51
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Vermeesch JR, Melotte C, Froyen G, Van Vooren S, Dutta B, Maas N, Vermeulen S, Menten B, Speleman F, De Moor B, Van Hummelen P, Marynen P, Fryns JP, Devriendt K. Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2016; 53:413-22. [PMID: 15750031 DOI: 10.1369/jhc.4a6436.2005] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Array CGH (comparative genomic hybridization) enables the identification of chromosomal copy number changes. The availability of clone sets covering the human genome opens the possibility for the widespread use of array CGH for both research and diagnostic purposes. In this manuscript we report on the parameters that were critical for successful implementation of the technology, assess quality criteria, and discuss the potential benefits and pitfalls of the technology for improved pre- and postnatal constitutional genetic diagnosis. We propose to name the genome-wide array CGH “molecular karyotyping,” in analogy with conventional karyotyping that uses staining methods to visualize chromosomes.
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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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53
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Ozantürk A, Davis EE, Sabo A, Weiss MM, Muzny D, Dugan-Perez S, Sistermans EA, Gibbs RA, Özgül KR, Yalnızoglu D, Serdaroglu E, Dursun A, Katsanis N. A t(5;16) translocation is the likely driver of a syndrome with ambiguous genitalia, facial dysmorphism, intellectual disability, and speech delay. Cold Spring Harb Mol Case Stud 2016; 2:a000703. [PMID: 27148584 PMCID: PMC4849851 DOI: 10.1101/mcs.a000703] [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] [Indexed: 12/25/2022] Open
Abstract
Genetic studies grounded on monogenic paradigms have accelerated both gene discovery and molecular diagnosis. At the same time, complex genomic rearrangements are also appreciated as potent drivers of disease pathology. Here, we report two male siblings with a dysmorphic face, ambiguous genitalia, intellectual disability, and speech delay. Through quad-based whole-exome sequencing and concomitant molecular cytogenetic testing, we identified two copy-number variants (CNVs) in both affected individuals likely arising from a balanced translocation: a 13.5-Mb duplication on Chromosome 16 (16q23.1 → 16qter) and a 7.7-Mb deletion on Chromosome 5 (5p15.31 → 5pter), as well as a hemizygous missense variant in CXorf36 (also known as DIA1R). The 5p terminal deletion has been associated previously with speech delay, whereas craniofacial dysmorphia and genital/urinary anomalies have been reported in patients with a terminal duplication of 16q. However, dosage changes in either genomic region alone could not account for the overall clinical presentation in our family; functional testing of CXorf36 in zebrafish did not induce defects in neurogenesis or the craniofacial skeleton. Notably, literature and database analysis revealed a similar dosage disruption in two siblings with extensive phenotypic overlap with our patients. Taken together, our data suggest that dosage perturbation of genes within the two chromosomal regions likely drives the syndromic manifestations of our patients and highlight how multiple genetic lesions can contribute to complex clinical pathologies.
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Affiliation(s)
- Ayşegül Ozantürk
- Department of Pediatrics, Metabolism Unit, Hacettepe University, Ankara 06410, Turkey;; Department of Biology, Molecular Biology Section, Hacettepe University, Ankara 06800, Turkey;; Center for Human Disease Modeling, Duke University, Durham, North Carolina 27701, USA
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina 27701, USA
| | - Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Marjan M Weiss
- Department of Clinical Genetics, VU University Medical Center (Amsterdam), NL-1081 HV Amsterdam, The Netherlands
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Shannon Dugan-Perez
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Erik A Sistermans
- Department of Clinical Genetics, VU University Medical Center (Amsterdam), NL-1081 HV Amsterdam, The Netherlands
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Köksal R Özgül
- Department of Pediatrics, Metabolism Unit, Hacettepe University, Ankara 06410, Turkey
| | - Dilek Yalnızoglu
- Department of Pediatrics, Pediatric Neurology Unit, Hacettepe University, Ankara 06410, Turkey
| | - Esra Serdaroglu
- Department of Pediatrics, Pediatric Neurology Unit, Hacettepe University, Ankara 06410, Turkey
| | - Ali Dursun
- Department of Pediatrics, Metabolism Unit, Hacettepe University, Ankara 06410, Turkey
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina 27701, USA
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Stamoulis C, Betensky RA. Optimization of Signal Decomposition Matched Filtering (SDMF) for Improved Detection of Copy-Number Variations. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2016; 13:584-591. [PMID: 27295643 PMCID: PMC4905595 DOI: 10.1109/tcbb.2015.2448077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We aim to improve the performance of the previously proposed signal decomposition matched filtering (SDMF) method [26] for the detection of copy-number variations (CNV) in the human genome. Through simulations, we show that the modified SDMF is robust even at high noise levels and outperforms the original SDMF method, which indirectly depends on CNV frequency. Simulations are also used to develop a systematic approach for selecting relevant parameter thresholds in order to optimize sensitivity, specificity and computational efficiency. We apply the modified method to array CGH data from normal samples in the cancer genome atlas (TCGA) and compare detected CNVs to those estimated using circular binary segmentation (CBS) [19], a hidden Markov model (HMM)-based approach [11] and a subset of CNVs in the Database of Genomic Variants. We show that a substantial number of previously identified CNVs are detected by the optimized SDMF, which also outperforms the other two methods.
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Affiliation(s)
- Catherine Stamoulis
- Department of Radiology, Harvard Medical School and Boston Children’s Hospital, Boston, MA 02115
| | - Rebecca A. Betensky
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115
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55
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Wou K, Levy B, Wapner RJ. Chromosomal Microarrays for the Prenatal Detection of Microdeletions and Microduplications. Clin Lab Med 2016; 36:261-76. [PMID: 27235911 DOI: 10.1016/j.cll.2016.01.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chromosomal microarray analysis has replaced conventional G-banded karyotype in prenatal diagnosis as the first-tier test for the cytogenetic detection of copy number imbalances in fetuses with/without major structural abnormalities. This article reviews the basic technology of microarray; the value and clinical significance of the detection of microdeletions, microduplications, and other copy number variants; as well as the importance of genetic counseling for prenatal diagnosis. It also discusses the current status of noninvasive screening for some of these microdeletion and microduplication syndromes.
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Affiliation(s)
- Karen Wou
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Medical Center, 3959 Broadway, CHN 718, New York, NY 10032, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Medical Center, 3959 Broadway, CHC 406b, New York, NY 10032, USA
| | - Ronald J Wapner
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Medical Center, 622 West 168th Street, PH 16-66, New York, NY 10032, USA.
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56
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Hu J, Zhang L, Wang HJ. Sequential model selection-based segmentation to detect DNA copy number variation. Biometrics 2016; 72:815-26. [PMID: 26954760 DOI: 10.1111/biom.12478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 08/01/2015] [Accepted: 09/01/2015] [Indexed: 12/16/2022]
Abstract
Array-based CGH experiments are designed to detect genomic aberrations or regions of DNA copy-number variation that are associated with an outcome, typically a state of disease. Most of the existing statistical methods target on detecting DNA copy number variations in a single sample or array. We focus on the detection of group effect variation, through simultaneous study of multiple samples from multiple groups. Rather than using direct segmentation or smoothing techniques, as commonly seen in existing detection methods, we develop a sequential model selection procedure that is guided by a modified Bayesian information criterion. This approach improves detection accuracy by accumulatively utilizing information across contiguous clones, and has computational advantage over the existing popular detection methods. Our empirical investigation suggests that the performance of the proposed method is superior to that of the existing detection methods, in particular, in detecting small segments or separating neighboring segments with differential degrees of copy-number variation.
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Affiliation(s)
- Jianhua Hu
- Department of Biostatistics, UT M. D. Anderson Cancer Center, Houston, Texas 77030, U.S.A..
| | - Liwen Zhang
- School of Economics, Shanghai University, Shanghai 200444, China.
| | - Huixia Judy Wang
- Department of Statistics, George Washington University, Washington D.C. 20052, U.S.A..
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57
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58
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Abstract
Microarray-based technology to conduct array comparative genomic hybridization (aCGH) has made a significant impact on the diagnosis of human genetic diseases. Such diagnoses, previously undetectable by traditional G-banding chromosome analysis, are now achieved by identifying genomic copy number variants (CNVs) using the microarray. Not only can hundreds of well-characterized genetic syndromes be detected in a single assay, but new genomic disorders and disease-causing genes can also be discovered through the utilization of aCGH technology. Although other platforms such as single nucleotide polymorphism (SNP) arrays can be used for detecting CNVs, in this chapter we focus on describing the methods for performing aCGH using Agilent oligonucleotide arrays for both prenatal (e.g., amniotic fluid and chorionic villus sample) and postnatal samples (e.g., blood).
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Affiliation(s)
- Ankita Patel
- Medical Genetics Laboratories, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Sau W Cheung
- Medical Genetics Laboratories, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
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59
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Corrado KR, Andrade SC, Bellizzi J, D'Souza-Li L, Arnold A. Polyclonality of Parathyroid Tumors in Neonatal Severe Hyperparathyroidism. J Bone Miner Res 2015; 30:1797-802. [PMID: 25828954 DOI: 10.1002/jbmr.2516] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 03/20/2015] [Accepted: 03/22/2015] [Indexed: 11/11/2022]
Abstract
Neonatal severe hyperparathyroidism (NSHPT) is a rare disorder characterized by major hypercalcemia, elevated parathyroid hormone levels, and marked enlargement of multiple parathyroid glands, usually associated with germline mutations in the calcium receptor gene CASR. However, little is known about the outgrowth of parathyroid tumors in NSHPT, including whether they represent monoclonal or polyclonal expansions. We sought to examine the clonality of parathyroid tissues resected from a patient with NSHPT and biallelic CASR mutations. DNA from two distinct parathyroid tumors resected from a girl with NSHPT, plus polyclonal/monoclonal control samples, were subjected to analyses of clonality by two independent methods, X-chromosome inactivation analysis at the androgen receptor locus (HUMARA) and BAC array comparative genomic hybridization (CGH). Both parathyroid tumor samples revealed polyclonal patterns by X-inactivation analysis, with polyclonal and monoclonal controls yielding the expected patterns. Similarly, by BAC array CGH, neither parathyroid sample contained monoclonal copy number changes and both appeared identical to the patient-matched polyclonal controls. Our observations provide direct experimental evidence that the markedly enlarged parathyroid tumors in the setting of NSHPT constitute polyclonal, generalized hyperplastic growths rather than monoclonal neoplasms.
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Affiliation(s)
- Kristin R Corrado
- Center for Molecular Medicine, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Simone Caixeta Andrade
- Pediatric Endocrinology Laboratory, Center for Investigation in Pediatrics, Department of Pediatrics, Faculty of Medical Science, State University of Campinas, São Paulo, Brazil
| | - Justin Bellizzi
- Center for Molecular Medicine, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Lilia D'Souza-Li
- Pediatric Endocrinology Laboratory, Center for Investigation in Pediatrics, Department of Pediatrics, Faculty of Medical Science, State University of Campinas, São Paulo, Brazil
| | - Andrew Arnold
- Center for Molecular Medicine, University of Connecticut School of Medicine, Farmington, CT, USA
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60
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Tattini L, D'Aurizio R, Magi A. Detection of Genomic Structural Variants from Next-Generation Sequencing Data. Front Bioeng Biotechnol 2015; 3:92. [PMID: 26161383 PMCID: PMC4479793 DOI: 10.3389/fbioe.2015.00092] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 06/10/2015] [Indexed: 01/16/2023] Open
Abstract
Structural variants are genomic rearrangements larger than 50 bp accounting for around 1% of the variation among human genomes. They impact on phenotypic diversity and play a role in various diseases including neurological/neurocognitive disorders and cancer development and progression. Dissecting structural variants from next-generation sequencing data presents several challenges and a number of approaches have been proposed in the literature. In this mini review, we describe and summarize the latest tools – and their underlying algorithms – designed for the analysis of whole-genome sequencing, whole-exome sequencing, custom captures, and amplicon sequencing data, pointing out the major advantages/drawbacks. We also report a summary of the most recent applications of third-generation sequencing platforms. This assessment provides a guided indication – with particular emphasis on human genetics and copy number variants – for researchers involved in the investigation of these genomic events.
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Affiliation(s)
- Lorenzo Tattini
- Department of Neurosciences, Psychology, Pharmacology and Child Health, University of Florence , Florence , Italy
| | - Romina D'Aurizio
- Laboratory of Integrative Systems Medicine (LISM), Institute of Informatics and Telematics and Institute of Clinical Physiology, National Research Council , Pisa , Italy
| | - Alberto Magi
- Department of Clinical and Experimental Medicine, University of Florence , Florence , Italy
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61
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Asim A, Kumar A, Muthuswamy S, Jain S, Agarwal S. "Down syndrome: an insight of the disease". J Biomed Sci 2015; 22:41. [PMID: 26062604 PMCID: PMC4464633 DOI: 10.1186/s12929-015-0138-y] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 04/22/2015] [Indexed: 01/19/2023] Open
Abstract
Down syndrome (DS) is one of the commonest disorders with huge medical and social cost. DS is associated with number of phenotypes including congenital heart defects, leukemia, Alzeihmer's disease, Hirschsprung disease etc. DS individuals are affected by these phenotypes to a variable extent thus understanding the cause of this variation is a key challenge. In the present review article, we emphasize an overview of DS, DS-associated phenotypes diagnosis and management of the disease. The genes or miRNA involved in Down syndrome associated Alzheimer's disease, congenital heart defects (AVSD), leukemia including AMKL and ALL, hypertension and Hirschprung disease are discussed in this article. Moreover, we have also reviewed various prenatal diagnostic method from karyotyping to rapid molecular methods - MLPA, FISH, QF-PCR, PSQ, NGS and noninvasive prenatal diagnosis in detail.
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Affiliation(s)
- Ambreen Asim
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, 226014, India.
| | - Ashok Kumar
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, 226014, India.
| | - Srinivasan Muthuswamy
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, 226014, India.
| | - Shalu Jain
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, 226014, India.
| | - Sarita Agarwal
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, 226014, India.
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62
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Hybrid algorithms for multiple change-point detection in biological sequences. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 823:41-61. [PMID: 25381101 DOI: 10.1007/978-3-319-10984-8_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Array comparative genomic hybridization (aCGH) is one of the techniques that can be used to detect copy number variations in DNA sequences in high resolution. It has been identified that abrupt changes in the human genome play a vital role in the progression and development of many complex diseases. In this study we propose two distinct hybrid algorithms that combine efficient sequential change-point detection procedures (the Shiryaev-Roberts procedure and the cumulative sum control chart (CUSUM) procedure) with the Cross-Entropy method, which is an evolutionary stochastic optimization technique to estimate both the number of change-points and their corresponding locations in aCGH data. The proposed hybrid algorithms are applied to both artificially generated data and real aCGH experimental data to illustrate their usefulness. Our results show that the proposed methodologies are effective in detecting multiple change-points in biological sequences of continuous measurements.
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63
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Weinmann A, Storath M. Iterative Potts and Blake-Zisserman minimization for the recovery of functions with discontinuities from indirect measurements. Proc Math Phys Eng Sci 2015; 471:20140638. [PMID: 27547074 DOI: 10.1098/rspa.2014.0638] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Signals with discontinuities appear in many problems in the applied sciences ranging from mechanics, electrical engineering to biology and medicine. The concrete data acquired are typically discrete, indirect and noisy measurements of some quantities describing the signal under consideration. The task is to restore the signal and, in particular, the discontinuities. In this respect, classical methods perform rather poor, whereas non-convex non-smooth variational methods seem to be the correct choice. Examples are methods based on Mumford-Shah and piecewise constant Mumford-Shah functionals and discretized versions which are known as Blake-Zisserman and Potts functionals. Owing to their non-convexity, minimization of such functionals is challenging. In this paper, we propose a new iterative minimization strategy for Blake-Zisserman as well as Potts functionals and a related jump-sparsity problem dealing with indirect, noisy measurements. We provide a convergence analysis and underpin our findings with numerical experiments.
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Affiliation(s)
- Andreas Weinmann
- Research Group Fast Algorithms for Biomedical Imaging, Helmholtz Center Munich, and Department of Mathematics , Technische Universität München , , Germany
| | - Martin Storath
- Biomedical Imaging Group , École Polytechnique Fédérale de Lausanne , Lausanne, Switzerland
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64
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Priyadarshana WJRM, Sofronov G. Multiple Break-Points Detection in Array CGH Data via the Cross-Entropy Method. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015; 12:487-498. [PMID: 26357234 DOI: 10.1109/tcbb.2014.2361639] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Array comparative genome hybridization (aCGH) is a widely used methodology to detect copy number variations of a genome in high resolution. Knowing the number of break-points and their corresponding locations in genomic sequences serves different biological needs. Primarily, it helps to identify disease-causing genes that have functional importance in characterizing genome wide diseases. For human autosomes the normal copy number is two, whereas at the sites of oncogenes it increases (gain of DNA) and at the tumour suppressor genes it decreases (loss of DNA). The majority of the current detection methods are deterministic in their set-up and use dynamic programming or different smoothing techniques to obtain the estimates of copy number variations. These approaches limit the search space of the problem due to different assumptions considered in the methods and do not represent the true nature of the uncertainty associated with the unknown break-points in genomic sequences. We propose the Cross-Entropy method, which is a model-based stochastic optimization technique as an exact search method, to estimate both the number and locations of the break-points in aCGH data. We model the continuous scale log-ratio data obtained by the aCGH technique as a multiple break-point problem. The proposed methodology is compared with well established publicly available methods using both artificially generated data and real data. Results show that the proposed procedure is an effective way of estimating number and especially the locations of break-points with high level of precision. Availability: The methods described in this article are implemented in the new R package breakpoint and it is available from the Comprehensive R Archive Network at http://CRAN.R-project.org/package=breakpoint.
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65
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[Current methods in genetic analysis : an approach for genetics-based preventive medicine]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2014; 58:113-20. [PMID: 25446309 DOI: 10.1007/s00103-014-2088-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Modern genetic analysis methods such as DNA arrays (gene chips) or high-throughput DNA sequencing of the next generation (Next Generation Sequencing, NGS) have once again accelerated the pace of innovation that has been powered by genome research over the past 10 years of the "post-genomic era". The present paper introduces array and NGS methods as two important innovation driving methods and provides examples for their application in large-scale scientific projects. However, a broad application of these very powerful technologies for genetic screening for the purpose of disease prevention is currently not yet in sight. The complexity of the interaction of genes, gene products and the environment has so far exceeded all expectations, suggesting that reliable statements about the medical relevance of common genetic variants can presently only be made in a few areas such as pharmacogenetics and oncology. We also discuss ethical issues raised by genetic population screening. The aim of this paper is to provide a brief outline of the development of methods in molecular genetics to the now dominant modern technologies and present their applications in research, in the diagnosis of rare diseases, and in terms of screening approaches.
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66
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Focal chromosomal copy number aberrations in cancer—Needles in a genome haystack. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:2698-2704. [DOI: 10.1016/j.bbamcr.2014.08.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 07/29/2014] [Accepted: 08/01/2014] [Indexed: 12/22/2022]
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67
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DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Res 2014; 24:2022-32. [PMID: 25236618 PMCID: PMC4248318 DOI: 10.1101/gr.175141.114] [Citation(s) in RCA: 295] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Detection of DNA copy number aberrations by shallow whole-genome sequencing (WGS) faces many challenges, including lack of completion and errors in the human reference genome, repetitive sequences, polymorphisms, variable sample quality, and biases in the sequencing procedures. Formalin-fixed paraffin-embedded (FFPE) archival material, the analysis of which is important for studies of cancer, presents particular analytical difficulties due to degradation of the DNA and frequent lack of matched reference samples. We present a robust, cost-effective WGS method for DNA copy number analysis that addresses these challenges more successfully than currently available procedures. In practice, very useful profiles can be obtained with ∼0.1× genome coverage. We improve on previous methods by first implementing a combined correction for sequence mappability and GC content, and second, by applying this procedure to sequence data from the 1000 Genomes Project in order to develop a blacklist of problematic genome regions. A small subset of these blacklisted regions was previously identified by ENCODE, but the vast majority are novel unappreciated problematic regions. Our procedures are implemented in a pipeline called QDNAseq. We have analyzed over 1000 samples, most of which were obtained from the fixed tissue archives of more than 25 institutions. We demonstrate that for most samples our sequencing and analysis procedures yield genome profiles with noise levels near the statistical limit imposed by read counting. The described procedures also provide better correction of artifacts introduced by low DNA quality than prior approaches and better copy number data than high-resolution microarrays at a substantially lower cost.
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68
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Sidonets IV, Meshkov AN. GENETICS FOR DIAGNOSTICS IN PREVENTIVE MEDICINE. КАРДИОВАСКУЛЯРНАЯ ТЕРАПИЯ И ПРОФИЛАКТИКА 2014. [DOI: 10.15829/1728-8800-2014-4-75-80] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The sequencing of first human genome followed by rapid development of technologies, that led to significant lowering of costs for genetic analyze and its fast performing, made possible a broad invention of genetic diagnostics methods into clinical practice. Contemporary methods of molecular genetics make possible to research on inherited factors on chromosome level with molecular cytogenetics methods, and on the level of local mutations with the use or polymeraze chain reaction, microchips and sequencing. Temps of the next generation sequencing methods provide the opportunity to predict soon inclusion in practice of the personalized medical analysis of large genetic data massive, that can be used for the disease outcome prediction, estimation of its course, and for the prescription and correction of pharmacotherapy. In this review, different (including novel) approaches to genetic diagnostics are explored for the rare as common diseases, their benefits and restrictions.
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Affiliation(s)
- I. V. Sidonets
- FSBI State Scientific-Research Centre for Preventive Medicine of the Ministry of Health, Moscow
| | - A. N. Meshkov
- FSBI State Scientific-Research Centre for Preventive Medicine of the Ministry of Health, Moscow
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69
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Xu Y, Trippa L, Müller P, Ji Y. Subgroup-Based Adaptive (SUBA) Designs for Multi-Arm Biomarker Trials. STATISTICS IN BIOSCIENCES 2014; 8:159-180. [PMID: 27617041 DOI: 10.1007/s12561-014-9117-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Targeted therapies based on biomarker profiling are becoming a mainstream direction of cancer research and treatment. Depending on the expression of specific prognostic biomarkers, targeted therapies assign different cancer drugs to subgroups of patients even if they are diagnosed with the same type of cancer by traditional means, such as tumor location. For example, Herceptin is only indicated for the subgroup of patients with HER2+ breast cancer, but not other types of breast cancer. However, subgroups like HER2+ breast cancer with effective targeted therapies are rare and most cancer drugs are still being applied to large patient populations that include many patients who might not respond or benefit. Also, the response to targeted agents in humans is usually unpredictable. To address these issues, we propose SUBA, subgroup-based adaptive designs that simultaneously search for prognostic subgroups and allocate patients adaptively to the best subgroup-specific treatments throughout the course of the trial. The main features of SUBA include the continuous reclassification of patient subgroups based on a random partition model and the adaptive allocation of patients to the best treatment arm based on posterior predictive probabilities. We compare the SUBA design with three alternative designs including equal randomization, outcome-adaptive randomization and a design based on a probit regression. In simulation studies we find that SUBA compares favorably against the alternatives.
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Affiliation(s)
- Yanxun Xu
- Division of Statistics and Scientific Computing, The University of Texas at Austin, Austin, TX, U.S.A
| | - Lorenzo Trippa
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, U.S.A
| | - Peter Müller
- Department of Mathematics, The University of Texas at Austin, Austin, TX, U.S.A
| | - Yuan Ji
- Center for Clinical and Research Informatics, NorthShore University Health System Evanston, IL, U.S.A; Department of Health Studies, The University of Chicago, Chicago, IL, U.S.A
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70
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Du Y, Murani E, Ponsuksili S, Wimmers K. biomvRhsmm: genomic segmentation with hidden semi-Markov model. BIOMED RESEARCH INTERNATIONAL 2014; 2014:910390. [PMID: 24995333 PMCID: PMC4065698 DOI: 10.1155/2014/910390] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 03/03/2014] [Accepted: 03/21/2014] [Indexed: 11/25/2022]
Abstract
High-throughput technologies like tiling array and next-generation sequencing (NGS) generate continuous homogeneous segments or signal peaks in the genome that represent transcripts and transcript variants (transcript mapping and quantification), regions of deletion and amplification (copy number variation), or regions characterized by particular common features like chromatin state or DNA methylation ratio (epigenetic modifications). However, the volume and output of data produced by these technologies present challenges in analysis. Here, a hidden semi-Markov model (HSMM) is implemented and tailored to handle multiple genomic profile, to better facilitate genome annotation by assisting in the detection of transcripts, regulatory regions, and copy number variation by holistic microarray or NGS. With support for various data distributions, instead of limiting itself to one specific application, the proposed hidden semi-Markov model is designed to allow modeling options to accommodate different types of genomic data and to serve as a general segmentation engine. By incorporating genomic positions into the sojourn distribution of HSMM, with optional prior learning using annotation or previous studies, the modeling output is more biologically sensible. The proposed model has been compared with several other state-of-the-art segmentation models through simulation benchmarking, which shows that our efficient implementation achieves comparable or better sensitivity and specificity in genomic segmentation.
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Affiliation(s)
- Yang Du
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, 18196 Dummerstorf, Germany
| | - Eduard Murani
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, 18196 Dummerstorf, Germany
| | - Siriluck Ponsuksili
- Research Group Functional Genomics, Leibniz Institute for Farm Animal Biology, 18196 Dummerstorf, Germany
| | - Klaus Wimmers
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, 18196 Dummerstorf, Germany
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71
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Briollais L, Durrieu G. Application of quantile regression to recent genetic and -omic studies. Hum Genet 2014; 133:951-66. [DOI: 10.1007/s00439-014-1440-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 03/10/2014] [Indexed: 12/01/2022]
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72
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Magbanua MJM, Roy R, Sosa EV, Hauranieh L, Kablanian A, Eisenbud LE, Ryazantsev A, Au A, Scott JH, Melisko M, Park JW. Genome-wide copy number analysis of cerebrospinal fluid tumor cells and their corresponding archival primary tumors. GENOMICS DATA 2014; 2:60-2. [PMID: 26484071 PMCID: PMC4535622 DOI: 10.1016/j.gdata.2014.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 04/02/2014] [Indexed: 11/10/2022]
Abstract
A debilitating complication of breast cancer is the metastatic spread of tumor cells to the leptomeninges or cerebrospinal fluid (CSF). Patients diagnosed with this aggressive clinical syndrome, known as leptomeningeal carcinomatosis, have very poor prognosis. Despite improvements in detecting cerebrospinal fluid tumor cells (CSFTCs), information regarding their molecular biology is extremely limited. In our recent work, we utilized a protocol previously used for circulating tumor cell isolation to purify tumor cells from the CSF. We then performed genomic characterization of CSFTCs as well as archival tumors from the same patient. Here, we describe the microarray data and quality controls associated with our study published in the Cancer Research journal in 2013 [1]. We also provide an R script containing code for quality control of microarray data and assessment of copy number calls. The microarray data has been deposited into Gene Expression Omnibus under accession # GSE46068.
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Affiliation(s)
- Mark Jesus M Magbanua
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Ritu Roy
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA ; Helen Diller Family Comprehensive Cancer Center Computational Biology Core, University of California San Francisco, San Francisco, California, USA
| | - Eduardo V Sosa
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Louai Hauranieh
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Andrea Kablanian
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Lauren E Eisenbud
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Artem Ryazantsev
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Alfred Au
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Janet H Scott
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Michelle Melisko
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - John W Park
- Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
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73
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Deficiency in asparagine synthetase expression in rectal cancers receiving concurrent chemoradiotherapy: negative prognostic impact and therapeutic relevance. Tumour Biol 2014; 35:6823-30. [DOI: 10.1007/s13277-014-1895-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 03/25/2014] [Indexed: 01/10/2023] Open
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Abstract
The field of cytogenetics has focused on studying the number, structure, function and origin of chromosomal abnormalities and the evolution of chromosomes. The development of fluorescent molecules that either directly or via an intermediate molecule bind to DNA has led to the development of fluorescent in situ hybridization (FISH), a technology linking cytogenetics to molecular genetics. This technique has a wide range of applications that increased the dimension of chromosome analysis. The field of cytogenetics is particularly important for medical diagnostics and research as well as for gene ordering and mapping. Furthermore, the increased application of molecular biology techniques, such as array-based technologies, has led to improved resolution, extending the recognized range of microdeletion/microduplication syndromes and genomic disorders. In adopting these newly expanded methods, cytogeneticists have used a range of technologies to study the association between visible chromosome rearrangements and defects at the single nucleotide level. Overall, molecular cytogenetic techniques offer a remarkable number of potential applications, ranging from physical mapping to clinical and evolutionary studies, making a powerful and informative complement to other molecular and genomic approaches. This manuscript does not present a detailed history of the development of molecular cytogenetics; however, references to historical reviews and experiments have been provided whenever possible. Herein, the basic principles of molecular cytogenetics, the technologies used to identify chromosomal rearrangements and copy number changes, and the applications for cytogenetics in biomedical diagnosis and research are presented and discussed.
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Affiliation(s)
- Mariluce Riegel
- Serviço de Genética Médica, Hospital de Clínicas, Porto Alegre, RS, Brazil . ; Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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75
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Feber A, Guilhamon P, Lechner M, Fenton T, Wilson GA, Thirlwell C, Morris TJ, Flanagan AM, Teschendorff AE, Kelly JD, Beck S. Using high-density DNA methylation arrays to profile copy number alterations. Genome Biol 2014; 15:R30. [PMID: 24490765 PMCID: PMC4054098 DOI: 10.1186/gb-2014-15-2-r30] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 02/03/2014] [Indexed: 12/17/2022] Open
Abstract
The integration of genomic and epigenomic data is an increasingly popular approach for studying the complex mechanisms driving cancer development. We have developed a method for evaluating both methylation and copy number from high-density DNA methylation arrays. Comparing copy number data from Infinium HumanMethylation450 BeadChips and SNP arrays, we demonstrate that Infinium arrays detect copy number alterations with the sensitivity of SNP platforms. These results show that high-density methylation arrays provide a robust and economic platform for detecting copy number and methylation changes in a single experiment. Our method is available in the ChAMP Bioconductor package: http://www.bioconductor.org/packages/2.13/bioc/html/ChAMP.html.
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Affiliation(s)
- Andrew Feber
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Paul Guilhamon
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Matthias Lechner
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Tim Fenton
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Gareth A Wilson
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Christina Thirlwell
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Tiffany J Morris
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Adrienne M Flanagan
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
- Royal National Orthopaedic Hospital, Stanmore, Brockly Hill, Middlesex HA7 4LP, UK
| | - Andrew E Teschendorff
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - John D Kelly
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
- Division of Surgery and Interventional Science, UCL Medical School, University College London, London WC1E 6BT, UK
| | - Stephan Beck
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
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Roa BB, Pulliam J, Eng CM, Cheung SW. Evolution of prenatal genetics: from point mutation testing to chromosomal microarray analysis. Expert Rev Mol Diagn 2014; 5:883-92. [PMID: 16255630 DOI: 10.1586/14737159.5.6.883] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Molecular genetic testing involves DNA analysis using various methods for the purpose of diagnosing genetic disorders. In the prenatal DNA diagnostic setting, fetal DNA is usually tested for a specific single-gene disorder for which the fetal risk is 25% or more. In contrast, cytogenetic testing is often used to detect fetal chromosomal abnormalities in cases that involve a wider range of indications. Classic cytogenetic and DNA-based testing methods provide a range of aberrations detected with different levels of genomic resolution. More recently developed molecular cytogenetic methods provide powerful tools to bridge the technical divide between these related areas. One such hybrid method is microarray-based comparative genomic hybridization. Chromosomal microarray analysis has been applied to clinical testing for unbalanced gains or losses of genomic regions associated with genetic disorders. This technology is poised to have a substantial impact on clinical genetics, including prenatal genetic testing.
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Affiliation(s)
- Benjamin B Roa
- Department of Molecular & Human Genetics, Baylor College of Medicine, NAB2015, Houston, TX 77030, USA.
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Nambiar S, Mirmohammadsadegh A, Bär A, Bardenheuer W, Roeder G, Hengge UR. Applications of array technology: melanoma research and diagnosis. Expert Rev Mol Diagn 2014; 4:549-57. [PMID: 15225102 DOI: 10.1586/14737159.4.4.549] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A complex set of genetic alterations occurs within a cell in order to permit neoplastic transformation. Human cancers undergo a continuous development from benign to malignant states, as most thoroughly documented in the mole-to-melanoma transition. Several specific genetic and transcriptional events correlate with the prolonged multistep sequence from early to late clinical stages of the disease. High-throughput microarrays are being used in expression profiling analyses with the aim of discovering genes and their pathways, functional characterization of genes and tumor subclassification. There are, however, many potential pitfalls in the use of microarrays that result in false leads and erroneous conclusions. This review summarizes the current status of the application of microarray technology in melanoma research. It also attempts to outline some of the steps needed to develop the key features to be observed in developing diagnostic and prognostic classification systems based upon gene expression profiling.
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Affiliation(s)
- Sandeep Nambiar
- Heine University, Department of Dermatology, Heinrich Heine, Moorenstr. 5, 40225 Dusseldorf, Germany.
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Abstract
The majority of melanocytic neoplasms can be correctly diagnosed using routine histopathologic analysis. However, a significant minority of tumors have ambiguous histopathologic attributes that overlap between melanocytic nevi and melanoma. Ancillary tests that assist in distinguishing potentially lethal melanomas from benign melanocytic nevi with atypical histopathologic features are available, but still need refining.Most melanomas have chromosomal copy number aberrations, frequently involving multiple chromosomes. With rare exceptions, such anomalies are not found in melanocytic nevi. This difference formed the basis to develop assays that can help distinguish melanoma from nevi by fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH). FISH can detect chromosomal copy number changes of a limited number of loci within individual cells. By contrast, CGH assesses copy number across the entire genome, but typically is performed on bulk cell populations so that copy number changes in individual cells or subpopulations of cells can go undetected. Both FISH and CGH have been used to provide genomic information in histopathologically ambiguous melanocytic tumors that can assist pathologists make correct diagnoses.
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Affiliation(s)
- Jeffrey P North
- Department of Dermatology, University of California San Francisco, San Francisco, CA, USA
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79
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Brito I, Hupé P, Neuvial P, Barillot E. Stability-based comparison of class discovery methods for DNA copy number profiles. PLoS One 2013; 8:e81458. [PMID: 24339933 PMCID: PMC3855312 DOI: 10.1371/journal.pone.0081458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 10/22/2013] [Indexed: 11/19/2022] Open
Abstract
MOTIVATION Array-CGH can be used to determine DNA copy number, imbalances in which are a fundamental factor in the genesis and progression of tumors. The discovery of classes with similar patterns of array-CGH profiles therefore adds to our understanding of cancer and the treatment of patients. Various input data representations for array-CGH, dissimilarity measures between tumor samples and clustering algorithms may be used for this purpose. The choice between procedures is often difficult. An evaluation procedure is therefore required to select the best class discovery method (combination of one input data representation, one dissimilarity measure and one clustering algorithm) for array-CGH. Robustness of the resulting classes is a common requirement, but no stability-based comparison of class discovery methods for array-CGH profiles has ever been reported. RESULTS We applied several class discovery methods and evaluated the stability of their solutions, with a modified version of Bertoni's [Formula: see text]-based test [1]. Our version relaxes the assumption of independency required by original Bertoni's [Formula: see text]-based test. We conclude that Minimal Regions of alteration (a concept introduced by [2]) for input data representation, sim [3] or agree [4] for dissimilarity measure and the use of average group distance in the clustering algorithm produce the most robust classes of array-CGH profiles. AVAILABILITY The software is available from http://bioinfo.curie.fr/projects/cgh-clustering. It has also been partly integrated into "Visualization and analysis of array-CGH"(VAMP)[5]. The data sets used are publicly available from ACTuDB [6].
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Affiliation(s)
- Isabel Brito
- Institut Curie, Paris, France
- INSERM, U900, Paris, France
- Mines ParisTech, Fontainebleau, France
| | - Philippe Hupé
- Institut Curie, Paris, France
- INSERM, U900, Paris, France
- Mines ParisTech, Fontainebleau, France
- CNRS UMR144, Paris, France
| | - Pierre Neuvial
- Laboratoire Statistique & Génome, Université d′Évry Val d′Essonne, UMR CNRS 8071-USC INRA, Évry, France
| | - Emmanuel Barillot
- Institut Curie, Paris, France
- INSERM, U900, Paris, France
- Mines ParisTech, Fontainebleau, France
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80
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Identification and functional analysis of miRNAs in developing kernels of a viviparous mutant in maize. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.cj.2013.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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81
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Luong TM, Rozenholc Y, Nuel G. Fast estimation of posterior probabilities in change-point analysis through a constrained hidden Markov model. Comput Stat Data Anal 2013. [DOI: 10.1016/j.csda.2013.06.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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82
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Lohberger B, Stuendl N, Wolf E, Liegl-Atzwanger B, Leithner A, Rinner B. The novel myxofibrosarcoma cell line MUG-Myx1 expresses a tumourigenic stem-like cell population with high aldehyde dehydrogenase 1 activity. BMC Cancer 2013; 13:563. [PMID: 24289252 PMCID: PMC4219478 DOI: 10.1186/1471-2407-13-563] [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: 08/01/2013] [Accepted: 11/26/2013] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Myxofibrosarcoma comprises a spectrum of malignant neoplasms withprominent myxoid stromata, cellular pleomorphism, and distinct curvilinear vascular patterns. These neoplasms mainly affect patients in the sixth to eighth decades of life and the overall 5-year survival rate is 60-70%. METHODS After the establishment of the novel myxofibrosarcoma cell lines MUG-Myx1, cells were characterized using short tandem repeat (STR), copy number variation (CNV), and genotype/loss-of-heterozygosity (LOH) analyses. The growth behaviour of the cells was analyzed with the xCELLigence system and an MTS assay. The tumourigenicity of MUG-Myx1 was proved in NOD/SCID mice. Additionally, a stem-like cell population with high enzymatic activity of aldehyde dehydrogenase 1 (ALDH1(high)) was isolated for the first time from myxofibrosarcoma cells using the Aldefluor® assay followed by FACS analysis. RESULTS The frozen primary parental tumour tissue and the MUG-Myx1 cell line showed the same STR profile at the markers D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, Amelogenin, D8S1179, TPOX, and FGY. Typically, myxofibrosarcoma gain and/or amplification was mapped to 7p21.3-q31.1, q31.1-q31.33, q33-q36.2, p21.3, p21.2, p14.1-q11.23, q31.33-q33, p21.2-p14.1, q11.23-q21.3, q36.2-q36.3, which, respectively are known to harbour tumour-associated genes, including TIF, BRAF, MLL3, SMO, and MET. Typically an LOH for myxofibrosarcoma on chr5 q21 was found. In addition, MUG-Myx1 ALDH1(high) cells showed an upregulation of the ABC transporter ABCB1 and ABCG2; higher c-Myc, E-cadherin and SOX-2 expression; and a higher potential for tumourigenicity and proliferation levels. CONCLUSION The new myxofibrosarcoma cell line MUG-Myx1 was established to enrich the bank of publicly available cell lines, with respect to providing comprehensive genetic and epigenetic characterization. Furthermore, because of their tumourigenicity, the cell line is also suitable for in vivo experiments.
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Affiliation(s)
- Birgit Lohberger
- Department of Orthopaedic Surgery, Medical University of Graz, Auenbruggerplatz 5, A-8036, Graz, Austria.
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Reijnders CMA, van Essen HW, van Rens BTTM, van Beek JHGM, Ylstra B, Blankenstein MA, Lips P, Bravenboer N. Increased expression of matrix extracellular phosphoglycoprotein (MEPE) in cortical bone of the rat tibia after mechanical loading: identification by oligonucleotide microarray. PLoS One 2013; 8:e79672. [PMID: 24255709 PMCID: PMC3821845 DOI: 10.1371/journal.pone.0079672] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 09/24/2013] [Indexed: 11/18/2022] Open
Abstract
Skeletal integrity in humans and animals is maintained by daily mechanical loading. It has been widely accepted that osteocytes function as mechanosensors. Many biochemical signaling molecules are involved in the response of osteocytes to mechanical stimulation. The aim of this study was to identify genes involved in the translation of mechanical stimuli into bone formation. The four-point bending model was used to induce a single period of mechanical loading on the right tibia, while the contra lateral left tibia served as control. Six hours after loading, the effects of mechanical loading on gene-expression were determined with microarray analysis. Protein expression of differentially regulated genes was evaluated with immunohistochemistry. Nine genes were found to exhibit a significant differential gene expression in LOAD compared to control. MEPE, Garnl1, V2R2B, and QFG-TN1 olfactory receptor were up-regulated, and creatine kinase (muscle form), fibrinogen-B beta-polypeptide, monoamine oxidase A, troponin-C and kinesin light chain-C were down-regulated. Validation with real-time RT-PCR analysis confirmed the up-regulation of MEPE and the down-regulation of creatine kinase (muscle form) and troponin-C in the loaded tibia. Immunohistochemistry showed that the increase of MEPE protein expression was already detectable six hours after mechanical loading. In conclusion, these genes probably play a role during translation of mechanical stimuli six hours after mechanical loading. The modulation of MEPE expression may indicate a connection between bone mineralization and bone formation after mechanical stimulation.
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Affiliation(s)
- Christianne M. A. Reijnders
- Department of Internal Medicine, Endocrine Section, VU University Medical Center, Amsterdam, The Netherlands
| | - Huib W. van Essen
- Department of Clinical Chemistry, VU University Medical Center, Amsterdam, The Netherlands
| | - Birgitte T. T. M. van Rens
- Department of Internal Medicine, Endocrine Section, VU University Medical Center, Amsterdam, The Netherlands
- Faculty of Human Movement Sciences, VU University, Amsterdam, The Netherlands
| | - Johannes H. G. M. van Beek
- Department of Clinical Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
- Research Institute MOVE, Amsterdam, The Netherlands
| | | | - Paul Lips
- Department of Internal Medicine, Endocrine Section, VU University Medical Center, Amsterdam, The Netherlands
| | - Nathalie Bravenboer
- Department of Clinical Chemistry, VU University Medical Center, Amsterdam, The Netherlands
- * E-mail:
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Balbás-Martínez C, Sagrera A, Carrillo-de-Santa-Pau E, Earl J, Márquez M, Vazquez M, Lapi E, Castro-Giner F, Beltran S, Bayés M, Carrato A, Cigudosa JC, Domínguez O, Gut M, Herranz J, Juanpere N, Kogevinas M, Langa X, López-Knowles E, Lorente JA, Lloreta J, Pisano DG, Richart L, Rico D, Salgado RN, Tardón A, Chanock S, Heath S, Valencia A, Losada A, Gut I, Malats N, Real FX. Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy. Nat Genet 2013; 45:1464-9. [PMID: 24121791 PMCID: PMC3840052 DOI: 10.1038/ng.2799] [Citation(s) in RCA: 192] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Accepted: 09/16/2013] [Indexed: 12/11/2022]
Abstract
Urothelial bladder cancer (UBC) is heterogeneous at the clinical, pathological, and genetic levels. Tumor invasiveness (T) and grade (G) are the main factors associated with outcome and determine patient management (1). A discovery exome sequencing screen (n=17), followed by a prevalence screen (n=60), identified new genes mutated in this tumor coding for proteins involved in chromatin modification (MLL2, ASXL2, BPTF), cell division (STAG2, SMC1A, SMC1B), and DNA repair (ATM, ERCC2, FANCA). STAG2, a subunit of cohesin, was significantly and commonly mutated/lost in UBC, mainly in tumors of low stage/grade, and its loss was associated with improved outcome. Loss of expression was often observed in chromosomally-stable tumors and STAG2 knockdown in bladder cancer cells did not increase aneuploidy. STAG2 reintroduction in non-expressing cells led to reduced colony formation. Our findings indicate that STAG2 is a novel UBC tumor suppressor acting through mechanisms that are different from its role to prevent aneuploidy.
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Affiliation(s)
- Cristina Balbás-Martínez
- Epithelial Carcinogenesis Group, Molecular Pathology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
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Shin SJ, Lal A, De Vries S, Suzuki J, Roy R, Hwang ES, Schnitt SJ, Waldman FM, Chen YY. Florid lobular carcinoma in situ: molecular profiling and comparison to classic lobular carcinoma in situ and pleomorphic lobular carcinoma in situ. Hum Pathol 2013; 44:1998-2009. [DOI: 10.1016/j.humpath.2013.04.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 04/10/2013] [Accepted: 04/12/2013] [Indexed: 11/16/2022]
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86
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Plummer PJ, Chen J. A Bayesian approach for locating change points in a compound Poisson process with application to detecting DNA copy number variations. J Appl Stat 2013. [DOI: 10.1080/02664763.2013.840272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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87
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Abstract
MOTIVATION Data quality is a critical issue in the analyses of DNA copy number alterations obtained from microarrays. It is commonly assumed that copy number alteration data can be modeled as piecewise constant and the measurement errors of different probes are independent. However, these assumptions do not always hold in practice. In some published datasets, we find that measurement errors are highly correlated between probes that interrogate nearby genomic loci, and the piecewise-constant model does not fit the data well. The correlated errors cause problems in downstream analysis, leading to a large number of DNA segments falsely identified as having copy number gains and losses. METHOD We developed a simple tool, called autocorrelation scanning profile, to assess the dependence of measurement error between neighboring probes. RESULTS Autocorrelation scanning profile can be used to check data quality and refine the analysis of DNA copy number data, which we demonstrate in some typical datasets. CONTACT lzhangli@mdanderson.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Liangcai Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA and Department of Biophysics, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
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88
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Zhao M, Wang Q, Wang Q, Jia P, Zhao Z. Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinformatics 2013; 14 Suppl 11:S1. [PMID: 24564169 PMCID: PMC3846878 DOI: 10.1186/1471-2105-14-s11-s1] [Citation(s) in RCA: 333] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Copy number variation (CNV) is a prevalent form of critical genetic variation that leads to an abnormal number of copies of large genomic regions in a cell. Microarray-based comparative genome hybridization (arrayCGH) or genotyping arrays have been standard technologies to detect large regions subject to copy number changes in genomes until most recently high-resolution sequence data can be analyzed by next-generation sequencing (NGS). During the last several years, NGS-based analysis has been widely applied to identify CNVs in both healthy and diseased individuals. Correspondingly, the strong demand for NGS-based CNV analyses has fuelled development of numerous computational methods and tools for CNV detection. In this article, we review the recent advances in computational methods pertaining to CNV detection using whole genome and whole exome sequencing data. Additionally, we discuss their strengths and weaknesses and suggest directions for future development.
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89
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Werdich XQ, Jakobiec FA, Singh AD, Kim IK. A review of advanced genetic testing for clinical prognostication in uveal melanoma. Semin Ophthalmol 2013; 28:361-71. [PMID: 24010756 DOI: 10.3109/08820538.2013.825290] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Uveal melanoma (UM) has a strong propensity to metastasize and the prognosis for metastatic disease is very poor. It has been suggested that occult micrometastases are already present, but undetectable, in many patients at the time when the primary ocular tumor is diagnosed and treated. To identify high-risk patients for close monitoring and early intervention with prophylactic adjuvant systemic therapy, an accurate predictive system is necessary for stratifying those patients at risk of developing metastatic disease. To date, many clinical and histopathological features, molecular pathway characteristics, and genetic fingerprints of UM have been suggested for disease prognostication. Among the newest of them, tumor genetics has received the most attention in demonstrating promise as a prognostic tool. Because of the plethora of recent developments, we summarize and compare in this review the important standard and more advanced cytogenetic prognostic markers. We further describe the variety of genetic tests available for prognostication of UM, and provide a critical assessment of the respective advantages and disadvantages of these tools.
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Affiliation(s)
- Xiang Q Werdich
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School , Boston, Massachusetts , USA and
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90
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Lan J, Tai HC, Lee SW, Chen TJ, Huang HY, Li CF. Deficiency in expression and epigenetic DNA Methylation of ASS1 gene in nasopharyngeal carcinoma: negative prognostic impact and therapeutic relevance. Tumour Biol 2013; 35:161-9. [DOI: 10.1007/s13277-013-1020-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 07/11/2013] [Indexed: 11/28/2022] Open
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91
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Trentini F, Ji Y, Iwamoto T, Qi Y, Pusztai L, Müller P. Bayesian mixture models for assessment of gene differential behaviour and prediction of pCR through the integration of copy number and gene expression data. PLoS One 2013; 8:e68071. [PMID: 23874497 PMCID: PMC3709899 DOI: 10.1371/journal.pone.0068071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 05/23/2013] [Indexed: 11/18/2022] Open
Abstract
We consider modeling jointly microarray RNA expression and DNA copy number data. We propose Bayesian mixture models that define latent Gaussian probit scores for the DNA and RNA, and integrate between the two platforms via a regression of the RNA probit scores on the DNA probit scores. Such a regression conveniently allows us to include additional sample specific covariates such as biological conditions and clinical outcomes. The two developed methods are aimed respectively to make inference on differential behaviour of genes in patients showing different subtypes of breast cancer and to predict the pathological complete response (pCR) of patients borrowing strength across the genomic platforms. Posterior inference is carried out via MCMC simulations. We demonstrate the proposed methodology using a published data set consisting of 121 breast cancer patients.
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Affiliation(s)
- Filippo Trentini
- University Centre of Statistics in the Biomedical Sciences, Vita-Salute San Raffaele University, Milan, Italy
| | - Yuan Ji
- Center for Clinical and Research Informatics, NorthShore University HealthSystem, Evanston, Illinois, United States of America
- * E-mail:
| | - Takayuki Iwamoto
- Department of Breast and Endocrine Surgery, Okayama University Hospital, Okayama, Japan
| | - Yuan Qi
- Division of Quantitative Sciences, MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Lajos Pusztai
- Chief of Breast Medical Oncology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Peter Müller
- Department of Mathematics, University of Texas, Austin, Texas, United States of America
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92
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Knierim E, Schwarz JM, Schuelke M, Seelow D. CNVinspector: a web-based tool for the interactive evaluation of copy number variations in single patients and in cohorts. J Med Genet 2013; 50:529-33. [PMID: 23729504 DOI: 10.1136/jmedgenet-2012-101497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Many genetic disorders are caused by copy number variations (CNVs) in the human genome. However, the large number of benign CNV polymorphisms makes it difficult to delineate causative variants for a certain disease phenotype. Hence, we set out to create software that accumulates and visualises locus-specific knowledge and enables clinicians to study their own CNVs in the context of known polymorphisms and disease variants. METHODS CNV data from healthy cohorts (Database of Genomic Variants) and from disease-related databases (DECIPHER) were integrated into a joint resource. Data are presented in an interactive web-based application that allows inspection, evaluation and filtering of CNVs in single individuals or in entire cohorts. RESULTS CNVinspector provides simple interfaces to upload CNV data, compare them with own or published control data and visualise the results in graphical interfaces. Beyond choosing control data from different public studies, platforms and methods, dedicated filter options allow the detection of CNVs that are either enriched in patients or depleted in controls. Alternatively, a search can be restricted to those CNVs that appear in individuals of similar clinical phenotype. For each gene of interest within a CNV, we provide a link to NCBI, ENSEMBL and the GeneDistiller search engine to browse for potential disease-associated genes. CONCLUSIONS With its user-friendly handling, the integration of control data and the filtering options, CNVinspector will facilitate the daily work of clinical geneticists and accelerate the delineation of new syndromes and gene functions. CNVinspector is freely accessible under http://www.cnvinspector.org.
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93
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Tian M, Wang Y, Gu X, Feng C, Fang S, Hu X, Li N. Copy number variants in locally raised Chinese chicken genomes determined using array comparative genomic hybridization. BMC Genomics 2013; 14:262. [PMID: 23594354 PMCID: PMC3637819 DOI: 10.1186/1471-2164-14-262] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 04/15/2013] [Indexed: 11/10/2022] Open
Abstract
Background Copy number variants contribute to genetic variation in birds. Analyses of copy number variants in chicken breeds had focused primarily on those from commercial varieties with nothing known about the occurrence and diversity of copy number variants in locally raised Chinese chicken breeds. To address this deficiency, we characterized copy number variants in 11 chicken breeds and compared the variation among these breeds. Results We presented a detailed analysis of the copy number variants in locally raised Chinese chicken breeds identified using a customized comparative genomic hybridization array. We identified 833 copy number variants contained within 308 copy number variant regions. The median and mean sizes of the copy number variant regions were 14.6 kb and 35.1 kb, respectively. Of the copy number variant regions, 138 (45%) involved gain of DNA, 159 (52%) involved loss of DNA, and 11 (3%) involved both gain and loss of DNA. Principal component analysis and agglomerative hierarchical clustering revealed the close relatedness of the four locally raised chicken breeds, Shek-Ki, Langshan, Qingyuan partridge, and Wenchang. Biological process enrichment analysis of the copy number variant regions confirmed the greater variation among the four aforementioned varieties than among the seven other breeds studied. Conclusion Our description of the distribution of the copy number variants and comparison of the differences among the copy number variant regions of the 11 chicken breeds supplemented the information available concerning the copy number variants of other Chinese chicken breeds. In addition to its relevance for functional analysis, our results provided the first insight into how chicken breeds can be clustered on the basis of their genomic copy number variation.
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Huang HY, Wu WR, Wang YH, Wang JW, Fang FM, Tsai JW, Li SH, Hung HC, Yu SC, Lan J, Shiue YL, Hsing CH, Chen LT, Li CF. ASS1 as a novel tumor suppressor gene in myxofibrosarcomas: aberrant loss via epigenetic DNA methylation confers aggressive phenotypes, negative prognostic impact, and therapeutic relevance. Clin Cancer Res 2013; 19:2861-72. [PMID: 23549872 DOI: 10.1158/1078-0432.ccr-12-2641] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The principal goals were to identify and validate targetable metabolic drivers relevant to myxofibrosarcoma pathogenesis using a published transcriptome. EXPERIMENTAL DESIGN As the most significantly downregulated gene regulating amino acid metabolism, argininosuccinate synthetase (ASS1) was selected for further analysis by methylation-specific PCR, pyrosequencing, and immunohistochemistry of myxofibrosarcoma samples. The roles of ASS1 in tumorigenesis and the therapeutic relevance of the arginine-depriving agent pegylated arginine deiminase (ADI-PEG20) were elucidated in ASS1-deficient myxofibrosarcoma cell lines and xenografts with and without stable ASS1 reexpression. RESULTS ASS1 promoter hypermethylation was detected in myxofibrosarcoma samples and cell lines and was strongly linked to ASS1 protein deficiency. The latter correlated with increased tumor grade and stage and independently predicted a worse survival. ASS1-deficient cell lines were auxotrophic for arginine and susceptible to ADI-PEG20 treatment, with dose-dependent reductions in cell viability and tumor growth attributable to cell-cycle arrest in the S-phase. ASS1 expression was restored in 2 of 3 ASS1-deficient myxofibrosarcoma cell lines by 5-aza-2'-deoxycytidine, abrogating the inhibitory effect of ADI-PEG20. Conditioned media following ASS1 reexpression attenuated HUVEC tube-forming capability, which was associated with suppression of MMP-9 and an antiangiogenic effect in corresponding myxofibrosarcoma xenografts. In addition to delayed wound closure and fewer invading cells in a Matrigel assay, ASS1 reexpression reduced tumor cell proliferation, induced G1-phase arrest, and downregulated cyclin E with corresponding growth inhibition in soft agar and xenograft assays. CONCLUSIONS Our findings highlight ASS1 as a novel tumor suppressor in myxofibrosarcomas, with loss of expression linked to promoter methylation, clinical aggressiveness, and sensitivity to ADI-PEG20.
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Affiliation(s)
- Hsuan-Ying Huang
- Department of Pathology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
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95
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Tsai PC, Breen M. Array-based comparative genomic hybridization-guided identification of reference genes for normalization of real-time quantitative polymerase chain reaction assay data for lymphomas, histiocytic sarcomas, and osteosarcomas of dogs. Am J Vet Res 2013; 73:1335-43. [PMID: 22924713 DOI: 10.2460/ajvr.73.9.1335] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To identify suitable reference genes for normalization of real-time quantitative PCR (RT-qPCR) assay data for common tumors of dogs. SAMPLE Malignant lymph node (n = 8), appendicular osteosarcoma (9), and histiocytic sarcoma (12) samples and control samples of various nonneoplastic canine tissues. PROCEDURES Array-based comparative genomic hybridization (aCGH) data were used to guide selection of 9 candidate reference genes. Expression stability of candidate reference genes and 4 commonly used reference genes was determined for tumor samples with RT-qPCR assays and 3 software programs. RESULTS LOC611555 was the candidate reference gene with the highest expression stability among the 3 tumor types. Of the commonly used reference genes, expression stability of HPRT was high in histiocytic sarcoma samples, and expression stability of Ubi and RPL32 was high in osteosarcoma samples. Some of the candidate reference genes had higher expression stability than did the commonly used reference genes. CONCLUSIONS AND CLINICAL RELEVANCE Data for constitutively expressed genes with high expression stability are required for normalization of RT-qPCR assay results. Without such data, accurate quantification of gene expression in tumor tissue samples is difficult. Results of the present study indicated LOC611555 may be a useful RT-qPCR assay reference gene for multiple tissue types. Some commonly used reference genes may be suitable for normalization of gene expression data for tumors of dogs, such as lymphomas, osteosarcomas, or histiocytic sarcomas.
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Affiliation(s)
- Pei-Chien Tsai
- Department of Molecular Biomedical Science, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606, USA
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96
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Broderick AH, Carter MCD, Lockett MR, Smith LM, Lynn DM. Fabrication of oligonucleotide and protein arrays on rigid and flexible substrates coated with reactive polymer multilayers. ACS APPLIED MATERIALS & INTERFACES 2013; 5:351-9. [PMID: 23237360 PMCID: PMC3553252 DOI: 10.1021/am302285n] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We report a top-down approach to the fabrication of oligonucleotide and protein arrays on surfaces coated with ultrathin, amine-reactive polymer multilayers fabricated by the covalent "layer-by-layer" (LbL) assembly of polyethyleneimine (PEI) and the amine-reactive, azlactone-functionalized polymer poly(2-vinyl-4,4-dimethylazlactone) (PVDMA). Manual spotting of amine-terminated oligonucleotide probe sequences on planar glass slides coated with PEI/PVDMA multilayers (~35 nm thick) yielded arrays of immobilized probes that hybridized fluorescently labeled complementary sequences with high signal intensities, high signal-to-noise ratios, and high sequence specificity. Treatment of residual azlactone functionality with the nonfouling small-molecule amine d-glucamine resulted in regions between the features of these arrays that resisted adsorption of protein and permitted hybridization in complex media containing up to 10 mg/mL protein. The residual azlactone groups in these films were also exploited to immobilize proteins on film-coated surfaces and fabricate functional arrays of proteins and enzymes. The ability to deposit PEI/PVDMA multilayers on substrates of arbitrary size, shape, and composition permitted the fabrication of arrays of oligonucleotides on the surfaces of multilayer-coated sheets of poly(ethylene terephthalate) and heat-shrinkable polymer film. Arrays fabricated on these flexible plastic substrates can be bent, cut, resized, and manipulated physically in ways that are difficult using more conventional rigid substrates. This approach could thus contribute to the development of new assay formats and new applications of biomolecule arrays. The methods described here are straightforward to implement, do not require access to specialized equipment, and should also be compatible with automated liquid-handling methods used to fabricate higher-density arrays of oligonucleotides and proteins on more traditional surfaces.
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Affiliation(s)
- Adam H Broderick
- Department of Chemical and Biological Engineering, 1415 Engineering Drive, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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97
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Banerjee D. Array comparative genomic hybridization: an overview of protocols, applications, and technology trends. Methods Mol Biol 2013; 973:1-13. [PMID: 23412780 DOI: 10.1007/978-1-62703-281-0_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
From the earliest observations of human chromosomes in the late 1800s to modern day next generation sequencing technologies, much has been learned about human cancers by the vigorous application of the techniques of the day. In general, resolution has improved tremendously, and correspondingly the size of the datasets generated has grown exponentially such that computational methods required to handle massive datasets have had to be devised. This chapter provides a brief synopsis of the evolution of such techniques as an introduction to the subsequent chapters that provide methods and applications, relevant to research, and clinical diagnostics.
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Affiliation(s)
- Diponkar Banerjee
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital, Ottawa, BC, Canada.
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98
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Abstract
Genomic profiling of mantle cell lymphoma (MCL) cells has enabled a better understanding of the complex mechanisms underlying the pathogenesis of disease. Besides the t(11;14)(q13;q32) leading to cyclin D1 overexpression, MCL exhibits a characteristic pattern of DNA copy number aberrations that differs from those detected in other B-cell lymphomas. These genomic changes disrupt selected oncogenes and suppressor genes that are required for lymphoma development and progression, many of which are components of cell cycle, DNA damage response and repair, apoptosis, and cell-signaling pathways. Additionally, some of them may represent effective therapeutic targets. A number of genomic and molecular abnormalities have been correlated with the clinical outcome of patients with MCL and are considered prognostic factors. However, only a few genomic markers have been shown to predict the response to current or novel targeted therapies. One representative example is the high-level amplification of the BCL2 gene, which predicts a good response to pro-apoptotic BH3 mimetic drugs. In summary, genomic analyses have contributed to the substantial advances made in the comprehension of the pathogenesis of MCL, providing a solid basis for the identification of optimal therapeutic targets and for the design of new molecular therapies aiming to cure this fatal disease.
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Affiliation(s)
- Melissa Rieger Menanteau
- Division of Oncology, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
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99
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Wei Y, Xu F, Li P. Technology-Driven and Evidence-Based Genomic Analysis for Integrated Pediatric and Prenatal Genetics Evaluation. J Genet Genomics 2013; 40:1-14. [DOI: 10.1016/j.jgg.2012.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 12/14/2012] [Indexed: 10/27/2022]
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Abstract
Alterations in the copy number of the cancer genome are frequently observed in brain tumors especially gliomas. Some pertinent examples include amplification of the EGFR locus in chromosome 7p and loss of the PTEN locus in 10q in glioblastoma. Meningiomas are often associated with loss of the NF2 locus in 22q. Array CGH or aCGH probes provide a reliable, consistent, and economical method of profiling genome-wide copy number alterations (CNAs) of cancer specimens at fairly robust resolution. This has allowed for the systematic assessment of brain tumors for recurrent genomic CNAs. In addition, recent technical advancements have increased the robustness of this technique to accommodate DNA derived from formalin-fixed paraffin-embedded (FFPE) tissue. Lastly, novel technologies such as next-generation sequencing and multiplex digital gene counting technology such as NanoString will expand the -repertoire of techniques for assessing CNAs in brain tumors.
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Affiliation(s)
- Gayatry Mohapatra
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
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