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Journal articles on the topic 'DNA Copy Number Variations'

Author: Grafiati

Published: 4 June 2021

Last updated: 9 February 2022

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1

Vijay, Aatira, Iti Garg, and Mohammad Zahid Ashraf. "Perspective: DNA Copy Number Variations in Cardiovascular Diseases." Epigenetics Insights 11 (January 2018): 251686571881883. http://dx.doi.org/10.1177/2516865718818839.

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Human genome contains many variations, often called mutations, which are difficult to detect and have remained a challenge for years. A substantial part of the genome encompasses repeats and when such repeats are in the coding region they may lead to change in the gene expression profile followed by pathological conditions. Structural variants are alterations which change one or more sequence feature in the chromosome such as change in the copy number, rearrangements, and translocations of a sequence and can be balanced or unbalanced. Copy number variants (CNVs) may increase or decrease the copies of a given region and have a pivotal role in the onset of many diseases including cardiovascular disorders. Cardiovascular disorders have a magnitude of well-established risk factors and etiology, but their correlation with CNVs is still being studied. In this article, we have discussed history of CNVs and a summary on the diseases associated with CNVs. To detect such variations, we shed light on the number of techniques introduced so far and their limitations. The lack of studies on cardiovascular diseases to determine the frequency of such variants needs clinical studies with larger cohorts. This review is a compilation of articles suggesting the importance of CNVs in multitude of cardiovascular anomalies. Finally, future perspectives for better understanding of CNVs and cardiovascular disorders have also been discussed.

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2

Harrison, Steven M., Casey Seideman, and Linda A. Baker. "DNA Copy Number Variations in Patients with Persistent Cloaca." Journal of Urology 191, no. 5S (May 2014): 1543–46. http://dx.doi.org/10.1016/j.juro.2013.09.056.

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3

Hovhannisyan, Galina, Tigran Harutyunyan, Rouben Aroutiounian, and Thomas Liehr. "DNA Copy Number Variations as Markers of Mutagenic Impact." International Journal of Molecular Sciences 20, no. 19 (September 24, 2019): 4723. http://dx.doi.org/10.3390/ijms20194723.

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DNA copy number variation (CNV) occurs due to deletion or duplication of DNA segments resulting in a different number of copies of a specific DNA-stretch on homologous chromosomes. Implications of CNVs in evolution and development of different diseases have been demonstrated although contribution of environmental factors, such as mutagens, in the origin of CNVs, is poorly understood. In this review, we summarize current knowledge about mutagen-induced CNVs in human, animal and plant cells. Differences in CNV frequencies induced by radiation and chemical mutagens, distribution of CNVs in the genome, as well as adaptive effects in plants, are discussed. Currently available information concerning impact of mutagens in induction of CNVs in germ cells is presented. Moreover, the potential of CNVs as a new endpoint in mutagenicity test-systems is discussed.

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4

Wineinger, Nathan E., Richard E. Kennedy, Stephen W. Erickson, Mary K. Wojczynski, Carl E. Bruder, and Hemant K. Tiwari. "Statistical issues in the analysis of DNA Copy Number Variations." International Journal of Computational Biology and Drug Design 1, no. 4 (2008): 368. http://dx.doi.org/10.1504/ijcbdd.2008.022208.

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5

Liu, Yan, Leslie Cope, Wenyue Sun, Yongchun Wang, Nijaguna Prasad, Lauren Sangenario, Kristen Talbot, et al. "DNA Copy Number Variations Characterize Benign and Malignant Thyroid Tumors." Journal of Clinical Endocrinology & Metabolism 98, no. 3 (March 1, 2013): E558—E566. http://dx.doi.org/10.1210/jc.2012-3113.

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6

Iacocca, Michael A., Jacqueline S. Dron, and Robert A. Hegele. "Progress in finding pathogenic DNA copy number variations in dyslipidemia." Current Opinion in Lipidology 30, no. 2 (April 2019): 63–70. http://dx.doi.org/10.1097/mol.0000000000000581.

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7

Jaimes-Bernal, Claudia P., Monte Trujillo, Francisco José Márquez, and Antonio Caruz. "Complement C4 Gene Copy Number Variation Genotyping by High Resolution Melting PCR." International Journal of Molecular Sciences 21, no. 17 (August 31, 2020): 6309. http://dx.doi.org/10.3390/ijms21176309.

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Background: Complement C4 gene copy number variation plays an important role as a determinant of genetic susceptibility to common diseases, such as systemic lupus erythematosus, schizophrenia, rheumatoid arthritis, and infectious diseases. This study aimed to develop an assay for the quantification of copy number variations in the C4 locus. Methods: the assay was based on a gene ratio analysis copy enumeration (GRACE) PCR combined with high resolution melting (HRM) PCR. The test was optimized using samples of a known genotype and validated with 72 DNA samples from healthy blood donors. Results: to validate the assay, standard curves were generated by plotting the C4/RP1 ratio values against copy number variation (CNV) for each gene, using genomic DNA with known C4 CNV. The range of copy numbers in control individuals was comparable to distributions observed in previous studies of European descent. Conclusions: the method herein described significantly simplifies C4 CNV diagnosis to validate the assay.

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8

Niu, Yue S., and Heping Zhang. "The screening and ranking algorithm to detect DNA copy number variations." Annals of Applied Statistics 6, no. 3 (September 2012): 1306–26. http://dx.doi.org/10.1214/12-aoas539.

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9

Villela, Darine, Claudia K. Suemoto, Renata Leite, Carlos Augusto Pasqualucci, Lea T. Grinberg, Peter Pearson, and Carla Rosenberg. "Increased DNA Copy Number Variation Mosaicism in Elderly Human Brain." Neural Plasticity 2018 (June 28, 2018): 1–9. http://dx.doi.org/10.1155/2018/2406170.

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Aging is a complex process strongly determined by genetics. Previous reports have shown that the genome of neuronal cells displays somatic genomic mosaicism including DNA copy number variations (CNVs). CNVs represent a significant source of genetic variation in the human genome and have been implicated in several disorders and complex traits, representing a potential mechanism that contributes to neuronal diversity and the etiology of several neurological diseases and provides new insights into the normal, complex functions of the brain. Nonetheless, the features of somatic CNV mosaicism in nondiseased elderly brains have not been investigated. In the present study, we demonstrate a highly significant increase in the number of CNVs in nondiseased elderly brains compared to the blood. In two neural tissues isolated from paired postmortem samples (same individuals), we found a significant increase in the frequency of deletions in both brain areas, namely, the frontal cortex and cerebellum. Also, deletions were found to be significantly larger when present only in the cerebellum. The sizes of the variants described here were in the 150–760 kb range, and importantly, nearly all of them were present in the Database of Genomic Variants (common variants). Nearly all evidence of genome structural variation in human brains comes from studies detecting changes in single cells which were interpreted as derived from independent, isolated mutational events. The observations based on array-CGH analysis indicate the existence of an extensive clonal mosaicism of CNVs within and between the human brains revealing a different type of variation that had not been previously characterized.

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10

Ahmad, Niaz, and Brent L. Nielsen. "Plant Organelle DNA Maintenance." Plants 9, no. 6 (May 28, 2020): 683. http://dx.doi.org/10.3390/plants9060683.

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Plant cells contain two double membrane bound organelles, plastids and mitochondria, that contain their own genomes. There is a very large variation in the sizes of mitochondrial genomes in higher plants, while the plastid genome remains relatively uniform across different species. One of the curious features of the organelle DNA is that it exists in a high copy number per mitochondria or chloroplast, which varies greatly in different tissues during plant development. The variations in copy number, morphology and genomic content reflect the diversity in organelle functions. The link between the metabolic needs of a cell and the capacity of mitochondria and chloroplasts to fulfill this demand is thought to act as a selective force on the number of organelles and genome copies per organelle. However, it is not yet clear how the activities of mitochondria and chloroplasts are coordinated in response to cellular and environmental cues. The relationship between genome copy number variation and the mechanism(s) by which the genomes are maintained through different developmental stages are yet to be fully understood. This Special Issue has several contributions that address current knowledge of higher plant organelle DNA. Here we briefly introduce these articles that discuss the importance of different aspects of the organelle genome in higher plants.

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11

Твеленёва, А. А., and Н. В. Шилова. "Methods for verification of submicroscopic pathogenic copy number variations." Nauchno-prakticheskii zhurnal «Medicinskaia genetika», no. 3() (March 29, 2019): 26–38. http://dx.doi.org/10.25557/2073-7998.2019.03.26-38.

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Геномная вариабельность является основой эволюции генома человека и включает в себя вариации последовательности ДНК и структурную вариабельность. К структурной вариабельности относят вариации числа копий участка ДНК (copy number variation - CNV), размером от 1000 п.н. до нескольких десятков млн п.н. Среди них выделяют субмикроскопические CNV размером от 1000 п.н. до 3 млн п.н., часть из которых является клинически значимой, то есть ассоциирована с задержкой психомоторного развития, врожденными пороками и/или аномалиями развития, а также заболеваниями аутистического спектра. Для анализа CNV используют широкий спектр методов с различной разрешающей способностью. В качестве универсального метода детекции субмикроскопических CNV в клинической практике используется хромосомный микроматричный анализ. Однако все чаще для анализа CNV используются методы высокопроизводительного секвенирования. Наряду с развитием полногеномных технологий, разрабатывается большое количество биоинформатических алгоритмов анализа CNV, имеющих разную эффективность. В связи с этим возрастает потребность в подтверждении полученных данных с целью исключения ложноположительных результатов. Кроме того, информации только о наличии или отсутствии CNV недостаточно для медико-генетического консультирования. Для оценки повторного риска хромосомной патологии необходимо определить структуру и происхождение обнаруженной CNV. С этой целью используются молекулярно-генетические и молекулярно-цитогенетические методы. Ряд молекулярно-генетических методов, основанных на использовании ПЦР, имеют разрешающую способность, достаточную для подтверждения субмикроскопических CNV. Молекулярно-цитогенетические методы включают в себя различные модификации метода флуоресцентной in situ гибридизации. Анализ субмикроскопических CNV с использованием FISH-метода ограничен длиной и спецификой фрагментов ДНК в зондах, используемых в традиционных протоколах исследования. Поэтому актуальным становится использование методов на основе in situ гибридизации с ДНК-зондами длиной порядка нескольких т.п.н., что позволяет не только подтвердить CNV и установить ее происхождение, но и определить структуру хромосомной перестройки, лежащей в основе хромосомного/геномного дисбаланса. В статье обсуждаются возможности, преимущества и недостатки различных методов, используемых для верификации клинически значимых CNV. Genomic variability is the basis of genetic diversity and evolution and includes sequence and structural variability. Structural variability refers to variations in the number of copies of DNA (copy number variations - CNVs), ranging from 1000 bp up to several megabases (Mb) in size. Among them, some submicroscopic CNVs up to 3 Mb, can lead to clinical signs such as developmental delay, intellectual disability, congenital malformations and/or dysmorphic features, as well as autism spectrum disorders. A wide range of methods with different resolution is used for CNVs analysis. To date, chromosomal microarray analysis (CMA) is a universal method for CNVs detection. However, with the advent methods of next-generation sequencing, their applicability for CNV analysis is increasingly being estimated. Therefore, with the development of genome-wide technologies and bioinformatic tools for CNV analysis, there is an increasing need to confirm the obtained data in order to establish the true values of their sensitivity and specificity. In addition, information only about localization and gene content of CNVs is not enough for genetic counseling for the family. It is necessary to define structure and origin of the detected CNV to assess accurate recurrence risk of chromosome imbalance. For this purpose, molecular genetics and molecular cytogenetic methods are used. There are some methods of molecular genetics based on PCR with sufficient resolution to confirm submicroscopic CNV longer than 1000 bp. Analysis of submicroscopic CNVs by various modifications of FISH-method is limited by the length and specificity of DNA fragments in probes used in conventional FISH-protocols. Therefore, application of DNA probes of the order of several kb in length becomes relevant. If both group of methods allow to confirm CNVs detected by wide-genome technologies, than the latter are used to estimate the structure of chromosomal imbalance. Possibilities, advantages and disadvantages of different methods for CNVs verification are discussed.

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12

Cabianca, Daphne Selvaggia, and Davide Gabellini. "FSHD: copy number variations on the theme of muscular dystrophy." Journal of Cell Biology 191, no. 6 (December 13, 2010): 1049–60. http://dx.doi.org/10.1083/jcb.201007028.

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In humans, copy number variations (CNVs) are a common source of phenotypic diversity and disease susceptibility. Facioscapulohumeral muscular dystrophy (FSHD) is an important genetic disease caused by CNVs. It is an autosomal-dominant myopathy caused by a reduction in the copy number of the D4Z4 macrosatellite repeat located at chromosome 4q35. Interestingly, the reduction of D4Z4 copy number is not sufficient by itself to cause FSHD. A number of epigenetic events appear to affect the severity of the disease, its rate of progression, and the distribution of muscle weakness. Indeed, recent findings suggest that virtually all levels of epigenetic regulation, from DNA methylation to higher order chromosomal architecture, are altered at the disease locus, causing the de-regulation of 4q35 gene expression and ultimately FSHD.

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13

Xie, Mian, Chao-sheng He, and Shen-hai Wei. "Integrated analyses of DNA copy number variations and gene expression in inflammatory breast cancer (IBC)." Journal of Clinical Oncology 31, no. 26_suppl (September 10, 2013): 28. http://dx.doi.org/10.1200/jco.2013.31.26_suppl.28.

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28 Background: Inflammatory breast cancer (IBC) is an aggressive form of BC poorly defined at the molecular level. We aim to perform genome-wide analyses of copy number variation and gene expression to identify genes reproducibly associated with survival in IBC patients. Methods: We performed concurrent genome-wide microarray analyses of copy number variable regions (CNVRs) and gene expression in IBC patients. Fifty-six pairs of breast cancer and normal specimens from IBC patients were analyzed by using Affymetrix SNP 6.0 and Affymetrix U133 plus 2.0 microarrays. To investigate genomic alterations, we used an Affymetrix Genome-Wide Human SNP 6.0 array containing 1.8 million SNP and CNV probes in total. The microarray data were imported into the Partek Genomic Suite to perform CNV analysis. Ingenuity Pathway Analysis was carried out to describe gene-gene interaction networks and canonical pathways. Cox regression model was used to evaluate the association between expression of these CNV-driven genes and survival outcomes. Results: The genomic landscape of frequent copy number variable regions (CNVRs) in at least 35% of samples was revealed. Further statistical analysis for genes located in the CNVRs identified 387 genes differentially expressed between tumor and normal tissues (p < 0.001). We demonstrated the concordance between copy number variations and gene expression changes by elevated Pearson correlation coefficients. Fisher’s exact test identified five canonical pathways that were significantly enriched among the 387 CNV-driven genes. Pathway analysis revealed two major dysregulated functions in IBC: survival regulation via Rac/PAK and PTEN/PI3K/AKT signaling pathway. Further validation using three independent cohorts demonstrated prediction of survival. Conclusions: We identified genes/pathways that may serve as prognostic markers for IBC patients by integrating gene expression profiles and copy number variations.

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14

Couzin, J. "HUMAN GENETICS: Interest Rises in DNA Copy Number Variations--Along With Questions." Science 322, no. 5906 (November 28, 2008): 1314. http://dx.doi.org/10.1126/science.322.5906.1314.

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15

Zmienko, Agnieszka, Malgorzata Marszalek-Zenczak, Pawel Wojciechowski, Anna Samelak-Czajka, Magdalena Luczak, Piotr Kozlowski, Wojciech M. Karlowski, and Marek Figlerowicz. "AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome." Plant Cell 32, no. 6 (April 7, 2020): 1797–819. http://dx.doi.org/10.1105/tpc.19.00640.

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16

Li, Jian, Rachel L. Dittmar, Shu Xia, Huijuan Zhang, Meijun Du, Chiang-Ching Huang, Brooke R. Druliner, Lisa Boardman, and Liang Wang. "Cell-free DNA copy number variations in plasma from colorectal cancer patients." Molecular Oncology 11, no. 8 (June 6, 2017): 1099–111. http://dx.doi.org/10.1002/1878-0261.12077.

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17

Pinkel, D., Y. P. Shi, J. Gray, G. Mohapatra, B. Feuerstein, D. Sudar, J. Mullikin, et al. "Analysis of DNA sequence copy number variations by comparative genomic hybridization (CGH)." Cancer Genetics and Cytogenetics 84, no. 2 (October 1995): 138. http://dx.doi.org/10.1016/0165-4608(96)85242-3.

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18

Iacocca, Michael A., and Robert A. Hegele. "Role of DNA copy number variation in dyslipidemias." Current Opinion in Lipidology 29, no. 2 (April 2018): 125–32. http://dx.doi.org/10.1097/mol.0000000000000483.

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19

Mascagni, Flavia, Alberto Vangelisti, Tommaso Giordani, Andrea Cavallini, and Lucia Natali. "Specific LTR-Retrotransposons Show Copy Number Variations between Wild and Cultivated Sunflowers." Genes 9, no. 9 (August 29, 2018): 433. http://dx.doi.org/10.3390/genes9090433.

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The relationship between variation of the repetitive component of the genome and domestication in plant species is not fully understood. In previous work, variations in the abundance and proximity to genes of long terminal repeats (LTR)-retrotransposons of sunflower (Helianthus annuus L.) were investigated by Illumina DNA sequencingtocompare cultivars and wild accessions. In this study, we annotated and characterized 22 specific retrotransposon families whose abundance varies between domesticated and wild genotypes. These families mostly belonged to the Chromovirus lineage of the Gypsy superfamily and were distributed overall chromosomes. They were also analyzed in respect to their proximity to genes. Genes close to retrotransposon were classified according to biochemical pathways, and differences between domesticated and wild genotypes are shown. These data suggest that structural variations related to retrotransposons might have occurred to produce phenotypic variation between wild and domesticated genotypes, possibly by affecting the expression of genes that lie close to inserted or deleted retrotransposons and belong to specific biochemical pathways as those involved in plant stress responses.

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20

Blokhin, Andrei, Tamara Vyshkina, Samuel Komoly, and Bernadette Kalman. "Variations in Mitochondrial DNA Copy Numbers in MS Brains." Journal of Molecular Neuroscience 35, no. 3 (June 20, 2008): 283–87. http://dx.doi.org/10.1007/s12031-008-9115-1.

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21

Morton, Elizabeth A., Ashley N. Hall, Elizabeth Kwan, Calvin Mok, Konstantin Queitsch, Vivek Nandakumar, John Stamatoyannopoulos, Bonita J. Brewer, Robert Waterston, and Christine Queitsch. "Challenges and Approaches to Genotyping Repetitive DNA." G3: Genes|Genomes|Genetics 10, no. 1 (November 22, 2019): 417–30. http://dx.doi.org/10.1534/g3.119.400771.

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Individuals within a species can exhibit vast variation in copy number of repetitive DNA elements. This variation may contribute to complex traits such as lifespan and disease, yet it is only infrequently considered in genotype-phenotype associations. Although the possible importance of copy number variation is widely recognized, accurate copy number quantification remains challenging. Here, we assess the technical reproducibility of several major methods for copy number estimation as they apply to the large repetitive ribosomal DNA array (rDNA). rDNA encodes the ribosomal RNAs and exists as a tandem gene array in all eukaryotes. Repeat units of rDNA are kilobases in size, often with several hundred units comprising the array, making rDNA particularly intractable to common quantification techniques. We evaluate pulsed-field gel electrophoresis, droplet digital PCR, and Nextera-based whole genome sequencing as approaches to copy number estimation, comparing techniques across model organisms and spanning wide ranges of copy numbers. Nextera-based whole genome sequencing, though commonly used in recent literature, produced high error. We explore possible causes for this error and provide recommendations for best practices in rDNA copy number estimation. We present a resource of high-confidence rDNA copy number estimates for a set of S. cerevisiae and C. elegans strains for future use. We furthermore explore the possibility for FISH-based copy number estimation, an alternative that could potentially characterize copy number on a cellular level.

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22

Jeon, Jae-Pil, Sung-Mi Shim, Jongsun Jung, Hye-Young Nam, Hye-Jin Lee, Bermseok Oh, Kuchan Kimm, Hyung-Lae Kim, and Bok-Ghee Han. "A comprehensive profile of DNA copy number variations in a Korean population: identification of copy number invariant regions among Koreans." Experimental and Molecular Medicine 41, no. 9 (2009): 618. http://dx.doi.org/10.3858/emm.2009.41.9.068.

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23

Yang, Shengping, Donald E. Mercante, Kun Zhang, and Zhide Fang. "An Integrated Approach for RNA-seq Data Normalization." Cancer Informatics 15 (January 2016): CIN.S39781. http://dx.doi.org/10.4137/cin.s39781.

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Background DNA copy number alteration is common in many cancers. Studies have shown that insertion or deletion of DNA sequences can directly alter gene expression, and significant correlation exists between DNA copy number and gene expression. Data normalization is a critical step in the analysis of gene expression generated by RNA-seq technology. Successful normalization reduces/removes unwanted nonbiological variations in the data, while keeping meaningful information intact. However, as far as we know, no attempt has been made to adjust for the variation due to DNA copy number changes in RNA-seq data normalization. Results In this article, we propose an integrated approach for RNA-seq data normalization. Comparisons show that the proposed normalization can improve power for downstream differentially expressed gene detection and generate more biologically meaningful results in gene profiling. In addition, our findings show that due to the effects of copy number changes, some housekeeping genes are not always suitable internal controls for studying gene expression. Conclusions Using information from DNA copy number, integrated approach is successful in reducing noises due to both biological and nonbiological causes in RNA-seq data, thus increasing the accuracy of gene profiling.

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Nagirnaja, L., L. Kasak, P. Palta, K. Rull, O. B. Christiansen, T. Esko, M. Remm, M. Metspalu, and M. Laan. "Role of DNA copy number variations in genetic predisposition to recurrent pregnancy loss." Journal of Reproductive Immunology 90, no. 2 (August 2011): 145. http://dx.doi.org/10.1016/j.jri.2011.06.028.

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25

Harrison, Steven M., Candace F. Granberg, Melise Keays, Martinez Hill, Gwen M. Grimsby, and Linda A. Baker. "DNA Copy Number Variations in Patients with 46,XY Disorders of Sex Development." Journal of Urology 192, no. 6 (December 2014): 1801–6. http://dx.doi.org/10.1016/j.juro.2014.06.040.

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26

Gu, Zhaohui, and Charles G. Mullighan. "ShinyCNV: a Shiny/R application to view and annotate DNA copy number variations." Bioinformatics 35, no. 1 (July 2, 2018): 126–29. http://dx.doi.org/10.1093/bioinformatics/bty546.

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27

Buis, Jeffrey, Tom Goodman, Julie Kim, Adele Kruger, Brendan Tarrier, Jie Ma, and Jay Stoerker. "Quantitation of DNA methylation and copy number variations by targeted sequencing of retrotransposon." Journal of Clinical Oncology 34, no. 15_suppl (May 20, 2016): e23139-e23139. http://dx.doi.org/10.1200/jco.2016.34.15_suppl.e23139.

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28

Liang, Dong, Kirk M. McHugh, Pat D. Brophy, Nader Shaikh, J. Robert Manak, Peter Andrews, Inessa Hakker, Zihua Wang, Andrew L. Schwaderer, and David S. Hains. "DNA copy number variations in children with vesicoureteral reflux and urinary tract infections." PLOS ONE 14, no. 8 (August 12, 2019): e0220617. http://dx.doi.org/10.1371/journal.pone.0220617.

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29

Muñoz-Minjares, Jorge, Yuriy S. Shmaliy, and Jesús Cabal-Aragón. "Confidence limits for genome DNA copy number variations in HR-CGH array measurements." Biomedical Signal Processing and Control 10 (March 2014): 166–73. http://dx.doi.org/10.1016/j.bspc.2013.11.007.

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30

Fukunaga, Hisanori. "Mitochondrial DNA Copy Number and Developmental Origins of Health and Disease (DOHaD)." International Journal of Molecular Sciences 22, no. 12 (June 21, 2021): 6634. http://dx.doi.org/10.3390/ijms22126634.

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Mitochondrial dysfunction is known to contribute to mitochondrial diseases, as well as to a variety of aging-based pathologies. Mitochondria have their own genomes (mitochondrial DNA (mtDNA)) and the abnormalities, such as point mutations, deletions, and copy number variations, are involved in mitochondrial dysfunction. In recent years, several epidemiological studies and animal experiments have supported the Developmental Origin of Health and Disease (DOHaD) theory, which states that the environment during fetal life influences the predisposition to disease and the risk of morbidity in adulthood. Mitochondria play a central role in energy production, as well as in various cellular functions, such as apoptosis, lipid metabolism, and calcium metabolism. In terms of the DOHaD theory, mtDNA copy number may be a mediator of health and disease. This paper summarizes the results of recent epidemiological studies on the relationship between environmental factors and mtDNA copy number during pregnancy from the perspective of DOHaD theory. The results of these studies suggest a hypothesis that mtDNA copy number may reflect environmental influences during fetal life and possibly serve as a surrogate marker of health risks in adulthood.

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Kidwell, K. K., and T. C. Osborn. "Variation among alfalfa somaclones in copy number of repeated DNA sequences." Genome 36, no. 5 (October 1, 1993): 906–12. http://dx.doi.org/10.1139/g93-119.

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Repeated DNA sequences of alfalfa (Medicago sativa L.) somaclonal variants were analyzed to determine if changes in copy number had occurred during tissue culture. DNA clones containing highly repeated nuclear sequences from the diploid line HG2 (2x = 16) were slot blotted and probed with labeled DNAs from HG2 and several somaclones of HG2. Two DNA clones that differed visually in hybridization intensity among the plant DNAs and one clone that had constant hybridization intensity were selected and used as probes on Southern blots and slot blots containing equal quantities of DNAs from HG2 and 15 régénérants. Statistically significant differences were detected in the copy number of two anonymous DNA sequences initially selected as variable and in the copy number of sequences homologous to pea ribosomal DNA. Based on Southern blot analysis, these sequences appeared to be arranged as tandem repeats. The cloned sequence initially selected as stable did not vary significantly in copy number and it appeared to be arranged as a dispersed repeat. Both increases and decreases in copy number of repeated sequences were observed in plants from successive regeneration cycles. Results from this study indicate that specific repeated nuclear DNA sequences have changed copy number in plants regenerated from tissue culture.Key words: somaclonal variation, repeated DNA, slot blot, quantitative variation.

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Freede, Peggy, and Sabine Brantl. "Transcriptional Repressor CopR: Use of SELEX To Study the copR Operator Indicates that Evolution Was Directed at Maximal Binding Affinity." Journal of Bacteriology 186, no. 18 (September 15, 2004): 6254–64. http://dx.doi.org/10.1128/jb.186.18.6254-6264.2004.

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ABSTRACT CopR is one of the two copy number control elements of the streptococcal plasmid pIP501. It represses transcription of the repR mRNA encoding the essential replication initiator protein about 10- to 20-fold by binding to its operator region upstream of the repR promoter pII. CopR binds at two consecutive sites in the major groove of the DNA that share the consensus motif 5′-CGTG. Previously, the minimal operator was narrowed down to 17 bp, and equilibrium dissociation constants for DNA binding and dimerization were determined to be 0.4 nM and 1.4 μM, respectively. In this work, we used a SELEX procedure to study copR operator sequences of different lengths in combination with electrophoretic mobility shift assays of mutated copR operators as well as copy number determinations to assess the sequence requirements for CopR binding. The results suggest that in vivo evolution was directed at maximal binding affinity. Three simultaneous nucleotide exchanges outside the bases directly contacted by CopR only slightly affected CopR binding in vitro or copy numbers in vivo. Furthermore, the optimal spacer sequence was found to comprise 7 bp, to be AT rich, and to need an A/T and a T at the 3′ positions, whereas broad variations in the sequences flanking the minimal 17-bp operator were well tolerated.

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Chen, Jian-Min, David N. Cooper, and Claude Férec. "Local DNA sequence determinants of FUT2 copy number variation." Transfusion 51, no. 6 (June 2011): 1359–61. http://dx.doi.org/10.1111/j.1537-2995.2011.03080.x.

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Egan, Chris M., Srinath Sridhar, Michael Wigler, and Ira M. Hall. "Recurrent DNA copy number variation in the laboratory mouse." Nature Genetics 39, no. 11 (October 28, 2007): 1384–89. http://dx.doi.org/10.1038/ng.2007.19.

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Tam, Gloria W. C., Richard Redon, Nigel P. Carter, and Seth G. N. Grant. "The Role of DNA Copy Number Variation in Schizophrenia." Biological Psychiatry 66, no. 11 (December 2009): 1005–12. http://dx.doi.org/10.1016/j.biopsych.2009.07.027.

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Jenner, Matthew W., David C. Johnson, Paola E. Leone, Brian A. Walker, David Gonzalez, Nicholas J. Dickens, Faith E. Davies, and Gareth J. Morgan. "The Impact of Constitutional Copy Number Variants in Myeloma." Blood 112, no. 11 (November 16, 2008): 496. http://dx.doi.org/10.1182/blood.v112.11.496.496.

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Abstract Single nucleotide polymorphisms (SNPs) have been long regarded as being important in determining variation and disease predisposition. Recently, chromosomal structural variation in the form of deletions, insertions and duplifications have been identified frequently in the genome of the general population. Such copy number variations (CNVs) have been shown to contribute to a range of human diseases. In recent studies we have utilized Affymetrix 50K and 500K arrays to identify acquired copy number change in myeloma tumor samples. In those studies we had access to paired constitutional DNA and in the present study have been able to report for the first time a CNV map of the constitutional genome of myeloma patients. Affymetrix 500K mapping arrays were used to identify copy number changes in 63 paired samples using DNA from peripheral blood and CD138 selected plasma cells. Tumor samples were analyzed in CNAG using both a paired and unpaired analysis to distinguish between inherited and acquired copy number change. Constitutional DNA was analyzed by both CNAG and GEMCA using 90 Caucasian samples from the Hapmap database as a reference set. For maximum calling accuracy, only those regions identified by both algorithms were called as CNVs. As with similar studies, overlapping CNVs identified using this approach were merged to generate a list of CNV regions (CNVRs) characteristic of the constitutional DNA of these myeloma cases. Using this approach, we identified 292 CNVs across 63 cases, with a median of 4 regions per sample. There were 155 discrete CNVRs, of which 46 were recurrent. The recurrent CNVRs were found most frequently in the pericentric regions of chromosome 14 and 15 in keeping with other studies. We then compared these recurrent CNVRs with a comparable dataset of normal individuals generated using Affymetrix 500K arrays. In this analysis, 25/46 recurrent CNVRs in the myeloma cases were novel. The two most frequent novel CNVRs in the myeloma cases were gains on chromosome 21 and 15. We also compared the characteristics of the constitutional CNVs with the acquired copy number changes in the corresponding tumor samples and identified that the constitutional CNVs were generally considerably smaller. However, using unpaired analysis it was possible to determine the presence of the constitutional CNV in the tumor sample, providing validation of the CNVs. We were also able to demonstrate that acquired copy number change in the tumor cells can either exaggerate or ameliorate the effect of the inherited CNV in the tumor genome, such as cases with acquired trisomy 15 and deletion or gain of regions of 15q in the constitutional DNA. These findings also reinforce the need for paired non-tumor DNA when undertaking copy number analysis of tumor DNA using SNP arrays. In this study we have been able to identify for the first time the presence of CNVs in the constitutional genome of individuals with myeloma. We have been able to systematically catalogue these CNVRs. These results provide the basis for future studies aimed at identifying how this type of genomic variation may influence the development of and outcome of myeloma and a broad range of other hematological conditions.

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Nielsen, Helene Myrtue, Alexandre How-Kit, Carole Guerin, Frederic Castinetti, Hans Kristian Moen Vollan, Catherine De Micco, Antoine Daunay, et al. "Copy number variations alter methylation and parallel IGF2 overexpression in adrenal tumors." Endocrine-Related Cancer 22, no. 6 (September 23, 2015): 953–67. http://dx.doi.org/10.1530/erc-15-0086.

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Overexpression of insulin growth factor 2 (IGF2) is a hallmark of adrenocortical carcinomas and pheochromocytomas. Previous studies investigating the IGF2/H19 locus have mainly focused on a single molecular level such as genomic alterations or altered DNA methylation levels and the causal changes underlying IGF2 overexpression are still not fully established. In the current study, we analyzed 62 tumors of the adrenal gland from patients with Conn's adenoma (CA, n=12), pheochromocytomas (PCC, n=10), adrenocortical benign tumors (ACBT, n=20), and adrenocortical carcinomas (ACC, n=20). Gene expression, somatic copy number variation of chr11p15.5, and DNA methylation status of three differential methylated regions of the IGF2/H19 locus including the H19 imprinting control region were integratively analyzed. IGF2 overexpression was found in 85% of the ACCs and 100% of the PCCs compared to 23% observed in CAs and ACBTs. Copy number aberrations of chr11p15.5 were abundant in both PCCs and ACCs but while PCCs retained a diploid state, ACCs were frequently tetraploid (7/19). Loss of either a single allele or loss of two alleles of the same parental origin in tetraploid samples resulted in a uniparental disomy-like genotype. These copy number changes correlated with hypermethylation of the H19 ICR suggesting that the lost alleles were the unmethylated maternal alleles. Our data provide conclusive evidence that loss of the maternal allele correlates with IGF2 overexpression in adrenal tumors and that hypermethylation of the H19 ICR is a consequence thereof.

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Shafie, Alaa, Mingzhan Xue, Paul J. Thornalley, and Naila Rabbani. "Copy number variation of glyoxalase I." Biochemical Society Transactions 42, no. 2 (March 20, 2014): 500–503. http://dx.doi.org/10.1042/bst20140011.

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The glyoxalase I gene GLO1 is a hotspot for copy number variation in the human and mouse genomes. The additional copies are often functional, giving rise to 2–4-fold increased glyoxalase I expression and activity. The prevalence of GLO1 copy number increase in the human population appears to be approximately 2% and may be linked to a risk of obesity, diabetes and aging. Increased GLO1 copy number has been found in human tumour cell lines and primary human tumours. The minimum common copy number increase region was approximately 1 Mb and it contained GLO1 and seven other genes. The increased copy number was generally functional, being associated with increased glyoxalase I protein and multidrug resistance in cancer chemotherapy. Glo1 duplication in the mouse genome is found within approximately 0.5 Mb of duplicated DNA. It was claimed to be linked to anxiety phenotypes, but other related discordant findings have doubted the association with glyoxalase I and further investigation is required.

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Kumar, Bhupender, Zafar Iqbal Bhat, Savita Bansal, Sunil Saini, Afreen Naseem, Khushnuma Wahabi, Archana Burman, Geeta Trilok Kumar, Sundeep Singh Saluja, and M. Moshahid Alam Rizvi. "Association of mitochondrial copy number variation and T16189C polymorphism with colorectal cancer in North Indian population." Tumor Biology 39, no. 11 (November 2017): 101042831774029. http://dx.doi.org/10.1177/1010428317740296.

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Globally, colorectal cancer is the third most common type of cancer. Genetic instability leading to cancer development is one of the major causes for development of cancer. Alterations in mitochondrial genome, that is, mutations, single-nucleotide polymorphisms, and copy number variations are known to contribute in cancer development. The aim of our study was to investigate association of mitochondrial T16189C polymorphism and copy number variation with colorectal cancer in North Indian population. DNA isolated from peripheral blood of 126 colorectal cancer patients and 114 healthy North Indian subjects was analyzed for T16189C polymorphism and half of them for mitochondrial copy number variation. Genotyping was done using polymerase chain reaction–restriction fragment length polymorphism, and copy number variation was estimated using real-time polymerase chain reaction, numbers of mitochondrial copies and found to be significantly higher in colorectal cancer patients than healthy controls (88 (58–154), p = 0.001). In the regression analysis, increased mitochondrial copy number variation was associated with risk of colorectal cancer (odds ratio = 2.885, 95% confidence interval = 1.3–6.358). However, T16189C polymorphism was found to be significantly associated with the risk of rectal cancer (odds ratio = 5.213, p = 0.001) and non-significantly with colon cancer (odds ratio = 0.867, p = 0.791). Also, false-positive report probability analysis was done to validate the significant findings. Our results here indicate that mitochondrial copy number variation may be playing an important role in the development of colorectal cancer, and detection of mitochondrial copy number variation can be used as a biomarker for predicting the risk of colorectal cancer in North Indian subjects.

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Brezina, Stefanie, Moritz Feigl, Tanja Gumpenberger, Ricarda Staudinger, Andreas Baierl, and Andrea Gsur. "Genome-wide association study of germline copy number variations reveals an association with prostate cancer aggressiveness." Mutagenesis 35, no. 3 (April 7, 2020): 283–90. http://dx.doi.org/10.1093/mutage/geaa010.

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Abstract Prostate cancer is a major health burden, being the second most commonly diagnosed malignancy in men worldwide. Overtreatment represents a major problem in prostate cancer therapy, leading to significant long-term quality-of-life effects for patients and a broad socio-ecological burden. Biomarkers that could facilitate risk stratification of prostate cancer aggressiveness at the time of diagnosis may help to guide clinical treatment decisions and reduce overtreatment. Previous research on genetic variations in prostate cancer has shown that germline copy number variations as well as somatic copy number alterations are commonly present in cancer patients, altering a greater portion of the cancer genome than any other type of genetic variation. To investigate the effect of germline copy number variations on cancer aggressiveness we have compared genome-wide screening data from genomic DNA isolated from the blood of 120 patients with aggressive prostate cancer, 231 patients with non-aggressive prostate cancer and 87 controls with benign prostatic hyperplasia from the Prostate Cancer Study of Austria biobank using the Affymetrix SNP 6.0 array. We could show that patients with an aggressive form of prostate cancer had a higher frequency of copy number variations [mean count of copy number segments (CNS) = 12.9, median count of CNS = 9] compared to patients with non-aggressive prostate cancer (mean count of CNS = 10.4, median count of CNS = 8) or control patients diagnosed with benign prostatic hyperplasia (mean count of CNS = 9.3, median count of CNS = 8). In general, we observed that copy number gain is a rarer event, compared to copy number loss within all three patient groups. Furthermore, we could show a significant effect of copy number losses located on chromosomes 8, 9 and 10 on prostate cancer aggressiveness (P = 0.040, P = 0.037 and P = 0.005, respectively). Applying a cross-validation analysis yielded an area under the curve of 0.63. Our study reports promising findings suggesting that copy number losses might play an important role in the establishment of novel biomarkers to predict prostate cancer aggressiveness at the time of diagnosis. Such markers could be used to facilitate risk stratification to reduce overtreatment of prostate cancer patients.

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Guha, Subharup, Yuan Ji, and Veerabhadran Baladandayuthapani. "Bayesian Disease Classification Using Copy Number Data." Cancer Informatics 13s2 (January 2014): CIN.S13785. http://dx.doi.org/10.4137/cin.s13785.

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DNA copy number variations (CNVs) have been shown to be associated with cancer development and progression. The detection of these CNVs has the potential to impact the basic knowledge and treatment of many types of cancers, and can play a role in the discovery and development of molecular-based personalized cancer therapies. One of the most common types of high-resolution chromosomal microarrays is array-based comparative genomic hybridization (aCGH) methods that assay DNA CNVs across the whole genomic landscape in a single experiment. In this article we propose methods to use aCGH profiles to predict disease states. We employ a Bayesian classification model and treat disease states as outcome, and aCGH profiles as covariates in order to identify significant regions of the genome associated with disease subclasses. We propose a principled two-stage method where we first make inferences on the underlying copy number states associated with the aCGH emissions based on hidden Markov model (HMM) formulations to account for serial dependencies in neighboring probes. Subsequently, we infer associations with disease outcomes, conditional on the copy number states, using Bayesian linear variable selection procedures. The selected probes and their effects are parameters that are useful for predicting the disease categories of any additional individuals on the basis of their aCGH profiles. Using simulated datasets, we investigate the method's accuracy in detecting disease category. Our methodology is motivated by and applied to a breast cancer dataset consisting of aCGH profiles assayed on patients from multiple disease subtypes.

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Yang, Lu, Ya-Zhe Wang, Hong-Hu Zhu, Yan Chang, Ling-Di Li, Wen-Min Chen, Ling-Yu Long, et al. "PRAME Gene Copy Number Variation Is Related to Its Expression in Multiple Myeloma." DNA and Cell Biology 36, no. 12 (December 2017): 1099–107. http://dx.doi.org/10.1089/dna.2017.3951.

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43

Xia, Yun, Chiang-Ching Huang, Rachel Dittmar, Meijun Du, Yuan Wang, Hongyan Liu, Niraj Shenoy, Liang Wang, and Manish Kohli. "Copy number variations in urine cell free DNA as biomarkers in advanced prostate cancer." Oncotarget 7, no. 24 (April 26, 2016): 35818–31. http://dx.doi.org/10.18632/oncotarget.9027.

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44

Komura, D., F. Shen, S. Ishikawa, K. R. Fitch, W. Chen, J. Zhang, G. Liu, et al. "Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays." Genome Research 16, no. 12 (October 19, 2006): 1575–84. http://dx.doi.org/10.1101/gr.5629106.

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45

Chen, Jie, Ayten Yiğiter, Yu-Ping Wang, and Hong-Wen Deng. "A Bayesian Analysis for Identifying DNA Copy Number Variations Using a Compound Poisson Process." EURASIP Journal on Bioinformatics and Systems Biology 2010 (2010): 1–10. http://dx.doi.org/10.1155/2010/268513.

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46

McGowan, Ruth, Graham Tydeman, David Shapiro, Tracey Craig, Norma Morrison, Susan Logan, Adam H. Balen, et al. "DNA copy number variations are important in the complex genetic architecture of müllerian disorders." Fertility and Sterility 103, no. 4 (April 2015): 1021–30. http://dx.doi.org/10.1016/j.fertnstert.2015.01.008.

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Cho, Soonweng, Hyun-Seok Kim, Martha A. Zeiger, Christopher B. Umbricht, and Leslie M. Cope. "Measuring DNA Copy Number Variation Using High-Density Methylation Microarrays." Journal of Computational Biology 26, no. 4 (April 2019): 295–304. http://dx.doi.org/10.1089/cmb.2018.0143.

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48

Crooijmans, Richard PMA, Mark S. Fife, Tomas W. Fitzgerald, Shurnevia Strickland, Hans H. Cheng, Pete Kaiser, Richard Redon, and Martien AM Groenen. "Large scale variation in DNA copy number in chicken breeds." BMC Genomics 14, no. 1 (2013): 398. http://dx.doi.org/10.1186/1471-2164-14-398.

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Xu, Baoshan, Hua Li, John M. Perry, Vijay Pratap Singh, Jay Unruh, Zulin Yu, Musinu Zakari, William McDowell, Linheng Li, and Jennifer L. Gerton. "Ribosomal DNA copy number loss and sequence variation in cancer." PLOS Genetics 13, no. 6 (June 22, 2017): e1006771. http://dx.doi.org/10.1371/journal.pgen.1006771.

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Huckaby, Adam C., Claire S. Granum, Maureen A. Carey, Karol Szlachta, Basel Al-Barghouthi, Yuh-Hwa Wang, and Jennifer L. Guler. "Complex DNA structures trigger copy number variation across thePlasmodium falciparumgenome." Nucleic Acids Research 47, no. 4 (December 21, 2018): 1615–27. http://dx.doi.org/10.1093/nar/gky1268.

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