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Journal articles on the topic 'Whole genome amplification'

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Author: Grafiati

Published: 4 June 2021

Last updated: 9 March 2023

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1

Arneson, N., S. Hughes, R. Houlston, and S. Done. "GenomePlex Whole-Genome Amplification." Cold Spring Harbor Protocols 2008, no. 2 (January 1, 2008): pdb.prot4920. http://dx.doi.org/10.1101/pdb.prot4920.

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2

Li, Ying, Hyun-Jin Kim, Chunyang Zheng, Wing Huen A. Chow, Jeonghwa Lim, Brendan Keenan, Xiaojing Pan, Bertrand Lemieux, and Huimin Kong. "Primase-based whole genome amplification." Nucleic Acids Research 36, no. 13 (June 17, 2008): e79-e79. http://dx.doi.org/10.1093/nar/gkn377.

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3

Seong, Ji-Yeong, Young-Jun Ko, Hyeon-Koon Myeong, and Se-Wook Oh. "Development of a Rapid Foodborne-pathogen-detection Method Involving Whole-genome Amplification." Korean Journal of Food Science and Technology 48, no. 2 (April 30, 2016): 128–32. http://dx.doi.org/10.9721/kjfst.2016.48.2.128.

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4

Sun, Fengzhu, and Michael S. Waterman. "Whole Genome Amplification and Branching Processes." Advances in Applied Probability 29, no. 3 (September 1997): 629–68. http://dx.doi.org/10.2307/1428080.

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Whole genome amplification is important for multipoint mapping by sperm or oocyte typing and genetic disease diagnosis. Polymerase chain reaction is not suitable for amplifying long DNA sequences. This paper studies a new technique, designated PEP-primer-extension-preamplification, for amplifying long DNA sequences using the theory of branching processes. A mathematical model for PEP is constructed and a closed formula for the expected target yield is obtained. A central limit theorem and a strong law of large numbers for the number of kth generation target sequences are proved.

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5

Höckner, M., M. Erdel, A. Spreiz, G. Utermann, and D. Kotzot. "Whole Genome Amplification from Microdissected Chromosomes." Cytogenetic and Genome Research 125, no. 2 (2009): 98–102. http://dx.doi.org/10.1159/000227832.

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6

Hawkins, Trevor L., John C. Detter, and Paul M. Richardson. "Whole genome amplification — applications and advances." Current Opinion in Biotechnology 13, no. 1 (February 2002): 65–67. http://dx.doi.org/10.1016/s0958-1669(02)00286-0.

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7

Sun, Fengzhu, and Michael S. Waterman. "Whole Genome Amplification and Branching Processes." Advances in Applied Probability 29, no. 03 (September 1997): 629–68. http://dx.doi.org/10.1017/s0001867800028287.

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Whole genome amplification is important for multipoint mapping by sperm or oocyte typing and genetic disease diagnosis. Polymerase chain reaction is not suitable for amplifying long DNA sequences. This paper studies a new technique, designated PEP-primer-extension-preamplification, for amplifying long DNA sequences using the theory of branching processes. A mathematical model for PEP is constructed and a closed formula for the expected target yield is obtained. A central limit theorem and a strong law of large numbers for the number of kth generation target sequences are proved.

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8

Bassaganyas, Laia, George Freedman, Dedeepya Vaka, Eunice Wan, Richard Lao, Flavia Chen, Mark Kvale, Robert J. Currier, Jennifer M. Puck, and Pui-Yan Kwok. "Whole exome and whole genome sequencing with dried blood spot DNA without whole genome amplification." Human Mutation 39, no. 1 (November 6, 2017): 167–71. http://dx.doi.org/10.1002/humu.23356.

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9

Zheng, Ying-ming, Ning Wang, Lei Li, and Fan Jin. "Whole genome amplification in preimplantation genetic diagnosis." Journal of Zhejiang University SCIENCE B 12, no. 1 (January 2011): 1–11. http://dx.doi.org/10.1631/jzus.b1000196.

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10

Burtt, N. P. "Whole-Genome Amplification Using 29 DNA Polymerase." Cold Spring Harbor Protocols 2011, no. 1 (January 1, 2011): pdb.prot5552. http://dx.doi.org/10.1101/pdb.prot5552.

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11

Garcia-Chapa, Meritxell, Assumpció Batlle, Djaouida Rekab, Michel Ruiz Rosquete, and Giuseppe Firrao. "PCR-mediated whole genome amplification of phytoplasmas." Journal of Microbiological Methods 56, no. 2 (February 2004): 231–42. http://dx.doi.org/10.1016/j.mimet.2003.10.010.

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12

Lao, Kaiqin, Nan Lan Xu, and Neil A. Straus. "Whole genome amplification using single-primer PCR." Biotechnology Journal 3, no. 3 (March 2008): 378–82. http://dx.doi.org/10.1002/biot.200700253.

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13

Tu, Jing, Yi Qiao, Yuhan Luo, Naiyun Long, and Zuhong Lu. "Quantifying genome DNA during whole-genome amplification via quantitative real-time multiple displacement amplification." RSC Advances 11, no. 8 (2021): 4617–21. http://dx.doi.org/10.1039/d0ra09021b.

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14

Sujayanont, Patcharawan, Kwanrutai Chininmanu, Boonrat Tassaneetrithep, Nattaya Tangthawornchaikul, Prida Malasit, and Prapat Suriyaphol. "Comparison of phi29-based whole genome amplification and whole transcriptome amplification in dengue virus." Journal of Virological Methods 195 (January 2014): 141–47. http://dx.doi.org/10.1016/j.jviromet.2013.10.005.

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15

Tay, Andy, Rajan P. Kulkarni, Armin Karimi, and Dino Di Carlo. "Research highlights: enhancing whole genome amplification using compartmentalization." Lab on a Chip 15, no. 23 (2015): 4379–82. http://dx.doi.org/10.1039/c5lc90117k.

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16

Raz, Ofir, Liming Tao, Tamir Biezuner, Tzipy Marx, Yaara Neumeier, Narek Tumanyan, and Ehud Shapiro. "Whole-Genome Amplification—Surveying Yield, Reproducibility, and Heterozygous Balance, Reported by STR-Targeting MIPs." International Journal of Molecular Sciences 23, no. 11 (May 31, 2022): 6161. http://dx.doi.org/10.3390/ijms23116161.

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Whole-genome amplification is a crucial first step in nearly all single-cell genomic analyses, with the following steps focused on its products. Bias and variance caused by the whole-genome amplification process add numerous challenges to the world of single-cell genomics. Short tandem repeats are sensitive genomic markers used widely in population genetics, forensics, and retrospective lineage tracing. A previous evaluation of common whole-genome amplification targeting ~1000 non-autosomal short tandem repeat loci is extended here to ~12,000 loci across the entire genome via duplex molecular inversion probes. Other than its improved scale and reduced noise, this system detects an abundance of heterogeneous short tandem repeat loci, allowing the allelic balance to be reported. We show here that while the best overall yield is obtained using RepliG-SC, the maximum uniformity between alleles and reproducibility across cells are maximized by Ampli1, rendering it the best candidate for the comparative heterozygous analysis of single-cell genomes.

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17

Nyaku, S. T., V. R. Sripathi, K. Lawrence, and G. Sharma. "Characterizing Repeats in Two Whole-Genome Amplification Methods in the Reniform Nematode Genome." International Journal of Genomics 2021 (March 6, 2021): 1–8. http://dx.doi.org/10.1155/2021/5532885.

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One of the major problems in the U.S. and global cotton production is the damage caused by the reniform nematode, Rotylenchulus reniformis. Amplification of DNA from single nematodes for further molecular analysis can be challenging sometimes. In this research, two whole-genome amplification (WGA) methods were evaluated for their efficiencies in DNA amplification from a single reniform nematode. The WGA was carried out using both REPLI-g Mini and Midi kits, and the GenomePlex single cell whole-genome amplification kit. Sequence analysis produced 4 Mb and 12 Mb of genomic sequences for the reniform nematode using REPLI-g and SIGMA libraries. These sequences were assembled into 28,784 and 24,508 contigs, respectively, for REPLI-g and SIGMA libraries. The highest repeats in both libraries were of low complexity, and the lowest for the REPLI-g library were for satellites and for the SIGMA library, RTE/BOV-B. The same kind of repeats were observed for both libraries; however, the SIGMA library had four other repeat elements (Penelope (long interspersed nucleotide element (LINE)), RTE/BOV-B (LINE), PiggyBac, and Mirage/P-element/Transib), which were not seen in the REPLI-g library. DNA transposons were also found in both libraries. Both reniform nematode 18S rRNA variants (RN_VAR1 and RN_VAR2) could easily be identified in both libraries. This research has therefore demonstrated the ability of using both WGA methods, in amplification of gDNA isolated from single reniform nematodes.

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18

Karere, Genesio M., Leslie A. Lyons, and Lutz Froenicke. "Enhancing radiation hybrid mapping through whole genome amplification." Hereditas 147, no. 2 (May 4, 2010): 103–12. http://dx.doi.org/10.1111/j.1601-5223.2010.02166.x.

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19

Hosono, S. "Unbiased Whole-Genome Amplification Directly From Clinical Samples." Genome Research 13, no. 5 (April 14, 2003): 954–64. http://dx.doi.org/10.1101/gr.816903.

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20

Kaper, F., S. Swamy, B. Klotzle, S. Munchel, J. Cottrell, M. Bibikova, H. Y. Chuang, et al. "Whole-genome haplotyping by dilution, amplification, and sequencing." Proceedings of the National Academy of Sciences 110, no. 14 (March 18, 2013): 5552–57. http://dx.doi.org/10.1073/pnas.1218696110.

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21

Lack, Justin B., Lawrence J. Weider, and Punidan D. Jeyasingh. "Whole genome amplification and sequencing of aDaphniaresting egg." Molecular Ecology Resources 18, no. 1 (October 14, 2017): 118–27. http://dx.doi.org/10.1111/1755-0998.12720.

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22

Kwok, Pui-Yan. "Making ‘random amplification’ predictable in whole genome analysis." Trends in Biotechnology 20, no. 10 (October 2002): 411–12. http://dx.doi.org/10.1016/s0167-7799(02)02034-6.

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23

Keller, Martin. "Whole genome amplification: watch out for the bias!" Environmental Microbiology 16, no. 3 (March 2014): 611. http://dx.doi.org/10.1111/1462-2920.12401.

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24

Spits, Claudia, Cédric Le Caignec, Martine De Rycke, Lindsey Van Haute, André Van Steirteghem, Inge Liebaers, and Karen Sermon. "Whole-genome multiple displacement amplification from single cells." Nature Protocols 1, no. 4 (November 2006): 1965–70. http://dx.doi.org/10.1038/nprot.2006.326.

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25

Chen, Lin, Andreas Manz, and Philip J. R. Day. "Whole genome amplification on poly(dimethylsiloxane) microchip array." Analytical Biochemistry 372, no. 1 (January 2008): 128–30. http://dx.doi.org/10.1016/j.ab.2007.07.036.

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26

Balogh, M. K., C. Børsting, P. Sánchez Diz, C. Thacker, D. Syndercombe-Court, A. Carracedo, N. Morling, and P. M. Schneider. "Application of whole genome amplification for forensic analysis." International Congress Series 1288 (April 2006): 725–27. http://dx.doi.org/10.1016/j.ics.2005.12.017.

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27

Abulencia, Carl B., Denise L. Wyborski, Joseph A. Garcia, Mircea Podar, Wenqiong Chen, Sherman H. Chang, Hwai W. Chang, et al. "Environmental Whole-Genome Amplification To Access Microbial Populations in Contaminated Sediments." Applied and Environmental Microbiology 72, no. 5 (May 2006): 3291–301. http://dx.doi.org/10.1128/aem.72.5.3291-3301.2006.

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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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28

Liu, C. L., B. E. Bernstein, and S. L. Schreiber. "Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): Overview." Cold Spring Harbor Protocols 2008, no. 6 (May 1, 2008): pdb.top42. http://dx.doi.org/10.1101/pdb.top42.

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29

Foster, Simon J., and Brendon J. Monahan. "Whole genome amplification from filamentous fungi using Phi29-mediated multiple displacement amplification." Fungal Genetics and Biology 42, no. 5 (May 2005): 367–75. http://dx.doi.org/10.1016/j.fgb.2005.01.013.

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30

Shortt, Jonathan A., Daren C. Card, Drew R. Schield, Yang Liu, Bo Zhong, Todd A. Castoe, Elizabeth J. Carlton, and David D. Pollock. "Whole Genome Amplification and Reduced-Representation Genome Sequencing of Schistosoma japonicum Miracidia." PLOS Neglected Tropical Diseases 11, no. 1 (January 20, 2017): e0005292. http://dx.doi.org/10.1371/journal.pntd.0005292.

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31

Kwon, Young M., and Mandy M. Cox. "Improved efficacy of whole genome amplification from bacterial cells." BioTechniques 37, no. 1 (July 2004): 40–44. http://dx.doi.org/10.2144/04371bm03.

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32

Hall, Eric, Samuel Kim, Visham Appadoo, and Richard Zare. "Lysis of a Single Cyanobacterium for Whole Genome Amplification." Micromachines 4, no. 3 (August 21, 2013): 321–32. http://dx.doi.org/10.3390/mi4030321.

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33

Lepere, Cécile, Mikihide Demura, Masanobu Kawachi, Sarah Romac, Ian Probert, and Daniel Vaulot. "Whole-genome amplification (WGA) of marine photosynthetic eukaryote populations." FEMS Microbiology Ecology 76, no. 3 (March 16, 2011): 513–23. http://dx.doi.org/10.1111/j.1574-6941.2011.01072.x.

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34

Brooks, R., R. J. Rose, M. B. Sheahan, and S. Kurdyukov. "Whole genome methylation scanning based on phi29 polymerase amplification." Biochemistry (Moscow) 76, no. 9 (September 2011): 999–1002. http://dx.doi.org/10.1134/s0006297911090021.

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35

Sun, Guangyun, Ritesh Kaushal, Prodipto Pal, Michael Wolujewicz, Diane Smelser, Hong Cheng, Mei Lu, Ranajit Chakraborty, Li Jin, and Ranjan Deka. "Whole-genome amplification: relative efficiencies of the current methods." Legal Medicine 7, no. 5 (October 2005): 279–86. http://dx.doi.org/10.1016/j.legalmed.2005.05.001.

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36

Yu, Zhilong, Sijia Lu, and Yanyi Huang. "Microfluidic Whole Genome Amplification Device for Single Cell Sequencing." Analytical Chemistry 86, no. 19 (September 22, 2014): 9386–90. http://dx.doi.org/10.1021/ac5032176.

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37

Bergen, A. W. "Effects of Electron-Beam Irradiation on Whole Genome Amplification." Cancer Epidemiology Biomarkers & Prevention 14, no. 4 (April 1, 2005): 1016–19. http://dx.doi.org/10.1158/1055-9965.epi-04-0686.

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38

Fu, Yusi, Chunmei Li, Sijia Lu, Wenxiong Zhou, Fuchou Tang, X. Sunney Xie, and Yanyi Huang. "Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification." Proceedings of the National Academy of Sciences 112, no. 38 (September 4, 2015): 11923–28. http://dx.doi.org/10.1073/pnas.1513988112.

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Whole-genome amplification (WGA) for next-generation sequencing has seen wide applications in biology and medicine when characterization of the genome of a single cell is required. High uniformity and fidelity of WGA is needed to accurately determine genomic variations, such as copy number variations (CNVs) and single-nucleotide variations (SNVs). Prevailing WGA methods have been limited by fluctuation of the amplification yield along the genome, as well as false-positive and -negative errors for SNV identification. Here, we report emulsion WGA (eWGA) to overcome these problems. We divide single-cell genomic DNA into a large number (105) of picoliter aqueous droplets in oil. Containing only a few DNA fragments, each droplet is led to reach saturation of DNA amplification before demulsification such that the differences in amplification gain among the fragments are minimized. We demonstrate the proof-of-principle of eWGA with multiple displacement amplification (MDA), a popular WGA method. This easy-to-operate approach enables simultaneous detection of CNVs and SNVs in an individual human cell, exhibiting significantly improved amplification evenness and accuracy.

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39

Buffart, Tineke E., Marianne Tijssen, Thijs Krugers, Beatriz Carvalho, Serge J. Smeets, Ruud H. Brakenhoff, Heike Grabsch, Gerrit A. Meijer, Henry B. Sadowski, and Bauke Ylstra. "DNA Quality Assessment for Array CGH by Isothermal Whole Genome Amplification." Analytical Cellular Pathology 29, no. 4 (January 1, 2007): 351–59. http://dx.doi.org/10.1155/2007/709290.

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Background: Array Comparative Genomic Hybridization (array CGH) is increasingly applied on DNA obtained from formalin-fixed paraffin-embedded (FFPE) tissue, but in a proportion of cases this type of DNA is unsuitable. Due to the high experimental costs of array CGH and unreliable methods for DNA quality testing, better prediction methods are needed. The aim of this study was to accurately determine the quality of FFPE DNA input in order to predict quality of array CGH outcome. Material and Methods: DNA quality was assessed by isothermal amplification and compared to array CGH quality on 59 FFPE gastric cancer samples, one FFPE colorectal cancer sample, two FFPE normal uvula samples, one fresh frozen and six FFPE HNSCC samples. Gastric cancer DNA was also quality tested by β-globin PCR. Results: Accurate prediction of DNA quality using the isothermal amplification was observed in the colorectal carcinoma, HNSCC and uvula samples. In gastric cancer samples, the isothermal amplification was a more accurate method for selecting good quality DNA for array CGH compared to using PCR product lengths. The isothermal amplification product was used for array CGH and compared to the results achieved using non-amplified DNA in four of the samples. DNAs before and after amplification yielded the same segmentation patterns of chromosomal copy number changes for both the fresh DNA sample and the FFPE samples. Conclusion: The efficiency of isothermal DNA amplification is a reliable predictor for array CGH quality. The amplification product itself can be used for array CGH, even starting with FFPE derived DNA samples.

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40

Bourrier, Chantal, Jean-Yves Pierga, Laura Xuereb, Hélène Salaun, Charlotte Proudhon, Michael R. Speicher, Jelena Belic, Ellen Heitzer, Brian Paul Lockhart, and Nolwen Guigal-Stephan. "Shallow Whole-Genome Sequencing from Plasma Identifies FGFR1 Amplified Breast Cancers and Predicts Overall Survival." Cancers 12, no. 6 (June 6, 2020): 1481. http://dx.doi.org/10.3390/cancers12061481.

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Background: Focal amplification of fibroblast growth factor receptor 1 (FGFR1) defines a subgroup of breast cancers with poor prognosis and high risk of recurrence. We sought to demonstrate the potential of circulating cell-free DNA (cfDNA) analysis to evaluate FGFR1 copy numbers from a cohort of 100 metastatic breast cancer (mBC) patients. Methods: Formalin-fixed paraffin-embedded (FFPE) tissue samples were screened for FGFR1 amplification by FISH, and positive cases were confirmed with a microarray platform (OncoscanTM). Subsequently, cfDNA was evaluated by two approaches, i.e., mFAST-SeqS and shallow whole-genome sequencing (sWGS), to estimate the circulating tumor DNA (ctDNA) allele fraction (AF) and to evaluate the FGFR1 status. Results: Tissue-based analyses identified FGFR1 amplifications in 20/100 tumors. All cases with a ctDNA AF above 3% (n = 12) showed concordance for FGFR1 status between tissue and cfDNA. In one case, we were able to detect a high-level FGFR1 amplification, although the ctDNA AF was below 1%. Furthermore, high levels of ctDNA indicated an association with unfavorable prognosis based on overall survival. Conclusions: Screening for FGFR1 amplification in ctDNA might represent a viable strategy to identify patients eligible for treatment by FGFR inhibition, and mBC ctDNA levels might be used for the evaluation of prognosis in clinical drug trials.

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41

Wang, Jian, Joy D. Van Nostrand, Liyou Wu, Zhili He, Guanghe Li, and Jizhong Zhou. "Microarray-Based Evaluation of Whole-Community Genome DNA Amplification Methods." Applied and Environmental Microbiology 77, no. 12 (April 15, 2011): 4241–45. http://dx.doi.org/10.1128/aem.01834-10.

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ABSTRACTThree whole-community genome amplification methods,Bst, REPLI-g, and Templiphi, were evaluated using a microarray-based approach. The amplification biases of all methods were <3-fold. For pure-culture DNA, REPLI-g and Templiphi showed less bias thanBst. For community DNA, REPLI-g showed the least bias and highest number of genes, whileBsthad the highest success rate and was suitable for low-quality DNA.

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42

Luka, Martha M., Everlyn Kamau, Zaydah R. de Laurent, John Mwita Morobe, Leonard K. Alii, D. James Nokes, and Charles N. Agoti. "Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018." Wellcome Open Research 6 (September 23, 2021): 178. http://dx.doi.org/10.12688/wellcomeopenres.16911.2.

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Background: Virus genome sequencing is increasingly utilized in epidemiological surveillance. Genomic data allows comprehensive evaluation of underlying viral diversity and epidemiology to inform control. For human rhinovirus (HRV), genomic amplification and sequencing is challenging due to numerous types, high genetic diversity and inadequate reference sequences. Methods: We developed a tiled amplicon type-specific protocol for genome amplification and sequencing on the Illumina MiSeq platform of two HRV types, A15 and A101. We then assessed added value in analyzing whole genomes relative to the VP4/2 region only in the investigation of HRV molecular epidemiology within the community in Kilifi, coastal Kenya. Results: We processed 73 nasopharyngeal swabs collected between 2016-2018, and 48 yielded at least 70% HRV genome coverage. These included all A101 samples (n=10) and 38 (60.3%) A15 samples. Phylogenetic analysis revealed that the Kilifi A101 sequences interspersed with global A101 genomes available in GenBank collected between 1999-2016. On the other hand, our A15 sequences formed a monophyletic group separate from the global genomes collected in 2008 and 2019. An improved phylogenetic resolution was observed with the genome phylogenies compared to the VP4/2 phylogenies. Conclusions: We present a type-specific full genome sequencing approach for obtaining HRV genomic data and characterizing infections.

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43

Luka, Martha M., Everlyn Kamau, Zaydah R. de Laurent, John Mwita Morobe, Leonard K. Alii, D. James Nokes, and Charles N. Agoti. "Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018." Wellcome Open Research 6 (July 8, 2021): 178. http://dx.doi.org/10.12688/wellcomeopenres.16911.1.

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Background: Virus genome sequencing is increasingly utilized in epidemiological surveillance. Genomic data allows comprehensive evaluation of underlying viral diversity and epidemiology to inform control. For human rhinovirus (HRV), genomic amplification and sequencing is challenging due to numerous types, high genetic diversity and inadequate reference sequences. Methods: We developed a tiled amplicon type-specific protocol for genome amplification and sequencing on the Illumina MiSeq platform of two HRV types, A15 and A101. We then assessed added value in analyzing whole genomes relative to the VP4/2 region only in the investigation of HRV molecular epidemiology within the community in Kilifi, coastal Kenya. Results: We processed 73 samples collected between 2016-2018, and 48 yielded at least 70% HRV genome coverage. These included all A101 samples (n=10) and 38 (60.3%) A15 samples. Phylogenetic analysis revealed that the Kilifi A101 sequences interspersed with global A101 genomes available in GenBank collected between 1999-2016. On the other hand, our A15 sequences formed a monophyletic group separate from the global genomes collected in 2008 and 2019. Improved phylogenetic resolution was observed with the genome phylogenies compared to the VP4/2 phylogenies. Conclusions: We present a type-specific full genome sequencing approach for obtaining HRV genomic data and characterizing infections.

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44

Pappoe-Ashong, Prince Jonathan, and Kwamena Sagoe. "Optimization of a Polymerase Chain Reaction System for Whole Genome Amplification of Human Immunodeficiency Virus Type 2 (HIV-2)." Open Forum Infectious Diseases 4, suppl_1 (2017): S359. http://dx.doi.org/10.1093/ofid/ofx163.871.

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Abstract Background In this study, attempts were made to amplify the whole genome of HIV-2 using polymerase chain reaction (PCR) from viral RNA and proviral DNA extracted from archived human plasma and whole blood, respectively. The aim this study is to develop a PCR system that can be used to amplify the entire genome of all known subtypes and recombinant forms of HIV-2 Methods Proviral DNA and viral RNA were extracted from archived human whole blood and plasma using Zymo Research Viral DNA kit and Zymo Research Viral nucleic acids kit, respectively. Primers that target the conserved sites of the 3’ and 5’ long terminal repeat were selected based on in silico analysis using Snapgene® tool version 2.1.0. Eight overlapping Primers for PCR whole genome amplification of HIV-2 were also selected and used for overlap PCR amplification of whole genome of HIV-2. Long range and overlapping PCR of whole genome of HIV-2 were carried out using long range Kit (New England Biolabs Inc., Ipswich, MA, USA) and cDNA synthesized using NEB ProtoScript II for proviral DNA and viral RNA templates. Amplified whole genome of HIV-2 was gel purified and PCR confirmed using two sets of primers ENVF/ENVG and EB2/EB5 and gel electrophoresis. Results Proviral DNA and viral RNA were successfully extracted from archived whole blood and plasma. Six primers were selected out of the 68 primer sequences retrieved using in silico analysis for long range single PCR amplification of HIV-2 whole genome. Primers P1/P8 and HIV2upA/HIV2lowA were successfully used in the whole genome amplification of HIV-2. Overlapping primers P1/P4, P6/P8, PolF/EnvG and Pol4F/EnvG covering the entire genome of HIV-2 were also successfully used in the whole genome amplification of HIV-2. The amplified whole genome fragment was confirmed to be HIV-2 by PCR using primers EB2/EB5 and EnvF/EnvG. Conclusion The techniques of long-range and overlapping amplification of HIV-2 whole genome may be useful in HIV-2 genotyping using viral RNA and proviral DNA. This study has led to the selection and shown novel primer combinations of already existing primers which can be used to amplify the entire genome of HIV-2. Disclosures All authors: No reported disclosures.

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Paunio, T., I. Reima, and A. C. Syvänen. "Preimplantation diagnosis by whole-genome amplification, PCR amplification, and solid-phase minisequencing of blastomere DNA." Clinical Chemistry 42, no. 9 (September 1, 1996): 1382–90. http://dx.doi.org/10.1093/clinchem/42.9.1382.

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Abstract We have developed a new method for preimplantation diagnosis of inherited diseases. Our procedure for the identification of point mutations in single cells combines whole-genome amplification using 15-mer random primers (primer extension preamplification, PEP) with a single locus-specific PCR amplification, followed by detection of the mutation by solid-phase minisequencing. The procedure was evaluated by detecting three disease-causing mutations and seven polymorphic nucleotides located on different human chromosomes from single granuloma and blastomere cells. The correct genotype of the cell was identified at 96% of the nucleotide positions analyzed, showing that a representative part of the genome is amplified during PEP. We estimate that PEP yielded at least 1000 copies of the genome. The quantitative nature of the solid-phase minisequencing method allowed us to notice that preferential amplification of one allele occurs at heterozygous loci during PEP, which is a potential problem in preimplantation diagnosis.

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Gardner, Shea N., Crystal J. Jaing, Maher M. Elsheikh, José Peña, David A. Hysom, and Monica K. Borucki. "Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes." Advances in Bioinformatics 2014 (August 3, 2014): 1–8. http://dx.doi.org/10.1155/2014/101894.

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Background. Targeted enrichment improves coverage of highly mutable viruses at low concentration in complex samples. Degenerate primers that anneal to conserved regions can facilitate amplification of divergent, low concentration variants, even when the strain present is unknown. Results. A tool for designing multiplex sets of degenerate sequencing primers to tile overlapping amplicons across multiple whole genomes is described. The new script, run_tiled_primers, is part of the PriMux software. Primers were designed for each segment of South American hemorrhagic fever viruses, tick-borne encephalitis, Henipaviruses, Arenaviruses, Filoviruses, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus, and Japanese encephalitis virus. Each group is highly diverse with as little as 5% genome consensus. Primer sets were computationally checked for nontarget cross reactions against the NCBI nucleotide sequence database. Primers for murine hepatitis virus were demonstrated in the lab to specifically amplify selected genes from a laboratory cultured strain that had undergone extensive passage in vitro and in vivo. Conclusions. This software should help researchers design multiplex sets of primers for targeted whole genome enrichment prior to sequencing to obtain better coverage of low titer, divergent viruses. Applications include viral discovery from a complex background and improved sensitivity and coverage of rapidly evolving strains or variants in a gene family.

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Brochet, Mathieu, Elisabeth Couvé, Mohamed Zouine, Claire Poyart, and Philippe Glaser. "A Naturally Occurring Gene Amplification Leading to Sulfonamide and Trimethoprim Resistance in Streptococcus agalactiae." Journal of Bacteriology 190, no. 2 (November 16, 2007): 672–80. http://dx.doi.org/10.1128/jb.01357-07.

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ABSTRACT Gene amplifications have been detected as a transitory phenomenon in bacterial cultures. They are predicted to contribute to rapid adaptation by simultaneously increasing the expression of genes clustered on the chromosome. However, genome amplifications have rarely been described in natural isolates. Through DNA array analysis, we have identified two Streptococcus agalactiae strains carrying tandem genome amplifications: a fourfold amplification of 13.5 kb and a duplication of 92 kb. Both amplifications were located close to the terminus of replication and originated independently from any long repeated sequence. They probably arose in the human host and showed different stabilities, the 13.5-kb amplification being lost at a frequency of 0.003 per generation and the 92-kb tandem duplication at a frequency of 0.035 per generation. The 13.5-kb tandem amplification carried the five genes required for dihydrofolate biosynthesis and led to both trimethoprim (TMP) and sulfonamide (SU) resistance. Resistance to SU probably resulted from the increased synthesis of dihydropteroate synthase, the target of this antibiotic, whereas the amplification of the whole pathway was responsible for TMP resistance. This revealed a new mechanism of resistance to TMP involving an increased dihydrofolate biosynthesis. This is, to our knowledge, the first reported case of naturally occurring antibiotic resistance resulting from genome amplification in bacteria. The low stability of DNA segment amplifications suggests that their role in antibiotic resistance might have been underestimated.

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Wu, Liyou, Xueduan Liu, Christopher W. Schadt, and Jizhong Zhou. "Microarray-Based Analysis of Subnanogram Quantities of Microbial Community DNAs by Using Whole-Community Genome Amplification." Applied and Environmental Microbiology 72, no. 7 (July 2006): 4931–41. http://dx.doi.org/10.1128/aem.02738-05.

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ABSTRACT Microarray technology provides the opportunity to identify thousands of microbial genes or populations simultaneously, but low microbial biomass often prevents application of this technology to many natural microbial communities. We developed a whole-community genome amplification-assisted microarray detection approach based on multiple displacement amplification. The representativeness of amplification was evaluated using several types of microarrays and quantitative indexes. Representative detection of individual genes or genomes was obtained with 1 to 100 ng DNA from individual or mixed genomes, in equal or unequal abundance, and with 1 to 500 ng community DNAs from groundwater. Lower concentrations of DNA (as low as 10 fg) could be detected, but the lower template concentrations affected the representativeness of amplification. Robust quantitative detection was also observed by significant linear relationships between signal intensities and initial DNA concentrations ranging from (i) 0.04 to 125 ng (r 2 = 0.65 to 0.99) for DNA from pure cultures as detected by whole-genome open reading frame arrays, (ii) 0.1 to 1,000 ng (r 2 = 0.91) for genomic DNA using community genome arrays, and (iii) 0.01 to 250 ng (r 2 = 0.96 to 0.98) for community DNAs from ethanol-amended groundwater using 50-mer functional gene arrays. This method allowed us to investigate the oligotrophic microbial communities in groundwater contaminated with uranium and other metals. The results indicated that microorganisms containing genes involved in contaminant degradation and immobilization are present in these communities, that their spatial distribution is heterogeneous, and that microbial diversity is greatly reduced in the highly contaminated environment.

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Sobol, Morgan S., and Anne-Kristin Kaster. "Back to Basics: A Simplified Improvement to Multiple Displacement Amplification for Microbial Single-Cell Genomics." International Journal of Molecular Sciences 24, no. 5 (February 21, 2023): 4270. http://dx.doi.org/10.3390/ijms24054270.

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Microbial single-cell genomics (SCG) provides access to the genomes of rare and uncultured microorganisms and is a complementary method to metagenomics. Due to the femtogram-levels of DNA in a single microbial cell, sequencing the genome requires whole genome amplification (WGA) as a preliminary step. However, the most common WGA method, multiple displacement amplification (MDA), is known to be costly and biased against specific genomic regions, preventing high-throughput applications and resulting in uneven genome coverage. Thus, obtaining high-quality genomes from many taxa, especially minority members of microbial communities, becomes difficult. Here, we present a volume reduction approach that significantly reduces costs while improving genome coverage and uniformity of DNA amplification products in standard 384-well plates. Our results demonstrate that further volume reduction in specialized and complex setups (e.g., microfluidic chips) is likely unnecessary to obtain higher-quality microbial genomes. This volume reduction method makes SCG more feasible for future studies, thus helping to broaden our knowledge on the diversity and function of understudied and uncharacterized microorganisms in the environment.

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Rouse, Nicholas A., Michael F. Nagy, Paul Smith, and Peter L. Nagy. "ASSESSMENT OF BIOSKRYB WHOLE GENOME AMPLIFICATION METHODOLOGY FOR GENOME-WIDE ASSESSMENT FOR SNPs AND INDELS USING ILLUMINA WHOLE GENOME SEQUENCING." Fertility and Sterility 116, no. 3 (September 2021): e391. http://dx.doi.org/10.1016/j.fertnstert.2021.07.1046.

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