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Open Access Highly Accessed Research article

A direct comparison of next generation sequencing enrichment methods using an aortopathy gene panel- clinical diagnostics perspective

Whitney L Wooderchak-Donahue1, Brendan O’Fallon1, Larissa V Furtado2, Jacob D Durtschi1, Parker Plant1, Perry G Ridge1, Alan F Rope3, Angela T Yetman4 and Pinar Bayrak-Toydemir125*

Author Affiliations

1 ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, USA

2 Department of Pathology, University of Utah, Salt Lake City, USA

3 Department of Pediatrics, Division of Medical Genetics, University of Utah, Salt Lake City, USA

4 Department of Pediatrics, Division of Cardiology, University of Utah, Salt Lake City, USA

5 Molecular Genetics Department, ARUP Institute for Clinical and Experimental Pathology, 500 Chipeta Way, Salt Lake City, UT, 84108, USA

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BMC Medical Genomics 2012, 5:50  doi:10.1186/1755-8794-5-50

Published: 14 November 2012

Abstract

Background

Aortopathies are a group of disorders characterized by aneurysms, dilation, and tortuosity of the aorta. Because of the phenotypic overlap and genetic heterogeneity of diseases featuring aortopathy, molecular testing is often required for timely and correct diagnosis of affected individuals. In this setting next generation sequencing (NGS) offers several advantages over traditional molecular techniques.

Methods

The purpose of our study was to compare NGS enrichment methods for a clinical assay targeting the nine genes known to be associated with aortopathy. RainDance emulsion PCR and SureSelect RNA-bait hybridization capture enrichment methods were directly compared by enriching DNA from eight samples. Enriched samples were barcoded, pooled, and sequenced on the Illumina HiSeq2000 platform. Depth of coverage, consistency of coverage across samples, and the overlap of variants identified were assessed. This data was also compared to whole-exome sequencing data from ten individuals.

Results

Read depth was greater and less variable among samples that had been enriched using the RNA-bait hybridization capture enrichment method. In addition, samples enriched by hybridization capture had fewer exons with mean coverage less than 10, reducing the need for followup Sanger sequencing. Variants sets produced were 77% concordant, with both techniques yielding similar numbers of discordant variants.

Conclusions

When comparing the design flexibility, performance, and cost of the targeted enrichment methods to whole-exome sequencing, the RNA-bait hybridization capture enrichment gene panel offers the better solution for interrogating the aortopathy genes in a clinical laboratory setting.

Keywords:
Aortopathy; Hybridization capture; Marfan syndrome; Next generation sequencing (NGS); Target enrichment; Emulsion PCR