole genome sequencing data from 10,847 unrelated individuals. Overall, we extracted 14,984 distinct structural variants (SVs) ranging in size from 50 bp to 106 Mb. Each individual harbored on average 10.3 and 1.5 SVs with putative functional effects that affected the coding regions of ADME genes and drug targets, respectively. In addition, by cross-referencing pharmacogenomic SVs with experimentally determined binding data of 224 transcription factors across 130 cell types, we identified 1276 non-coding SVs that overlapped with gene regulatory elements. Based on these data, we estimate that non-coding structural variants account for 22% of the genetically encoded pharmacogenomic variability. Combined, these analyses provide the first comprehensive map of structural variability across pharmacogenes, derive estimates for the functional impact of non-coding SVs and incentivize the incorporation of structural genomic data into personalized drug response predictions.
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Affiliation(s)
- Roman Tremmel
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University Tübingen, Tübingen, Germany
| | - Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Matthias Schwab
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University Tübingen, Tübingen, Germany
- Departments of Clinical Pharmacology and Pharmacy and Biochemistry, University Tübingen, Tübingen, Germany
| | - Volker M Lauschke
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.
- University Tübingen, Tübingen, Germany.
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
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Drug Response Prediction Based on 1D Convolutional Neural Network and Attention Mechanism. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:8671348. [PMID: 36164615 PMCID: PMC9509240 DOI: 10.1155/2022/8671348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/18/2022] [Indexed: 11/30/2022]
Abstract
There are multiple methods based on gene expression, copy number variation, and methylation biomarkers for screening drug response have been developed. On the other hand, many machine learning algorithms have been applied in recent years to predict drug response, such as neural networks and random forests for the discovery of genomic markers of drug sensitivity for individual drugs in cancer cell lines. In this paper, we propose a drug response prediction algorithm based on 1D convolutional neural networks with attention mechanism and combined with pathway networks, which combines the individual histological data affecting drug response and considers the topological nature of the pathways to find the subpathways highly correlated with drug response and use this as a feature to predict drug response by training using convolutional neural networks. Thus, the output values will represent the probability of occurrence of each of these two categories. In this experiment, using five-fold cross-validation, the identification accuracy reached an average of 84.6%, which is 4.5% higher than the direct random forest approach for drug prediction with an AUC value. This proves that the use of the one-dimensional1D convolutional neural network with attention mechanism to predict the response of low-grade glioma patients and drugs has better prediction results.
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Gu KN, Bang SY, Lee HS, Park Y, Kang JY, Kim JS, Nam B, Yoo HS, Shin JM, Lee YK, Lee TH, Chun S, Cho SK, Choi CB, Sung YK, Kim TH, Jun JB, Yoo DH, Kim K, Bae SC. Deletion at 2q14.3 is associated with worse response to TNF-α blockers in patients with rheumatoid arthritis. Arthritis Res Ther 2019; 21:195. [PMID: 31462329 PMCID: PMC6714408 DOI: 10.1186/s13075-019-1983-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 08/16/2019] [Indexed: 01/20/2023] Open
Abstract
Background Structural variations such as copy number variations (CNVs) have a functional impact on various human traits. This study profiled genome-wide CNVs in Korean patients with rheumatoid arthritis (RA) to investigate the efficacy of treatment with TNF-α blockers. Methods A total of 357 Korean patients with RA were examined for the efficacy of TNF-α blocker treatment. Disease activity indexes were measured at baseline and 6 months after the treatment. The patients were classified as responders and non-responders based on the change in disease activity indexes according to the EULAR response criteria. CNVs in the same patients were profiled using fluorescence signal intensity data generated by a genome-wide SNP array. The association of CNVs with response to TNF-α blockers was analyzed by multivariate logistic regression accounting for genetic background and clinical factors including body mass index, gender, baseline disease activity, TNF-α blocker used, and methotrexate treatment. Results The study subjects varied in their responses to TNF-α blockers and had 286 common CNVs in autosomes. We identified that the 3.8-kb deletion at 2q14.3 in 5% of the subjects was associated with response to TNF-α blockers (1.37 × 10− 5 ≤ P ≤ 4.07 × 10− 4) at a false discovery rate threshold of 5%. The deletion in the identified CNV was significantly more frequent in the non-responders than in the responders, indicating worse response to TNF-α blockers in the deletion carriers. The 3.8-kb deletion at 2q14.3 is located in an intergenic region with the binding sites of two transcription factors, MAFF and MAFK. Conclusions This study obtained the CNV landscape of Korean patients with RA and identified the common regional deletion associated with poor response to treatment with TNF-α blockers. Electronic supplementary material The online version of this article (10.1186/s13075-019-1983-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ki-Nam Gu
- Department of Biology, Kyung Hee University, Seoul, 02447, South Korea
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Youngho Park
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea.,Department of Business Statistics, Hannam University, Daejeon, 34430, South Korea
| | - Ju-Yeon Kang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Ji-Soong Kim
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Bora Nam
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Hyun-Seung Yoo
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Jung-Min Shin
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Yeon-Kyung Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Tae-Han Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Sehwan Chun
- Department of Biology, Kyung Hee University, Seoul, 02447, South Korea
| | - Soo-Kyung Cho
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Chan-Bum Choi
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Yoon-Kyoung Sung
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Tae-Hwan Kim
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Jae-Bum Jun
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Dae Hyun Yoo
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea
| | - Kwangwoo Kim
- Department of Biology, Kyung Hee University, Seoul, 02447, South Korea.
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, 04763, South Korea.
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Xu Y, Dong Q, Li F, Xu Y, Hu C, Wang J, Shang D, Zheng X, Yang H, Zhang C, Shao M, Meng M, Xiong Z, Li X, Zhang Y. Identifying subpathway signatures for individualized anticancer drug response by integrating multi-omics data. J Transl Med 2019; 17:255. [PMID: 31387579 PMCID: PMC6685260 DOI: 10.1186/s12967-019-2010-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 07/31/2019] [Indexed: 12/19/2022] Open
Abstract
Background Individualized drug response prediction is vital for achieving personalized treatment of cancer and moving precision medicine forward. Large-scale multi-omics profiles provide unprecedented opportunities for precision cancer therapy. Methods In this study, we propose a pipeline to identify subpathway signatures for anticancer drug response of individuals by integrating the comprehensive contributions of multiple genetic and epigenetic (gene expression, copy number variation and DNA methylation) alterations. Results Totally, 46 subpathway signatures associated with individual responses to different anticancer drugs were identified based on five cancer-drug response datasets. We have validated the reliability of subpathway signatures in two independent datasets. Furthermore, we also demonstrated these multi-omics subpathway signatures could significantly improve the performance of anticancer drug response prediction. In-depth analysis of these 46 subpathway signatures uncovered the essential roles of three omics types and the functional associations underlying different anticancer drug responses. Patient stratification based on subpathway signatures involved in anticancer drug response identified subtypes with different clinical outcomes, implying their potential roles as prognostic biomarkers. In addition, a landscape of subpathways associated with cellular responses to 191 anticancer drugs from CellMiner was provided and the mechanism similarity of drug action was accurately unclosed based on these subpathways. Finally, we constructed a user-friendly web interface-CancerDAP (http://bio-bigdata.hrbmu.edu.cn/CancerDAP/) available to explore 2751 subpathways relevant with 191 anticancer drugs response. Conclusions Taken together, our study identified and systematically characterized subpathway signatures for individualized anticancer drug response prediction, which may promote the precise treatment of cancer and the study for molecular mechanisms of drug actions. Electronic supplementary material The online version of this article (10.1186/s12967-019-2010-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yanjun Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Qun Dong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Feng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yingqi Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Congxue Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Jingwen Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Desi Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xuan Zheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Haixiu Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Chunlong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Mengting Shao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Mohan Meng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Zhiying Xiong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
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Bokhari Y, Arodz T. QuaDMutEx: quadratic driver mutation explorer. BMC Bioinformatics 2017; 18:458. [PMID: 29065872 PMCID: PMC5655866 DOI: 10.1186/s12859-017-1869-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 10/16/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Somatic mutations accumulate in human cells throughout life. Some may have no adverse consequences, but some of them may lead to cancer. A cancer genome is typically unstable, and thus more mutations can accumulate in the DNA of cancer cells. An ongoing problem is to figure out which mutations are drivers - play a role in oncogenesis, and which are passengers - do not play a role. One way of addressing this question is through inspection of somatic mutations in DNA of cancer samples from a cohort of patients and detection of patterns that differentiate driver from passenger mutations. RESULTS We propose QuaDMutEx, a method that incorporates three novel elements: a new gene set penalty that includes non-linear penalization of multiple mutations in putative sets of driver genes, an ability to adjust the method to handle slow- and fast-evolving tumors, and a computationally efficient method for finding gene sets that minimize the penalty, through a combination of heuristic Monte Carlo optimization and exact binary quadratic programming. Compared to existing methods, the proposed algorithm finds sets of putative driver genes that show higher coverage and lower excess coverage in eight sets of cancer samples coming from brain, ovarian, lung, and breast tumors. CONCLUSIONS Superior ability to improve on both coverage and excess coverage on different types of cancer shows that QuaDMutEx is a tool that should be part of a state-of-the-art toolbox in the driver gene discovery pipeline. It can detect genes harboring rare driver mutations that may be missed by existing methods. QuaDMutEx is available for download from https://github.com/bokhariy/QuaDMutEx under the GNU GPLv3 license.
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Affiliation(s)
- Yahya Bokhari
- Department of Computer Science, School of Engineering, Virginia Commonwealth University, 401 W. Main St., Richmond, 23284, VA, USA
| | - Tomasz Arodz
- Department of Computer Science, School of Engineering, Virginia Commonwealth University, 401 W. Main St., Richmond, 23284, VA, USA. .,Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, 23284, VA, USA.
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Li R, Kim D, Ritchie MD. Methods to analyze big data in pharmacogenomics research. Pharmacogenomics 2017; 18:807-820. [PMID: 28612644 DOI: 10.2217/pgs-2016-0152] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The scale and scope of pharmacogenomics research continues to expand as the cost and efficiency of molecular data generation techniques advance. These new technologies give rise to enormous opportunity for the identification of important genetic and genomic factors important for drug treatment response. With this opportunity come significant challenges. Most of these can be categorized as 'big data' issues, facing not only pharmacogenomics, but other fields in the life sciences as well. In this review, we describe some of the analysis techniques and tools being implemented for genetic/genomic discovery in pharmacogenomics.
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Affiliation(s)
- Ruowang Li
- Bioinformatics & Genomics Graduate Program, The Pennsylvania State University, University Park, PA 16802, USA
| | - Dokyoon Kim
- Biomedical & Translational Informatics Institute, Geisinger Health System, Danville, PA 17821, USA
| | - Marylyn D Ritchie
- Bioinformatics & Genomics Graduate Program, The Pennsylvania State University, University Park, PA 16802, USA.,Biomedical & Translational Informatics Institute, Geisinger Health System, Danville, PA 17821, USA
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7
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Tracking Cancer Genetic Evolution using OncoTrack. Sci Rep 2016; 6:29647. [PMID: 27412732 PMCID: PMC4944131 DOI: 10.1038/srep29647] [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: 11/11/2015] [Accepted: 06/20/2016] [Indexed: 02/07/2023] Open
Abstract
It is difficult for existing methods to quantify, and track the constant evolution of cancers due to high heterogeneity of mutations. However, structural variations associated with nucleotide number changes show repeatable patterns in localized regions of the genome. Here we introduce SPKMG, which generalizes nucleotide number based properties of genes, in statistical terms, at the genome-wide scale. It is measured from the normalized amount of aligned NGS reads in exonic regions of a gene. SPKMG values are calculated within OncoTrack. SPKMG values being continuous numeric variables provide a statistical metric to track DNA level changes. We show that SPKMG measures of cancer DNA show a normative pattern at the genome-wide scale. The analysis leads to the discovery of core cancer genes and also provides novel dynamic insights into the stage of cancer, including cancer development, progression, and metastasis. This technique will allow exome data to also be used for quantitative LOH/CNV analysis for tracking tumour progression and evolution with a higher efficiency.
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Niu N, Wang L. In vitro human cell line models to predict clinical response to anticancer drugs. Pharmacogenomics 2015; 16:273-85. [PMID: 25712190 DOI: 10.2217/pgs.14.170] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In vitro human cell line models have been widely used for cancer pharmacogenomic studies to predict clinical response, to help generate pharmacogenomic hypothesis for further testing, and to help identify novel mechanisms associated with variation in drug response. Among cell line model systems, immortalized cell lines such as Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) have been used most often to test the effect of germline genetic variation on drug efficacy and toxicity. Another model, especially in cancer research, uses cancer cell lines such as the NCI-60 panel. These models have been used mainly to determine the effect of somatic alterations on response to anticancer therapy. Even though these cell line model systems are very useful for initial screening, results from integrated analyses of multiple omics data and drug response phenotypes using cell line model systems still need to be confirmed by functional validation and mechanistic studies, as well as validation studies using clinical samples. Future models might include the use of patient-specific inducible pluripotent stem cells and the incorporation of 3D culture which could further optimize in vitro cell line models to improve their predictive validity.
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Affiliation(s)
- Nifang Niu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
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Seiser EL, Innocenti F. Hidden Markov Model-Based CNV Detection Algorithms for Illumina Genotyping Microarrays. Cancer Inform 2015; 13:77-83. [PMID: 25657572 PMCID: PMC4310714 DOI: 10.4137/cin.s16345] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 11/18/2014] [Accepted: 11/21/2014] [Indexed: 12/24/2022] Open
Abstract
Somatic alterations in DNA copy number have been well studied in numerous malignancies, yet the role of germline DNA copy number variation in cancer is still emerging. Genotyping microarrays generate allele-specific signal intensities to determine genotype, but may also be used to infer DNA copy number using additional computational approaches. Numerous tools have been developed to analyze Illumina genotype microarray data for copy number variant (CNV) discovery, although commonly utilized algorithms freely available to the public employ approaches based upon the use of hidden Markov models (HMMs). QuantiSNP, PennCNV, and GenoCN utilize HMMs with six copy number states but vary in how transition and emission probabilities are calculated. Performance of these CNV detection algorithms has been shown to be variable between both genotyping platforms and data sets, although HMM approaches generally outperform other current methods. Low sensitivity is prevalent with HMM-based algorithms, suggesting the need for continued improvement in CNV detection methodologies.
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Affiliation(s)
- Eric L Seiser
- Center for Pharmacogenomics and Individualized Therapy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Federico Innocenti
- Center for Pharmacogenomics and Individualized Therapy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. ; UNC Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Nakanishi H, Shojo H, Ohmori T, Hara M, Takada A, Adachi N, Saito K. A novel method for sex determination by detecting the number of X chromosomes. Int J Legal Med 2014; 129:23-9. [DOI: 10.1007/s00414-014-1065-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 08/07/2014] [Indexed: 10/24/2022]
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Copy Number Variation in Chickens: A Review and Future Prospects. MICROARRAYS 2014; 3:24-38. [PMID: 27605028 PMCID: PMC5003453 DOI: 10.3390/microarrays3010024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 12/19/2022]
Abstract
DNA sequence variations include nucleotide substitution, deletion, insertion, translocation and inversion. Deletion or insertion of a large DNA segment in the genome, referred to as copy number variation (CNV), has caught the attention of many researchers recently. It is believed that CNVs contribute significantly to genome variability, and thus contribute to phenotypic variability. In chickens, genome-wide surveys with array comparative genome hybridization (aCGH), SNP chip detection or whole genome sequencing have revealed a large number of CNVs. A large portion of chicken CNVs involves protein coding or regulatory sequences. A few CNVs have been demonstrated to be the determinant factors for single gene traits, such as late-feathering, pea-comb and dermal hyperpigmentation. The phenotypic effects of the majority of chicken CNVs are to be delineated.
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Zhang W, Zheng Y, Hou L. Pharmacogenomic Discovery Delineating the Genetic Basis of Drug Response. CURRENT GENETIC MEDICINE REPORTS 2013; 1:143-149. [PMID: 24015375 DOI: 10.1007/s40142-013-0019-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Personalized medicine has the promise to tailor medical care based on the patient's genetic make-up and clinical variables such as gender, race and exposure to environmental stimuli. Recent progress in pharmacogenetic and pharmacogenomic studies has suggested that drug response to therapeutic treatments is likely a complex trait influenced by a variety of genetic and non-genetic factors. Identifying molecular targets (e.g., genetic variants) delineating the genetic basis of drug response could help understand the complex nature of drug response. The last decade has witnessed significant advances in genome-wide profiling technologies for genetic/epigenetic variations and gene expression. As an unbiased, cell-based model for pharmacogenomic discovery, a tremendous resource of whole-genome molecular targets has been accumulated for the HapMap lymphoblastoid cell lines (LCLs) during the past decade. The current progress, particularly in cancer pharmacogenomics, using the LCL model was reviewed to illustrate the potential impact of systems biology approaches on pharmacogenomic discovery.
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Affiliation(s)
- Wei Zhang
- Department of Pediatrics, University of Illinois, Chicago, Illinois, USA ; Institute of Human Genetics, University of Illinois, Chicago, Illinois, USA ; University of Illinois Cancer Center, Chicago, Illinois, USA
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Ochs-Balcom HM, Preus L, Wactawski-Wende J, Nie J, Johnson NA, Zakharia F, Tang H, Carlson C, Carty C, Chen Z, Hoffman T, Hutter CM, Jackson RD, Kaplan RC, Li L, Liu S, Neuhouser ML, Peters U, Robbins J, Seldin MF, Thornton TA, Thompson CL, Kooperberg C, Sucheston LE. Association of DXA-derived bone mineral density and fat mass with African ancestry. J Clin Endocrinol Metab 2013; 98:E713-7. [PMID: 23436924 PMCID: PMC3615193 DOI: 10.1210/jc.2012-3921] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Both genes and environment have been implicated in determining the complex body composition phenotypes in individuals of European ancestry; however, few studies have been conducted in other race/ethnic groups. OBJECTIVE We conducted a genome-wide admixture mapping study in an attempt to localize novel genomic regions associated with genetic ancestry. SETTING/PARTICIPANTS We selected a sample of 842 African-American women from the Women's Health Initiative single nucleotide polymorphism (SNP) Health Association Resource for whom several dual-energy X-ray absorptiometry (DXA)-derived bone mineral density (BMD) and fat mass phenotypes were available. METHODS We derived both global and local ancestry estimates for each individual from Affymetrix 6.0 data and analyzed the correlation of DXA phenotypes with global African ancestry. For each phenotype, we examined the association of local genetic ancestry (number of African ancestral alleles at each marker) and each DXA phenotype at 570 282 markers across the genome in additive models with adjustment for important covariates. RESULTS We identified statistically significant correlations of whole-body fat mass, trunk fat mass, and all 6 measures of BMD with a proportion of African ancestry. Genome-wide (admixture) significance for femoral neck BMD was achieved across 2 regions ∼3.7 MB and 0.3 MB on chromosome 19q13; similarly, total hip and intertrochanter BMD were associated with local ancestry in these regions. Trunk fat was the most significant fat mass phenotype showing strong, but not genomewide significant associations on chromosome Xp22. CONCLUSIONS Our results suggest that genomic regions in postmenopausal African-American women contribute to variance in BMD and fat mass existence and warrant further study.
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Affiliation(s)
- Heather M Ochs-Balcom
- Department of Social and Preventive Medicine, University at Buffalo, Buffalo, NY14214-8001, USA.
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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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15
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Mu W, Zhang W. Molecular Approaches, Models, and Techniques in Pharmacogenomic Research and Development. Pharmacogenomics 2013. [DOI: 10.1016/b978-0-12-391918-2.00008-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Gamazon ER, Huang RS, Cox NJ. SCAN: a systems biology approach to pharmacogenomic discovery. Methods Mol Biol 2013; 1015:213-24. [PMID: 23824859 DOI: 10.1007/978-1-62703-435-7_14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Genome-wide association (GWA) studies have identified thousands of genetic variants that contribute to disease and pharmacologic traits. More recently, high-throughput sequencing studies promise to provide a more complete catalog of genetic variants with roles in human phenotypic variation. Yet, characterizing the influence of functional variants on genes, RNAs, proteins, and ultimately disease or pharmacologic traits is a critical challenge for a vast majority of the implicated susceptibility loci. Here we describe SCAN, a bioinformatics resource we have developed to elucidate the functional consequences of genetic variants identified by genome-wide scans. In particular, this public resource implements a systems biology approach to pharmacogenomic discovery.
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Affiliation(s)
- Eric R Gamazon
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
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17
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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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Abstract
OBJECTIVE The goal of pharmacogenomics is the translation of genomic discoveries into individualized patient care. Recent advances in the means to survey human genetic variation are fundamentally transforming our understanding of the genetic basis of interindividual variation in therapeutic response. The goal of this study was to systematically evaluate high-throughput genotyping technologies for their ability to assay variation in pharmacogenetically important genes (pharmacogenes). These platforms are either being proposed for or are already being widely used for clinical implementation; therefore, knowledge of coverage of pharmacogenes on these platforms would serve to better evaluate current or proposed pharmacogenetic association studies. METHOD Among the genes included in our study are drug-metabolizing enzymes, transporters, receptors, and drug targets, of interest to the entire pharmacogenetic community. We considered absolute and linkage disequilibrium (LD)-informed coverage, minor allele frequency spectrum, and functional annotation for a Caucasian population. We also examined the effect of LD, effect size, and cohort size on the power to detect single nucleotide polymorphism associations. RESULTS In our analysis of 253 pharmacogenes, we found that no platform showed more than 85% coverage of these genes (after accounting for LD). Furthermore, the lack of coverage showed a marked increase at minor allele frequencies of less than 20%. Even after accounting for LD, only 30% of the missense polymorphisms (which are enriched for low-frequency alleles) were covered by HapMap, with still lower coverage on the other platforms. CONCLUSION We have conducted the first systematic evaluation of the Axiom Genomic Database, Omni 2.5 M, and the Drug Metabolizing Enzymes and Transporters chip. This study is the first to utilize the 1000 Genomes Project to present a comprehensive evaluative framework. Our results provide a much-needed assessment of microarray-based genotyping and next-generation sequencing technologies' ability to survey fully the variation in genes of particular interest to the pharmacogenetics community. Our findings demonstrate the limitations of genome-wide methods and the challenges of implementing pharmacogenomic tests into the clinical context.
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Ziliak D, Gamazon ER, Lacroix B, Kyung Im H, Wen Y, Huang RS. Genetic variation that predicts platinum sensitivity reveals the role of miR-193b* in chemotherapeutic susceptibility. Mol Cancer Ther 2012; 11:2054-61. [PMID: 22752226 DOI: 10.1158/1535-7163.mct-12-0221] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Platinum agents are the backbone of cancer chemotherapy. Recently, we identified and replicated the role of a single nucleotide polymorphism (SNP, rs1649942) in predicting platinum sensitivity both in vitro and in vivo. Using the CEU samples from the International HapMap Project, we found the same SNP to be a master regulator of multiple gene expression phenotypes, prompting us to investigate whether rs1649942-mediated regulation of miRNAs may in part contribute to variation in platinum sensitivity. To these ends, 60 unrelated HapMap CEU I/II samples were used for our discovery-phase study using high-throughput genome-wide miRNA and gene expression profiling. Examining the relationships among rs1649942, its gene expression targets, genome-wide miRNA expression, and cellular sensitivity to carboplatin and cisplatin, we identified 2 platinum-associated miRNAs (miR-193b* and miR-320) that inhibit the expression of 5 platinum-associated genes (CRIM1, IFIT2, OAS1, KCNMA1, and GRAMD1B). We further replicated the relationship between the expression of miR-193b*, CRIM1, IFIT2, KCNMA1, and GRAMD1B, and platinum sensitivity in a separate HapMap CEU III dataset. We then showed that overexpression of miR-193b* in a randomly selected HapMap cell line results in resistance to both carboplatin and cisplatin. This relationship was also found in 7 ovarian cancer cell lines from NCI60 dataset and confirmed in an OVCAR-3 that overexpression of miR-193b* leads to increased resistance to carboplatin. Our findings highlight a potential mechanism of action for a previously observed genotype-survival outcome association. Further examination of miR-193b* in platinum sensitivity in ovarian cancer is warranted.
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Affiliation(s)
- Dana Ziliak
- Section of Hematology/Oncology, The University of Chicago, Chicago, Illinois 60637, USA
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Ueno T, Emi M, Sato H, Ito N, Muta M, Kuroi K, Toi M. Genome-wide copy number analysis in primary breast cancer. Expert Opin Ther Targets 2012; 16 Suppl 1:S31-5. [PMID: 22313367 DOI: 10.1517/14728222.2011.636739] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Carcinogenesis is considered to be a multistep process that may involve cumulative genomic alterations. Loss of chromosomal material would inactivate tumor suppressor genes and gain of chromosomal material has the potential to activate tumor-promoting genes. AREAS COVERED Recent intensive studies by array comparative genomic hybridization (aCGH) have demonstrated frequent alterations in multiple regions of the genome. This suggests that these regions contain a variety of oncogenes and tumor suppressor genes associated with breast cancer development. The patterns of copy number variations (CNVs) have been suggested to be associated with breast cancer subtypes, indicating the importance of genomic instability in the development of breast cancer. EXPERT OPINION To further clarify the complexity of gene alterations, one approach is to employ a CNV-targeted platform that harbors a large number of direct CNV markers located in the repeat-rich unstable regions of the human genome. Next generation sequencing is another approach to overcome the limitations of aCGH such as the repeat-rich regions. Genomic analysis should be combined with expression analysis to elucidate individual genes relevant to breast cancer development and progression. The elucidation of the functions of the affected genes would lead to identification of new molecular targets for breast cancer eradication.
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Affiliation(s)
- Takayuki Ueno
- Kyoto University, Graduate School of Medicine, Department of Breast Surgery, Kyoto 606-8507, Japan.
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