scholarly journals Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation

2010 ◽  
Vol 20 (12) ◽  
pp. 1719-1729 ◽  
Author(s):  
M. D. Robinson ◽  
C. Stirzaker ◽  
A. L. Statham ◽  
M. W. Coolen ◽  
J. Z. Song ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Copy Number Variation ◽  
Copy Number ◽  
Methylation Data ◽  
Amplification Bias ◽  
Genome Wide ◽  
Number Variation

scholarly journals An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1897
Author(s):  
Clarence K. Mah ◽  
Jill P. Mesirov ◽  
Lukas Chavez
Keyword(s):  
Dna Methylation ◽  
Copy Number Variation ◽  
Copy Number ◽  
Cost Effective ◽  
Copy Number Alterations ◽  
Software Environment ◽  
Link Type ◽  
Genome Wide ◽  
Effective Technology ◽  
Number Variation

Illumina Infinium DNA methylation arrays are a cost-effective technology to measure DNA methylation at CpG sites genome-wide and across cohorts of normal and cancer samples. While copy number alterations are commonly inferred from array-CGH, SNP arrays, or whole-genome DNA sequencing, Illumina Infinium DNA methylation arrays have been shown to detect copy number alterations at comparable sensitivity. Here we present an accessible, interactive GenePattern notebook for the analysis of copy number variation using Illumina Infinium DNA methylation arrays. The notebook provides a graphical user interface to a workflow using the R/Bioconductor packages minfi and conumee. The environment allows analysis to be performed without the installation of the R software environment, the packages and dependencies, and without the need to write or manipulate code.

scholarly journals Genome-Wide Copy Number Variation Scan Identifies Complement Component C4 as Novel Susceptibility Gene for Crohnʼs Disease

2016 ◽  
Vol 22 (3) ◽  
pp. 505-515 ◽  
Author(s):  
Isabelle Cleynen ◽  
Peter Konings ◽  
Caroline Robberecht ◽  
Debby Laukens ◽  
Leila Amininejad ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Susceptibility Gene ◽  
Complement Component ◽  
Genome Wide ◽  
Number Variation

scholarly journals Genome-Wide Detection of Allele Specific Copy Number Variation Associated with Insulin Resistance in African Americans from the HyperGEN Study

PLoS ONE ◽  
2011 ◽  
Vol 6 (8) ◽  
pp. e24052 ◽  
Author(s):  
Marguerite R. Irvin ◽  
Nathan E. Wineinger ◽  
Treva K. Rice ◽  
Nicholas M. Pajewski ◽  
Edmond K. Kabagambe ◽  
...  
Keyword(s):  
Insulin Resistance ◽  
African Americans ◽  
Copy Number Variation ◽  
Copy Number ◽  
Genome Wide ◽  
Number Variation ◽  
Allele Specific

Copy-number variation in sporadic amyotrophic lateral sclerosis: a genome-wide screen

2008 ◽  
Vol 7 (4) ◽  
pp. 319-326 ◽  
Author(s):  
Hylke M Blauw ◽  
Jan H Veldink ◽  
Michael A van Es ◽  
Paul W van Vught ◽  
Christiaan GJ Saris ◽  
...  
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Copy Number Variation ◽  
Copy Number ◽  
Sporadic Amyotrophic Lateral Sclerosis ◽  
Genome Wide ◽  
A Genome ◽  
Number Variation ◽  
Lateral Sclerosis

scholarly journals A genome-wide analysis of copy number variation in Murciano-Granadina goats

2020 ◽  
Vol 52 (1) ◽  
Author(s):  
Dailu Guan ◽  
Amparo Martínez ◽  
Anna Castelló ◽  
Vincenzo Landi ◽  
María Gracia Luigi-Sierra ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Number Variation

scholarly journals DNA methylation and copy number variation profiling of T-cell lymphoblastic leukemia and lymphoma

2020 ◽  
Vol 10 (4) ◽  
Author(s):  
Zahra Haider ◽  
Mattias Landfors ◽  
Irina Golovleva ◽  
Martin Erlanson ◽  
Kjeld Schmiegelow ◽  
...  
Keyword(s):  
Dna Methylation ◽  
T Cell ◽  
Copy Number Variation ◽  
Copy Number ◽  
Cpg Island ◽  
Lymphoblastic Leukemia ◽  
Clinical Manifestations ◽  
Cpg Island Methylator Phenotype ◽  
Genetic Landscape ◽  
Number Variation

AbstractDespite having common overlapping immunophenotypic and morphological features, T-cell lymphoblastic leukemia (T-ALL) and lymphoma (T-LBL) have distinct clinical manifestations, which may represent separate diseases. We investigated and compared the epigenetic and genetic landscape of adult and pediatric T-ALL (n = 77) and T-LBL (n = 15) patient samples by high-resolution genome-wide DNA methylation and Copy Number Variation (CNV) BeadChip arrays. DNA methylation profiling identified the presence of CpG island methylator phenotype (CIMP) subgroups within both pediatric and adult T-LBL and T-ALL. An epigenetic signature of 128 differentially methylated CpG sites was identified, that clustered T-LBL and T-ALL separately. The most significant differentially methylated gene loci included the SGCE/PEG10 shared promoter region, previously implicated in lymphoid malignancies. CNV analysis confirmed overlapping recurrent aberrations between T-ALL and T-LBL, including 9p21.3 (CDKN2A/CDKN2B) deletions. A significantly higher frequency of chromosome 13q14.2 deletions was identified in T-LBL samples (36% in T-LBL vs. 0% in T-ALL). This deletion, encompassing the RB1, MIR15A and MIR16-1 gene loci, has been reported as a recurrent deletion in B-cell malignancies. Our study reveals epigenetic and genetic markers that can distinguish between T-LBL and T-ALL, and deepen the understanding of the biology underlying the diverse disease localization.

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