SNPWave: a flexible multiplexed SNP genotyping technology.
Scalable multiplexed amplification technologies are needed for cost-effective large-scale genotyping of genetic markers such as single nucleotide polymorphisms (SNPs). We present SNPWave, a novel SNP genotyping technology to detect various subsets of sequences in a flexible fashion in a fixed detection format. SNPWave is based on highly multiplexed ligation, followed by amplification of up to 20 ligated probes in a single PCR. Depending on the multiplexing level of the ligation reaction, the latter employs selective amplification using the amplified fragment length polymorphism (AFLP) technology. Detection of SNPWave reaction products is based on size separation on a sequencing instrument with multiple fluorescence labels and short run times. The SNPWave technique is illustrated by a 100-plex genotyping assay for Arabidopsis, a 40-plex assay for tomato and a 10-plex assay for Caenorhabditis elegans, detected on the MegaBACE 1000 capillary sequencer.
van Eijk
Michiel J T
MJ
Keygene NV, Agro Business Park 90, PO Box 216, 6700 AE Wageningen, The Netherlands. michiel.van-eijk@keygene.com
Broekhof
José L N
JL
van der Poel
Hein J A
HJ
Hogers
René C J
RC
Schneiders
Harrie
H
Kamerbeek
Judith
J
Verstege
Esther
E
van Aart
Joris W
JW
Geerlings
Henk
H
Buntjer
Jaap B
JB
van Oeveren
A Jan
AJ
Vos
Pieter
P
D000483:Alleles; D000818:Animals; D017360:Arabidopsis / Q000235:genetics*; D017173:Caenorhabditis elegans / Q000235:genetics*; D004247:DNA / Q000032:analysis / Q000235:genetics; D015342:DNA Probes / Q000235:genetics; D005838:Genotype; D018551:Solanum lycopersicum / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012015:Reference Standards; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
D015342:DNA Probes; D004247:DNA