We are analyzing https://link.springer.com/article/10.1186/1471-2164-7-216.

Title:
Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing | BMC Genomics
Description:
Background Whole genome amplification is an increasingly common technique through which minute amounts of DNA can be multiplied to generate quantities suitable for genetic testing and analysis. Questions of amplification-induced error and template bias generated by these methods have previously been addressed through either small scale (SNPs) or large scale (CGH array, FISH) methodologies. Here we utilized whole genome sequencing to assess amplification-induced bias in both coding and non-coding regions of two bacterial genomes. Halobacterium species NRC-1 DNA and Campylobacter jejuni were amplified by several common, commercially available protocols: multiple displacement amplification, primer extension pre-amplification and degenerate oligonucleotide primed PCR. The amplification-induced bias of each method was assessed by sequencing both genomes in their entirety using the 454 Sequencing System technology and comparing the results with those obtained from unamplified controls. Results All amplification methodologies induced statistically significant bias relative to the unamplified control. For the Halobacterium species NRC-1 genome, assessed at 100 base resolution, the D-statistics from GenomiPhi-amplified material were 119 times greater than those from unamplified material, 164.0 times greater for Repli-G, 165.0 times greater for PEP-PCR and 252.0 times greater than the unamplified controls for DOP-PCR. For Campylobacter jejuni, also analyzed at 100 base resolution, the D-statistics from GenomiPhi-amplified material were 15 times greater than those from unamplified material, 19.8 times greater for Repli-G, 61.8 times greater for PEP-PCR and 220.5 times greater than the unamplified controls for DOP-PCR. Conclusion Of the amplification methodologies examined in this paper, the multiple displacement amplification products generated the least bias, and produced significantly higher yields of amplified DNA.
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Keywords {🔍}

genome, amplification, dna, unamplified, bias, pubmed, amplified, samples, halobacterium, jejuni, control, reads, sequence, article, coverage, google, scholar, sequencing, dop, methods, size, analysis, table, cas, regions, genomes, replig, reference, genomiphi, genomic, populations, pep, number, relative, content, nrc, sample, campylobacter, pcr, mda, figure, counts, central, generated, species, base, comparison, high, wga, population,

Topics {✒️}

primer extension preamplification open access article primer extension pre-amplification isothermal rolling-circle amplification processive pcr-based methods multiple displacement amplification pcr-based methodologies renders microarray-based survey restricted great medical/scientific importance article download pdf degenerate oligonucleotide-primed pcr distribution-free kolmogorov-smirnov test pcr-based amplification methods pcr-based methods generated amplifications versus pcr-based multiple bacterial species pcr-based wga methods single-nucleotide-polymorphism genotyping ks-test d-statistic values genome amplification-related loss mda-based methodologies produce array-hybridization results revealed conducted sequence-based karyotyping log-log plots display genome amplification-induced bias genome-wide snp genotyping assess amplification-induced bias permit polymerase access dop-pcr uniformity found privacy choices/manage cookies bmc genomics 7 high-throughput sequencing methodologies multiple sequencing runs related subjects full size image mda-amplified templates improved authors’ original file pcr-related bias multiple mutation analyses pcr-based methods double-stranded adaptors halobacterium species nrc-1 halobacterium chromosome reveals degenerate oligonucleotide primer detecting statistically significant article pinard pcr-based wga pep-pcr produced reads double stranded dna sophisticated statistical assessment

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         headline:Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing
         description:Whole genome amplification is an increasingly common technique through which minute amounts of DNA can be multiplied to generate quantities suitable for genetic testing and analysis. Questions of amplification-induced error and template bias generated by these methods have previously been addressed through either small scale (SNPs) or large scale (CGH array, FISH) methodologies. Here we utilized whole genome sequencing to assess amplification-induced bias in both coding and non-coding regions of two bacterial genomes. Halobacterium species NRC-1 DNA and Campylobacter jejuni were amplified by several common, commercially available protocols: multiple displacement amplification, primer extension pre-amplification and degenerate oligonucleotide primed PCR. The amplification-induced bias of each method was assessed by sequencing both genomes in their entirety using the 454 Sequencing System technology and comparing the results with those obtained from unamplified controls. All amplification methodologies induced statistically significant bias relative to the unamplified control. For the Halobacterium species NRC-1 genome, assessed at 100 base resolution, the D-statistics from GenomiPhi-amplified material were 119 times greater than those from unamplified material, 164.0 times greater for Repli-G, 165.0 times greater for PEP-PCR and 252.0 times greater than the unamplified controls for DOP-PCR. For Campylobacter jejuni, also analyzed at 100 base resolution, the D-statistics from GenomiPhi-amplified material were 15 times greater than those from unamplified material, 19.8 times greater for Repli-G, 61.8 times greater for PEP-PCR and 220.5 times greater than the unamplified controls for DOP-PCR. Of the amplification methodologies examined in this paper, the multiple displacement amplification products generated the least bias, and produced significantly higher yields of amplified DNA.
         datePublished:2006-08-23T00:00:00Z
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            Multiple Displacement Amplification
            Main Chromosome
            Prime Extension Preamplification
            Multiple Displacement Amplification Reaction
            Life Sciences
            general
            Microarrays
            Proteomics
            Animal Genetics and Genomics
            Microbial Genetics and Genomics
            Plant Genetics and Genomics
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      headline:Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing
      description:Whole genome amplification is an increasingly common technique through which minute amounts of DNA can be multiplied to generate quantities suitable for genetic testing and analysis. Questions of amplification-induced error and template bias generated by these methods have previously been addressed through either small scale (SNPs) or large scale (CGH array, FISH) methodologies. Here we utilized whole genome sequencing to assess amplification-induced bias in both coding and non-coding regions of two bacterial genomes. Halobacterium species NRC-1 DNA and Campylobacter jejuni were amplified by several common, commercially available protocols: multiple displacement amplification, primer extension pre-amplification and degenerate oligonucleotide primed PCR. The amplification-induced bias of each method was assessed by sequencing both genomes in their entirety using the 454 Sequencing System technology and comparing the results with those obtained from unamplified controls. All amplification methodologies induced statistically significant bias relative to the unamplified control. For the Halobacterium species NRC-1 genome, assessed at 100 base resolution, the D-statistics from GenomiPhi-amplified material were 119 times greater than those from unamplified material, 164.0 times greater for Repli-G, 165.0 times greater for PEP-PCR and 252.0 times greater than the unamplified controls for DOP-PCR. For Campylobacter jejuni, also analyzed at 100 base resolution, the D-statistics from GenomiPhi-amplified material were 15 times greater than those from unamplified material, 19.8 times greater for Repli-G, 61.8 times greater for PEP-PCR and 220.5 times greater than the unamplified controls for DOP-PCR. Of the amplification methodologies examined in this paper, the multiple displacement amplification products generated the least bias, and produced significantly higher yields of amplified DNA.
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         Multiple Displacement Amplification
         Main Chromosome
         Prime Extension Preamplification
         Multiple Displacement Amplification Reaction
         Life Sciences
         general
         Microarrays
         Proteomics
         Animal Genetics and Genomics
         Microbial Genetics and Genomics
         Plant Genetics and Genomics
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