Pathogen genome sequencing directly from clinical samples is quickly gaining importance in genetic and medical research studies. However, low DNA yield from blood-borne pathogens is often a limiting factor. The problem worsens in extremely base-biased genomes such as the AT-rich Plasmodium falciparum. We present a strategy for whole-genome amplification (WGA) of low-yield samples from P. falciparum prior to short-read sequencing. We have developed WGA conditions that incorporate tetramethylammonium chloride for improved amplification and coverage of AT-rich regions of the genome. We show that this method reduces amplification bias and chimera formation. Our data show that this method is suitable for as low as 10 pg input DNA, and offers the possibility of sequencing the parasite genome from small blood samples.

Original publication

DOI

10.1093/dnares/dsu028

Type

Journal article

Journal

DNA Res

Publication Date

12/2014

Volume

21

Pages

661 - 671

Keywords

AT-rich, malaria, tetramethylammonium chloride, whole-genome amplification, DNA, Protozoan, Genome, Protozoan, High-Throughput Nucleotide Sequencing, Nucleic Acid Amplification Techniques, Plasmodium falciparum