scholarly journals A new whole genome amplification method for studying clonal evolution patterns in malignant colorectal polyps

2012 ◽  
Vol 51 (5) ◽  
pp. 490-500 ◽  
Author(s):  
Daniela Hirsch ◽  
Jordi Camps ◽  
Sudhir Varma ◽  
Ralf Kemmerling ◽  
Mark Stapleton ◽  
...  
Keyword(s):  
Whole Genome Amplification ◽  
Clonal Evolution ◽  
Colorectal Polyps ◽  
Whole Genome ◽  
Genome Amplification ◽  
Amplification Method

scholarly journals Species Identification of Pinus Pollen Found in Belukha Glacier, Russian Altai Mountains, Using a Whole-Genome Amplification Method

Forests ◽  
2018 ◽  
Vol 9 (8) ◽  
pp. 444
Author(s):  
Fumio Nakazawa ◽  
Yoshihisa Suyama ◽  
Satoshi Imura ◽  
Hideaki Motoyama
Keyword(s):  
Species Identification ◽  
Whole Genome Amplification ◽  
Pollen Grains ◽  
Pollen Grain ◽  
Pinus Sibirica ◽  
Whole Genome ◽  
Accurate Identification ◽  
Closely Related Species ◽  
Genome Amplification ◽  
Amplification Method

Pollen taxa in sediment samples can be identified based on morphology. However, closely related species do not differ substantially in pollen morphology, and accurate identification is generally limited to genera or families. Because many pollen grains in glaciers contain protoplasm, genetic information obtained from pollen grains should enable the identification of plant taxa at the species level. In the present study, species identification of Pinus pollen grains was attempted using whole-genome amplification (WGA). We used pollen grains extracted from surface snow (depth, 1.8–1.9 m) from the Belukha glacier in the summer of 2003. WGA was performed using a single pollen grain. Some regions of the chloroplast genome were amplified by PCR, and the DNA products were sequenced to identify the pollen grain. Pinus includes approximately 111 recognized species in two subgenera, four sections, and 11 subsections. The tree species Pinus sibirica and P. sylvestris are currently found at the periphery of the glacier. We identified the pollen grains from the Belukha glacier to the level of section or subsection to which P. sibirica and P. sylvestris belong. Moreover, we specifically identified two pollen grains as P. sibirica or P. cembra. Fifteen species, including P. sibirica, were candidates for the remaining pollen grain.

scholarly journals Pushing the limits of whole genome amplification: Successful sequencing of RADseq libraries from single micro-hymenoptera (Chalcidoidea, Trichogramma)

2018 ◽  
Author(s):  
Astrid Cruaud ◽  
Géraldine Groussier ◽  
Guenaëlle Genson ◽  
Laure Sauné ◽  
Jean-Yves Rasplus
Keyword(s):  
High Throughput ◽  
Whole Genome Amplification ◽  
Multiple Displacement Amplification ◽  
Mendelian Inheritance ◽  
Whole Genome ◽  
Genome Amplification ◽  
Amplification Method ◽  
As Species ◽  
F1 Generation ◽  
Genomic Material

A major obstacle to high-throughput genotyping of micro-hymenoptera is their small size. As species are difficult to discriminate and because complexes may exist, the sequencing of a pool of specimens is hazardous. Thus, one should be able to sequence pangenomic markers (e.g. RADtags) from a single specimen. To date, whole genome amplification (WGA) prior to library construction is still a necessity as only ca 10ng of DNA can be obtained from single specimens. However this amount of DNA is not compatible with manufacturer’s requirements for commercialised kits. Here we tested the accuracy of the GenomiPhi kit V2 on Trichogramma wasps by comparing RAD libraries obtained from the WGA of single specimens (generation F0 and F1, ca 1 ng input DNA for the WGA) and a biological amplification of genomic material (the pool of the progeny of the F1 generation). Globally, we found that ca 99% of the examined loci (up to 48,189; 109 bp each) were compatible with the mode of reproduction of the studied model (haplodiploidy) or a Mendelian inheritance of alleles. The remaining 1% (ca 0.01% of the analysed nucleotides) could represent WGA bias or other experimental / analytical bias. This study shows that the multiple displacement amplification method on which the GenomiPhi kit relies, could also be of great help for the high-throughput genotyping of micro-hymenoptera used for biological control or other organisms from which only a very low amount of DNA can be extracted such as human disease vectors (e.g. sand flies, fleas, ticks etc.).

scholarly journals Pushing the limits of whole genome amplification: Successful sequencing of RADseq libraries from single micro-hymenoptera (Chalcidoidea, Trichogramma)

2018 ◽  
Author(s):  
Astrid Cruaud ◽  
Géraldine Groussier ◽  
Guenaëlle Genson ◽  
Laure Sauné ◽  
Jean-Yves Rasplus
Keyword(s):  
High Throughput ◽  
Whole Genome Amplification ◽  
Multiple Displacement Amplification ◽  
Mendelian Inheritance ◽  
Whole Genome ◽  
Genome Amplification ◽  
Amplification Method ◽  
As Species ◽  
F1 Generation ◽  
Genomic Material

A major obstacle to high-throughput genotyping of micro-hymenoptera is their small size. As species are difficult to discriminate and because complexes may exist, the sequencing of a pool of specimens is hazardous. Thus, one should be able to sequence pangenomic markers (e.g. RADtags) from a single specimen. To date, whole genome amplification (WGA) prior to library construction is still a necessity as only ca 10ng of DNA can be obtained from single specimens. However this amount of DNA is not compatible with manufacturer’s requirements for commercialised kits. Here we tested the accuracy of the GenomiPhi kit V2 on Trichogramma wasps by comparing RAD libraries obtained from the WGA of single specimens (generation F0 and F1, ca 1 ng input DNA for the WGA) and a biological amplification of genomic material (the pool of the progeny of the F1 generation). Globally, we found that ca 99% of the examined loci (up to 48,189; 109 bp each) were compatible with the mode of reproduction of the studied model (haplodiploidy) or a Mendelian inheritance of alleles. The remaining 1% (ca 0.01% of the analysed nucleotides) could represent WGA bias or other experimental / analytical bias. This study shows that the multiple displacement amplification method on which the GenomiPhi kit relies, could also be of great help for the high-throughput genotyping of micro-hymenoptera used for biological control or other organisms from which only a very low amount of DNA can be extracted such as human disease vectors (e.g. sand flies, fleas, ticks etc.).

A Whole Genome Amplification Method to Generate Long Fragments from Low Quantities of Genomic DNA

2002 ◽  
Vol 300 (2) ◽  
pp. 237-244 ◽  
Author(s):  
Ralf Kittler ◽  
Mark Stoneking ◽  
Manfred Kayser
Keyword(s):  
Genomic Dna ◽  
Whole Genome Amplification ◽  
Whole Genome ◽  
Genome Amplification ◽  
Amplification Method

scholarly journals Pushing the limits of whole genome amplification: successful sequencing of RADseq library from a single microhymenopteran (Chalcidoidea, Trichogramma)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5640 ◽  
Author(s):  
Astrid Cruaud ◽  
Géraldine Groussier ◽  
Guenaëlle Genson ◽  
Laure Sauné ◽  
Andrew Polaszek ◽  
...  
Keyword(s):  
High Throughput ◽  
Whole Genome Amplification ◽  
Multiple Displacement Amplification ◽  
Mendelian Inheritance ◽  
Whole Genome ◽  
Genome Amplification ◽  
Amplification Method ◽  
As Species ◽  
Commercial Kits ◽  
F1 Generation

A major obstacle to high-throughput genotyping of microhymenoptera is their small size. As species are difficult to discriminate, and because complexes may exist, the sequencing of a pool of specimens is hazardous. Thus, one should be able to sequence pangenomic markers (e.g., RADtags) from a single specimen. To date, whole genome amplification (WGA) prior to library construction is still a necessity as at most 10 ng of DNA can be obtained from single specimens (sometimes less). However, this amount of DNA is not compatible with manufacturer’s requirements for commercial kits. Here we test the accuracy of the GenomiPhi kit V2 on Trichogramma wasps by comparing RAD libraries obtained from the WGA of single specimens (F0 and F1 generation, about1 ng input DNA for the WGA (0.17–2.9 ng)) and a biological amplification of genomic material (the pool of the progeny of the F1 generation). Globally, we found that 99% of the examined loci (up to 48,189 for one of the crosses, 109 bp each) were compatible with the mode of reproduction of the studied model (haplodiploidy) and Mendelian inheritance of alleles. The remaining 1% (0.01% of the analysed nucleotides) could represent WGA bias or other experimental/analytical bias. This study shows that the multiple displacement amplification method on which the GenomiPhi kit relies, could also be of great help for the high-throughput genotyping of microhymenoptera used for biological control, or other organisms from which only a very small amount of DNA can be extracted, such as human disease vectors (e.g.,  sandflies, fleas, ticks etc.).

Evaluation of a whole-genome amplification method based on adaptor-ligation PCR of randomly sheared genomic DNA

2003 ◽  
Vol 38 (2) ◽  
pp. 168-176 ◽  
Author(s):  
Chikako Tanabe ◽  
Kazuhiko Aoyagi ◽  
Tokuki Sakiyama ◽  
Takashi Kohno ◽  
Noriko Yanagitani ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Whole Genome Amplification ◽  
Whole Genome ◽  
Genome Amplification ◽  
Amplification Method

A novel whole genome amplification method using type IIS restriction enzymes to create overhangs with random sequences

2014 ◽  
Vol 184 ◽  
pp. 1-6 ◽  
Author(s):  
Xiaoming Pan ◽  
Baihui Wan ◽  
Chunchuan Li ◽  
Yu Liu ◽  
Jing Wang ◽  
...  
Keyword(s):  
Whole Genome Amplification ◽  
Restriction Enzymes ◽  
Whole Genome ◽  
Genome Amplification ◽  
Random Sequences ◽  
Amplification Method
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