Abstract
Next-generation sequencing (NGS) technologies, by sequencing hundreds of thousands to millions of DNA templates in parallel, resulted in higher throughput (Gb scale) and lowered sequencing cost (Mardis 2008; Shendure and Ji 2008). This has permitted the definition of entire genome as well as the differences that exist between them. The ultimate goal is to routinely perform whole-genome sequencing to allow us to gain a deeper understanding of genetic variation and to define its role in phenotypic variation and the pathogenesis of complex traits (Mamanova et al. 2010). Due to the cost and time limitations, it is not yet feasible to sequence large numbers of complex genomes. Therefore, a significant effort has focused on the development of “target enrichment” methods, in which genomic regions are selectively captured from a DNA sample before sequencing (Fig. 3.1). This approach is more time- and cost-effective, and the resulting data are considerably less cumbersome to analyze, except in the case of exome capture (Chap. 8). Several approaches to target enrichment have been developed, and the performance parameters vary from one to another: (1) sensitivity, or the percentage of the target bases that are represented by one or more sequence reads; (2) specificity, or the percentage of sequences that map to the intended targets; (3) uniformity, or the variability in sequence coverage across target regions; (4) reproducibility, or how closely results obtained from replicate experiments correlate; (5) cost; (6) ease of use; and (7) amount of DNA required per experiment, or per megabase of target (Mamanova et al. 2010).
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Albert TJ, Molla MN, Muzny DM et al (2007) Direct selection of human genomic loci by microarray hybridization. Nat Methods 4:903–905. doi:10.1038/nmeth1111
Bainbridge MN, Wang M, Burgess DL et al (2010) Whole exome capture in solution with 3 Gbp of data. Genome Biol 11:R62. doi:10.1186/gb-2010-11-6-r62
Choi M, Scholl UI, Ji W et al (2009) Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci U S A 106:19096–19101. doi:10.1073/pnas.0910672106
Clark MJ, Chen R, Lam HYK et al (2011) Performance comparison of exome DNA sequencing technologies. Nat Biotechnol 29:908–914. doi:10.1038/nbt.1975
Daiger SP, Sullivan LS, Bowne SJ et al (2010) Targeted high-throughput DNA sequencing for gene discovery in retinitis pigmentosa. Adv Exp Med Biol 664:325–331. doi:10.1007/978-1-4419-1399-9_37
Deng J, Shoemaker R, Xie B et al (2009) Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nat Biotechnol 27:353–360. doi:10.1038/nbt.1530
Ding L, Getz G, Wheeler DA et al (2008) Somatic mutations affect key pathways in lung adenocarcinoma. Nature 455:1069–1075. doi:10.1038/nature07423
Ghosh S, Krux F, Binder V et al (2012) Array-based sequence capture and next-generation sequencing for the identification of primary immunodeficiencies. Scand J Immunol 75:350–354. doi:10.1111/j.1365-3083.2011.02658.x
Gnirke A, Melnikov A, Maguire J et al (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 27:182–189. doi:10.1038/nbt.1523
Hodges E, Xuan Z, Balija V et al (2007) Genome-wide in situ exon capture for selective resequencing. Nat Genet 39:1522–1527. doi:10.1038/ng.2007.42
Hodges E, Rooks M, Xuan Z et al (2009) Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nat Protoc 4:960–974. doi:10.1038/nprot.2009.68
Jones MA, Bhide S, Chin E et al (2011) Targeted polymerase chain reaction-based enrichment and next-generation sequencing for diagnostic testing of congenital disorders of glycosylation. Genet Med 13:921–932. doi:10.1097/GIM.0b013e318226fbf2
Kim PM, Lam HYK, Urban AE et al (2008) Analysis of copy number variants and segmental duplications in the human genome: evidence for a change in the process of formation in recent evolutionary history. Genome Res 18:1865–1874. doi:10.1101/gr.081422.108
Landegren U, Schallmeiner E, Nilsson M et al (2004) Molecular tools for a molecular medicine: analyzing genes, transcripts and proteins using padlock and proximity probes. J Mol Recognit 17:194–197. doi:10.1002/jmr.664
Lovett M, Kere J, Hinton LM (1991) Direct selection: a method for the isolation of cDNAs encoded by large genomic regions. Proc Natl Acad Sci U S A 88:9628–9632
Majewski J, Schwartzentruber J, Lalonde E et al (2011) What can exome sequencing do for you? J Med Genet 48:580–589. doi:10.1136/jmedgenet-2011-100223
Mamanova L, Coffey AJ, Scott CE et al (2010) Target-enrichment strategies for next-generation sequencing. Nat Methods 7:111–118. doi:10.1038/nmeth.1419
Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24:133–141. doi:10.1016/j.tig.2007.12.007
Meder B, Haas J, Keller A et al (2011) Targeted next-generation sequencing for the molecular genetic diagnostics of cardiomyopathies. Circ Cardiovasc Genet 4:110–122. doi:10.1161/CIRCGENETICS.110.958322
Nilsson M, Malmgren H, Samiotaki M et al (1994) Padlock probes: circularizing oligonucleotides for localized DNA detection. Science 265:2085–2088
Okou DT, Steinberg KM, Middle C et al (2007) Microarray-based genomic selection for high-throughput resequencing. Nat Methods 4:907–909. doi:10.1038/nmeth1109
Porreca GJ, Zhang K, Li JB et al (2007) Multiplex amplification of large sets of human exons. Nat Methods 4:931–936. doi:10.1038/nmeth1110
Shearer AE, DeLuca AP, Hildebrand MS et al (2010) Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing. Proc Natl Acad Sci U S A 107:21104–21109. doi:10.1073/pnas.1012989107
Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145. doi:10.1038/nbt1486
Simpson DA, Clark GR, Alexander S et al (2011) Molecular diagnosis for heterogeneous genetic diseases with targeted high-throughput DNA sequencing applied to retinitis pigmentosa. J Med Genet 48:145–151. doi:10.1136/jmg.2010.083568
Sivakumaran TA, Husami A, Kissell D et al (2013) Performance evaluation of the next-generation sequencing approach for molecular diagnosis of hereditary hearing loss. Otolaryngol Head Neck Surg 148:1007–1016. doi:10.1177/0194599813482294
Summerer D, Wu H, Haase B et al (2009) Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing. Genome Res 19:1616–1621. doi:10.1101/gr.091942.109
Tewhey R, Warner JB, Nakano M et al (2009) Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat Biotechnol 27:1025–1031. doi:10.1038/nbt.1583
Turner EH, Lee C, Ng SB et al (2009) Massively parallel exon capture and library-free resequencing across 16 genomes. Nat Methods 6:315–316. doi:10.1038/nmeth.f.248
Valencia CA, Rhodenizer D, Bhide S et al (2012) Assessment of target enrichment platforms using massively parallel sequencing for the mutation detection for congenital muscular dystrophy. J Mol Diagn 14:233–246. doi:10.1016/j.jmoldx.2012.01.009
Valencia CA, Ankala A, Rhodenizer D et al (2013) Comprehensive mutation analysis for congenital muscular dystrophy: a clinical PCR-based enrichment and next-generation sequencing panel. PLoS One 8:e53083. doi:10.1371/journal.pone.0053083
Voelkerding KV, Dames SA, Durtschi JD (2009) Next-generation sequencing: from basic research to diagnostics. Clin Chem 55:641–658. doi:10.1373/clinchem.2008.112789
Author information
Authors and Affiliations
Rights and permissions
Copyright information
© 2013 C. Alexander Valencia
About this chapter
Cite this chapter
Valencia, C.A., Pervaiz, M.A., Husami, A., Qian, Y., Zhang, K. (2013). A Review of DNA Enrichment Technologies. In: Next Generation Sequencing Technologies in Medical Genetics. SpringerBriefs in Genetics. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-9032-6_3
Download citation
DOI: https://doi.org/10.1007/978-1-4614-9032-6_3
Published:
Publisher Name: Springer, New York, NY
Print ISBN: 978-1-4614-9031-9
Online ISBN: 978-1-4614-9032-6
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)