Relevant bibliographies by topics / Genome-wide copy number analysis

Academic literature on the topic 'Genome-wide copy number analysis'

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Published: 9 March 2023
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Journal articles on the topic "Genome-wide copy number analysis"

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Baslan, Timour, Jude Kendall, Linda Rodgers, Hilary Cox, Mike Riggs, Asya Stepansky, Jennifer Troge, et al. "Genome-wide copy number analysis of single cells." Nature Protocols 7, no. 6 (May 3, 2012): 1024–41. http://dx.doi.org/10.1038/nprot.2012.039.

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SUN, Yu-Lin, Fei LIU, and Xiao-Hang ZHAO. "Genome-wide Association Analysis Based on Copy Number Variations*." PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS 36, no. 8 (October 16, 2009): 968–77. http://dx.doi.org/10.3724/sp.j.1206.2008.00881.

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Liu, Xiling, Zhenmin Zhao, Qiannan Xu, Zheng Wang, Yingnan Bian, Suhua Zhang, and Chengtao Li. "Genome-wide copy number variation analysis in monozygotic twins." Forensic Science International: Genetics Supplement Series 6 (December 2017): e218-e220. http://dx.doi.org/10.1016/j.fsigss.2017.09.075.

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Ueno, Takayuki, Mitsuru Emi, Hidenori Sato, Noriko Ito, Mariko Muta, Katsumasa Kuroi, and Masakazu Toi. "Genome-wide copy number analysis in primary breast cancer." Expert Opinion on Therapeutic Targets 16, sup1 (February 8, 2012): S31—S35. http://dx.doi.org/10.1517/14728222.2011.636739.

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Lin, Chien-hsing, Mei-chu Huang, Ling-hui Li, Jer-yuarn Wu, Yuan-tsong Chen, and Cathy S. J. Fann. "Genome-wide copy number analysis using copy number inferring tool (CNIT) and DNA pooling." Human Mutation 29, no. 8 (August 2008): 1055–62. http://dx.doi.org/10.1002/humu.20760.

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Michael Rothenberg, S., and Jeff Settleman. "Discovering Tumor Suppressor Genes Through Genome-Wide Copy Number Analysis." Current Genomics 11, no. 5 (August 1, 2010): 297–310. http://dx.doi.org/10.2174/138920210791616734.

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Baslan, Timour, Jude Kendall, Linda Rodgers, Hilary Cox, Mike Riggs, Asya Stepansky, Jennifer Troge, et al. "Erratum: Corrigendum: Genome-wide copy number analysis of single cells." Nature Protocols 11, no. 3 (February 25, 2016): 616. http://dx.doi.org/10.1038/nprot0316.616b.

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Smadbeck, James B., Sarah H. Johnson, Stephanie A. Smoley, Athanasios Gaitatzes, Travis M. Drucker, Roman M. Zenka, Farhad Kosari, et al. "Copy number variant analysis using genome-wide mate-pair sequencing." Genes, Chromosomes and Cancer 57, no. 9 (July 30, 2018): 459–70. http://dx.doi.org/10.1002/gcc.5.

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Lee, Il-Kwon, Nan Young Kim, Hee Nam Kim, Dong Kyun Han, Hee-Jo Baek, Tai Ju Hwang, Hoon Kook, and Hyeoung Joon Kim. "Genome-Wide Screening of Copy Number Variation In Childhood Neuroblastoma." Blood 116, no. 21 (November 19, 2010): 4454. http://dx.doi.org/10.1182/blood.v116.21.4454.4454.

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Abstract Abstract 4454 Background Structural genetic variation, including copy-number variation (CNV), constitutes a substantial fraction of total genetic variability and the importance of structural variants in modulating human disease is increasingly being recognized. Recent studies showed that chromosomal aberrations are detectable in childhood cancers and can be associated with susceptibility to childhood cancers. However its relationship with neuroblosatoma in particular is not fully understood. To gain insight into the incidence of the chromosomal aberrations in neuroblastoma in children, we examined Korean childhood neuroblastoma genomes using high-resolution single-nucleotide polymorphism (SNP) array-based analysis. Patients and Methods 13 cases analyzed had been diagnosed with neuroblastoma (5 male, 8 female). 620,901 SNP markers were considered on these samples using Human610Quad v1.0 DNA analysis BeadChip (Illumina). Fragmented DNAs were hybridized on bead chips. Data analysis was carried out with GenomeStudio v2009.1, Genotyping 1.1.9, cnvPartition_v2.4.4 softwares. Overall call rate were more than 99.8%. Genome-wide CNV, genotyping of markers including 7,577 non-synonymous SNPs, loss of heterozygosity (LOH) analyses were performed using the GenomeStudio v2010.1. Linkage disequilibrium was analyzed by Haploview 4.2. The gene set enrichment analysis was performed using GO software, Panther. Results The average call rates were 99.8 %. In total 343 CNVs were identified across the whole genome. Average number of CNVs per genome in this study (17.15) is higher than that of CNVs called in the recent studies using lower-resolution SNP- or CNV arrays. The median size of CNVs was 30,056 (range 569 ~ 1,260,297 bp). The largest portion of CNVs (235 calls) were found to be 10 kb~500 kb in length. Gain/loss of CNV was 2.05/4.90 having 2.4 fold higher frequencies in loss calls. We defined CNV regions (CNVRs) by merging overlapping CNVs (30% of overlap threshold) detected in two or more genomes. In total 155 CNVRs identified. The median size of CNVR was 27,482 (range 806 ~ 1,270,815 bp). Like CNVs, CNVRs-losses were more frequent than CNVR-gains. Defined CNVRs encompassing 13.4Mb accounted for ~0.5% of the human genome. Total of 1029 NM numbered transcripts were located near or within the 155 CNVRs. Through gene ontology (GO) analysis, putative target genes within the commonly gained or deleted region were categorized. Gene functions significantly enriched in the identified CNVRs include receptors for signal transduction pathways, transcription factors with nucleic acid binding proteins, transporters and regulatory molecule related functions involved in developmental processes. Genotype distributions for 7,577 non-synonymous SNPs in neuroblastoma were also examined and compared to two lab-specific as well as 90 Korean HapMap samples as control reference. Conclusions High-resolution single-nucleotide polymorphism (SNP) array-based analysis allowed us a high incidence of gains and losses in childhood neuroblastoma. Many of those detectable legions were found to be previously unidentified cryptic chromosomal aberrations. Those CNVRs could be potentially Korean-specific novel CNVRs indicating that previous CNV coverage of the human genome is incomplete and there is human genome diversity among different ethnic populations. Although results reveals high degrees of heterogeneity in the genomic alterations detectable in neuroblastoma, genes of the signal transduction pathway and transcriptional regulatory members were the most frequently altered targets whose deregulation may play a role in the pathogenesis of neuroblastoma in children. CNVs/CNVRs identified in the study will be solid resources for investigating chromosomal aberrations in childhood cancer and its potential association with childhood neuroblastoma. Further studies on larger sample size, as well as functional analyses will define their role in the pathogenesis of neuroblastoma in children. Disclosures: No relevant conflicts of interest to declare.
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Huang, Yen-Tsung, Thomas Hsu, and David C. Christiani. "TEGS-CN: A Statistical Method for Pathway Analysis of Genome-wide Copy Number Profile." Cancer Informatics 13s4 (January 2014): CIN.S13978. http://dx.doi.org/10.4137/cin.s13978.

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The effects of copy number alterations make up a significant part of the tumor genome profile, but pathway analyses of these alterations are still not well established. We proposed a novel method to analyze multiple copy numbers of genes within a pathway, termed Test for the Effect of a Gene Set with Copy Number data (TEGS-CN). TEGS-CN was adapted from TEGS, a method that we previously developed for gene expression data using a variance component score test. With additional development, we extend the method to analyze DNA copy number data, accounting for different sizes and thus various numbers of copy number probes in genes. The test statistic follows a mixture of X 2 distributions that can be obtained using permutation with scaled X 2 approximation. We conducted simulation studies to evaluate the size and the power of TEGS-CN and to compare its performance with TEGS. We analyzed a genome-wide copy number data from 264 patients of non-small-cell lung cancer. With the Molecular Signatures Database (MSigDB) pathway database, the genome-wide copy number data can be classified into 1814 biological pathways or gene sets. We investigated associations of the copy number profile of the 1814 gene sets with pack-years of cigarette smoking. Our analysis revealed five pathways with significant P values after Bonferroni adjustment (<2.8 x 10-5), including the PTEN pathway (7.8 x 10-7), the gene set up-regulated under heat shock (3.6 x 10-6), the gene sets involved in the immune profile for rejection of kidney transplantation (9.2 x 10-6) and for transcriptional control of leukocytes (2.2 x 10-5), and the ganglioside biosynthesis pathway (2.7 x 10-5). In conclusion, we present a new method for pathway analyses of copy number data, and causal mechanisms of the five pathways require further study.
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Dissertations / Theses on the topic "Genome-wide copy number analysis"

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Song, Lei. "Computational Analysis of Genome-Wide DNA Copy Number Changes." Thesis, Virginia Tech, 2011. http://hdl.handle.net/10919/32462.

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DNA copy number change is an important form of structural variation in human genome. Somatic copy number alterations (CNAs) can cause over expression of oncogenes and loss of tumor suppressor genes in tumorigenesis. Recent development of SNP array technology has facilitated studies on copy number changes at a genome-wide scale, with high resolution. Quantitative analysis of somatic CNAs on genes has found broad applications in cancer research. Most tumors exhibit genomic instability at chromosome scale as a result of dynamically accumulated genomic mutations during the course of tumor progression. Such higher level cancer genomic characteristics cannot be effectively captured by the analysis of individual genes. We introduced two definitions of chromosome instability (CIN) index to mathematically and quantitatively characterize genome-wide genomic instability. The proposed CIN indices are derived from detected CNAs using circular binary segmentation and wavelet transform, which calculates a score based on both the amplitude and frequency of the copy number changes. We generated CIN indices on ovarian cancer subtypesâ copy number data and used them as features to train a SVM classifier. The experimental results show promising and high classification accuracy estimated through cross-validations. Additional survival analysis is constructed on the extracted CIN scores from TCGA ovarian cancer dataset and showed considerable correlation between CIN scores and various events and severity in ovarian cancer development. Currently our methods have been integrated into G-DOC. We expect these newly defined CINs to be predictors in tumors subtype diagnosis and to be a useful tool in cancer research.
Master of Science
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Jarick, Ivonne [Verfasser], and Helmut [Akademischer Betreuer] Schäfer. "Strategies for Genome-Wide Association Analyses of Raw Copy Number Variation Data / Ivonne Jarick. Betreuer: Helmut Schäfer." Marburg : Philipps-Universität Marburg, 2013. http://d-nb.info/1045729884/34.

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Weck, Antoine de. "Development of methodologies for the analysis of copy number alterations in tumour samples." Thesis, University of Oxford, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.572470.

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The genetic basis of the different cancer phenotypes has been a continuous and accelerating subject of investigation. Data accumulated thanks to recently introduced genome-wide scanning technologies have revealed that human diversity and diseases susceptibility is also greatly influenced by structural alterations in the human genome, such as DNA copy number variants (CNVs) and copy number alterations (CNAs), which influence gene expression in both healthy and pathological cells. Our research aims to investigate the influence of structural alterations on gene expression in cancer cells using SNP microarray data. Specifically, we focus on analyzing DNA copy number alternations (CNAs), which can significantly influence gene expression in cancer cells. Several cancer-predisposing mutations affect genes that are responsible for maintaining the integrity of the chromosomes during cell division, which can result in translocations, gains or losses of large parts of chromosome. To our knowledge, there have been no publications that link whole-genome copy number alterations in cancer to gene expression variations using the full range of possibilities offered by SNP arrays. The accurate use of SNP arrays in the analysis of cancer has been difficult due to tumour purity, tumour heterogeneity, aneuploidy/polyploidy and complex patterns of CNA and loss-of-heterozygosity (LOH). In our work, we use and further extend a recently developed novel tool for tumour genome profiling called OncoSNP (Yau, Mouradov et al. 2010), in order to resolve some of those problems and accurately estimate copy number alterations (CNA) and loss-of-heterozygosity (LOH) from SNP array data in cancer cell samples. The methods developed in this thesis tackle the problem of cancer genomic investigation by developing and validating an extension (DPS smoothing) of a new method (OncoSNP). This approach is used in the analysis of global expression versus CNA patterns in experimental systems and large clinical datasets. We analyse various cancer SNP and gene expression arrays of increasing complexity and heterogeneity, starting with a dataset of head and neck squamous cell carcinoma (HNSCC) cell lines, followed by leukaemia samples and finally a large breast cancer dataset. The central findings of our research are multifold. In the HNSCC dataset we find that the level of genetic instability is not indicative of the pathological state; i.e. there are premalignant lesions displaying extensive mutations. However some genetic features are typical of certain lesion type; e.g. we consistently observe copy loss in the short arm of chromosome 3 in carcinoma. The pattern of homozygous deletion in the dataset reveals common deletion of cancer related genes, especially CDK4 (pI6). Furthermore we notice a significant positive correlation between the copy number and the expression on a systematic level. In Leukaemia, we do not observe extended uniparental disomy as previously published (Akagi, Shih et al. 2009) and expected. However large alterations (whole arm amplification) are observed in individual patients: copy loss in chromosome 7 (2 patients), copy gain in chromosome 8 (3 patients) as well as common alterations around the centromeres and telomeres. In the breast cancer dataset significantly different level of mutations were observed in the different subtypes in the cohort. Furthermore 499 genes were identified with significant correlation between their gene expression (GE) and underlying genomic alterations (either copy number (CN) or loss-of-heterozygosity (LOH)). Performing hierarchical clustering on the cohort using the 499 correlated genes enabled us to recover the subtypes' separation previously based on gene expression alone.
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Charoen, Pimphen. "Robust approaches for performing meta-analysis of genome-wide association studies to identify single nucleotide polymorphisms and copy number variations associated with complex traits." Thesis, Imperial College London, 2013. http://hdl.handle.net/10044/1/30165.

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From 2007, there has been a huge proliferation in the discovery of genetic variants affecting human traits and diseases, achieved largely by the integration of multiple genome-wide association studies (GWAS) via meta-analysis. The principal objective of this thesis is to develop robust approaches for meta-analysis GWAS in order to reduce false positive findings and optimise statistical power. I consider both Single Nucleotide Polymorphism (SNP) and Copy Number Variant (CNV) GWAS. First, to gain background knowledge in GWAS and meta-analysis, I was involved in a large-scale meta-analysis GWAS to identify genetic variants associated with alcohol consumption, as the main statistical analyst. This study provided me with the opportunity to investigate ways of reducing the probability of false positive findings, via quality control procedures. The main discovery from the study was the identification of the Autism susceptibility candidate 2 gene (AUTS2) as associated with alcohol consumption at genome-wide significance. In the alcohol study, different phenotype transformations were applied to the data according to the inclusion or exclusion of non-drinkers, which led to questioning which transformation of skewed continuous phenotypes optimises statistical power in GWAS in general, forming the second major investigation in my thesis. It was shown that while the inverse normal transformation (INT) may not be the preferable choice of transformation in many epidemiological studies where effect sizes are large, its application to non-normal phenotypes in GWAS, where effect sizes are small and the priority is discovery over interpretability, may lead to an increase in the discovery of genetic variants affecting continuous traits. Finally, as knowledge about CNVs has accumulated in recent years, the meta-analysis of GWAS on CNVs has become a natural next step forward in the field. Therefore, I investigated and developed an approach to enable CNV meta-analysis to proceed in a similar way as SNP meta-analyses. This approach was developed into a software package, cnvPipe, which was applied to investigate CNVs associated with height and weight in the meta-analysis setting.
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Rucker, James. "Whole genome analysis of copy number variation in a case control study of recurrent depressive disorder." Thesis, King's College London (University of London), 2012. https://kclpure.kcl.ac.uk/portal/en/theses/whole-genome-analysis-of-copy-number-variation-in-a-case-control-study-of-recurrent-depressive-disorder(c6719f93-999f-4cc5-9f8c-c0632194b608).html.

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Rare copy number variants (CNV), defined as deletions and duplications of genetic material over 1,000 base pairs in length, have become the focus of considerable interest in psychiatric disorders, where a proportion of individuals harbour rare and de novo events not usually seen in controls. We have performed a genome wide association study of copy number variation in 3,106 cases of recurrent depressive disorder, 1,731 controls screened for a lifetime absence of psychiatric disorder, and 5,619 population controls from phase 2 of the Wellcome Trust Case Control Consortium. Analysing our data with the PennCNV method, we found an enrichment of rare deletion CNVs in our case cohort, especially when compared to our screened control cohort. This finding was supported by further analysis with the iPattern method, but not by the QuantiSNP method. We followed up a selection of cases and controls with a comparative genomic hybridisation (CGH) array focussed on the region 22qll.2, which is a neuro-gene rich region of the human genome under current active evolutionary selection and resident to a deletion syndrome which commonly manifests with psychiatric disorders. We found no significant differences in CNV burden between our case and control cohorts. Finally we ran association analyses with our CNV call sets, including a high quality intersected call set derived from all three methods, against various phenotypes obtained from a combined database of all studies that contributed samples to this GWAS. We found no associations that survived Bonferroni correction for multiple testing.
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Khuzwayo, Sabelo Lethukuthula. "Functional analysis of subtelomeric breakage motifs using yeast as a model organism." Thesis, Georgia Institute of Technology, 2011. http://hdl.handle.net/1853/41119.

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Genome wide studies have uncovered the existence of large-scale copy number variation (CNV) in the human genome. The human genome of different individuals was initially estimated to be 99.9% similar, but population studies on CNV have revealed that it is 12-16% copy number variable. Abnormal genomic CNVs are frequently found in subtelomeres of patients with mental retardation (MR) and other neurological disorders. Rearrangements of chromosome subtelomeric regions represent a high proportion of cytogenetic abnormalities and account for approximately 30% of pathogenic CNVs. Although DNA double strand breaks (DSBs) are implicated as a major factor in chromosomal rearrangements, the causes of chromosome breakage in subtelomeric regions have not been elucidated. But due to the presence of repetitive sequences in subtelomeres, we hypothesized that chromosomal rearrangements in these regions are not stochastic but driven by specific sequence motifs. In a collaborative effort with Dr. Rudd (Department of human genetics at Emory University), we characterized subtelomeric breakpoints on different chromosome ends in search of common motifs that cause double-strand breaks. Using a yeast-based gross chromosomal rearrangement (GCR) system, we have identified a subtelomeric breakage motif from chromosome 2 (2q SBM) with a GCR rate that is 340 fold higher than background levels. To determine if the fragility of 2q SBM was driven by the formation of secondary structures, the helicase activities of Sgs1 and Pif1 were disrupted. These helicases have been shown to destabilize DNA secondary structures such as G-quadruplex structures. Disruption of these helicases augmented chromosomal rearrangements induced by 2q SBM, indicating that these helicases are required for maintenance of this sequence. We also donwregulated replication fork components to determine if 2q SBM was imposing any problems to the replication fork machinery. Downregulation of replication fork components increased chromosomal rearrangements, indicating that intact replication fork was a critical determinant of 2q SBM fragility. Using a yeast-based functional assay, these experiments have linked human subtelomeric repetitive sequences to chromosomal breakage that could give rise to human CNV in subtelomeric regions.
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LETTIERI, ANTONELLA. "Genomic and trascriptomic analyses of pediatric T-cell lynphoblastic leukemia/limphoma." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2011. http://hdl.handle.net/10281/20246.

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ABSTRACT In the first part of our work we focused our attention on the biological question about the differences between two pathologies: T-cell lymphoblastic leukemia and T-cell lymphoblastic lymphoma. These two diseases share many features such as immunophenotypic features, lymphoblast morphology and clinical characteristics and are differentially diagnosed only on the base of bone marrow involvement. We tried to understand whether T-cell leukemia and lymphoma are a unique pathology with a different manifestation or whether they are two different diseases. The results obtained by gene expression profiling revealed an intrinsic difference in the expression of 78 genes between T-ALL and T-LBL. In particular since these genes belong to the angiogenesis and the chemotactic response we supposed that the two malignancies have different ability to respond to several cyto- and chemokines and that T-LBL need to modulate transcription to promote angiogenesis as well as to deal with hypoxic conditions. Also by analysis of copy number we were able to identify some abnormalities that seemed to be specific for each group regardless the limited data set of patients. Although this work provides additional elements in the characterization of these two pathologies, many studies have yet to be done, especially on the comprehension of the different capability of cells to migrate and invade the bone marrow compartment. The complete understanding of the molecular characteristics of T-LBL and T-ALL represents the driving element toward the design of fully successful therapeutic approaches. The second part of the study focused on the genetic characterization of two different groups of T-ALL patients on the basis of MRD response. With the aim to find biological correlates with the outcome for HR and nonHR patients, we performed many analyses, starting from copy number analysis to microRNAs expression profiling. Furthermore, we tried to integrate all the data in order to delineate common characteristics for each group of patients. First of all, the study of copy number revealed the presence of multiple abnormalities in all patients: we found known and unknown lesions, and in some cases we were able to associate them with HR or nonHR patients. The improvement of copy number results was obtained by the study of translocations. Also in this case we found one or more translocation in the majority of patients and we identified that the most recurrent were SIL-TAL1 and TLX3 translocations. Moreover, we tested the Notch1 mutations and, as expected, about 60% of patients were mutated for Notch1, with a tendency for Notch1 mutations to be more frequent in the nonHR group. The second step was the analysis of gene and microRNAs expression. The initial unsupervised analysis between HR and nonHR group failed to distinguish the two groups; but the successively supervised analysis revealed the distribution of MR patients in an equal manner between HR and SR patients. Thus an unsupervised analysis without MR patients showed a specific pattern of expression for each group (SR and HR). The GSEA analysis performed highlighted the enrichment of two specific pathways: the mir-215/192 pathway and the methylation pathway. The results obtained by the expression profile of about 700 microRNAs in the HR and nonHR group and those achieved by the combined analysis of GEP and microRNAs suggested miR-215 and miR-107 as the most differentially expressed and provided some possible target genes of these microRNAs. Moreover, to delineate specific pattern of expression not driven by MRD but by other alterations, we used the data derived from copy number, translocation and mutational analyses to supervise genetic subgroups. Significant results were obtained for Nocth1 mutated vs non-mutated, TLX3 translocated vs non-translocated, PTEN and LEF1 deleted vs non-deleted. We also tried to integrate all the data provided by both genomic and trasncriptomic analyses to understand whether the distribution of MR and the different signature of HR and SR were correlated with specific gene lesions. SIL-TAL1 fusion gene and the deletion of LEF1 and PTEN seemed to be specific for the HR group while the TLX3-translocation seemed to be peculiar for the nonHR group of patients. In conclusion HR and nonHR patients seemed to show some peculiar lesions and patterns of expression that could be justify the different response to therapy. In summary, several high throughput methodologies have been applied to the selected subgroup of patients to study the biological correlates of the different response to therapy. By this work we tried to provide a better characterization of T-ALL and to give a way of interpretation for the different outcome of T-ALL patients.
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Li, Mura Ilena Egle Astrid. "Identification of novel loci and genes involved in Arrhythmogenic Right Ventricular Cardiomyopathy." Doctoral thesis, Università degli studi di Padova, 2012. http://hdl.handle.net/11577/3422950.

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Introduction: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited cardiac disease characterized by fibrofatty replacement of myocardial tissue and high incidence of serious ventricular tachyarrhythmias. To date, ten disease-genes have been identified, five of which encoding desmosomal proteins (PKP2, DSP, DSG2, DSC2 and JUP). Aim of the study: The study described in the present thesis aimed at determining the spectrum and prevalence of desmosomal mutations in 80 Italian unrelated index cases. Moreover, the identification of novel disease loci and genes in three ARVC families was attempted by integrating different approaches, including genome-wide linkage study, Copy Number Variations (CNVs) analysis, and exome-sequencing. Methods: Mutation screening of the desmosomal ARVC genes was performed by Denaturing High-Performance Liquid Chromatography (DHPLC) and direct sequencing. In order to map novel loci and, possibly, to identify novel genes, genome-wide linkage study and CNVs analysis was performed in three independent families with recurrence of ARVC, showing no mutations in any of the desmosomal genes. In addition, in Family #2 and in Family #3 a combined strategy of linkage analysis and exome sequencing was adopted to identify novel ARVC genes. Results: Mutation screening of five desmosomal ARVC genes in 80 Italian probands identified single point mutations in 32.5% of cases and multiple mutations in 12.5%. No mutations were identified in the remaining 55% of probands. The genes most frequently involved were PKP2, DSP and DSG2. Among the index cases negative for point mutations in the desmosomal genes, three belong to independent families with recurrence of ARVC. Assuming a further genetic heterogeneity in these families, a genome-wide scan was performed in order to identify novel loci and genes. In Family #1, a CNV involving a desmosomal ARVC gene was identified in all affected family members. In Family #2, a novel ARVC locus was mapped on chromosome 19 by linkage analysis. Finally, in Family #3, a possible novel candidate gene for ARVC was detected by a combined strategy of linkage analysis and exome-sequencing. Discussion: In the present study, genetic screening of five desmosomal ARVC genes in 80 Italian probands identified causative mutations in 45% of cases, mainly involving the “big3” genes PKP2, DSP, and DSG2, according to data reported in literature. Genetic analysis of available family members confirmed the high heterogeneity in the clinical expression of ARVC mutations even among relatives. Mutation screening of desmosomal genes failed to detect causative mutations in more than 50% of index cases, suggesting that additional and still unknown genes could be involved. In this perspective, a genome-wide scan was performed in three large ARVC families, showing no mutations in any of the desmosomal genes. In Family #1, a CNV was identified in a desmosomal ARVC gene, highlighting the importance of complementing the conventional mutation screening in ARVC genes with other approaches able to detect possible structural variations. In Family #2, genome-wide linkage results provided strong evidence for a novel ARVC locus on chromosome 19, highlighting the soundness of this strategy for identifying susceptibility regions in large, highly informative families and providing the basis for the identification of a novel disease gene. Finally, in Family #3, exome-sequencing identified a novel putative candidate gene for ARVC. Identification of novel ARVC genes is of great importance for understanding the molecular pathogenesis of this disease, as well as for increasing the power of genetic screening and developing successful targeted therapies
Introduzione: La Cardiomiopatia Aritmogena del Ventricolo Destro (ARVC) è una malattia ereditaria del muscolo cardiaco caratterizzata dalla progressiva perdita e sostituzione fibro-adiposa dei cardiomiociti che costituiscono la parete libera delventricolo destro. Tale disomogeneità del tessuto cardiaco altera la normale conduzione dell'impulso elettrico, determinando l'insorgenza di aritmie che occasionalmente portano a fibrillazione ventricolare e morte improvvisa per arresto cardiaco, soprattutto nei giovani e negli atleti. Attualmente, sono noti 10 geni implicati nella determinazione genetica dell’ARVC e cinque di questi codificano per proteine costituenti il desmosoma cardiaco: Placofilina-2 (PKP2), Desmoplachina (DSP), Desmogleina-2 (DSG2), Desmocollina-2 (DSC2) e Placoblobina (JUP). Scopo dello studio: Lo studio descritto nella presente tesi mira a valutare la prevalenza e lo spettro di mutazioni nei cinque geni ARVC desmosomali in un gruppo di 80 casi indice Italiani, non imparentati tra loro. Inoltre, in tre grandi famiglie con ricorrenza di casi ARVC e in cui non sono state identificate mutazioni nei geni desmosomali, è stata effettuata un'analisi genome-wide integrando diversi approcci, quali studio di linkage, analisi di Copy Number Variations (CNVs) e sequenziamento dell’esoma. Metodi: Lo screening per la ricerca di mutazioni nei cinque geni ARVC desmosomali ha coinvolto 80 casi indice ed è stato effettuato tramite analisi DHPLC (Denaturing High-Performance Liquid Chromatography) e sequenziamento diretto del DNA.I soggetti appartenenti a ciascuna delle tre famiglie selezionate per l'analisi genome-wide sono stati genotipizzati utilizzando un pannello di marcatori ad alta densità che include più di 370.000 polimorfismi di singolo nucleotide (SNPs) (Illumina HumanCNV370-Duo BeadChip). In ciascuna famiglia è stato effettuato uno studio di linkage ed un’analisi di CNVs. Inoltre, Nella Famiglia #2 e nella #3 l'identificazione del gene malattia è stata tentata integrando i risultati dello studio di linkage con i dati ottenuti dal sequenziamento dell'esoma di due soggetti affetti. Risultati: L'analisi delle sequenze codificanti dei geni PKP2, DSP, DSG2, DSC2 e JUP in 80 casi indice Italiani ha permesso di identificare mutazioni singole nel 32.5% dei casi e mutazioni multiple nel 12.5%. Il 55% dei probandi non è risultato portatore di alcuna mutazione nei geni desmosomali. La maggior parte delle mutazioni ha coinvolto i geni PKP2, DSP, DSG2, confermando i dati riportati in letteratura. Tra i casi indice in cui non sono state identificate mutazioni nei geni desmosomali, tre appartengono a famiglie indipendenti con ricorrenza di casi ARVC. In ognuna di queste famiglie è stata effettuata un'analisi genome-wide allo scopo di identificare nuovi loci e geni malattia. Nella Famiglia #1 è stata identificata una CNV che coinvolge uno dei geni ARVC desmosomali noti e co-segrega con il fenotipo patogeno. Nella Famiglia #2, l’analisi di linkage ha permesso di identificare un nuovo locus ARVC sul cromosoma 19. Infine, nella Famiglia #3 è stato identificato un nuovo potenziale gene candidato per l’ARVC. Discussione: L’analisi genetica delle sequenze codificanti dei cinque geni ARVC desmosomali, in un gruppo di 80 probandi italiani, ha permesso di identificare mutazioni nel 45% dei casi, confermando il prevalente coinvolgimento dei tre geni PKP2, DSP e DSG2, in accordo con i dati riportati in letteratura. L'analisi genetica dei familiari dei probandi ha confermato la penetranza incompleta e l'espressività variabile della malattia, anche all'interno della stessa famiglia. L'assenza di mutazioni in più del 50% dei casi suggerisce il coinvolgimento di altri geni nella determinazione genetica dell'ARVC. In quest' ottica, un'analisi genome-wide è stata effettuata in tre famiglie con ricorrenza di casi ARVC e in cui non sono state individuate mutazioni nei geni desmosomali. Nella Famiglia #1, l’identificazione di una CNV in uno dei geni ARVC desmosomali, presente in tutti i soggetti affetti, sottolinea l'importanza di associare alle metodiche tradizionali utilizzate per lo screening di mutazioni puntiformi approcci che permettano di identificare eventuali variazioni strutturali presenti nel genoma. Nella Famiglia #2, l'analisi di linkage ha fornito una significativa evidenza dell'esistenza di un nuovo locus ARVC sul cromosoma 19, fornendo le basi per l'identificazione di nuovi geni. Infine, nella Famiglia #3, il sequenziamento dell'esoma di due soggetti affetti ha identificato un nuovo gene come un possibile candidato per l'ARVC
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Giannoulatou, Eleni. "Single nucleotide polymorphism and copy number variant genotyping for genome wide association studies." Thesis, University of Oxford, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.543550.

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Enyakoit, George Ojula. "A genome-wide investigatin of DNA copy number aberrations in high malignancy grade astrocytomas." Thesis, University College London (University of London), 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.500063.

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Books on the topic "Genome-wide copy number analysis"

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Langley, Kate. ADHD genetics. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198739258.003.0003.

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This chapter reviews the evidence suggesting that there is a strong genetic component to ADHD and the efforts to identify the specific genetic factors that might be involved. It discusses the different types of genetic contributions, from common to rare variants, and the evidence that these are involved in the aetiology of the disorder. An overview of the methodological strategies employed, including genome-wide association studies (GWAS), polygenic risk score, and copy number variant (CNV) analyses, is undertaken, as well as discussion of the strengths and pitfalls of such work. The contradictory findings in the field and controversies that arise as a result are also explored. Finally, this chapter considers how the heritability of ADHD and specific genetic factors involved need to be examined in the context of clinical factors such as comorbidity and how these factors affect investigations into the genetics of ADHD.
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Canli, Turhan, ed. The Oxford Handbook of Molecular Psychology. Oxford University Press, 2014. http://dx.doi.org/10.1093/oxfordhb/9780199753888.001.0001.

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Determining the biological bases for behavior—and the extent to which we can observe and explain their neural underpinnings—requires a bold, broadly defined research methodology. The interdisciplinary entries in this handbook are organized around the principle of “molecular psychology,” which unites cutting-edge research from such wide-ranging disciplines as clinical neuroscience and genetics, psychology, behavioral neuroscience, and neuroethology. For the first time in a single volume, leaders from diverse research areas present their work in which they use molecular approaches to investigate social behavior, psychopathology, emotion, cognition, and stress in healthy volunteers, patient populations, and an array of nonhuman species including nonhuman primates, rodents, insects, and fish. Chapters draw on molecular methods covering candidate genes, genome-wide association studies, copy number variations, gene expression studies, and epigenetics while addressing the ethical, legal, and social issues to emerge from this new and exciting research approach.
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Book chapters on the topic "Genome-wide copy number analysis"

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Magbanua, Mark Jesus M., and John W. Park. "Genome-Wide Gene Copy Number Analysis of Circulating Tumor Cells." In Circulating Tumor Cells, 201–13. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3363-1_10.

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Shen, Wei, Philippe Szankasi, Jacob Durtschi, Todd W. Kelley, and Xinjie Xu. "Genome-Wide Copy Number Variation Detection Using NGS: Data Analysis and Interpretation." In Methods in Molecular Biology, 113–24. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9004-7_8.

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Ogawa, Seishi, Yasuhito Nanya, and Go Yamamoto. "Genome-wide Copy Number Analysis on GeneChip® Platform Using Copy Number Analyzer for Affymetrix GeneChip 2.0 Software." In Comparative Genomics, 185–206. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-515-2_13.

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Dimitriadou, Eftychia, Masoud Zamani Esteki, and Joris Robert Vermeesch. "Copy Number Variation Analysis by Array Analysis of Single Cells Following Whole Genome Amplification." In Whole Genome Amplification, 197–219. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2990-0_14.

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Vucic, Emily A., Kelsie L. Thu, Ariane C. Williams, Wan L. Lam, and Bradley P. Coe. "Copy Number Variations in the Human Genome and Strategies for Analysis." In Methods in Molecular Biology, 103–17. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60327-367-1_6.

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Sanders, Mathijs A., and Peter J. M. Valk. "Genome-Wide Gene Expression Profiling, Genotyping, and Copy Number Analyses of Acute Myeloid Leukemia Using Affymetrix GeneChips." In Methods in Molecular Biology, 155–77. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-435-7_10.

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Taniguchi, Yuichi. "Genome-Wide Analysis of Protein and mRNA Copy Numbers in Single Escherichia coli Cells with Single-Molecule Sensitivity." In Methods in Molecular Biology, 55–67. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2987-0_5.

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Rowsey, Ross, Iya Znoyko, and Daynna J. Wolff. "Whole-Genome Single Nucleotide Polymorphism Microarray for Copy Number and Loss of Heterozygosity Analysis in Tumors." In Methods in Molecular Biology, 89–111. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9004-7_7.

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Barseghyan, Hayk, Andy W. C. Pang, Yang Zhang, Nikhil S. Sahajpal, Yannick Delpu, Chi-Yu Jill Lai, Joyce Lee, et al. "Neurogenetic Variant Analysis by Optical Genome Mapping for Structural Variation Detection-Balanced Genomic Rearrangements, Copy Number Variants, and Repeat Expansions/Contractions." In Neuromethods, 155–72. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2357-2_9.

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Deleye, Lieselot, Dieter De Coninck, Dieter Deforce, and Filip Van Nieuwerburgh. "Genome-Wide Copy Number Alteration Detection in Preimplantation Genetic Diagnosis." In Methods in Molecular Biology, 27–42. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7514-3_3.

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Conference papers on the topic "Genome-wide copy number analysis"

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Gokgoz, Nalan, Jay S. Wunder, and Irene L. Andrulis. "Abstract 5075: Genome-wide analysis of DNA copy number variations in osteosarcoma." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-5075.

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Tsukamoto, Yoshiyuki, Tsuyoshi Noguchi, Tomohisa Uchida, Chisato Nakada, Tetsuya Aizawa, Naoki Hijiya, Keiko Matsuura, and Masatsugu Moriyama. "Abstract 5097: Genome-wide analysis of DNA copy number aberrations in gastric cancer." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-5097.

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Porat, Rinnat M., Ivan Pasic, Adan Shlien, Nalan Gokgoz, Irene Andrulis, Jay S. Wunder, and David Malkin. "Abstract 1447: Investigating susceptibility to sporadic osteosarcoma by genome-wide copy number analysis." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-1447.

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Rogers, Angela, Katayoon Darvishi, Jen-Hwa Chu, Iuliana Ionita-Laza, Barbara J. Klanderman, Charles Lee, and Benjamin Raby. "A Genome-wide Analysis Of The Role Of Copy Number Variants In Asthma." In American Thoracic Society 2010 International Conference, May 14-19, 2010 • New Orleans. American Thoracic Society, 2010. http://dx.doi.org/10.1164/ajrccm-conference.2010.181.1_meetingabstracts.a3732.

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Dai, Chao, Amy Xiaohong Wang, Zhixin Zhao, Feng Xie, Kemin Zhou, Shujun Luo, Shidong Jia, and Pan Du. "Abstract 2242: Blood-based genome-wide copy number analysis of 500 cancer patients." In Proceedings: AACR Annual Meeting 2021; April 10-15, 2021 and May 17-21, 2021; Philadelphia, PA. American Association for Cancer Research, 2021. http://dx.doi.org/10.1158/1538-7445.am2021-2242.

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Rogers, Angela J., Katayoon Darvishi, JenHwa Chu, Iuliana Ionita-Laza, Ute Geigenmuller, Charles Lee, and Benjamin A. Raby. "A Genome-Wide Analysis Of The Role Of Copy Number Variants In Asthma." In American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California. American Thoracic Society, 2012. http://dx.doi.org/10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a5596.

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Liu, Yang, Yiu Fai Lee, and K. Ng Michael. "Classification of genome-wide copy number variations and their associated SNP and gene networks analysis." In 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2010. http://dx.doi.org/10.1109/bibm.2010.5706526.

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Stefansson, Olafur A., Sebastian Moran, Antonio Gomez, Sergi Sayols Puig, Jorunn Eyfjord, and Manel Esteller. "Abstract 2018: Genome-wide analysis of DNA methylation and copy number changes in breast cancers." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-2018.

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Paolella, Brenton R., William J. Gibson, Laura M. Urbanski, John A. Alberta, Travis I. Zack, Pratiti Bandopadhayay, Caitlin A. Nichols, et al. "Abstract 4369: Genome-wide copy number dependency analysis identifies partial copy loss of SF3B1 as a novel cancer vulnerability." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-4369.

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Pietsch, Torsten, A. Carmichael, Christian Vokuhl, and Ivo Leuschner. "Abstract LB-205: Genome-wide copy number analysis of pediatric hepatocellular carcinomas: Identification of characteristic aberrations." In Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1538-7445.am2014-lb-205.

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Reports on the topic "Genome-wide copy number analysis"

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Seroussi, Eyal, and George Liu. Genome-Wide Association Study of Copy Number Variation and QTL for Economic Traits in Holstein Cattle. United States Department of Agriculture, September 2010. http://dx.doi.org/10.32747/2010.7593397.bard.

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Copy number variation (CNV) has been recently identified in human and other mammalian genomes and increasing awareness that CNV might be a major source for heritable variation in complex traits has emerged. Despite this, little has been published on CNVs in Holsteins. In order to fill this knowledge-gap, we proposed a genome-wide association study between quantitative trait loci (QTL) for economic traits and CNV in the Holstein cattle. The approved feasibility study was aimed at the genome-wide characterization of CNVs in Holstein cattle and at the demonstrating of their possible association with economic traits by performing the activities of preparation of DNA samples, Comparative Genomic Hybridization (CGH), initial association study between CNVs and production traits and characterization of CNVSNP associations. For both countries, 40 genomic DNA samples of bulls representing the extreme sub-populations for economically important traits were CGH analyzed using the same reference genome on a NimbleGen tiling array. We designed this array based on the latest build of the bovine genome (UMD3) with average probe spacing of 1150 bases (total number of probes was 2,166,672). Two CNV gene clusters, PLA2G2D on BTA2 and KIAA1683 on BTA7 revealed significant association with milk percentage and cow fertility, respectively, and were chosen for further characterization and verification in a larger sample using other methodologies including sequencing, tag SNPs and real time PCR (qPCR). Comparison between these four methods indicated that there is under estimation of the number of CNV loci in Holstein cattle and their complexity. The variation in sequence between different copies seemed to affect their functionality and thus the hybridization based methods were less informative than the methods that are based on sequencing. We thus conclude that large scale sequencing effort complemented by array CGH should be considered to better detect and characterize CNVs in order to effectively employ them in marker-assisted selection.
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Lehman, Donna, Robin Leach, and August Blackburn. Assessing the Role of Copy Number Variants in Prostate Cancer Risk and Progression Using a Novel Genome-Wide Screening Method. Fort Belvoir, VA: Defense Technical Information Center, October 2010. http://dx.doi.org/10.21236/ada542445.

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Lehman, Donna, August Blackburn, and Robin Leach. Assessing the Role of Copy Number Variants in Prostate Cancer Risk and Progression using a Novel Genome-Wide Screening Method. Fort Belvoir, VA: Defense Technical Information Center, October 2012. http://dx.doi.org/10.21236/ada568305.

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Lehman, Donna, and Robin Leach. Assessing the Role of Copy Number Variants in Prostate Cancer Risk and Progression Using a Novel Genome-Wide Screening Method. Fort Belvoir, VA: Defense Technical Information Center, October 2013. http://dx.doi.org/10.21236/ada594060.

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Lehman, Donna. Assessing the Role of Copy Number Variants in Prostate Cancer Risk and Progression Using a Novel Genome-Wide Screening Method. Fort Belvoir, VA: Defense Technical Information Center, October 2011. http://dx.doi.org/10.21236/ada554128.

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