A systematic comparison of two new releases of exome sequencing products: the aim of use determines the choice of product
-
Janine Altmüller
,
Susanne Motameny
Abstract
We received early access to the newest releases of exome sequencing products, namely Agilent SureSelect v6 (Agilent, Santa Clara, CA, USA) and NimbleGen MedExome (Roche NimbleGen, Basel, Switzerland), and we conducted whole exome sequencing (WES) of several DNA samples with each of these products in order to assess their performance. Here, we provide a detailed evaluation of the original, normalized (with respect to the different target sizes), and trimmed data sets and compare them in terms of the amount of duplicates, the reads on target, and the enrichment evenness. In addition to these general statistics, we performed a detailed analysis of the frequently mutated and newly described genes found in ‘The Deciphering Developmental Disorders Study’ published very recently (Fitzgerald, T.W., Gerety, S.S., Jones, W.D., van Kogelenberg, M., King, D.A., McRae, J., Morley, K.I., Parthiban, V., Al-Turki, S., Ambridge, K., et al. (2015). Large-scale discovery of novel genetic causes of developmental disorders. Nature 519, 223–228.). In our comparison, the Agilent v6 exome performs better than the NimbleGen’s MedExome both in terms of efficiency and evenness of coverage distribution. With its larger target size, it is also more comprehensive, and therefore the better choice in research projects that aim to identify novel disease-associated genes. In contrast, if the exomes are mainly used in a diagnostic setting, we see advantages for the new NimbleGen MedExome. We find a superior coverage here in those genes of high clinical relevance that likely allows for a better detection of relevant, disease-causing mutations.
Acknowledgments
All computations underlying the analyses presented in this review were performed on the CHEOPS high performance compute cluster of the Computing Center of the University of Cologne.
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©2016 Walter de Gruyter GmbH, Berlin/Boston
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Articles in the same Issue
- Frontmatter
- Reviews
- Endocytosis of pro-inflammatory cytokine receptors and its relevance for signal transduction
- The two faces of reactive oxygen species (ROS) in adipocyte function and dysfunction
- Research Articles/Short Communications
- Genes and Nucleic Acids
- Genetic association of NAD(P)H quinone oxidoreductase (NQO1*2) polymorphism with NQO1 levels and risk of diabetic nephropathy
- Protein Structure and Function
- Troponins, intrinsic disorder, and cardiomyopathy
- Molecular Medicine
- Molecular mechanisms mediating the beneficial metabolic effects of [Arg4]tigerinin-1R in mice with diet-induced obesity and insulin resistance
- Cell Biology and Signaling
- Adenovirus-mediated expression of vascular endothelial growth factor-a potentiates bone morphogenetic protein9-induced osteogenic differentiation and bone formation
- Proteolysis
- The intact Kunitz domain protects the amyloid precursor protein from being processed by matriptase-2
- Novel Techniques
- A systematic comparison of two new releases of exome sequencing products: the aim of use determines the choice of product
