Results 21 to 30 of about 288,493 (295)

DNA isolation protocol effects on nuclear DNA analysis by microarrays, droplet digital PCR, and whole genome sequencing, and on mitochondrial DNA copy number estimation. [PDF]

, 2017
Potential bias introduced during DNA isolation is inadequately explored, although it could have significant impact on downstream analysis. To investigate this in human brain, we isolated DNA from cerebellum and frontal cortex using spin columns under ...
A Bendich, A Koren, A Leo, A Pyle, Alan M. Pittman, AM D’Erchia, Anthony H. Schapira, Ayesha Ejaz, Aynur Soenmez, Christos Proukakis, Colin Grace, D Lindgren, D Sims, E Reznik, Elizabeth Nacheva, Emanuela Maserati, F Ye, FA Azevedo, GD Evrony, Henry Houlden, I Scheinin, Jan-Willem Taanman, JC Marioni, Jeong-Sun Seo, JF Huggett, K Jacobs, Katya Mokretar, L Aghili, L Atanesyan, L Kasak, L Kluwe, L Miotke, M Costantini, M O’Huallachain, M Sakai, MA van de Wiel, MG Ross, MJ McConnell, P Cozzi, R Aplenc, R Valli, Roberto Valli, S van Heesch, S Vattathil, S Vattathil, SE Antonarakis, Selina Vattathil, SJ Diskin, W Guo, X Cai   +49 more
core   +12 more sources

Measuring DNA Copy Number Variation Using High-Density Methylation Microarrays [PDF]

Journal of Computational Biology, 2019
Genetic and epigenetic changes drive carcinogenesis, and their integrated analysis provides insights into mechanisms of cancer development. Computational methods have been developed to measure copy number variation (CNV) from methylation array data, including ChAMP-CNV, CN450K, and, introduced here, Epicopy. Using paired single nucleotide polymorphism (
Soonweng, Cho, Hyun-Seok, Kim, Martha A, Zeiger, Christopher B, Umbricht, Leslie M, Cope   +4 more
openaire   +2 more sources

Cell-free DNA copy number variations in plasma from colorectal cancer patients. [PDF]

Mol Oncol, 2017
To evaluate the clinical utility of cell‐free DNA (cfDNA), we performed whole‐genome sequencing to systematically examine plasma cfDNA copy number variations (CNVs) in a cohort of patients with colorectal cancer (CRC, n = 80), polyps (n = 20), and healthy controls (n = 35).
Li J, Dittmar RL, Xia S, Zhang H, Du M, Huang CC, Druliner BR, Boardman L, Wang L.   +8 more
europepmc   +4 more sources

Mitochondrial DNA copy number variation in asthma risk, severity, and exacerbations

Journal of Allergy and Clinical Immunology, 2023
AbstractRationaleAlthough airway oxidative stress and inflammation are central to asthma pathogenesis, there is limited knowledge of the relationship of asthma risk, severity, or exacerbations to mitochondrial dysfunction, which is pivotal to oxidant generation and inflammation.ObjectivesWe investigated whether mitochondrial DNA copy number (mtDNA-CN ...
Xu, Weiling, Hong, Yun Soo, Hu, Bo, Comhair, Suzy A. A., Janocha, Allison J., Zein, Joe G., Chen, Ruoying, Meyers, Deborah A., Mauger, David T., Ortega, Victor E., Bleecker, Eugene R., Castro, Mario, Denlinger, Loren C., Fahy, John V., Israel, Elliot, Levy, Bruce D., Jarjour, Nizar N., Moore, Wendy C., Wenzel, Sally E., Gaston, Benjamin, Liu, Chunyu, Arking, Dan E., Erzurum, Serpil C., National Heart, Lung, and Blood Institute (NHLBI) Severe Asthma Research Program (SARP) and TOPMed mtDNA Working Group in NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium   +23 more
openaire   +4 more sources

Identifying Copy Number Variants under Selection in Geographically Structured Populations Based on -statistics [PDF]

Genomics & Informatics, 2012
Large-scale copy number variants (CNVs) in the human provide the raw material for delineating population differences, as natural selection may have affected at least some of the CNVs thus far discovered.
Hae-Hiang Song, Hae-Jin Hu, In-Hae Seok, Yeun-Jun Chung   +3 more
doaj   +1 more source

A normalization technique for next generation sequencing experiments [PDF]

, 2010
Next generation sequencing (NGS) are these days one of the key technologies in biology. NGS' cost effectiveness and capability of finding the smallest variations in the genome makes them increasingly popular.
Andreas Mayr, Günter Klambauer, Günter Klambauer, Karin Schwarzbauer, Sepp Hochreiter   +4 more
core   +3 more sources

Identifying Copy Number Variations based on Next Generation Sequencing Data by a Mixture of Poisson Model [PDF]

, 2010
Next generation sequencing (NGS) technologies have profoundly impacted biological research and are becoming more and more popular due to cost effectiveness and their speed.
Andreas Mayr, Günter Klambauer, Karin Schwarzbauer, Karin Schwarzbauer, Sepp Hochreiter   +4 more
core   +2 more sources

Statistical issues in the analysis of DNA Copy Number Variations [PDF]

International Journal of Computational Biology and Drug Design, 2008
Approaches to assess copy number variation have advanced rapidly and are being incorporated into genetic studies. While the technology exists for CNV genotyping, a further understanding and discussion of how to use the CNV data for association analyses is warranted. We present the options available for processing and analysing CNV data.
Nathan E, Wineinger, Richard E, Kennedy, Stephen W, Erickson, Mary K, Wojczynski, Carl E, Bruder, Hemant K, Tiwari   +5 more
openaire   +2 more sources

Quantification of Plasmid Copy Number with Single Colour Droplet Digital PCR. [PDF]

PLoS ONE, 2017
Bacteria can be considered as biological nanofactories that manufacture a cornucopia of bioproducts most notably recombinant proteins. As such, they must perfectly match with appropriate plasmid vectors to ensure successful overexpression of target genes.
Magdalena Plotka, Mateusz Wozniak, Tadeusz Kaczorowski   +2 more
doaj   +1 more source

DNA copy number changes define spatial patterns of heterogeneity in colorectal cancer [PDF]

, 2017
Genetic heterogeneity between and within tumours is a major factor determining cancer progression and therapy response. Here we examined DNA sequence and DNA copy-number heterogeneity in colorectal cancer (CRC) by targeted high-depth sequencing of 100 ...
Aust, Daniela, Childs, Liam Harold, Heim, Daniel, Mamlouk, Soulafa, Melching, Friederike, Oliveira, Cristiano, Sers, Christine [u. v. m.]   +6 more
core   +1 more source