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.
References
Altmüller, J., Budde, B.S., and Nürnberg, P. (2014). Enrichment of target sequences for next-generation sequencing applications in research and diagnostics. Biol. Chem. 395, 231–237.10.1515/hsz-2013-0199Suche in Google Scholar PubMed
Asan, Xu, Y., Jiang, H., Tyler-Smith, C., Xue, Y., Jiang, T., Wang, J., Wu, M., Liu, X., Tian, G., et al. (2011). Comprehensive comparison of three commercial human whole-exome capture platforms. Genome Biol. 12, R95.10.1186/gb-2011-12-9-r95Suche in Google Scholar PubMed PubMed Central
Beleggia, F., Li, Y., Fan, J., Elcioğlu, N.H., Toker, E., Wieland, T., Maumenee, I.H., Akarsu, N.A., Meitinger, T., Strom, T.M., et al. (2015). CRIM1 haploinsufficiency causes defects in eye development in human and mouse. Hum. Mol. Genet. 24, 2267–2273.10.1093/hmg/ddu744Suche in Google Scholar PubMed PubMed Central
Chilamakuri, C.S., Lorenz, S., Madoui, M.A., Vodák, D., Sun, J., Hovig, E., Myklebost, O., and Meza-Zepeda, L.A. (2014). Performance comparison of four exome capture systems for deep sequencing. BMC Genomics 15, 449.10.1186/1471-2164-15-449Suche in Google Scholar PubMed PubMed Central
Clark, M.J., Chen, R., Lam, H.Y., Karczewski, K.J., Chen, R., Euskirchen, G., Butte, A.J., and Snyder, M. (2011). Performance comparison of exome DNA sequencing technologies. Nat. Biotechnol. 29, 908–914.10.1038/nbt.1975Suche in Google Scholar PubMed PubMed Central
Filges, I. and Friedman, J.M. (2015). Exome sequencing for gene discovery in lethal fetal disorders - harnessing the value of extreme phenotypes. Prenat. Diagn. 35, 1005–1009.10.1002/pd.4464Suche in Google Scholar PubMed
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, 223–228.10.1038/nature14135Suche in Google Scholar PubMed PubMed Central
Flickinger, M., Jun, G., Abecasis, G.R., Boehnke, M., and Kang, H.M. (2015). Correcting for sample contamination in genotype calling of DNA sequence data. Am. J. Hum. Genet. 97, 284–290.10.1016/j.ajhg.2015.07.002Suche in Google Scholar PubMed PubMed Central
Frommolt, P., Abdallah, A.T., Altmüller, J., Motameny, S., Thiele, H., Becker, C., Stemshorn, K., Fischer, M., Freilinger, T., and Nürnberg, P. (2012). Assessing the enrichment performance in targeted resequencing experiments. Hum. Mutat. 33, 635–641.10.1002/humu.22036Suche in Google Scholar PubMed
Li, H. and Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760.10.1093/bioinformatics/btp324Suche in Google Scholar PubMed PubMed Central
Jun, G., Flickinger, M., Hetrick, K.N., Romm, J.M., Doheny, K.F., Abecasis, G.R., Boehnke M., and Kang H.M. (2012). Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data. Am. J. Hum. Genet. 91, 839–848.10.1016/j.ajhg.2012.09.004Suche in Google Scholar PubMed PubMed Central
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010). The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303.10.1101/gr.107524.110Suche in Google Scholar PubMed PubMed Central
Shigemizu, D., Momozawa, Y., Abe, T., Morizono, T., Boroevich, K.A., Takata, S., Ashikawa, K., Kubo, M., and Tsunoda, T. (2015). Performance comparison of four commercial human whole-exome capture platforms. Sci. Rep. 5, 12742.10.1038/srep12742Suche in Google Scholar PubMed PubMed Central
Smedley, D. and Robinson, P.N. (2015). Phenotype-driven strategies for exome prioritization of human Mendelian disease genes. Genome Med. 7, 81.10.1186/s13073-015-0199-2Suche in Google Scholar PubMed PubMed Central
Sulonen, A.M., Ellonen, P., Almusa, H., Lepist, Ã.M., Eldfors, S., Hannula, S., Miettinen, T., Tyynismaa, H., Salo, P., Heckman, C., et al. (2011). Comparison of solution-based exome capture methods for next generation sequencing. Genome Biol. 12, R94.10.1186/gb-2011-12-9-r94Suche in Google Scholar PubMed PubMed Central
van der Werf, I.M., Kooy, R.F., Vandeweyer, G. (2014). A robust protocol to increase NimbleGen SeqCap EZ multiplexing capacity to 96 samples. PLoS One 10, e0123872.10.1371/journal.pone.0123872Suche in Google Scholar PubMed PubMed Central
Zhang, X. (2014). Exome sequencing greatly expedites the progressive research of Mendelian diseases. Front Med. 8, 42–57.10.1007/s11684-014-0303-9Suche in Google Scholar PubMed
Zhang, G., Wang, J., Yang, J., Li, W., Deng, Y., Li, J., Huang, J., Hu, S., and Zhang, B. (2015). Comparison and evaluation of two exome capture kits and sequencing platforms for variant calling. BMC Genomics 16, 581.10.1186/s12864-015-1796-6Suche in Google Scholar PubMed PubMed Central
©2016 Walter de Gruyter GmbH, Berlin/Boston
Artikel in diesem Heft
- 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
Artikel in diesem Heft
- 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
