Overview of Target Enrichment Strategies

Iwanka Kozarewa1, Javier Armisen2, Andrew F. Gardner3, Barton E. Slatko3, C.L. Hendrickson4

1 Oncology Translational Science, Innovative Medicines & Early Development, AstraZeneca, Cambridge, 2 Horizon Discovery Group, Cambridge, United Kingdom, 3 New England BioLabs, Ipswich, Massachusetts, 4 Directed Genomics, Ipswich, Massachusetts
Publication Name:  Current Protocols in Molecular Biology
Unit Number:  Unit 7.21
DOI:  10.1002/0471142727.mb0721s112
Online Posting Date:  October, 2015
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library

Abstract

Target enrichment is commonly used in next generation sequencing (NGS) workflows to eliminate genomic DNA regions that are not of interest for a particular experiment. By only targeting specific regions such as exons, one can obtain greater depth of DNA sequencing coverage for regions of interest or increase the sampling numbers of individuals, thereby saving both time and cost. This overview of target enrichment strategies provides a high‐level review of distinct approaches to capture specific sequences: (a) hybridization‐based strategies, (b) transposon‐mediated fragmentation (tagmentation), (c) molecular inversion probes (MIPs), and (d) singleplex and multiplex polymerase chain reaction (PCR) target enrichment. Strategies for assay design and performance criteria are also discussed. Other platforms currently in development are also briefly described. © 2015 by John Wiley & Sons, Inc.

Keywords: target enrichment; DNA capture; hybridization based enrichment; PCR amplification

     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Table of Contents

  • Introduction
  • Hybridization‐Based Strategies
  • Target Enrichment Strategies Based on Transposon‐Mediated Fragmentation (Tagmentation)
  • Target Enrichment Strategies Based on the Use of Molecular Inversion Probes (MIPs)
  • PCR‐Based Target Enrichment Strategies
  • Choosing a Target Enrichment Strategy
  • Additional Target Enrichment Strategies on the Horizon
  • Literature Cited
  • Figures
  • Tables
     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Materials

GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Figures

Videos

Literature Cited

Literature Cited
  Akhras, M.S., Unemo, M., Thiyagarajan, S., Nyren, P., Davis, R.W., Fire, A.Z., and Pourmand, N. 2007. Connector inversion probe technology: A powerful one‐primer multiplex DNA amplification system for numerous scientific applications. PloS One 2:e915. doi: 10.1371/journal.pone.0000915
  Altmuller, J., Budde, B.S., and Nurnberg, P. 2014. Enrichment of target sequences for next‐generation sequencing applications in research and diagnostics. Biol. Chem. 395:231‐237. doi: 10.1515/hsz‐2013‐0199
  Anonymous. 2014. Method of the Year 2013. Nat. Methods 11:1. doi: 10.1038/nmeth.2801
  Bodi, K., Perera, A.G., Adams, P.S., Bintzler, D., Dewar, K., Grove, D.S., Kieleczawa, J., Lyons, R.H., Neubert, T.A., Noll, A.C., Singh, S., Steen, R., and Zianni, M. 2013. Comparison of commercially available target enrichment methods for next‐generation sequencing. J. Biomol. Tech. 24:73‐86.
  Boland, J.F., Chung, C.C., Roberson, D., Mitchell, J., Zhang, X., Im, K.M., He, J., Chanock, S.J., Yeager, M., and Dean, M. 2013. The new sequencer on the block: Comparison of Life Technology's Proton sequencer to an Illumina HiSeq for whole‐exome sequencing. Hum. Genet. 132:1153‐1163. doi: 10.1007/s00439‐013‐1321‐4
  Caruccio, N. 2011. Preparation of next‐generation sequencing libraries using Nextera technology: Simultaneous DNA fragmentation and adaptor tagging by in vitro transposition. Methods Mol. Biol. 733:241‐255.
  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. doi: 10.1038/nbt.1975
  Cosart, T., Beja‐Pereira, A., Chen, S., Ng, S.B., Shendure, J., and Luikart, G. 2011. Exome‐wide DNA capture and next generation sequencing in domestic and wild species. BMC Genomics 12:347. doi: 10.1186/1471‐2164‐12‐347
  Duncavage, E.J., Abel, H.J., Szankasi, P., Kelley, T.W., and Pfeifer, J.D. 2012. Targeted next generation sequencing of clinically significant gene mutations and translocations in leukemia. Mod. Pathol. 25:795‐804. doi: 10.1038/modpathol.2012.2
  Geniez, S., Foster, J.M., Kumar, S., Moumen, B., Leproust, E., Hardy, O., Guadalupe, M., Thomas, S.J., Boone, B., Hendrickson, C., Bouchon, D., Greve, P., and Slatko, B.E. 2012. Targeted genome enrichment for efficient purification of endosymbiont DNA from host DNA. Symbiosis 58:201‐207. doi: 10.1007/s13199‐012‐0215‐x
  Gnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E.M., Brockman, W., Fennell, T., Giannoukos, G., Fisher, S., Russ, C., Gabriel, S., Jaffe, D.B., Lander, E.S., and Nusbaum, C. 2009. Solution hybrid selection with ultra‐long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27:182‐189. doi: 10.1038/nbt.1523
  Gole, J., Gore, A., Richards, A., Chiu, Y.J., Fung, H.L., Bushman, D., Chiang, H.I., Chun, J., Lo, Y.H., and Zhang, K. 2013. Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Nat. Biotechnol. 31:1126‐1132. doi: 10.1038/nbt.2720
  Hardenbol, P., Yu, F., Belmont, J., Mackenzie, J., Bruckner, C., Brundage, T., Boudreau, A., Chow, S., Eberle, J., Erbilgin, A., Falkowski, M., Fitzgerald, R., Ghose, S., Iartchouk, O., Jain, M., Karlin‐Neumann, G., Lu, X., Miao, X., Moore, B., Moorhead, M., Namsaraev, E., Pasternak, S., Prakash, E., Tran, K., Wang, Z., Jones, H.B., Davis, R.W., Willis, T.D., and Gibbs, R.A. 2005. Highly multiplexed molecular inversion probe genotyping: Over 10,000 targeted SNPs genotyped in a single tube assay. Genome Res. 15:269‐275. doi: 10.1101/gr.3185605
  Hedges, D.J., Guettouche, T., Yang, S., Bademci, G., Diaz, A., Andersen, A., Hulme, W.F., Linker, S., Mehta, A., Edwards, Y.J., Beecham, G.W., Martin, E.R., Pericak‐Vance, M.A., Zuchner, S., Vance, J.M., and Gilbert, J.R. 2011. Comparison of three targeted enrichment strategies on the SOLiD sequencing platform. PloS One 6:e18595. doi: 10.1371/journal.pone.0018595
  Kihana, M., Mizuno, F., Sawafuji, R., Wang, L., and Ueda, S. 2013. Emulsion PCR‐coupled target enrichment: An effective fishing method for high‐throughput sequencing of poorly preserved ancient DNA. Gene 528:347‐351. doi: 10.1016/j.gene.2013.07.040
  Kiialainen, A., Karlberg, O., Ahlford, A., Sigurdsson, S., Lindblad‐Toh, K., and Syvanen, A.C. 2011. Performance of microarray and liquid based capture methods for target enrichment for massively parallel sequencing and SNP discovery. PloS One 6:e16486. doi: 10.1371/journal.pone.0016486
  Lesnik, E.A. and Freier, S.M. 1995. Relative thermodynamic stability of DNA, RNA, and DNA:RNA hybrid duplexes: Relationship with base composition and structure. Biochemistry 34:10807‐10815. doi: 10.1021/bi00034a013
  Mamanova, L., Coffey, A.J., Scott, C.E., Kozarewa, I., Turner, E.H., Kumar, A., Howard, E., Shendure, J., and Turner, D.J. 2010. Target‐enrichment strategies for next‐generation sequencing. Nat. Methods 7:111‐118. doi: 10.1038/nmeth.1419
  Nilsson, M., Malmgren, H., Samiotaki, M., Kwiatkowski, M., Chowdhary, B.P., and Landegren, U. 1994. Padlock probes: Circularizing oligonucleotides for localized DNA detection. Science 265:2085‐2088. doi: 10.1126/science.7522346
  Saiki, R.K., Scharf, S., Faloona, F., Mullis, K.B., Horn, G.T., Erlich, H.A., and Arnheim, N. 1985. Enzymatic amplification of beta‐globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230:1350‐1354. doi: 10.1126/science.2999980
  Sulonen, A.M., Ellonen, P., Almusa, H., Lepisto, M., Eldfors, S., Hannula, S., Miettinen, T., Tyynismaa, H., Salo, P., Heckman, C., Joensuu, H., Raivio, T., Suomalainen, A., and Saarela, J. 2011. Comparison of solution‐based exome capture methods for next generation sequencing. Genome Biol. 12:R94. doi: 10.1186/gb‐2011‐12‐9‐r94
  Teer, J.K., Johnston, J.J., Anzick, S.L., Pineda, M., Stone, G., Program, N.C.S., Meltzer, P.S., Mullikin, J.C., and Biesecker, L.G. 2013. Massively‐parallel sequencing of genes on a single chromosome: A comparison of solution hybrid selection and flow sorting. BMC Genomics 14:253. doi: 10.1186/1471‐2164‐14‐253
  Tewhey, R., Warner, J.B., Nakano, M., Libby, B., Medkova, M., David, P.H., Kotsopoulos, S.K., Samuels, M.L., Hutchison, J.B., Larson, J.W., Topol, E.J., Weiner, M.P., Harismendy, O., Olson, J., Link, D.R., and Frazer, K.A. 2009. Microdroplet‐based PCR enrichment for large‐scale targeted sequencing. Nat. Biotechnol. 27:1025‐1031. doi: 10.1038/nbt.1583
  Thompson, J.D., Shibahara, G., Rajan, S., Pel, J., and Marziali, A. 2012. Winnowing DNA for rare sequences: Highly specific sequence and methylation based enrichment. PloS One 7:e31597. doi: 10.1371/journal.pone.0031597
  Valencia, C.A., Rhodenizer, D., Bhide, S., Chin, E., Littlejohn, M.R., Keong, L.M., Rutkowski, A., Bonnemann, C., and Hegde, M. 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
  Varley, K.E. and Mitra, R.D. 2008. Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes. Genome Res. 18:1844‐1850. doi: 10.1101/gr.078204.108
  Wiggin, M., Pel, J., Vysotskaia, V., Broemeling, D., Marziali, A., and Hanson, D. 2013. Highly Multiplexed Profiling of Low Abundance Tumor Mutations in Plasma. J. Biomol. Tech. 24:S73‐S73.
  Zong, C., Lu, S., Chapman, A.R., and Xie, X.S. 2012. Genome‐wide detection of single‐nucleotide and copy‐number variations of a single human cell. Science 338:1622‐1626. doi: 10.1126/science.1229164
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library