The GeneInsight Suite: a platform to support laboratory and provider use of DNA-based genetic testing.

The future of personalized medicine will hinge on effective management of patient genetic profiles. Molecular diagnostic testing laboratories need to track knowledge surrounding an increasingly large number of genetic variants, incorporate this knowledge into interpretative reports, and keep ordering clinicians up to date as this knowledge evolves. Treating clinicians need to track which variants have been identified in each of their patients along with the significance of these variants. The GeneInsight(SM) Suite assists in these areas. The suite also provides a basis for interconnecting laboratories and clinicians in a manner that increases the scalability of personalized medicine processes.

Evaluation of second-generation sequencing of 19 dilated cardiomyopathy genes for clinical applications.

Medical sequencing for diseases with locus and allelic heterogeneities has been limited by the high cost and low throughput of traditional sequencing technologies. "Second-generation" sequencing (SGS) technologies allow the parallel processing of a large number of genes and, therefore, offer great promise for medical sequencing; however, their use in clinical laboratories is still in its infancy. Our laboratory offers clinical resequencing for dilated cardiomyopathy (DCM) using an array-based platform that interrogates 19 of more than 30 genes known to cause DCM. We explored both the feasibility and cost effectiveness of using PCR amplification followed by SGS technology for sequencing these 19 genes in a set of five samples enriched for known sequence alterations (109 unique substitutions and 27 insertions and deletions). While the analytical sensitivity for substitutions was comparable to that of the DCM array (98%), SGS technology performed better than the DCM array for insertions and deletions (90.6% versus 58%). Overall, SGS performed substantially better than did the current array-based testing platform; however, the operational cost and projected turnaround time do not meet our current standards. Therefore, efficient capture methods and/or sample pooling strategies that shorten the turnaround time and decrease reagent and labor costs are needed before implementing this platform into routine clinical applications.

DNA sequencing of cancer-related genes for biomarker discovery.

Dideoxy DNA sequencing is routinely used in research and, increasingly, in clinical care for the detection of DNA sequence variants, single nucleotide changes, or small insertions or deletions, when the spectrum of DNA variation is unknown. DNA sequence variation can be present in tumor tissue that is not present in the normal tissue from the same individual. This somatic DNA sequence variation is often the cause of abnormal cell growth and/or regulation and, ultimately, tumorigenesis. Identification of these oncogenic DNA sequence variants has successfully led to the development of cancer therapies, since the abnormal protein products created from genomic DNA containing mutations can serve as targets for pharmacologic inhibition. Somatic DNA sequence analysis will continue to be a valuable technique for biomarker discovery until the complete spectrum of DNA variation observed in tumor tissue is understood.

Platform evaluation for rapid genotyping of CYP2C9 and VKORC1 alleles.

AIMS: Warfarin is a commonly prescribed drug with a narrow therapeutic index. Adverse drug reactions owing to over- or under-dosing are common. It is now established that genetic differences between individuals play a major role in warfarin metabolism. In particular, common variants in CYP2C9 (*2 and *3) and VKORC1 (-1639G>A) have been associated with a reduced drug-dosage requirement. MATERIALS & METHODS: We have evaluated the performance of five platforms that can be used to genotype individuals for these variants. These include Third Wave Technologies Invader®, Applied Biosystems TaqMan®, AutoGenomics INFINITI™ 2C9-VKORC1 assay, Osmetech eSensor® XT-8 warfarin sensitivity test and the Idaho Technologies LightScanner®. RESULTS & CONCLUSIONS: Excluding failures, all of these technologies had 100% concordance rates with either Sanger sequencing or another validated technology. All of these platforms had high sensitivity and specificity and are therefore appropriate for clinical molecular diagnostics. Therefore, platform choice is likely to be driven by clinical laboratories interested in performing this service taking other factors into account, including turnaround time, capacity, cost and ease of use.