Multiple displacement amplification to create a long-lasting source of DNA for genetic studies

Abstract

In many situations there may not be sufficient DNA collected from patient or population cohorts to meet the requirements of genome-wide analysis of SNPs, genomic copy number polymorphisms, or acquired copy number alternations. When the amount of available DNA for genotype analysis is limited, high performance whole-genome amplification (WGA) represents a new development in genetic analysis. It is especially useful for analysis of DNA extracted from stored histology slides, tissue samples, buccal swabs, or blood stains collected on filter paper. The multiple displacement amplification (MDA) method, which relies on isothermal amplification using the DNA polymerase of the bacteriophage phi29, is a recently developed technique for high performance WGA. This review addresses new trends in the technical performance of MDA and its applications to genetic analyses. The main challenge of WGA methods is to obtain balanced and faithful replication of all chromosomal regions without the loss of or preferential amplification of any genomic loci or allele. In multiple comparisons to other WGA methods, MDA appears to be most reliable for genotyping, with the most favorable call rates, best genomic coverage, and lowest amplification bias.

Systematic evaluation of the effect of common SNPs on pre-mRNA splicing

“…The GenomiPhi method relies on the multiple displacement amplification (MDA) WGA reaction that was first described by (Dean et al, 2002), and has been recently considered developed technique for high performance WGA (Lovmar and Syvanen, 2006). The basic idea of MDA is that, the random hexamers anneal to the single stranded target molecule and as the DNA polymerase elongates the primer, the upstream DNA strands are displaced.…”

“…The displaced DNA strands can then serve as templates for new priming events, which results in primer elongation in the opposite direction. The MDA reaction continues, and new DNA strands are displaced to produce new templates and a hyperbranched structure, generating an abundance of copies of the original DNA molecule (Lovmar and Syvanen, 2006). Varying DNA concentrations in the initial sample will plateau during MDA, which is a potential benefit for MDA in large-scale genotyping applications because it unifies and increases the DNA concentrations of the samples (Lovmar and Syvanen, 2006).…”

“…The MDA reaction continues, and new DNA strands are displaced to produce new templates and a hyperbranched structure, generating an abundance of copies of the original DNA molecule (Lovmar and Syvanen, 2006). Varying DNA concentrations in the initial sample will plateau during MDA, which is a potential benefit for MDA in large-scale genotyping applications because it unifies and increases the DNA concentrations of the samples (Lovmar and Syvanen, 2006). The performance of MDA is dependent upon the quality of the input DNA (Lage et al, 2003).…”

Getting it right: designing microarray (and not ‘microawry') comparative genomic hybridization studies for cancer research

“…30 Multiple displacement amplification (MDA) is a non-PCRbased amplification method which uses bacteriophage Phi29 or large fragment-Bst DNA polymerase for WGA, and is supposed to have a much lower propensity for over/ under representation (three-fold vs 1000-fold) than PCRbased WGA methods. 24,31 In addition, MDA produces longer products from each priming event than PCR-based methods, theoretically generating equal representation of loci, thus providing nearly perfect coverage of the human genome. 24 Phi29 has only been successfully applied to fresh frozen tissue and cell line DNA in aCGH studies; 24,32,33 although there are anecdotal reports of successful Phi29 amplification of DNA amplified from FFPE tissue samples, 34 this has proven to be inconsistent to say the least.…”

Integrating Host Genomics with Surveillance for Invasive Bacterial Diseases

“…Genomic DNA was amplifi ed from 3-mm punches of 1/2″ nDBSs by using multiple displacement techniques (8) (12). Of 269 diallelic sites (SNPs), 173 (64%) were in the CC study samples and 59 (34%) were unique to the CC study samples (Table 2, online Technical Appendix).…”