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Maximum likelihood principle for DNA copy number analysis

Abdullah K. Alqallaf, Ahmed H. Tewfik
2009 2009 IEEE International Conference on Acoustics, Speech and Signal Processing  
In this paper, we present a robust procedure for the analysis of DNA copy number data based on maximum likelihood principle using global information of the entire data record.  ...  Microarray technologies had been used to measure DNA copy number data. The copy number represents the relative fluorescent intensity level between control and test DNA samples.  ...  These intensity ratios are informative about DNA copy number variations.  ... 
doi:10.1109/icassp.2009.4959630 dblp:conf/icassp/AlqallafT09 fatcat:pgalnq4snnbq7ac527fgsij3wq

Comprehensive Study Of Dna Copy Number Analysis Using Sigma Filter

Abdullah Alqallaf, A.H. Tewfik
2007 Zenodo  
Publication in the conference proceedings of EUSIPCO, Poznan, Poland, 2007  ...  It provides a high-resolution method to map and measure relative changes in DNA copy number simultaneously at thousands of genomic loci.  ...  PRIOR WORK Generally, DNA Copy Number (DCN) variation detection techniques fall into two categories: statistical model based approaches and smoothing techniques.  ... 
doi:10.5281/zenodo.40523 fatcat:e3xnumtphvfr7nx5hatwvlumyi

Copy Number Variation: Methods and Clinical Applications

Ondrej Pös, Jan Radvanszky, Jakub Styk, Zuzana Pös, Gergely Buglyó, Michal Kajsik, Jaroslav Budis, Bálint Nagy, Tomas Szemes
2021 Applied Sciences  
Gains and losses of large segments of genomic DNA, known as copy number variants (CNVs) gained considerable interest in clinical diagnostics lately, as particular forms may lead to inherited genetic diseases  ...  In this review, we summarize methodological progress from conventional approaches to current state of the art techniques capable of detecting CNVs from a few bases up to several megabases.  ...  of normalized read depth delineates relative copy number changes.  ... 
doi:10.3390/app11020819 fatcat:sqgril5tvrhprjf6bdbih2osyy

Functional Copy-Number Alterations in Cancer

Barry S. Taylor, Jordi Barretina, Nicholas D. Socci, Penelope DeCarolis, Marc Ladanyi, Matthew Meyerson, Samuel Singer, Chris Sander, Greg Gibson
2008 PLoS ONE  
To demonstrate the methodology, we experimentally profile copy number changes in a clinically aggressive subtype of softtissue sarcoma, pleomorphic liposarcoma, and computationally derive a portrait of  ...  Taken together, we present a statistically robust methodology applicable to high-resolution genomic data to assess the extent and function of copy-number alterations in cancer.  ...  Techniques based on microarray technologies can simultaneously measure thousands to millions of loci in the genome for DNA copy number changes.  ... 
doi:10.1371/journal.pone.0003179 pmid:18784837 pmcid:PMC2527508 fatcat:h7g3mdloirbnliehmjiykzs6zy

Using expression arrays for copy number detection: an example from E. coli

Dmitriy Skvortsov, Diana Abdueva, Michael E Stitzer, Steven E Finkel, Simon Tavaré
2007 BMC Bioinformatics  
Copy number is obtained from fluorescence signals after processing with novel normalization, spatial artifact correction, data transformation and deletion/duplication detection.  ...  Microarray-based comparative genomic hybridization (array CGH) has enabled the high-resolution detection of DNA copy number aberrations.  ...  In contrast, each DNA sample in this study was harvested from a single homogeneous E. coli colony, yielding changes in signal reflecting discrete changes in DNA copy number.  ... 
doi:10.1186/1471-2105-8-203 pmid:17570850 pmcid:PMC1914360 fatcat:2lwkntj3qvcctksd25l53vfa7e

Genome-wide profiling of copy number alterations in cancer: focus on melanoma

Luigi Pasini
2013 Biomedical Reviews  
Thanks to a never-before detailed view of the human genome, the last decade has brought to light the notion of DNA copy number variation (CNV) as the pivotal force contributing to population genomic diversity  ...  This review gives a brief overview of key developments in genome-wide SCNA profiling, with specific emphasis on array-based techniques and deep-sequencing, which indeed enabled us to identify the large  ...  The main limitation, however, of array-based techniques is the ability to detect aberration involving copy number changes only: balanced translocations and inversions are not detectable with this methodology  ... 
doi:10.14748/bmr.v24.18 fatcat:3ukwsalo7navjmlvkyssze2nmy

Copy number variation in livestock: A mini review

V. Bhanuprakash, Supriya Chhotaray, D. R. Pruthviraj, Chandrakanta Rawat, A. Karthikeyan, Manjit Panigrahi
2018 Veterinary World  
CNVs alter the gene expression and change the phenotype of an individual due to deletion and duplication of genes in the copy number variation regions (CNVRs).  ...  Copy number variation (CNV) is a phenomenon in which sections of the genome, ranging from one kilo base pair (Kb) to several million base pairs (Mb), are repeated and the number of repeats vary between  ...  Acknowledgments The authors would wish to acknowledge Director and Joint Director (R), IVRI-Bareilly, for their support and providing infrastructural facility to review this study.  ... 
doi:10.14202/vetworld.2018.535-541 pmid:29805222 pmcid:PMC5960796 fatcat:t5igt2damngnxc5dv4fftydx3m

Generating DNA profile from low copy number DNA: Strategies and associated risks

Rana Muhammad Mateen, Asma Tariq, Mureed Hussain
2020 Acta Scientiarum : Biological Sciences  
This review highlights different strategies used by forensic laboratories worldwide for creating complete DNA profiles from low copy number template for comparison purposes along with its associated risks  ...  Many shreds of evidence found on the crime scenes contain a trace amount of DNA which results in insignificant profiling results for subsequent comparison.  ...  low copy number template DNA.  ... 
doi:10.4025/actascibiolsci.v42i1.52239 fatcat:ecn4al7ryvb2lcdbwm3wfedaxm

Copy Number Variants in Alzheimer's Disease

Denis Cuccaro, Elvira Valeria De Marco, Rita Cittadella, Sebastiano Cavallaro, Dominique Campion
2016 Journal of Alzheimer's Disease  
of DNA) in AD.  ...  In the last years, in particular, new developments in genome-wide scanning methodologies have enabled the association of a number of previously uncharacterized copy number variants (CNVs, gain or loss  ...  The fluorescence intensity ratio obtained on each spot provides a locus-by-locus measure of DNA copy number changes.  ... 
doi:10.3233/jad-160469 pmid:27662298 pmcid:PMC5115612 fatcat:4pmnaqy4rrduffsfrm6rv3dk5q

CNARA: reliability assessment for genomic copy number profiles

Ni Ai, Haoyang Cai, Caius Solovan, Michael Baudis
2016 BMC Genomics  
DNA copy number profiles from microarray and sequencing experiments sometimes contain wave artefacts which may be introduced during sample preparation and cannot be removed completely by existing preprocessing  ...  Besides, large derivative log ratio spread (DLRS) of the probes correlating with poor DNA  ...  Availability of supporting data The GEO accession numbers of the arrays used in the study are provided in the Additional files and can be used to access GEO datasets as well as the corresponding processed  ... 
doi:10.1186/s12864-016-3074-7 pmid:27733115 pmcid:PMC5062840 fatcat:xhliw6dhave2llijovb7nt2gtm

Methods and strategies for analyzing copy number variation using DNA microarrays

Nigel P Carter
2007 Nature Genetics  
The association of DNA copy-number variation (CNV) with specific gene function and human disease has been long known, but the wide scope and prevalence of this form of variation has only recently been  ...  The latest studies using microarray technology have demonstrated that as much as 12% of the human genome and thousands of genes are variable in copy number, and this diversity is likely to be responsible  ...  As is true for clone and PCR product arrays, data from low-copy-number repeats and segmental duplications can be difficult to interpret, as the genomic location of detected copy-number changes could be  ... 
doi:10.1038/ng2028 pmid:17597776 pmcid:PMC2697494 fatcat:zhc2thg7bza6lkq7xgkp2ronqm

Distal 10q trisomy with copy number gain in chromosome region 10q23.1–10q25.1: the Wnt signaling pathway is the most pertinent to the gene content in the region of copy number gain: a case report

Siew-Lee Wong, Hsin-Hsu Chou, Chung-Nun Chao, Joseph Hang Leung, Yu-Hsin Chen, Cheng-Da Hsu
2015 BMC Research Notes  
Although abnormal chromosome phenotypes are commonly detected by visualization of chromosomes by traditional cytogenetic techniques, this approach is marginal in both diagnostic sensitivity and potential  ...  for biological interpretation, thus making implementation of advanced techniques and analysis methods an important consideration in a health service.  ...  To address the limitation that the CytoChip Oligo array cannot detect DNA copy number changes in genomic regions that are not represented on the microarray, we complemented the array-CGH result with qPCR  ... 
doi:10.1186/s13104-015-1213-x pmid:26088875 pmcid:PMC4473823 fatcat:27gmc2xxkvdzvlvcwv7hmvrlku

High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers

Mayumi Oda, Jacob L. Glass, Reid F. Thompson, Yongkai Mo, Emmanuel N. Olivier, Maria E. Figueroa, Rebecca R. Selzer, Todd A. Richmond, Xinmin Zhang, Luke Dannenberg, Roland D. Green, Ari Melnick (+5 others)
2009 Nucleic Acids Research  
We also show that the MspI representation generates information about copy-number variation, that the assay can be used on as little as 10 ng of DNA and that massively parallel sequencing can be used as  ...  The use of enzymes sensitive to cytosine methylation allows high-throughput analysis of this epigenetic regulatory process.  ...  and copy-number changes (30) are frequent.  ... 
doi:10.1093/nar/gkp260 pmid:19386619 pmcid:PMC2709560 fatcat:4fu5loxvlbf6zgbxc4dbhcsisi

Reconstructing DNA copy number by penalized estimation and imputation

Zhongyang Zhang, Kenneth Lange, Roel Ophoff, Chiara Sabatti
2010 Annals of Applied Statistics  
Recent advances in genomics have underscored the surprising ubiquity of DNA copy number variation (CNV). Fortunately, modern genotyping platforms also detect CNVs with fairly high reliability.  ...  Together these changes enable us to minimize the fused-lasso criterion in a highly effective way. We also reframe the reconstruction problem in terms of imputation via discrete optimization.  ...  Acknowledgments We thank Joe de Young for help in reclustering the genotype signal and Jacobine Buizer-Voskamp for providing us with detailed information in real data analysis.  ... 
doi:10.1214/10-aoas357 pmid:21572975 pmcid:PMC3092301 fatcat:ur7f6wtywrfura3uwpj6ke45ay

Genomic copy number variation, human health, and disease

Louise V Wain, John AL Armour, Martin D Tobin
2009 The Lancet  
Acknowledgments We thank Ammar Al-Chalabi, Cother Hajat, Ed Hollox, and James R Lupski for providing comments on the report; and anonymous reviewers for their helpful comments and suggestions.  ...  sperm in the human beta-globin gene region, Hum Mol Genet 15 (2006), pp. 1099-1111. 53 KW Lam and AJ Jeffreys, Processes of copy number change in human DNA: the dynamics of {alpha}-globin gene deletion  ...  Even when changes to the BAC signal ratios indicate a real copy number variant, a deletion in the test sample would be indistinguishable from a duplication in the reference sample.  ... 
doi:10.1016/s0140-6736(09)60249-x pmid:19535135 fatcat:q7qqm3mqq5epxakyjvc6oepzhe
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