scholarly journals Evaluation of genome coverage and fidelity of multiple displacement amplification from single cells by SNP array

2009 ◽  
Vol 15 (11) ◽  
pp. 739-747 ◽  
Author(s):  
J. Ling ◽  
G. Zhuang ◽  
B. Tazon-Vega ◽  
C. Zhang ◽  
B. Cao ◽  
...  
Keyword(s):  
Multiple Displacement Amplification ◽  
Single Cells ◽  
Snp Array ◽  
Genome Coverage

scholarly journals Development of Microbial Genome-Probing Microarrays using Digital Multiple Displacement Amplification of Uncultivated Microbial Single Cells

2008 ◽  
Vol 42 (22) ◽  
pp. 8614-8614
Author(s):  
Ho-Won Chang ◽  
Youboong Sung ◽  
Kyoung-Ho Kim ◽  
Young-Do Nam ◽  
Seong Woon Roh ◽  
...  
Keyword(s):  
Multiple Displacement Amplification ◽  
Single Cells ◽  
Microbial Genome

Reaction parameter comparison and optimization of multiple displacement amplification

2020 ◽  
Vol 12 (1) ◽  
pp. 46-53 ◽  
Author(s):  
Mengting Huang ◽  
Fang Yang ◽  
Jiye Fu ◽  
Pengfeng Xiao ◽  
Jing Tu ◽  
...  
Keyword(s):  
Multiple Displacement Amplification ◽  
Dna Denaturation ◽  
Reaction Parameter ◽  
Genome Coverage

After analysed MDA under different conditions, we found that different DNA denaturation methods before isothermal incubation can influence the amplification speed of MDA, and genome coverage uniformity was correlated with the amplification temperature.

scholarly journals SCELLECTOR: ranking amplification bias in single cells using shallow sequencing

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Vivekananda Sarangi ◽  
Alexandre Jourdon ◽  
Taejeong Bae ◽  
Arijit Panda ◽  
Flora Vaccarino ◽  
...  
Keyword(s):  
Single Cell ◽  
Multiple Displacement Amplification ◽  
Single Cells ◽  
Sequencing Data ◽  
High Coverage ◽  
Amplification Bias ◽  
Single Cell Profiling ◽  
High Concordance ◽  
Human Neuronal Cells

Abstract Background The study of mosaic mutation is important since it has been linked to cancer and various disorders. Single cell sequencing has become a powerful tool to study the genome of individual cells for the detection of mosaic mutations. The amount of DNA in a single cell needs to be amplified before sequencing and multiple displacement amplification (MDA) is widely used owing to its low error rate and long fragment length of amplified DNA. However, the phi29 polymerase used in MDA is sensitive to template fragmentation and presence of sites with DNA damage that can lead to biases such as allelic imbalance, uneven coverage and over representation of C to T mutations. It is therefore important to select cells with uniform amplification to decrease false positives and increase sensitivity for mosaic mutation detection. Results We propose a method, Scellector (single cell selector), which uses haplotype information to detect amplification quality in shallow coverage sequencing data. We tested Scellector on single human neuronal cells, obtained in vitro and amplified by MDA. Qualities were estimated from shallow sequencing with coverage as low as 0.3× per cell and then confirmed using 30× deep coverage sequencing. The high concordance between shallow and high coverage data validated the method. Conclusion Scellector can potentially be used to rank amplifications obtained from single cell platforms relying on a MDA-like amplification step, such as Chromium Single Cell profiling solution.

O▪28 Validating multiple displacement amplification for analysis of single cells

2005 ◽  
Vol 10 ◽  
pp. 10
Author(s):  
AR Thornhill ◽  
KV Schowalter ◽  
JR Fredrickson ◽  
DL Walker ◽  
SN Thibodeau
Keyword(s):  
Multiple Displacement Amplification ◽  
Single Cells

scholarly journals Genome sequencing and de novo assembly of the giant unicellular alga Acetabularia acetabulum using droplet MDA

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ina J. Andresen ◽  
Russell J. S. Orr ◽  
Anders K. Krabberød ◽  
Kamran Shalchian-Tabrizi ◽  
Jon Bråte
Keyword(s):  
Genome Sequencing ◽  
Cell Biology ◽  
De Novo ◽  
Multiple Displacement Amplification ◽  
Single Cells ◽  
Model System ◽  
Genomic Information ◽  
Unicellular Alga ◽  
Acetabularia Acetabulum ◽  
Genomic Material

AbstractThe macroscopic single-celled green alga Acetabularia acetabulum has been a model system in cell biology for more than a century. However, no genomic information is available from this species. Since the alga has a long life cycle, is difficult to grow in dense cultures, and has an estimated diploid genome size of almost 2 Gb, obtaining sufficient genomic material for genome sequencing is challenging. Here, we have attempted to overcome these challenges by amplifying genomic DNA using multiple displacement amplification (MDA) combined with microfluidics technology to distribute the amplification reactions across thousands of microscopic droplets. By amplifying and sequencing DNA from five single cells we were able to recover an estimated ~ 7–11% of the total genome, providing the first draft of the A. acetabulum genome. We highlight challenges associated with genome recovery and assembly of MDA data due to biases arising during genome amplification, and hope that our study can serve as a reference for future attempts on sequencing the genome from non-model eukaryotes.

Towards the analysis of the genomes of single cells: Further characterisation of the multiple displacement amplification

Gene ◽  
2006 ◽  
Vol 372 ◽  
pp. 1-7 ◽  
Author(s):  
Simona Panelli ◽  
Giuseppe Damiani ◽  
Luca Espen ◽  
Gioacchino Micheli ◽  
Vittorio Sgaramella
Keyword(s):  
Multiple Displacement Amplification ◽  
Single Cells

Development of Microbial Genome-Probing Microarrays Using Digital Multiple Displacement Amplification of Uncultivated Microbial Single Cells

2008 ◽  
Vol 42 (16) ◽  
pp. 6058-6064 ◽  
Author(s):  
Ho-Won Chang ◽  
Youlboong Sung ◽  
Kyoung-Ho Kim ◽  
Young-Do Nam ◽  
Seong Woon Roh ◽  
...  
Keyword(s):  
Multiple Displacement Amplification ◽  
Single Cells ◽  
Microbial Genome

scholarly journals Development of a maize 55 K SNP array with improved genome coverage for molecular breeding

2017 ◽  
Vol 37 (3) ◽  
Author(s):  
Cheng Xu ◽  
Yonghong Ren ◽  
Yinqiao Jian ◽  
Zifeng Guo ◽  
Yan Zhang ◽  
...  
Keyword(s):  
Molecular Breeding ◽  
Snp Array ◽  
Genome Coverage

scholarly journals Comparison of seven single cell Whole Genome Amplification commercial kits using targeted sequencing

2017 ◽  
Author(s):  
Tamir Biezuner ◽  
Ofir Raz ◽  
Shiran Amir ◽  
Lilach Milo ◽  
Rivka Adar ◽  
...  
Keyword(s):  
Single Cell ◽  
Whole Genome Amplification ◽  
Single Cells ◽  
Targeted Sequencing ◽  
Whole Genome ◽  
Genome Coverage ◽  
Genome Amplification ◽  
Cell Experiment ◽  
Commercial Kits ◽  
Genomic Regions

AbstractAdvances in biochemical technologies have led to a boost in the field of single cell genomics. Observation of the genome at a single cell resolution is currently achieved by pre-amplification using whole genome amplification (WGA) techniques that differ by their biochemical aspects and as a result by biased amplification of the original molecule. Several comparisons between commercially available single cell dedicated WGA kits (scWGA) were performed, however, these comparisons are costly, were only performed on selected scWGA kit and more notably, are limited by the number of analyzed cells, making them limited for reproducibility analysis. We benchmarked an economical assay to compare all commercially available scWGA kits that is based on targeted sequencing of thousands of genomic regions, including highly mutable genomic regions (microsatellites), from a large cohort of human single cells (125 cells in total). Using this approach, we could analyze the genome coverage, the reproducibility of genome coverage and the error rate of each kit. Our experimental design provides an affordable and reliable comparative assay that simulates a real single cell experiment. Results demonstrate the needfor a dedicated kit selection depending on the desired single cell assay.

scholarly journals Environmental Whole-Genome Amplification To Access Microbial Populations in Contaminated Sediments

2006 ◽  
Vol 72 (5) ◽  
pp. 3291-3301 ◽  
Author(s):  
Carl B. Abulencia ◽  
Denise L. Wyborski ◽  
Joseph A. Garcia ◽  
Mircea Podar ◽  
Wenqiong Chen ◽  
...  
Keyword(s):  
Contaminated Soils ◽  
Whole Genome Amplification ◽  
Multiple Displacement Amplification ◽  
Department Of Energy ◽  
Contaminated Site ◽  
Small Subset ◽  
Whole Genome ◽  
Genome Coverage ◽  
Genome Amplification ◽  
Amplification Bias

ABSTRACT Low-biomass samples from nitrate and heavy metal contaminated soils yield DNA amounts that have limited use for direct, native analysis and screening. Multiple displacement amplification (MDA) using φ29 DNA polymerase was used to amplify whole genomes from environmental, contaminated, subsurface sediments. By first amplifying the genomic DNA (gDNA), biodiversity analysis and gDNA library construction of microbes found in contaminated soils were made possible. The MDA method was validated by analyzing amplified genome coverage from approximately five Escherichia coli cells, resulting in 99.2% genome coverage. The method was further validated by confirming overall representative species coverage and also an amplification bias when amplifying from a mix of eight known bacterial strains. We extracted DNA from samples with extremely low cell densities from a U.S. Department of Energy contaminated site. After amplification, small-subunit rRNA analysis revealed relatively even distribution of species across several major phyla. Clone libraries were constructed from the amplified gDNA, and a small subset of clones was used for shotgun sequencing. BLAST analysis of the library clone sequences showed that 64.9% of the sequences had significant similarities to known proteins, and “clusters of orthologous groups” (COG) analysis revealed that more than half of the sequences from each library contained sequence similarity to known proteins. The libraries can be readily screened for native genes or any target of interest. Whole-genome amplification of metagenomic DNA from very minute microbial sources, while introducing an amplification bias, will allow access to genomic information that was not previously accessible.

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