Primer Design and Marker Clustering for Multiplex SNP-IT Primer Extension Genotyping Assay using Statistical Modeling

Predicting the success of primer extension genotyping assays using statistical modeling.

Using an empirical panel of more than 20 000 single base primer extension (SNP-IT) assays we have developed a set of statistical scores for evaluating and rank ordering various parameters of the SNP-IT reaction to facilitate high-throughput assay primer design with improved likelihood of success. Each score predicts either signal magnitude from primer extension or signal noise caused by misprim...

Hierarchical high-throughput SNP genotyping of the human Y chromosome using MALDI-TOF mass spectrometry.

We have established the use of a primer extension/mass spectrometry method (the PinPoint assay) for high-throughput SNP genotyping of the human Y chromosome. 118 markers were used to define 116 haplogroups and typing was organised in a hierarchical fashion. Twenty multiplex PCR/primer extension reactions were set up and each sample could be assigned to a haplogroup with only two to five of thes...

Competitive enzymatic reaction to control allele-specific extensions

Here, we present a novel method for SNP genotyping based on protease-mediated allele-specific primer extension (PrASE), where the two allele-specific extension primers only differ in their 3'-positions. As reported previously [Ahmadian,A., Gharizadeh,B., O'Meara,D., Odeberg,J. and Lundeberg,J. (2001), Nucleic Acids Res., 29, e121], the kinetics of perfectly matched primer extension is faster th...

Author's response to reviews Title: Robust SNP genotyping by multiplex PCR and arrayed primer extension Authors:

MACGT: multi-dimensional automated clustering genotyping tool for analysis of microarray-based mini-sequencing data

SUMMARY Multi-dimensional Automated Clustering Genotyping Tool (MACGT) is a Java application that clusters complex multi-dimensional vector data derived from single nucleotide polymorphism (SNP) genotyping experiments using mini-sequencing based microarray chemistries such as arrayed primer extension (APEX). Spot intensity output files from microarray experiments across multiple samples are imp...