A Comparative Study of Five Technologically Diverse CFTR Testing Platforms

Abstract

Multiple cystic fibrosis (CF) testing platforms, using diverse and rapidly evolving technologies, are available to clinical laboratories commercially or for evaluation. Considerations when choosing a CF platform may include: sensitivity, specificity, accuracy, signal discrimination, ability to genotype, ability to reflex test, no calls/repeat rate, composition of mutation panel, hands-on time, start-to-finish time, integration into laboratory workflow, data analysis methods, flexibility regarding custom test design, and required instrumentation. Mindful of these considerations, we evaluated five technologically diverse CF platforms: 1) eSensor, an electronic detection assay system; 2) InPlex, a signal amplification methodology using a microfluidics card; 3) oligonucleotide ligation assay, an electrophoretic-based separation of amplicon-derived ligation-generated products; and two liquid bead arrays; 4) Signature, a direct hybridization assay using allele-specific capture probes; and 5) Tag-It, an assay using allele-specific primer extension and a universal microarray. A core of 150 samples, focusing on mutations in the American College of Medical Genetics/ American College of Obstetricians and Gynecologists mutation panel, was tested throughout several runs for each platform. All of the platforms performed comparably in respect to sensitivity, specificity, and no-call rate. As our results indicate, consideration of all of the parameters evaluated may be useful when selecting the most appropriate platform for the specific setting. (J Mol Diagn 2007, 9:401-407;

Comparison of the GenMark Diagnostics eSensor Respiratory Viral Panel to Real-Time PCR for Detection of Respiratory Viruses in Children

“…Molecular assays utilizing this technology and instrumentation and targeting other genetic markers of human disease have previously been licensed by the FDA (1,11,13,21,27).…”

Perioperative Genomic Profiles Using Structure-Specific Oligonucleotide Probes

“…Recently, the performance of another Invader platform (i.e., InPlex for cystic fibrosis genotyping on a microfluidics card) was compared with eSensor (Osmetech Molecular Diagnostics, Pasadena, CA), CF v3.0 oligonucleotide ligation assay (Abbott Laboratories, Abbott Park, IL/Celera Diagnostics, Alameda, CA), Signature CF 2.0 ASR (Asuragen, Austin, TX), and Tag-It Mutation Detection Kit for CFTR (TM Biosciences, Toronto, Canada) technologies on the same sample of CFTR templates. 77 The Invader assay exhibited the least cost for instrumentation ($12,900 vs. $45,000 to $145,000), the least cost of reagents per patient sample ($39.00 vs. $45.00 to $64.00), the least hands-on operator time (<1 hour vs. 1 to 2.5 hours), and the least start to finish time (4 hours vs. 5 to 8 hours). While the Inplex microfluidics card and the PCR-independent and PCR-dependent microtiter platforms of the present investigation lack a number of features in common, they are generally equivalent in consumption of reagents other than oligonucleotide probes, instrumentation, operator time and start to finish time.…”

Visual DNA as a diagnostic tool

“…Since 2001, when the American College of Obstetricians and Gynecologists and the American College of Medical Genetics established a recommended screening panel of 25 CFTR mutations [15,21], a number of commercial kits have been introduced to the market [16]. The methods are in most cases based on DNA hybridization and/or enzymatic interrogation but differ in their detection setup.…”

“…For this reason newborn screening is routinely recommended and procedures applied by hospitals encompass immunoreactive trypsinogen test [11], sweat tests [13,14],] as well as genetic tests [15]. The latter, which often involves hybridization, ligation, or polymerization to interrogate DNA variations [16], is the most informative while also requiring advanced detection instrumentation, hence it is also the most expensive. Therefore, as a proof of concept, a panel of mutations was selected to demonstrate the concept of making DNA sequence variation visible to the naked eye as a part of an efficient diagnostic assay using only standard laboratory instrumentation.…”