Suspension arrays for high throughput, multiplexed single nucleotide polymorphism genotyping

Abstract

We demonstrate, for the first time, the feasibility of multiplexed genotyping with suspension arrays using direct hybridization analyses. Our approach enables probes to be removed from or added to an array, enhancing flexibility over conventional chips. The ability to multiplex both the PCR preparation and the hybridization should enhance the throughput, cost, and speed of the assay.

High-Throughput Detection of Pathogenic Yeasts of the Genus Trichosporon

“…However, adding a few base pairs to some probe sequences does not always improve probe performance, as was the case for the Porosum clade-specific probe (P30b) (results not shown). Similar effects have been reported by others, for which a substantial decrease in resolution and specificity was found when probes underwent length modifications of a few nucleotides (3). Reports in the literature indicate that when a length of a probe is increased, a mismatched base pair in the probe-target duplex will have a marginal effect on the stability of the duplex.…”

Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput

“…Except for clinical applications, accuracy and sensitivity seldom are an issue, as the accuracy and sensitivity of all commercially available techniques have been tested and verified by many independent groups. For example, there are many reports for SBE with MS detection, 12,16,17,20,76,95 SBE with microarray 23 and microbeads [96][97][98][99] detection, the FP-TDI, [100][101][102] the TaqMan assay, 64,88,103 pyrosequencing, [104][105][106] the Invader assay 46,107-109 and ligation-based methods. 53,84,110,111 The issue becomes more salient when users intend to try out newly developed but not widely used methods.…”

Technical standards and guidelines: Venous thromboembolism (Factor V Leiden and prothrombin 20210G>A testing): A disease-specific supplement to the standards and guidelines for clinical genetics laboratories

“…Laboratories most easily use bead arrays in the context of validated ASRs because the reagents incorporate proprietary elements and none of the commercially available products are FDA cleared. [37][38][39][40] FV/PT 3.10.2 Multiplex PCR amplification. All general guidelines for multiplex PCR amplification apply to liquid bead array-based detection.…”

“…One commercial platform uses biotin-modified PCR products that are hybridized to allele-specific capture probes on different beads. [37][38][39] Another uses allele-specific primer extensions of the PCR product such that "universal tags" are incorporated into the product for allele discrimination. 40 The biotinylated PCR product, or extended PCR product, is then hybridized to either capture probes or "universal antitags," respectively, that are covalently bound to the beads.…”