Clarification to: Evaluation of a whole-genome amplification method based on adaptor-ligation PCR of randomly sheared genomic DNA. Tanabe C, Aoyagi K, Sakiyama T, Kohno T, Yanagitani N, Akimoto S, Sakamoto M, Sakamoto H, Yokota J, Ohki M, Terada M, Yoshida T, Sasaki H. Genes Chromosomes Cancer 38(2):168-176; 2003.

2003 ◽  
Vol 39 (2) ◽  
pp. 170-170
Keyword(s):  
Genomic Dna ◽  
Whole Genome Amplification ◽  
Whole Genome ◽  
Genome Amplification ◽  
Amplification Method

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

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.

187 EMBRYO GENOTYPING FROM IN VIVO BIOPSIED BOVINE EMBRYOS AFTER WHOLE GENOME AMPLIFICATION

2009 ◽  
Vol 21 (1) ◽  
pp. 192 ◽  
Author(s):  
D. Le Bourhis ◽  
Y. Amigues ◽  
F. Charreaux ◽  
S. Lacaze ◽  
M. Tissier ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Detection Rate ◽  
Whole Genome Amplification ◽  
Field Conditions ◽  
Bovine Embryo ◽  
Whole Genome ◽  
Bovine Embryos ◽  
Genome Amplification ◽  
Number Of Cells

Genomic tools are now available for most livestock species and used routinely for marker-assisted selection (MAS) in cattle. The detection of a large number of markers that are widespread over the genome is generally limited by the amount of genomic DNA available in an embryo biopsy of a small size not to be detrimental to embryonic survival. Amplification of DNA from such a biopsy is then necessary. In this study, the efficiency of embryo genotyping for 45 microsatellites (MS) following whole-genome amplification (WGA) was evaluated from samples of a variable number of cells isolated from cattle embryos. In a second part, this work aims to test the reliability of the MAS method for 45 MS and 13 single nucleotide polymorphisms (SNP) from bovine embryo biopsies under field conditions. In experiment 1, in vitro bovine morulae (n = 10) were produced, and 1, 5, and 10 embryonic cells were removed from each morula. Cells were dry frozen in tubes before further processing. Whole-genome amplification was performed using the commercial Qiagen REPLI-g® Mini Kit according to the manufacturer instructions (Qiagen, Valencia, CA, USA). WGA solution was then diluted, processed by PCR with 45 markers, and the resulting data were genotyped with GeneMapper software® (Applied Biosystems Europe). Accuracy and reliability of genotyping were assessed using different samples of cells from the same embryo. In experiment 2, after superovulation (10 cows), bovine embryos were in vivo-produced and collected at day 6 or day 7 of pregnancy. Only grade 1 embryos were washed and biopsied using a microblade. Biopsied embryos were either frozen or transferred back to synchronized recipients. Individual biopsies were transferred as dry samples to the laboratory. Genomic DNA was amplified using WGA, and embryos were genotyped. The results of experiment 1 clearly indicate that a conventional biopsy of 5 to 10 cells was sufficient for multi-markers detection after whole-genome amplification as 98% of the 45 markers were detected compared to 45% of marker detection using 1 cell (P < 0.01). In experiment 2, from 123 collected embryos, 79 were classified as grade I or II transferable embryos (64.2%) and 57 were biopsied (34 were classified as stage 4–5 and 23 as stage 5–6, according to the IETS criteria). Using the stereomicroscopic analysis, 44 biopsies had a number of cells ranging from 4 to 7 (5.6 ± 1.4) and 13 biopsies from 8 to 10 (8.4 ± 1.6). Overall, at least 95% of markers (MS + SNP) were detected in 49.1% of biopsies (28/57). The total detection rate for SNP was significantly higher than for MS; 70.2% (40/57) v. 31.6% (18/57), respectively, (chi-square, P < 0.01). The detection rate of the markers was not significantly affected by the embryo stage or the biopsy size. Our results confirm that genotyping a large number of markers from biopsy samples after whole-genome amplification is possible under field conditions. A larger number of biopsies is required to assess the reliability of this method that may allow the development of MAS from early embryo. This work has been performed through the programme TYPAGENAE (GENANIMAL 4-03) with the financial support of FRT/ANR and Apis-Genes.

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.).

scholarly journals Whole-Genome Amplification by Adaptor-Ligation PCR of Randomly Sheared Genomic DNA (PRSG)

2008 ◽  
Vol 2008 (2) ◽  
pp. pdb.prot4922-pdb.prot4922 ◽  
Author(s):  
N. Arneson ◽  
S. Hughes ◽  
R. Houlston ◽  
S. Done
Keyword(s):  
Genomic Dna ◽  
Whole Genome Amplification ◽  
Whole Genome ◽  
Genome Amplification

Whole genome amplification of buccal cell DNA: genotyping concordance before and after multiple displacement amplification

2005 ◽  
Vol 43 (2) ◽  
Author(s):  
Miles D. Thompson ◽  
Raffick A. R. Bowen ◽  
Betty Y. L. Wong ◽  
Joan Antal ◽  
Zhanqin Liu ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Whole Genome Amplification ◽  
Multiple Displacement Amplification ◽  
Buccal Cell ◽  
Whole Genome ◽  
Buccal Cells ◽  
Genome Amplification ◽  
Dna Yield ◽  
Epidemiological Surveys ◽  
Before And After

AbstractWhile buccal cells provide an easily accessible source of genomic DNA, the amount extracted may be insufficient for many studies. Whole genome amplification (WGA) using multiple displacement amplification (MDA) may optimize buccal cell genomic DNA yield. We compared the usefulness, in epidemiological surveys, of DNA derived from buccal cells collected by alcohol mouthwash and amplified by WGA protocol and standard protocols. Buccal cell collection kits were mailed to 300 randomly selected members of a large cohort study, and 189 subjects returned buccal cell samples. We determined: (i) which QIAamp

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