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Genome‐wide single‐nucleotide polymorphism arrays demonstrate high fidelity of multiple displacement‐based whole‐genome amplification
Author(s) -
Tzvetkov Mladen V.,
Becker Christian,
Kulle Bettina,
Nürnberg Peter,
Brockmöller Jürgen,
Wojnowski Leszek
Publication year - 2005
Publication title -
electrophoresis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.666
H-Index - 158
eISSN - 1522-2683
pISSN - 0173-0835
DOI - 10.1002/elps.200410121
Subject(s) - molecular inversion probe , genotyping , multiple displacement amplification , single nucleotide polymorphism , biology , snp genotyping , genetics , human genome , genome , snp array , dna , genotype , microbiology and biotechnology , polymerase chain reaction , gene , dna extraction
Whole‐genome DNA amplification by multiple displacement (MD‐WGA) is a promising tool to obtain sufficient DNA amounts from samples of limited quantity. Using Affymetrix' GeneChip Human Mapping 10K Arrays, we investigated the accuracy and allele amplification bias in DNA samples subjected to MD‐WGA. We observed an excellent concordance (99.95%) between single‐nucleotide polymorphisms (SNPs) called both in the nonamplified and the corresponding amplified DNA. This concordance was only 0.01% lower than the intra‐assay reproducibility of the genotyping technique used. However, MD‐WGA failed to amplify an estimated 7% of polymorphic loci. Due to the algorithm used to call genotypes, this was detected only for heterozygous loci. We achieved a 4.3‐fold reduction of noncalled SNPs by combining the results from two independent MD‐WGA reactions. This indicated that inter‐reaction variations rather than specific chromosomal loci reduced the efficiency of MD‐WGA. Consistently, we detected no regions of reduced amplification, with the exception of several SNPs located near chromosomal ends. Altogether, despite a substantial loss of polymorphic sites, MD‐WGA appears to be the current method of choice to amplify genomic DNA for array‐based SNP analyses. The number of nonamplified loci can be substantially reduced by amplifying each DNA sample in duplicate.