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Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
Open accessAbstract
Targeting genomic loci by massively parallel sequencing requires new methods to enrich templates to be sequenced. We developed a capture method that uses biotinylated RNA 'baits' to fish targets out of a 'pond' of DNA fragments. The RNA is transcribed from PCR-amplified oligodeoxynucleotides originally synthesized on a microarray, generating sufficient bait for multiple captures at concentrations high enough to drive the hybridization. We tested this method with 170-mer baits that target >15,000 coding exons (2.5 Mb) and four regions (1.7 Mb total) using Illumina sequencing as read-out. About 90% of uniquely aligning bases fell on or near bait sequence; up to 50% lay on exons proper. The uniformity was such that approximately 60% of target bases in the exonic 'catch', and approximately 80% in the regional catch, had at least half the mean coverage. One lane of Illumina sequence was sufficient to call high-confidence genotypes for 89% of the targeted exon space.
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“In genome research, an average depth of sequence coverage of 30-fold has been accepted as sufficient for single-nucleotide polymorphism (SNP) and nucleotide insertion or deletion (indel) detection (15–22).”
From Carrier testing for severe childhood recessive diseases by next-generation sequencing (2011) · cites this paper as [15]
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“Target capture and next-generation sequencing (NGS) have shown efficacy and, recently, scalability for resequencing human genomes and exomes, providing an alternative potential paradigm for comprehensive carrier testing (15–22).”
From Carrier testing for severe childhood recessive diseases by next-generation sequencing (2011) · cites this paper as [15]
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“Preliminary experiments suggested that existing protocols for Agilent SureSelect hybrid capture (15) and RainDance microdroplet polymerase chain reaction (PCR) (16) but not Febit HybSelect microarray-based biochip capture (30) or Olink padlock probe ligation and PCR (31) yielded consistent target enrichment.”
From Carrier testing for severe childhood recessive diseases by next-generation sequencing (2011) · cites this paper as [15]
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Carrier testing for severe childhood recessive diseases by next-generation sequencing
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“SureSelect enrichment of 6-, 8-, or 12-plex pooled libraries was per Agilent protocols (15), with 100 ng of custom bait library, blocking oligonucleotides specific for paired-end sequencing libraries and 60-hour hybridization.”
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Vaishnavi, A., Capelletti, M., Le, A. T., Kako, S. L., Butaney, M., Ercan, D., Mahale, S., Davies, K. D., Aisner, D. L., Pilling, A. B., et al. (2013) · Nature Medicine · doi:10.1038/nm.3352 · Cited by 615
DNA analysis of an early modern human from Tianyuan Cave, China
Fu, Q., Meyer, M., Gao, X., Stenzel, U., Burbano, H. A., Kelso, J., & Pääbo, S. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1221359110 · Cited by 608
“(25) that uses oligonucleotides synthesized on arrays to construct probe libraries that are then amplified and converted into biotinylated RNA capture probes through in vitro transcription.”
BackgroundAdvancements in Next-Generation Sequencing
Levy, S., & Myers, R. (2016) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-083115-022413 · Cited by 630
Rademakers, R., Baker, M., Nicholson, A. M., Rutherford, N. J., Finch, N., Soto-Ortolaza, A., Lash, J., Wider, C., Wojtas, A., DeJesus-Hernandez, M., et al. (2012) · Nature Genetics · doi:10.1038/ng.1027 · Cited by 571
Parks, M., Cronn, R., & Liston, A. (2009) · BMC Biology · doi:10.1186/1741-7007-7-84 · Cited by 587
The impact of next-generation sequencing on genomics
Zhang, J., Chiodini, R., Badr, A., & Zhang, G. (2011) · Journal of Genetics and Genomics · doi:10.1016/j.jgg.2011.02.003 · Cited by 577
“The most common techniques for targeted sequence enrichment are either microarray-based (Summerer et al., 2009, 2010; Zheng et al., 2009; Igartua et al., 2010) or solution hybrid-based (Gnirke et al., 2009; Tewhey et al., 2009; Bainbridge et al., 2010).”
MethodAncient gene flow from early modern humans into Eastern Neanderthals
Kuhlwilm, M., Gronau, I., Hubisz, M. J., de Filippo, C., Prado-Martinez, J., Kircher, M., Fu, Q., Burbano, H. A., Lalueza-Fox, C., de la Rasilla, M., et al. (2016) · Nature · doi:10.1038/nature16544 · Cited by 577
Partial uracil–DNA–glycosylase treatment for screening of ancient DNA
Rohland, N., Harney, E., Mallick, S., Nordenfelt, S., & Reich, D. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2013.0624 · Cited by 572
The Genomic Landscape of Pediatric Ewing Sarcoma
Crompton, B. D., Stewart, C., Taylor-Weiner, A. N., Alexe, G., Kurek, K. C., Calicchio, M. L., Kieżun, A., Carter, S. L., Shukla, S. A., Mehta, S. S., et al. (2014) · Cancer Discovery · doi:10.1158/2159-8290.cd-13-1037 · Cited by 592
“Whole-exome sequencing Library construction followed procedures as previously reported (60).”
MethodMultiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products
Maričić, T., Whitten, M., & Pääbo, S. (2010) · PLoS ONE · doi:10.1371/journal.pone.0014004 · Cited by 581
Zanoni, P., Khetarpal, S. A., Larach, D. B., Hancock-Cerutti, W. F., Millar, J. S., Cuchel, M., DerOhannessian, S., Kontush, A., Surendran, P., Saleheen, D., et al. (2016) · Science · doi:10.1126/science.aad3517 · Cited by 545
Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations
Eleveld, T. F., Oldridge, D. A., Bernard, V., Köster, J., Daage, L. C., Diskin, S. J., Schild, L. G., Bessoltane, N., Bellini, A., Chicard, M., et al. (2015) · Nature Genetics · doi:10.1038/ng.3333 · Cited by 536
Wagle, N., Berger, M. F., Davis, M. J., Blumenstiel, B. S., DeFelice, M. T., Pochanard, P., Ducar, M. D., Hummelen, P. V., MacConaill, L. E., Hahn, W. C., et al. (2011) · Cancer Discovery · doi:10.1158/2159-8290.cd-11-0184 · Cited by 529
Self-citationGenetic heterogeneity of diffuse large B-cell lymphoma
Zhang, J., Grubor, V. D., Love, C., Banerjee, A., Richards, K. L., Mieczkowski, P. A., Dunphy, C. H., Choi, W., Au, W. Y., Srivastava, G., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1205299110 · Cited by 543
“These overall patterns of genetic variation in the DLBCL exomes are quite similar to what we would expect in the variation of normal exomes We performed whole-exome sequencing for all of these DLBCL and paired normal cases using the Agilent solution– based system of exon capture, which targets the NCBI Consensus CDS d…”
MethodCostello, M., Pugh, T. J., Fennell, T. J., Stewart, C., Lichtenstein, L., Meldrim, J. C., Fostel, J., Friedrich, D. C., Perrin, D., Dionne, D. A., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gks1443 · Cited by 520
Self-citationPlimack, E. R., Dunbrack, R. L., Brennan, T. A., Andrake, M., Zhou, Y., Serebriiskii, I. G., Slifker, M. J., Alpaugh, K. R., Dulaimi, E., Palma, N. A., et al. (2015) · European Urology · doi:10.1016/j.eururo.2015.07.009 · Cited by 521
“and ligation of indexed Illumina (San Diego, CA, USA) sequencing adaptors [11].”
BackgroundPerformance comparison of exome DNA sequencing technologies
Clark, M. J., Chen, R., Lam, H. Y. K., Karczewski, K. J., Chen, R., Euskirchen, G. M., Butte, A. J., & Snyder, M. P. (2011) · Nature Biotechnology · doi:10.1038/nbt.1975 · Cited by 531
High-Throughput Genomic Data in Systematics and Phylogenetics
Lemmon, E. M., & Lemmon, A. R. (2013) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-110512-135822 · Cited by 522
“The biotinylated probes, which form RNA-DNA complexes with target regions, are then captured with magnetic streptavidin-coated beads, unbound DNA is washed from the beads, and the captured DNA is then amplified via PCR using primers specific to adapters added during DNA library construction (Gnirke et al. 2009).”
BackgroundMethodInfluentialMethods for mapping 3D chromosome architecture
Kempfer, R., & Pombo, A. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0195-2 · Cited by 533
Recurrent AAV2-related insertional mutagenesis in human hepatocellular carcinomas
Nault, J.-C., Datta, S., Imbeaud, S., Franconi, A., Mallet, M., Couchy, G., Letouzé, E., Pilati, C., Verret, B., Blanc, J.-F., et al. (2015) · Nature Genetics · doi:10.1038/ng.3389 · Cited by 489
Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes
Briggs, A. W., Good, J. M., Green, R. E., Krause, J., Maričić, T., Stenzel, U., Lalueza‐Fox, C., Rudan, P., Brajković, D., Kućan, Ž., et al. (2009) · Science · doi:10.1126/science.1174462 · Cited by 508
A TALEN Genome-Editing System for Generating Human Stem Cell-Based Disease Models
Ding, Q., Lee, Y., Schaefer, E. A. K., Peters, D., Veres, A., Kim, K. J., Kuperwasser, N., Motola, D., Meissner, T. B., Hendriks, W. T. J., et al. (2012) · Cell stem cell · doi:10.1016/j.stem.2012.11.011 · Cited by 515
“Exome and Whole-Genome Sequence Analyses Exome sequencing and whole-genome sequencing were performed as previously described (Gnirke et al., 2009; Stransky et al., 2011).”
MethodDeng, J., Shoemaker, R., Xie, B., Gore, A., LeProust, E. M., Antosiewicz‐Bourget, J., Egli, D. M., Maherali, N., Park, I., Yu, J., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1530 · Cited by 502
Self-citationRAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping
Ali, O. A., O’Rourke, S. M., Amish, S. J., Meek, M. H., Luikart, G., Jeffres, C. A., & Miller, M. R. (2015) · Genetics · doi:10.1534/genetics.115.183665 · Cited by 496
“Multiple plate libraries are pooled, hybridized to biotinylated oligonucleotide baits corresponding to the targeted RAD tag loci, and captured to produce the final library enriched for the loci of interest.”
BackgroundMethodMolecular Diagnosis of Infantile Mitochondrial Disease with Targeted Next-Generation Sequencing
Calvo, S. E., Compton, A. G., Hershman, S. G., Lim, S. C., Lieber, D. S., Tucker, E. J., Laskowski, A., Garone, C., Liu, S., Jaffe, D. B., et al. (2012) · Science Translational Medicine · doi:10.1126/scitranslmed.3003310 · Cited by 476
Self-citationThe pluripotent regulatory circuitry connecting promoters to their long-range interacting elements
Schoenfelder, S., Furlan-Magaril, M., Mifsud, B., Tavares-Cadete, F., Sugar, R., Javierre, B.-M., Nagano, T., Katsman, Y., Sakthidevi, M., Wingett, S. W., et al. (2015) · Genome Research · doi:10.1101/gr.185272.114 · Cited by 460
“6% for FLC, in line with previously reported sequence capture approaches (Gnirke et al. 2009).”
InfluentialSelf-citationExome sequencing identifies GRIN2A as frequently mutated in melanoma
Program, N. C. S., Wei, X., Walia, V., Lin, J., Teer, J. K., Prickett, T. D., Gartner, J. J., Davis, S. R., Stemke‐Hale, K., Davies, M. A., et al. (2011) · Nature Genetics · doi:10.1038/ng.810 · Cited by 471
Hagman, K. D. F., Shahmirzadi, L., El‐Khechen, D., Powis, Z., Chao, E., Davis, B. T., Baxter, R. M., Zeng, W., Mroske, C., Parra, M. C., et al. (2014) · Genetics in Medicine · doi:10.1038/gim.2014.154 · Cited by 469
Exome sequencing supports a de novo mutational paradigm for schizophrenia
Xu, B., Roos, J. L., Dexheimer, P. J., Boone, B. E., Plummer, B., Levy, S., Gogos, J. A., & Karayiorgou, M. (2011) · Nature Genetics · doi:10.1038/ng.902 · Cited by 474
Annotating non-coding regions of the genome.
Alexander, R. P., Fang, G., Rozowsky, J., Snyder, M., & Gerstein, M. B. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2814 · Cited by 464
Recurrent SomaticDICER1Mutations in Nonepithelial Ovarian Cancers
Heravi‐Moussavi, A., Anglesio, M. S., Cheng, S., Senz, J., Yang, W., Prentice, L., Fejes, A. P., Chow, C., Tone, A. A., Kalloger, S. E., et al. (2011) · New England Journal of Medicine · doi:10.1056/nejmoa1102903 · Cited by 465
Adaptive mutability of colorectal cancers in response to targeted therapies
Russo, M., Crisafulli, G., Sogari, A., Reilly, N. M., Arena, S., Lamba, S., Bartolini, A., Amodio, V., Magrì, A., Novara, L., et al. (2019) · Science · doi:10.1126/science.aav4474 · Cited by 433
Microdroplet-based PCR enrichment for large-scale targeted sequencing
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., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1583 · Cited by 454
Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes
Beliveau, B. J., Joyce, E. F., Apostolopoulos, N., Yilmaz, F., Fonseka, C. Y., McCole, R. B., Chang, Y. K., Li, J. B., Senaratne, T. N., Williams, B. R., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1213818110 · Cited by 456
“(46, XY) metaphase spreads were obtained from Abbott Molecular (30-806010).”
BackgroundMethodClimate refugia: joint inference from fossil records, species distribution models and phylogeography
Gavin, D. G., Fitzpatrick, M. C., Gugger, P. F., Heath, K. D., Rodríguez‐Sánchez, F., Dobrowski, S. Z., Hampe, A., Hu, F. S., Ashcroft, M. B., Bartlein, P. J., et al. (2014) · New Phytologist · doi:10.1111/nph.12929 · Cited by 475
Jiménez-Sánchez, A., Memon, D., Pourpe, S., Veeraraghavan, H., Li, Y., Vargas, H. A., Gill, M. B., Park, K. J., Zivanovic, O., Konner, J. A., et al. (2017) · Cell · doi:10.1016/j.cell.2017.07.025 · Cited by 456
Mutation Profiling in Cholangiocarcinoma: Prognostic and Therapeutic Implications
Churi, C. R., Shroff, R. T., Wang, Y., Rashid, A., Kang, H. C., Weatherly, J., Zuo, M., Zinner, R., Hong, D. S., Meric‐Bernstam, F., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0115383 · Cited by 450
“NGS performed by Foundation Medicine used the Illumina Hiseq 2000 Platform for 236 targetable GA’s and the methods for the same have been described previously [13, 14].”
MethodPrognostic and predictive biomarkers in breast cancer: Past, present and future
Nicolini, A., Ferrari, P., & Duffy, M. J. (2017) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2017.08.010 · Cited by 442
Readfish enables targeted nanopore sequencing of gigabase-sized genomes
Payne, A., Holmes, N., Clarke, T., Munro, R., Debebe, J., & Loose, M. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-00746-x · Cited by 408
What can exome sequencing do for you?
Majewski, J., Schwartzentruber, J., Lalonde, E., Montpetit, A., & Jabado, N. (2011) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2011-100223 · Cited by 417
DNA sequencing technologies: 2006–2016
Mardis, E. R. (2017) · Nature Protocols · doi:10.1038/nprot.2016.182 · Cited by 421
Mutational Profile of Metastatic Breast Cancers: A Retrospective Analysis
Lefèbvre, C., Bachelot, T., Filleron, T., Pedrero, M., Campone, M., Soria, J., Massard, C., Lévy, C., Arnedos, M., Lacroix‐Triki, M., et al. (2016) · PLoS Medicine · doi:10.1371/journal.pmed.1002201 · Cited by 398
Massively Parallel Sequencing: The Next Big Thing in Genetic Medicine
Tucker, T., Marra, M. A., & Friedman, J. M. (2009) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2009.06.022 · Cited by 393
Metadata
- Authors
- 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., & Nusbaum, C.
- Affiliations
- Broad Institute (US)
- Agilent Technologies (United States) (US)
- Corresponding author
- Gnirke, Andreas
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2009-02
- Volume
- 27
- Issue
- 2
- Pages
- 182-189
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC2663421
- OpenAlex
- W2121531763
- Cited by
- 1,433
- References
- 25
- Citations by year
- 2026: 23 · 2025: 48 · 2024: 70 · 2023: 54 · 2022: 56 · 2021: 64 · 2020: 67 · 2019: 70 · 2018: 86 · 2017: 85 · 2016: 105 · 2015: 108 · 2014: 105 · 2013: 110 · 2012: 130
- FWCI
- 51.05
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Broad Institute
- National Human Genome Research Institute (U54HG003067, HG03067-05)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- targeted sequencing, DNA capture, exon capture, next-generation sequencing, genotype calling, human genome
- MeSH terms
- Base Composition, Bayes Theorem, Exons, Humans, Nucleic Acid Hybridization, Oligonucleotides, Sensitivity and Specificity, Reproducibility of Results, Polymerase Chain Reaction, Sequence Analysis, DNA, Biotinylation, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Genomics
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