scholarly journals Laser capture microdissection (LCM) and whole genome amplification (WGA) of DNA from normal breast tissue --- optimization for genome wide array analyses

2011 ◽  
Vol 4 (1) ◽  
Author(s):  
Kristina E Aaltonen ◽  
Anna Ebbesson ◽  
Caroline Wigerup ◽  
Ingrid Hedenfalk
Keyword(s):  
Laser Capture Microdissection ◽  
Breast Tissue ◽  
Whole Genome Amplification ◽  
Normal Breast Tissue ◽  
Normal Breast ◽  
Whole Genome ◽  
Genome Amplification ◽  
Genome Wide ◽  
Laser Capture ◽  
Array Analyses

Genome-wide abundance of 5-hydroxymethylcytosine in breast tissue reveals unique function in dynamic gene regulation and carcinogenesis

2018 ◽  
Author(s):  
Owen M. Wilkins ◽  
Kevin C. Johnson ◽  
E. Andres Houseman ◽  
Jessica E. King ◽  
Carmen J. Marsit ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Breast Tissue ◽  
Cell Function ◽  
Immune Cell ◽  
Normal Breast Tissue ◽  
Wide Distribution ◽  
Normal Breast ◽  
Lactate Oxidation ◽  
Genome Wide ◽  
A Genome

Abstract5-hydroxymethylcytosine (5hmC) is generated by oxidation of 5-methylcytosine (5mC), however little is understood regarding the distribution and functions of 5hmC in mammalian cells. We determined the genome-wide distribution of 5hmC and 5mC in normal breast tissue from disease-free women. Although less abundant than 5mC, 5hmC is differentially distributed, and consistently enriched among breast-specific enhancers and transcriptionally active chromatin. In contrast, regulatory regions associated with transcriptional inactivity were relatively depleted of 5hmC. Gene regions containing abundant 5hmC were significantly associated with lactate oxidation, immune cell function, and prolactin signaling pathways. In independent data sets, normal breast tissue 5hmC was significantly enriched among CpG loci demonstrated to have altered methylation in pre-invasive breast cancer and invasive breast tumors. Our findings provide a genome-wide map of nucleotide-level 5hmC in normal breast tissue and demonstrate that 5hmC is positioned to contribute to gene regulatory functions which protect against carcinogenesis.

Genome-wide single-nucleotide polymorphism arrays demonstrate high fidelity of multiple displacement-based whole-genome amplification

2005 ◽  
Vol 26 (3) ◽  
pp. 710-715 ◽  
Author(s):  
Mladen V. Tzvetkov ◽  
Christian Becker ◽  
Bettina Kulle ◽  
Peter Nürnberg ◽  
Jürgen Brockmöller ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Whole Genome Amplification ◽  
High Fidelity ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Amplification ◽  
Genome Wide ◽  
Displacement Based

scholarly journals PD2-2-7: Two wrongs make a right: the use of whole genome amplification for pair-wise genome-wide copy number analysis of limited patient material

2007 ◽  
Vol 2 (8) ◽  
pp. S442-S443
Author(s):  
Trevor J. Pugh ◽  
Allen D. Delaney ◽  
Stephane Flibotte ◽  
Noushin Farnoud ◽  
Irene Li ◽  
...  
Keyword(s):  
Copy Number ◽  
Whole Genome Amplification ◽  
Whole Genome ◽  
Copy Number Analysis ◽  
Genome Amplification ◽  
Genome Wide

scholarly journals A streamlined workflow for single-cells genome-wide copy-number profiling by low-pass sequencing of LM-PCR whole-genome amplification products

PLoS ONE ◽  
2018 ◽  
Vol 13 (3) ◽  
pp. e0193689 ◽  
Author(s):  
Alberto Ferrarini ◽  
Claudio Forcato ◽  
Genny Buson ◽  
Paola Tononi ◽  
Valentina del Monaco ◽  
...  
Keyword(s):  
Copy Number ◽  
Whole Genome Amplification ◽  
Single Cells ◽  
Whole Genome ◽  
Genome Amplification ◽  
Genome Wide ◽  
Low Pass

scholarly journals Whole genome amplification and exome sequencing of archived schistosome miracidia

Parasitology ◽  
2018 ◽  
Vol 145 (13) ◽  
pp. 1739-1747 ◽  
Author(s):  
Winka Le Clec'h ◽  
Frédéric D. Chevalier ◽  
Marina McDew-White ◽  
Fiona Allan ◽  
Bonnie L. Webster ◽  
...  
Keyword(s):  
Whole Genome Amplification ◽  
Population Genomics ◽  
Exome Capture ◽  
Whole Genome ◽  
Genetic Studies ◽  
Genome Amplification ◽  
History Museum ◽  
Fta Cards ◽  
Genome Wide ◽  
Polymorphism Data

AbstractAdult schistosomes live in the blood vessels and cannot easily be sampled from humans, so archived miracidia larvae hatched from eggs expelled in feces or urine are commonly used for population genetic studies. Large collections of archived miracidia on FTA cards are now available through the Schistosomiasis Collection at the Natural History Museum (SCAN). Here we describe protocols for whole genome amplification of Schistosoma mansoni and Schistosome haematobium miracidia from these cards, as well as real time PCR quantification of amplified schistosome DNA. We used microgram quantities of DNA obtained for exome capture and sequencing of single miracidia, generating dense polymorphism data across the exome. These methods will facilitate the transition from population genetics, using limited numbers of markers to population genomics using genome-wide marker information, maximising the value of collections such as SCAN.

scholarly journals Genome-wide characterization of cytosine-specific 5-hydroxymethylation in normal breast tissue

Epigenetics ◽  
2019 ◽  
Vol 15 (4) ◽  
pp. 398-418 ◽  
Author(s):  
Owen M. Wilkins ◽  
Kevin C. Johnson ◽  
E. Andres Houseman ◽  
Jessica E. King ◽  
Carmen J. Marsit ◽  
...  
Keyword(s):  
Breast Tissue ◽  
Normal Breast Tissue ◽  
Normal Breast ◽  
Genome Wide

scholarly journals Accurate Genomic Variant Detection in Single Cells with Primary Template-Directed Amplification

2020 ◽  
Author(s):  
Veronica Gonzalez ◽  
Sivaraman Natarajan ◽  
Yuntao Xia ◽  
David Klein ◽  
Robert Carter ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Cell ◽  
Whole Genome Amplification ◽  
Single Cells ◽  
Variant Calling ◽  
Whole Genome ◽  
Genome Amplification ◽  
Genome Wide ◽  
Variant Detection ◽  
Genomic Variant

AbstractImprovements in whole genome amplification (WGA) would enable new types of basic and applied biomedical research, including studies of intratissue genetic diversity that require more accurate single-cell genotyping. Here we present primary template-directed amplification (PTA), a new isothermal WGA method that reproducibly captures >95% of the genomes of single cells in a more uniform and accurate manner than existing approaches, resulting in significantly improved variant calling sensitivity and precision. To illustrate the new types of studies that are enabled by PTA, we developed direct measurement of environmental mutagenicity (DMEM), a new tool for mapping genome-wide interactions of mutagens with single living human cells at base pair resolution. In addition, we utilized PTA for genome-wide off-target indel and structural variant detection in cells that had undergone CRISPR-mediated genome editing, establishing the feasibility for performing single-cell evaluations of biopsies from edited tissues. The improved precision and accuracy of variant detection with PTA overcomes the current limitations of accurate whole genome amplification, which is the major obstacle to studying genetic diversity and evolution at cellular resolution.

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