Investigating the utility of combining phi29 whole genome amplification and highly multiplexed single nucleotide polymorphism BeadArray genotyping.
BACKGROUND
Sustainable DNA resources and reliable high-throughput genotyping methods are required for large-scale, long-term genetic association studies. In the genetic dissection of common disease it is now recognised that thousands of samples and hundreds of thousands of markers, mostly single nucleotide polymorphisms (SNPs), will have to be analysed. In order to achieve these aims, both an ability to boost quantities of archived DNA and to genotype at low costs are highly desirable. We have investigated phi29 polymerase Multiple Displacement Amplification (MDA)-generated DNA product (MDA product), in combination with highly multiplexed BeadArray genotyping technology. As part of a large-scale BeadArray genotyping experiment we made a direct comparison of genotyping data generated from MDA product with that from genomic DNA (gDNA) templates.


RESULTS
Eighty-six MDA product and the corresponding 86 gDNA samples were genotyped at 345 SNPs and a concordance rate of 98.8% was achieved. The BeadArray sample exclusion rate, blind to sample type, was 10.5% for MDA product compared to 5.8% for gDNA.


CONCLUSIONS
We conclude that the BeadArray technology successfully produces high quality genotyping data from MDA product. The combination of these technologies improves the feasibility and efficiency of mapping common disease susceptibility genes despite limited stocks of gDNA samples.
Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes, Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge, CB2 2XY, UK. rebecca.pask@cimr.cam.ac.uk
Rebecca
R
Pask
Helen E
HE
Rance
Bryan J
BJ
Barratt
Sarah
S
Nutland
Deborah J
DJ
Smyth
Meera
M
Sebastian
Rebecca C J
RC
Twells
Anne
A
Smith
Alex C
AC
Lam
Luc J
LJ
Smink
Neil M
NM
Walker
John A
JA
Todd
D017103:Bacillus Phages / Q000201:enzymology*; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism*; D015894:Genome, Human; D005838:Genotype; D006684:HLA-DR Antigens / Q000235:genetics; D059811:HLA-DRB1 Chains; D006801:Humans; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D013698:Templates, Genetic
D006684:HLA-DR Antigens; D059811:HLA-DRB1 Chains; D004259:DNA-Directed DNA Polymerase