scholarly journals REPLI-g Pooled DNA

2020 ◽  
Author(s):  
Keyword(s):  
Pooled Dna

scholarly journals Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 16 ◽  
Author(s):  
Michael P Mullen ◽  
Christopher J Creevey ◽  
Donagh P Berry ◽  
Matt S McCabe ◽  
David A Magee ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Allele Frequency ◽  
High Throughput ◽  
Frequency Estimation ◽  
Allele Frequency Estimation ◽  
Polymorphism Discovery ◽  
Pooled Dna ◽  
High Throughput Dna Sequencing

Detectability vs. time and costs in pooled DNA extraction of cutaneous swabs: a study on the amphibian chytrid fungi

2019 ◽  
Vol 40 (1) ◽  
pp. 29-39 ◽  
Author(s):  
Joana Sabino-Pinto ◽  
E. Tobias Krause ◽  
Molly C. Bletz ◽  
An Martel ◽  
Frank Pasmans ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Pathogen Detection ◽  
Batrachochytrium Dendrobatidis ◽  
Quantitative Polymerase Chain Reaction ◽  
Large Fraction ◽  
Work Load ◽  
Detection Sensitivity ◽  
Pooled Dna ◽  
Reaction Volumes ◽  
User Friendly

Abstract Epidemiology relies on understanding the distribution of pathogens which often can be detected through DNA-based techniques, such as quantitative Polymerase Chain Reaction (qPCR). Typically, the DNA of each individual sample is separately extracted and undergoes qPCR analysis. However, when performing field surveys and long-term monitoring, a large fraction of the samples is generally expected to be negative, especially in geographical areas still considered free of the pathogen. If pathogen detection within a population – rather than determining its individual prevalence – is the focus, work load and monetary costs can be reduced by pooling samples for DNA extraction. We test and refine a user-friendly technique where skin swabs can be pooled during DNA extraction to detect the amphibian chytrid fungi, Batrachochytrium dendrobatidis and B. salamandrivorans (Bsal). We extracted pools with different numbers of samples (from one to four swabs), without increasing reaction volumes, and each pool had one sample inoculated with a predetermined zoospore amount. Pool size did not reduce the ability to detect the two fungi, except if inoculated with extremely low zoospore amounts (one zoospore). We confirm that pooled DNA extraction of cutaneous swabs can substantially reduce processing time and costs without minimizing detection sensitivity. This is of relevance especially for the new emerging pathogen Bsal, for which pooled DNA extraction had so far not been tested and massive monitoring efforts in putatively unaffected regions are underway.

scholarly journals Pooled-DNA sequencing identifies genomic regions of selection in Nigerian isolates of Plasmodium falciparum

2017 ◽  
Vol 10 (1) ◽  
Author(s):  
Kolapo M. Oyebola ◽  
Emmanuel T. Idowu ◽  
Yetunde A. Olukosi ◽  
Taiwo S. Awolola ◽  
Alfred Amambua-Ngwa
Keyword(s):  
Plasmodium Falciparum ◽  
Dna Sequencing ◽  
Pooled Dna ◽  
Genomic Regions

scholarly journals Mapping of transgenic alleles in soybean using a nanopore-based sequencing strategy

2019 ◽  
Vol 70 (15) ◽  
pp. 3825-3833 ◽  
Author(s):  
Shengjun Li ◽  
Shangang Jia ◽  
Lili Hou ◽  
Hanh Nguyen ◽  
Shirley Sato ◽  
...  
Keyword(s):  
High Throughput ◽  
Soybean Genome ◽  
Transgenic Technology ◽  
Transgenic Soybean ◽  
Pooled Dna ◽  
Sequencing Strategy ◽  
Ds Element ◽  
Soybean Plants ◽  
Cost Efficient ◽  
Transgene Insertion

Abstract Transgenic technology was developed to introduce transgenes into various organisms to validate gene function and add genetic variations >40 years ago. However, the identification of the transgene insertion position is still challenging in organisms with complex genomes. Here, we report a nanopore-based method to map the insertion position of a Ds transposable element originating in maize in the soybean genome. In this method, an oligo probe is used to capture the DNA fragments containing the Ds element from pooled DNA samples of transgenic soybean plants. The Ds element-enriched DNAs are then sequenced using the MinION-based platform of Nanopore. This method allowed us to rapidly map the Ds insertion positions in 51 transgenic soybean lines through a single sequencing run. This strategy is high throughput, convenient, reliable, and cost-efficient. The transgenic allele mapping protocol can be easily translated to other eukaryotes with complex genomes.

scholarly journals 326 Comparison of Genomic Relationship Matrices Using Differing Number of SNP in Pooled DNA Analyses.

2018 ◽  
Vol 96 (suppl_3) ◽  
pp. 124-124
Author(s):  
R Boldt ◽  
J Keele ◽  
L Kuehn ◽  
T McDaneld ◽  
T Smith ◽  
...  
Keyword(s):  
Genomic Relationship ◽  
Dna Analyses ◽  
Pooled Dna

Association screen for atopic dermatitis candidate gene regions using microsatellite markers in pooled DNA samples

2006 ◽  
Vol 33 (6) ◽  
pp. 401-409 ◽  
Author(s):  
S. Hoffjan ◽  
Q. Parwez ◽  
E. Petrasch-Parwez ◽  
D. Falkenstein ◽  
M. Nothnagel ◽  
...  
Keyword(s):  
Atopic Dermatitis ◽  
Microsatellite Markers ◽  
Candidate Gene ◽  
Pooled Dna

Screening for candidate gene regions in narcolepsy using a microsatellite based approach and pooled DNA

2004 ◽  
Vol 82 (10) ◽  
pp. 696-705 ◽  
Author(s):  
Stefan Wieczorek ◽  
Peter Jagiello ◽  
Larissa Arning ◽  
Norbert Dahmen ◽  
Joerg T. Epplen
Keyword(s):  
Candidate Gene ◽  
Pooled Dna
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