RT Journal Article
SR Electronic
T1 Improved DOP-PCR (iDOP-PCR): a robust and simple WGA method for efficient amplification of low copy number genomic DNA
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 128736
DO 10.1101/128736
A1 Konstantin A. Blagodatskikh
A1 Vladimir M. Kramarov
A1 Ekaterina V. Barsova
A1 Alexey V. Garkovenko
A1 Dmitriy S. Shcherbo
A1 Andrew A. Shelenkov
A1 Vera V. Ustinova
A1 Maria R. Tokarenko
A1 Simon C. Baker
A1 Tatiana V. Kramarova
A1 Konstantin B. Ignatov
YR 2017
UL http://biorxiv.org/content/early/2017/04/19/128736.abstract
AB Whole-genome amplification (WGA) techniques are used for non-specific amplification of low-copy number DNA, and especially for single-cell genome and transcriptome amplification. There are a number of WGA methods that have been developed over the years. One example is degenerate oligonucleotide-primed PCR (DOP-PCR), which is a very simple, fast and inexpensive WGA technique. Although DOP-PCR has been regarded as one of the pioneering methods for WGA, it only provides low genome coverage and a high allele dropout rate when compared to more modern techniques. Here we describe an improved DOP-PCR (iDOP-PCR). We have modified the classic DOP-PCR by using a new thermostable DNA polymerase (SD polymerase) with a strong strand-displacement activity and by adjustments in primers design. We compared iDOP-PCR, classic DOP-PCR and the well-established PicoPlex technique for whole genome amplification of both high- and low-copy number human genomic DNA. The amplified DNA libraries were evaluated by analysis of short tandem repeat genotypes and NGS data. In summary, iDOP-PCR provided a better quality of the amplified DNA libraries compared to the other WGA methods tested, especially when low amounts of genomic DNA were used as an input material.