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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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A Genome-Scale RNA Interference Screen Implicates NF1 Loss in Resistance to RAF Inhibition
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BackgroundCell-free DNA (cfDNA): Clinical Significance and Utility in Cancer Shaped By Emerging Technologies
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“However, development of the solution-based hybridization workflows (80) and refinements in sequencing library construction protocols such as improvements of ligation efficiency allowed drastic reduction of the quality and quantity of input DNA requirements, resulting in the development of the capability to analyze DNA…”
BackgroundNext-generation sequencing in the clinic: Promises and challenges
Xuan, J., Yu, Y., Qing, T., Guo, L., & Shi, L. M. (2012) · Cancer Letters · doi:10.1016/j.canlet.2012.11.025 · Cited by 355
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“For example, whole exomes [23] or regions associated with particular traits [19,24] can be targeted.”
BackgroundMethodResultInfluentialExome sequencing identifies GATA1 mutations resulting in Diamond-Blackfan anemia
Sankaran, V. G., Ghazvinian, R., Do, R., Thiru, P., Vergilio, J.-A., Beggs, A. H., Sieff, C. A., Orkin, S. H., Nathan, D. G., Lander, E. S., et al. (2012) · Journal of Clinical Investigation · doi:10.1172/jci63597 · Cited by 342
Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing
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Integrative analysis of the melanoma transcriptome
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Self-citationGenotyping-by-Sequencing in Plants
Deschamps, S., Llaca, V., & May, G. D. (2012) · Biology · doi:10.3390/biology1030460 · Cited by 348
“strategies for genome reduction such as multiplexed amplification of target sequences [105], molecular inversion probes (MIPs) [106] or the use of probes to capture DNA fragments by direct hybridization prior to sequencing [107,108] are available but can be labor intensive and rely heavily on existing sequence informa…”
BackgroundMutations in BCKD-kinase Lead to a Potentially Treatable Form of Autism with Epilepsy
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“To enrich targeted UCE loci, we followed an established workflow (Gnirke et al. 2009; Blumenstiel et al. 2010) incorporating several modifications to the protocol detailed in Faircloth et al.”
MethodPHF6 mutations in T-cell acute lymphoblastic leukemia
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Genetic Mapping and Exome Sequencing Identify Variants Associated with Five Novel Diseases
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Self-citationRecurrent and functional regulatory mutations in breast cancer
Rheinbay, E., Parasuraman, P., Grimsby, J., Tiao, G., Engreitz, J., Kim, J., Lawrence, M. S., Taylor-Weiner, A. N., Rodriguez-Cuevas, S. A., Rosenberg, M. W., et al. (2017) · Nature · doi:10.1038/nature22992 · Cited by 311
Self-citationThe expanding scope of DNA sequencing
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Exome sequencing: the sweet spot before whole genomes
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Archaeogenomic evidence reveals prehistoric matrilineal dynasty
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Implementing personalized cancer genomics in clinical trials
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The National Institutes of Health Undiagnosed Diseases Program: insights into rare diseases
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Adaptive evolution of multiple traits through multiple mutations at a single gene
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Comprehensive omic characterization of breast cancer in Mexican-Hispanic women
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ContEst: estimating cross-contamination of human samples in next-generation sequencing data
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Self-citationGenetic and Clonal Dissection of Murine Small Cell Lung Carcinoma Progression by Genome Sequencing
McFadden, D. G., Papagiannakopoulos, T. Y., Taylor-Weiner, A. N., Stewart, C., Carter, S. L., Cibulskis, K., Bhutkar, A. J., McKenna, A., Dooley, A. L., Vernon, A. N., et al. (2014) · Cell · doi:10.1016/j.cell.2014.02.031 · Cited by 284
Self-citationSequence capture of ultraconserved elements from bird museum specimens
McCormack, J. E., Tsai, W. L. E., & Faircloth, B. C. (2015) · Molecular Ecology Resources · doi:10.1111/1755-0998.12466 · Cited by 294
“We followed an established workflow for target enrichment (Gnirke et al. 2009) with modifications specified in Faircloth et al.”
MethodInfluentialPlimack, E. R., Hoffman-Censits, J. H., Viterbo, R., Trabulsi, E. J., Ross, E. A., Greenberg, R. E., Chen, D. Y. T., Lallas, C. D., Wong, Y., Lin, J., et al. (2014) · Journal of Clinical Oncology · doi:10.1200/jco.2013.53.2465 · Cited by 287
“Extracted DNA (200 ng) was sheared to approximately 100 to 400 bp by sonication, followed by end repair, dA addition, and ligation of indexed Illumina (San Diego, CA) sequencing adaptors.(19) Sequencing libraries were hybridization captured using a pool of 5 -biotinylated DNA oligonucleotides (Integrated DNA Technolog…”
MethodHigh-resolution characterization of a hepatocellular carcinoma genome
Totoki, Y., Tatsuno, K., Yamamoto, S., Arai, Y., Hosoda, F., Ishikawa, S., Tsutsumi, S., Sonoda, K., Totsuka, H., Shirakihara, T., et al. (2011) · Nature Genetics · doi:10.1038/ng.804 · Cited by 284
Yaeger, R., Cercek, A., O'Reilly, E. M., Reidy, D. L., Kemeny, N., Wolinsky, T., Capanu, M., Gollub, M. J., Rosen, N., Berger, M. F., et al. (2015) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-14-2779 · Cited by 276
“Target-specific probes for hybrid selection were designed as previously described (22, 23) to capture all protein-coding exons of 341 oncogenes, tumor suppressor genes, and components of pathways deemed actionable by targeted therapies (for full list see Supplementary Table S1).”
Evaluation of Hybridization Capture Versus Amplicon‐Based Methods for Whole‐Exome Sequencing
Samorodnitsky, E., Jewell, B. M., Hagopian, R., Miya, J., Wing, M. R., Lyon, E., Damodaran, S., Bhatt, D., Reeser, J. W., Datta, J., et al. (2015) · Human Mutation · doi:10.1002/humu.22825 · Cited by 271
“Yet, such array-mediated capture functions best on DNA fragments around 500-bp long, thus limiting targeting of closely spaced regions [Hodges et al., 2007; Gnirke et al., 2009], such as human exons [Clamp et al., 2007].”
BackgroundMethodInfluentialBi, K., Vanderpool, D., Singhal, S., Linderoth, T. P., Moritz, C. C., & Good, J. M. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-403 · Cited by 267
“Exon capture involves the hybridization of genomic libraries to short oligonucleotide baits complementary to complete or partial exomes printed on a microarray [7] or attached to magnetic beads in solution [11].”
BackgroundComparison of solution-based exome capture methods for next generation sequencing
Sulonen, A.-M., Ellonen, P., Almusa, H., Lepistö, M., Eldfors, S., Hannula, S., Miettinen, T., Tyynismaa, H., Salo, P. P., Heckman, C. A., et al. (2011) · Genome biology · doi:10.1186/gb-2011-12-9-r94 · Cited by 265
Exome Sequencing Can Improve Diagnosis and Alter Patient Management
Dixon‐Salazar, T., Silhavy, J. L., Udpa, N., Schroth, J., Bielas, S. L., Schaffer, A. E., Olvera, J., Bafna, V., Zaki, M. S., Abdel‐Salam, G. M. H., et al. (2012) · Science Translational Medicine · doi:10.1126/scitranslmed.3003544 · Cited by 262
“This kit provides >95% coverage at 1×, and >88% at 10× coverage, and paired-end sequencing of 75–base pair sequencing length was done with Illumina GAIIx or HiSeq2000 instruments (42).”
MethodSelf-citationSequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics
Harvey, M. G., Smith, B. T., Glenn, T. C., Faircloth, B. C., & Brumfield, R. T. (2016) · Systematic Biology · doi:10.1093/sysbio/syw036 · Cited by 263
“Streptavidin-coated paramagnetic beads are used to attract the biotinylated probes and hybridized (target) DNA library fragments, unwanted (non-target) portions of the DNA library are washed away, and targeted fragments are then released from the beads for sequencing (Gnirke et al. 2009; Fisher et al. 2011).”
BackgroundMethodInfluentialŻemojtel, T., Köhler, S., Mackenroth, L., Jäger, M., Hecht, J., Krawitz, P. M., Graul-Neumann, L. M., Doelken, S. C., Ehmke, N., Spielmann, M., et al. (2014) · Science Translational Medicine · doi:10.1126/scitranslmed.3009262 · Cited by 258
“Since our aim was to obtain nearly complete coverage of the DAG, we designed enrichment probes for the DAG using SureSelect technology ( 38 ).”
MethodPacific biosciences sequencing technology for genotyping and variation discovery in human data
Carneiro, M. O., Russ, C., Ross, M. G., Gabriel, S., Nusbaum, C., & DePristo, M. A. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-375 · Cited by 255
“Illumina HiSeq data are validated with 454 sequencing); for examples see[1,13-15].”
MethodSelf-citationTargeted enrichment of genomic DNA regions for next-generation sequencing
Mertes, F., ElSharawy, A., Sauer, S., van Helvoort, J. M. L. M., van der Zaag, P. J., Franke, A., Nilsson, M. F., Lehrach, H., & Brookes, A. J. (2011) · Briefings in Functional Genomics · doi:10.1093/bfgp/elr033 · Cited by 269
Mosaic PPM1D mutations are associated with predisposition to breast and ovarian cancer
Ruark, E., Snape, K. M. G., Humburg, P., Loveday, C., Bajrami, I., Brough, R., Rodrigues, D. N., Renwick, A., Seal, S., Ramsay, E., et al. (2012) · Nature · doi:10.1038/nature11725 · Cited by 250
Recurrent Mutations of MYD88 and TBL1XR1 in Primary Central Nervous System Lymphomas
González-Aguilar, A., Idbaïh, A., Boisselier, B., Habbita, N., Rossetto, M., Laurenge, A., Bruno, A., Jouvet, A., Polivka, M., Adam, C., et al. (2012) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-12-0845 · Cited by 243
“Clin Cancer Res; 18(19) October 1, 2012 Clinical Cancer Research5204 probes library (Human All Exon v2-46 Mb, Agilent), followed by paired-end 75b massively parallel sequencing on Illumina GAIIX (13).”
MethodInfluentialChiu, C. Y. (2013) · Current Opinion in Microbiology · doi:10.1016/j.mib.2013.05.001 · Cited by 247
“Another complementary approach is to perform target enrichment using biotinylated probes to enrich NGS libraries for sequences corresponding to pathogens, akin to now well-established techniques that have been developed in the cancer field [85].”
BackgroundClinical Implications of the Cancer Genome
MacConaill, L. E., & Garraway, L. A. (2010) · Journal of Clinical Oncology · doi:10.1200/jco.2009.27.4944 · Cited by 234
Fast-forward genetics enabled by new sequencing technologies
Schneeberger, K., & Weigel, D. (2011) · Trends in Plant Science · doi:10.1016/j.tplants.2011.02.006 · Cited by 225
Specific Capture and Whole-Genome Sequencing of Viruses from Clinical Samples
Depledge, D. P., Palser, A. L., Watson, S. J., Lai, I. Y.-C., Gray, E. R., Grant, P. R., Kanda, R. K., LeProust, E. M., Kellam, P., & Breuer, J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0027805 · Cited by 232
Self-citationA genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture
O'Geen, H., Henry, I. M., Bhakta, M. S., Meckler, J. F., & Segal, D. J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv137 · Cited by 219
“Next, we wanted to evaluate sequence capture as a highthroughput approach to simultaneously screen hundreds of potential off-target regions for indels and assess Cas9 activity at potential off-target sites (46).”
BackgroundMethodHER2/neu-directed therapy for biliary tract cancer
Javle, M. M., Churi, C. R., Kang, H. C., Shroff, R. T., Jankú, F., Surapaneni, R., Zuo, M., Barrera, C., Al-Shamsi, H. O., Krishnan, S., et al. (2015) · Journal of Hematology & Oncology · doi:10.1186/s13045-015-0155-z · Cited by 229
“For four samples, NGS was performed by Foundation Medicine using the Illumina Hiseq 2000 Platform (Illumina, San Diego, CA, USA) for 236 targetable GAs; the methods have been described previously [20, 21].”
MethodPierson, T. M., Adams, D. R., Bonn, F., Martinelli, P., Cherukuri, P. F., Teer, J. K., Hansen, N. F., Cruz, P., Mullikin, J. C., Blakesley, R. W., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002325 · Cited by 226
A Paleogenomic Perspective on Evolution and Gene Function: New Insights from Ancient DNA
Shapiro, B., & Hofreiter, M. (2014) · Science · doi:10.1126/science.1236573 · Cited by 192
“Large-scale enrichment approaches rely on a process of selective hybridization, whereby synthesized bait molecules representing targeted regions hybridize with and immobilize ancient DNA sequences in the library, and anything that does not hybridize is washed away (67).”
BackgroundPopulation genomics based on low coverage sequencing: how low should we go?
Buerkle, C. A., & Gompert, Z. (2012) · Molecular Ecology · doi:10.1111/mec.12105 · Cited by 220
“…al. 2010; Cao et al. 2011; Jones et al. 2012; genotyping-by-sequencing: van Orsouw et al. 2007; Baird et al. 2008; Andolfatto et al. 2011; Elshire et al. 2011; Parchman et al. 2012; and sequence capture: Gnirke et al. 2009; Li et al. 2010; Yi et al. 2010; Nadeau et al. 2011; Rohland & Reich 2012).”
BackgroundAncient goat genomes reveal mosaic domestication in the Fertile Crescent
Daly, K. G., Delser, P. M., Mullin, V. E., Scheu, A., Mattiangeli, V., Teasdale, M. D., Hare, A. J., Bürger, J., Verdugo, M. P., Collins, M. J., et al. (2018) · Science · doi:10.1126/science.aas9411 · Cited by 236
Targeted enrichment strategies for next‐generation plant biology
Cronn, R., Knaus, B. J., Liston, A., Maughan, P. J., Parks, M., Syring, J. V., & Udall, J. A. (2012) · American Journal of Botany · doi:10.3732/ajb.1100356 · Cited by 218
The genetic landscape of intellectual disability arising from chromosome X
Gécz, J., Shoubridge, C., & Corbett, M. (2009) · Trends in Genetics · doi:10.1016/j.tig.2009.05.002 · Cited by 207
High-throughput bisulfite sequencing in mammalian genomes
Smith, Z. D., Gu, H., Bock, C., Gnirke, A., & Meissner, A. (2009) · Methods · doi:10.1016/j.ymeth.2009.05.003 · Cited by 216
Self-citationVoss, M. H., Hakimi, A. A., Pham, C. G., Brannon, A. R., Chen, Y., Cunha, L. F., Akın, O., Liu, H., Takeda, S., Scott, S. N., et al. (2014) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-13-2345 · Cited by 219
“Target-specific probes for hybrid selection were designed as previously described (11, 12) to capture all protein-coding exons of 230 oncogenes, tumor suppressor genes, and components of pathways deemed actionable by targeted therapies (for full list see Supplementary Table S2).”
BackgroundBeaudoin, M., Goyette, P., Boucher, G., Lo, K. S., Rivas, M. A., Stevens, C. R., Alikashani, A., Ladouceur, M., Ellinghaus, D., Törkvist, L., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003723 · Cited by 218
“Sequencing and variant discovery The combined PCR products from each pooled DNA group were concatenated using the NotI adapters and sheared into fragments as previously described [36].”
MethodThe use of museum specimens with high-throughput DNA sequencers
Burrell, A. S., Disotell, T. R., & Bergey, C. M. (2014) · Journal of Human Evolution · doi:10.1016/j.jhevol.2014.10.015 · Cited by 224
“This method involves hybridizing genomic DNA to DNA or RNA probes or ‘baits’ present either in a solution (e.g., Gnirke et al., 2009) or on an array (e.g., Albert et al., 2007; Okou et al., 2007) and then washing away unbound, non-target DNA.”
MethodNext-generation sequencing: impact of exome sequencing in characterizing Mendelian disorders
Rabbani, B., Mahdieh, N., Hosomichi, K., Nakaoka, H., & Inoue, I. (2012) · Journal of Human Genetics · doi:10.1038/jhg.2012.91 · Cited by 217
Do, R., Balick, D. J., Li, H., Adzhubei, I. A., Sunyaev, S. R., & Reich, D. (2015) · Nature Genetics · doi:10.1038/ng.3186 · Cited by 206
Accurate and exact CNV identification from targeted high-throughput sequence data
Nord, A. S., Lee, M. J., King, M., & Walsh, T. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-184 · Cited by 209
Identifying conserved genomic elements and designing universal bait sets to enrich them
Faircloth, B. C. (2017) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12754 · Cited by 203
“One popular reduced representation approach is the targeted enrichment (Gnirke et al. 2009) of conserved or ultraconserved genomic elements (sensu Faircloth et al. 2012).”
BackgroundMethodBainbridge, M. N., Wang, M., Wu, Y., Newsham, I., Muzny, D. M., Jefferies, J. L., Albert, T. J., Burgess, D. L., & Gibbs, R. A. (2011) · Genome biology · doi:10.1186/gb-2011-12-7-r68 · Cited by 208
Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencingPreprint
Teer, J. K., Bonnycastle, L. L., Chines, P. S., Hansen, N. F., Aoyama, N., Swift, A. J., Abaan, H. Ö., Albert, T. J., Program, N. C. S., Margulies, E. H., et al. (2010) · Genome Research · doi:10.1101/gr.106716.110 · Cited by 206
Applications of Immunogenomics to Cancer
Liu, X. S., & Mardis, E. R. (2017) · Cell · doi:10.1016/j.cell.2017.01.014 · Cited by 207
A Robust Framework for Microbial Archaeology
Warinner, C., Herbig, A., Mann, A. E., Yates, J. A. F., Weiß, C. L., Burbano, H. A., Orlando, L., & Krause, J. (2017) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-091416-035526 · Cited by 204
“The key turning point was the availability of high-throughput sequencing (HTS), a transformative innovation in DNA sequencing (114, 115), and sequence capture enrichment methods (16, 20, 62, 75)—two techniques that increased both sample throughput and data output by orders of magnitude.”
BackgroundPD-1 Blockade in Advanced Adrenocortical Carcinoma
Raj, N. P., Zheng, Y., Kelly, V., Katz, S. S., Chou, J. F., Do, R. K. G., Capanu, M., Zamarin, D., Saltz, L. B., Ariyan, C. E., et al. (2019) · Journal of Clinical Oncology · doi:10.1200/jco.19.01586 · Cited by 208
“Age, years, median (range) 62 (19-87) Time since diagnosis to C1D1, months, median (range) 15 (1-131) Ethnicity”
BackgroundCapturing Protein-Coding Genes Across Highly Divergent Species
Li, C., Hofreiter, M., Straube, N., Corrigan, S. L., & Naylor, G. J. P. (2013) · BioTechniques · doi:10.2144/000114039 · Cited by 194
NMNAT1 mutations cause Leber congenital amaurosis
Falk, M. J., Zhang, Q., Nakamaru‐Ogiso, E., Kannabiran, C., Fonseca-Kelly, Z., Chakarova, C. F., Audo, I. S., Mackay, D. S., Zeitz, C., Borman, A. D., et al. (2012) · Nature Genetics · doi:10.1038/ng.2361 · Cited by 201
Yaeger, R. D., Shah, M. A., Miller, V. A., Kelsen, J. R., Wang, K., Heins, Z. J., Ross, J. S., He, Y., Sanford, E. M., Yantiss, R. K., et al. (2016) · Gastroenterology · doi:10.1053/j.gastro.2016.04.001 · Cited by 200
Probiotic neoantigen delivery vectors for precision cancer immunotherapy
Redenti, A., Im, J., Redenti, B. J., Li, F., Rouanne, M., Sheng, Z., Sun, W. Y., Gurbatri, C. R., Huang, S., Komaranchath, M., et al. (2024) · Nature · doi:10.1038/s41586-024-08033-4 · Cited by 216
“Exome capture from mouse tumour and tail DNA tripli-cates was conducted using Agilent SureSelectXT All Exon kit for target enrichment DNA library preparation 56 , according to the manufacturer’s instructions (Agilent).”
Exploration of liver cancer genomes
Shibata, T., & Aburatani, H. (2014) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2014.6 · Cited by 202
Brownstein, Z., Friedman, L. M., Shahin, H., Oron‐Karni, V., Kol, N., Rayyan, A. A., Parzefall, T., Lev, D., Shalev, S. A., Frydman, M., et al. (2011) · Genome biology · doi:10.1186/gb-2011-12-9-r89 · Cited by 195
Levin, J. Z., Berger, M. F., Adiconis, X., Rogov, P., Melnikov, A., Fennell, T., Nusbaum, C., Garraway, L. A., & Gnirke, A. (2009) · Genome biology · doi:10.1186/gb-2009-10-10-r115 · Cited by 199
Self-citationPopulation‐level inferences from environmental DNA—Current status and future perspectives
Sigsgaard, E. E., Jensen, M. R., Winkelmann, I. E., Møller, P. R., Hansen, M. M., & Thomsen, P. F. (2019) · Evolutionary Applications · doi:10.1111/eva.12882 · Cited by 200
“Relatively small amounts of starting DNA material are required for this approach (Gnirke et al., 2009; Hodges et al., 2007), which has made it advantageous in studies where endogenous DNA content is low and fragment size is small, such as in ancient samples (Enk et al., 2014).”
BackgroundDerivation of HLA types from shotgun sequence datasets
Warren, R. M., Choe, G. H., Freeman, D. J., Castellarin, M. L., Munro, S., Moore, R. A., & Holt, R. A. (2012) · Genome Medicine · doi:10.1186/gm396 · Cited by 197
“In separate experiments, we removed HLA CDS, exonic regions and genes from 15K randomly selected Ensembl [26] transcripts, approximately 220K exon regions [27] (SureSelect Target Enrichment, Agilent Technologies, Inc.”
MethodNext Generation Sequencing of Ancient DNA: Requirements, Strategies and Perspectives
Knapp, M., & Hofreiter, M. (2010) · Genes · doi:10.3390/genes1020227 · Cited by 207
The neandertal genome and ancient DNA authenticity
Green, R. E., Briggs, A. W., Krause, J., Prüfer, K., Burbano, H. A., Siebauer, M., Lachmann, M., & Pääbo, S. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.222 · Cited by 190
The impact of next-generation sequencing technologies on HLA research
Hosomichi, K., Shiina, T., Tajima, A., & Inoue, I. (2015) · Journal of Human Genetics · doi:10.1038/jhg.2015.102 · Cited by 193
Targeted exome sequencing of suspected mitochondrial disorders
Lieber, D. S., Calvo, S. E., Shanahan, K., Slate, N. G., Liu, S., Hershman, S. G., Gold, N. B., Chapman, B., Thorburn, D. R., Berry, G. T., et al. (2013) · Neurology · doi:10.1212/wnl.0b013e3182918c40 · Cited by 188
Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes
Ma, W., Ay, F., Lee, C., Gülsoy, G., Deng, X., Cook, S. M., Hesson, J., Cavanaugh, C., Ware, C. B., Krumm, A., et al. (2014) · Nature Methods · doi:10.1038/nmeth.3205 · Cited by 191
Performance comparison of four exome capture systems for deep sequencing
Chilamakuri, C. S. R., Lorenz, S., Madoui, M., Vodák, D., Sun, J., Hovig, E. J., Myklebost, O., & Meza‐Zepeda, L. A. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-449 · Cited by 185
“Base composition has been shown to bias sequencing efficiency, thus coverage may be low for sequences with high GC or AT content [17].”
BackgroundKerick, M., Isau, M., Timmermann, B., Sültmann, H., Herwig, R., Krobitsch, S., Schaefer, G., Verdorfer, I., Bartsch, G. H., Klocker, H., et al. (2011) · BMC Medical Genomics · doi:10.1186/1755-8794-4-68 · Cited by 181
DNA methylation in lung cells is associated with asthma endotypes and genetic risk
Nicodemus-Johnson, J., Myers, R. A., Sakabe, N. J., Sobreira, D. R., Hogarth, D. K., Naureckas, E. T., Sperling, A. I., Solway, J., White, S. R., Nobrega, M. A., et al. (2016) · JCI Insight · doi:10.1172/jci.insight.90151 · Cited by 180
“Promoter capture was performed as described previously (53) with the following changes: the in situ Hi-C library was hybridyzed to 81,735 biotinylated 120-bp custom RNA oligomers (Custom Array, Supplemental Table 7) targeting promoter regions.”
MethodPersonalized Diagnosis and Management of Congenital Cataract by Next-Generation Sequencing
Gillespie, R. L., O’Sullivan, J., Ashworth, J. L., Bhaskar, S. S., Williams, S. G., Biswas, S., Kehdi, E., Ramsden, S., Clayton‐Smith, J., Black, G. C. M., et al. (2014) · Ophthalmology · doi:10.1016/j.ophtha.2014.06.006 · Cited by 180
Hodges, E. C., Rooks, M. G., Xuan, Z., Bhattacharjee, A., Gordon, D. B., Brizuela, L., McCombie, W. R., & Hannon, G. J. (2009) · Nature Protocols · doi:10.1038/nprot.2009.68 · Cited by 174
Talkowski, M. E., Ernst, C., Heilbut, A. M., Chiang, C., Hanscom, C., Lindgren, A. M., Kirby, A. W., Liu, S., Muddukrishna, B., Ohsumi, T. K., et al. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.03.013 · Cited by 177
Tucker, E. J., Hershman, S. G., Köhrer, C., Belcher-Timme, C. A., Patel, J., Goldberger, O., Christodoulou, J., Silberstein, J. M., McKenzie, M., Ryan, M. T., et al. (2011) · Cell Metabolism · doi:10.1016/j.cmet.2011.07.010 · Cited by 176
From human genome to cancer genome: The first decadePreprint
Wheeler, D. A., & Wang, L. (2013) · Genome Research · doi:10.1101/gr.157602.113 · Cited by 183
“The introduction of DNA sequence enrichment technologies from NimbleGen and Agilent (Albert et al. 2007; Gnirke et al. 2009) enabled WES on large scales.”
MethodLeaché, A. D., Chavez, A. S., Jones, L. N., Grummer, J. A., Gottscho, A. D., & Linkem, C. W. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv026 · Cited by 173
“Sequence capture methods use short probes (60–120 nucleotides) to hybridize to specific genomic regions that are subsequently sequenced, and therefore these methods require some advanced level of knowledge of the genomes under investigation (Gnirke et al. 2009; Mamanova et al. 2010).”
MethodCapturing sequence diversity in metagenomes with comprehensive and scalable probe design
Metsky, H. C., Siddle, K. J., Gladden, A. D., Qu, J., Yang, D. K., Brehio, P., Goldfarb, A., Piantadosi, A. L., Wohl, S., Carter, A., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-018-0006-x · Cited by 172
Self-citationWei, X., Ju, X.-C., Yi, X., Zhu, Q., Qu, N., Liu, T., Chen, Y., Jiang, H., Yang, G., Ruan, Z., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0029500 · Cited by 169
The origin and evolution of maize in the Southwestern United States
da Fonseca, R. R., Smith, B. D., Wales, N., Cappellini, E., Skoglund, P., Fumagalli, M., Castruita, J. A. S., Carøe, C., Ávila‐Arcos, M. C., Hufnagel, D. E., et al. (2015) · Nature Plants · doi:10.1038/nplants.2014.3 · Cited by 168
Churko, J. M., Mantalas, G. L., Snyder, M. P., & Wu, J. C. (2013) · Circulation Research · doi:10.1161/circresaha.113.300939 · Cited by 183
Comparison of Next-Generation Sequencing Systems
Liu, L., Li, Y., Li, S., Hu, N., He, Y., Pong, R., Lin, D., Lü, L., & Law, M. (2014) · Apple Academic Press eBooks · doi:10.1201/b16568-3 · Cited by 168
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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