Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing
| Autor: | Karrie R. Tartaro, John H. Leamon, Michael Egholm, Robert Pinard, Jonathan M. Rothberg, Ramona Plant, Alex de Winter, Gary J. Sarkis, Mark Gerstein |
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| Jazyk: | angličtina |
| Rok vydání: | 2006 |
| Předmět: |
Halobacterium
Cancer genome sequencing lcsh:QH426-470 lcsh:Biotechnology Hybrid genome assembly Bacterial genome size Biology Statistics Nonparametric Campylobacter jejuni 03 medical and health sciences Bias lcsh:TP248.13-248.65 Genetics 030304 developmental biology Whole genome sequencing Whole Genome Amplification 0303 health sciences Massive parallel sequencing 030306 microbiology Multiple displacement amplification Genomics Sequence Analysis DNA Nucleic acid amplification technique Chromosomes Bacterial lcsh:Genetics DNA Probes Nucleic Acid Amplification Techniques Genome Bacterial Research Article Biotechnology |
| Zdroj: | BMC Genomics, Vol 7, Iss 1, p 216 (2006) BMC Genomics |
| ISSN: | 1471-2164 |
| Popis: | BackgroundWhole 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.Halobacteriumspecies NRC-1 DNA andCampylobacter jejuniwere 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.ResultsAll amplification methodologies induced statistically significant bias relative to the unamplified control. For theHalobacteriumspecies 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. ForCampylobacter 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.ConclusionOf the amplification methodologies examined in this paper, the multiple displacement amplification products generated the least bias, and produced significantly higher yields of amplified DNA. |
| Databáze: | OpenAIRE |
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