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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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Cites
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Padlock Probes: Circularizing Oligonucleotides for Localized DNA Detection
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A large genome center's improvements to the Illumina sequencing system
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“PCR amplification of the catch and sequencing itself is also known to introduce bia”
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Allen, E. M. V., Golay, H. G., Liu, Y., Koyama, S., Wong, K. K. W., Taylor-Weiner, A. N., Giannakis, M., Harden, M. V., Rojas‐Rudilla, V., Chevalier, A. A., et al. (2015) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-15-0024 · Cited by 69
The impact of GC bias on phylogenetic accuracy using targeted enrichment phylogenomic data
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“Faircloth et al.’s (2012) approach uses in-solution sequence capture (sensu Gnirke et al., 2009) of large quantities of so-called ‘‘ultraconserved elements” (UCEs).”
Mutation Scanning in Wheat by Exon Capture and Next-Generation Sequencing
King, R., Bird, N., Ramirez-Gonzalez, R. H., Coghill, J. A., Patil, A., Hassani‐Pak, K., Uauy, C., & Phillips, A. L. (2015) · PLoS ONE · doi:10.1371/journal.pone.0137549 · Cited by 69
“Similarly, analysis of the efficiency of exon capture at different G+C contents suggested that although the median G+C content of wheat exons is 48%, exons with a G+C content of 48–60% were captured most effectively whereas exons with unusually high or low G+C contents had low read coverage (S3 Fig), as has been noted…”
BackgroundKohsaka, S., Tatsuno, K., Ueno, T., Nagano, M., Shinozaki‐Ushiku, A., Ushiku, T., Takai, D., Ikegami, M., Kobayashi, H., Kage, H., et al. (2019) · Cancer Science · doi:10.1111/cas.13968 · Cited by 69
Dominant mutations in mtDNA maintenance gene SSBP1 cause optic atrophy and foveopathy
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“For a detailed explanation of the protocol, see the publication in Nature Methods(34).”
BackgroundMutation inSNAP25as a novel genetic cause of epilepsy and intellectual disability
Rohena, L. O., Neidich, J., Cho, M. T., Hagman, K. D. F., Tang, S., Devinsky, O., & Chung, W. K. (2013) · Rare Diseases · doi:10.4161/rdis.26314 · Cited by 67
“DNA from the parents and proband were prepared using the SureSelect Target Enrichment System (Agilent Technologies).(11) The exome libraries were then applied to the solid surface flow cell for clonal amplification and sequencing using paired-end, 100-cycle chemistry on the Illumina HiSeq 2000 (Illumina).”
MethodDapprich, J., Ferriola, D., Mackiewicz, K., Clark, P., Rappaport, E. F., D’Arcy, M. E., Sasson, A., Gai, X., Schug, J., Kaestner, K. H., et al. (2016) · BMC Genomics · doi:10.1186/s12864-016-2836-6 · Cited by 68
“They are typically based upon a multiplexed PCR amplification reaction [12], DNA hybridization to a capture oligonucleotide (either on an array or in solution) [13–15] or DNA capture via molecular inversion probe circularization [16, 17].”
MethodPast climate changes, population dynamics and the origin of Bison in Europe
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“For the production of complete mitogenome sequences, we developed a sequence capture approach using biotinylated RNA baits [47].”
Chang, D., Knapp, M., Enk, J. M., Lippold, S., Kircher, M., Lister, A. M., MacPhee, R. D. E., Widga, C., Czechowski, P., Sommer, R. S., et al. (2017) · Scientific Reports · doi:10.1038/srep44585 · Cited by 69
Beyond assembly: the increasing flexibility of single-molecule sequencing technology
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“For example, target regions (for example, ~750,000 bp 33 ) by tiling probes across the region in one reaction.”
Chou, L., Liu, C.-S. J., Boese, B., Zhang, X., & Mao, R. (2009) · Clinical Chemistry · doi:10.1373/clinchem.2009.132639 · Cited by 67
Mizuguchi, T., Suzuki, T., Abe, C., Umemura, A., Tokunaga, K., Kawai, Y., Nakamura, M., Nagasaki, M., Kinoshita, K., Okamura, Y., et al. (2019) · Journal of Human Genetics · doi:10.1038/s10038-019-0569-5 · Cited by 65
Zhao, Y., Fang, L. T., Shen, T.-W., Choudhari, S., Talsania, K., Chen, X., Shetty, J., Kriga, Y., Tran, B. Q., Zhu, B., et al. (2021) · Scientific Data · doi:10.1038/s41597-021-01077-5 · Cited by 67
Non-sequential and multi-step splicing of the dystrophin transcript
Gazzoli, I., Pulyakhina, I., Verwey, N. E., Ariyürek, Y., Laros, J. F. J., Hoen, P. A. C. ’., & Aartsma-Rus, A. M. (2015) · RNA Biology · doi:10.1080/15476286.2015.1125074 · Cited by 66
Won, H. H., Scott, S. N., Brannon, A. R., Shah, R. H., & Berger, M. F. (2013) · Journal of Visualized Experiments · doi:10.3791/50710 · Cited by 65
Moresco, E. M. Y., Li, X., & Beutler, B. (2013) · American Journal Of Pathology · doi:10.1016/j.ajpath.2013.02.002 · Cited by 69
Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing
Lee, E. J., Pei, L., Srivastava, G. P., Joshi, T., Kushwaha, G., Choi, J.-H., Robertson, K. D., Wang, X., Colbourne, J. K., Zhang, L., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr598 · Cited by 65
EVIDENCE OF ADAPTATION FROM ANCESTRAL VARIATION IN YOUNG POPULATIONS OF BEACH MICE
DOMINGUES, V. S., Poh, Y.-P., Peterson, B. K., Pennings, P. S., Jensen, J. D., & Hoekstra, H. E. (2012) · Evolution · doi:10.1111/j.1558-5646.2012.01669.x · Cited by 64
Origin and Health Status of First-Generation Africans from Early Colonial Mexico
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“Whole-genome and immune-genes captures Using in-solution capture based on modified immortalized probe sequences [151], target immunity genes sequences or a panel of around 1,237,207 single nucleotide polymorphisms (SNPs) were enriched via in-solution capture from the total DNA in the sequencing libraries [152–154].”
Ancient Plant Genomics in Archaeology, Herbaria, and the Environment
Kistler, L., Bieker, V. C., Martin, M. D., Pedersen, M. W., Ramos‐Madrigal, J., & Wales, N. (2020) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-081519-035837 · Cited by 69
“Following library preparation, samples can be treated similar to highly fragmented modern DNA for shotgun-sequenced or target enrichment using hybridization capture (45).”
BackgroundMethodGenome‐scale target capture of mitochondrial and nuclear environmental DNA from water samples
Jensen, M. R., Sigsgaard, E. E., Liu, S., Manica, A., Bach, S., Hansen, M. M., Møller, P. R., & Thomsen, P. F. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13293 · Cited by 64
“Target enrichment via DNA hybridization capture (“target capture”) (Gnirke et al., 2009), is a well-tested method for obtaining DNA data from samples with high nontarget content.”
MethodHybridization: a ‘double-edged sword’ for Neotropical plant diversity
Schley, R., Twyford, A. D., & Pennington, R. T. (2021) · Botanical Journal of the Linnean Society · doi:10.1093/botlinnean/boab070 · Cited by 64
The forest for the trees: evaluating molecular phylogenies with an emphasis on higher-level Decapoda
Timm, L. E., & Bracken‐Grissom, H. D. (2015) · Journal of Crustacean Biology · doi:10.1163/1937240x-00002371 · Cited by 62
“Such sequencing efforts allow analysis of hundreds to thousands of markers across the genomes of hundreds of individuals (Gnirke et al., 2009; Mamanova et al., 2010; Lemmon and Lemmon, 2012; Lemmon et al., 2012), generating unprecedented amounts of data while using fewer resources.”
BackgroundNext‐generation sequencing – feasibility and practicality in haematology
Kohlmann, A., Großmann, V., Nadarajah, N., & Haferlach, T. (2013) · British Journal of Haematology · doi:10.1111/bjh.12194 · Cited by 65
“Even more specifically, various capturing technologies and library preparation technologies allow the detailed targeted resequencing of candidate genes or chromosomal regions of interest (Albert et al, 2007; Gnirke et al, 2009; Teer et al, 2010).”
BackgroundThe GENCODE exome: sequencing the complete human exome
Coffey, A. J., Kokocinski, F., Calafato, M., Scott, C., Palta, P., Drury, E., Joyce, C. J., LeProust, E. M., Harrow, J., Hunt, S. E., et al. (2011) · European Journal of Human Genetics · doi:10.1038/ejhg.2011.28 · Cited by 64
Self-citationMulti‐locus phylogenetics, lineage sorting, and reticulation in Pinus subsection Australes
Gernandt, D. S., Dugua, X. A., Vázquez‐Lobo, A., Willyard, A., Moreno‐Letelier, A., de la Rosa, J. A. P., Piñero, D., & Liston, A. (2018) · American Journal of Botany · doi:10.1002/ajb2.1052 · Cited by 64
“We used targeted sequence capture (Gnirke et al., 2009) combined with genome skimming (HybSeq; Weitemier et al.”
MethodPastoret, C., Desmots, F., Drillet, G., Gallou, S. L., Boulland, M., Thannberger, A., Doncker, A., Salaün, V., Damaj, G. L., Veyrat‐Masson, R., et al. (2021) · Blood · doi:10.1182/blood.2020006721 · Cited by 65
Continuously tunable nucleic acid hybridization probes
Wu, L. R., Wang, J. S., Fang, J. Z., Evans, E. R., Pinto, A., Pekker, I., Boykin, R., Ngouenet, C., Webster, P. J., Beechem, J., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3626 · Cited by 64
“For example, allele-specific PCR primers may benefit from a controllable tradeoff between mutation sensitivity and amplification efficiency (i.e. Cq delay), and hybrid-capture probes for NGS target enrichment 27 could benefit from yield uniformity or allele-specific enrichment.”
High‐density SNP assay development for genetic analysis in maritime pine ( P inus pinaster)
Plomion, C., Bartholomé, J., Lesur, I., Boury, C., Rodríguez‐Quilón, I., Lagraulet, H., Ehrenmann, F., Bouffier, L., Gion, J., Grivet, D., et al. (2015) · Molecular Ecology Resources · doi:10.1111/1755-0998.12464 · Cited by 67
“Considering missing data allele drop out concerns, future development of marker technology in this species will be based on sequence capture and direct sequencing (Gnirke et al. 2009).”
BackgroundCao, H., Wu, J., Wang, Y., Jiang, H., Zhang, T., Liu, X., Xu, Y., Liang, D., Gao, P., Sun, Y., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0069388 · Cited by 64
“Target region capture sequencing was developed mainly to enrich and sequence specific regions of particular interest, such as specific exons or entire exomes [12,13].”
BackgroundCongenital lethal motor neuron disease with a novel defect in ribosome biogenesis
Butterfield, R. J., Stevenson, T. J., Xing, L., Newcomb, T. M., Nelson, B., Zeng, W., Li, X., Lu, H., Lu, H. Y., Hagman, K. D. F., et al. (2014) · Neurology · doi:10.1212/wnl.0000000000000305 · Cited by 63
“Genomic DNA was prepared for whole exome sequencing using the SureSelect Target Enrichment System (Agilent Technologies, Santa Clara, CA) according to the manufacturer’s protocol.(11) Briefly, each DNA sample was sheared, blunt-end repaired, and tagged using indexed adapters.”
MethodIdentification of rare alleles and their carriers using compressed se(que)nsing
Shental, N., Amir, A., & Zuk, O. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq675 · Cited by 69
The Limits of Hyb-Seq for Herbarium Specimens: Impact of Preservation Techniques
Forrest, L. L., Hart, M. L., Hughes, M., Wilson, H. P., Chung, K., Tseng, Y., & Kidner, C. A. (2019) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2019.00439 · Cited by 66
“Hybrid capture, or hybrid baits (Gnirke et al., 2009), by focusing sequencing effort on phylogenetically useful plant sequences, gives much higher coverage and less contamination.”
BackgroundTargeted Exon Sequencing by In‐Solution Hybrid Selection
Blumenstiel, B. S., Cibulskis, K., Fisher, S., DeFelice, M. T., Barry, A. J., Fennell, T. J., Abreu, J., Minie, B., Costello, M., Young, G., et al. (2010) · Current Protocols in Human Genetics · doi:10.1002/0471142905.hg1804s66 · Cited by 62
Self-citationMitchell, K. G., Diao, L., Karpinets, T. V., Negrao, M. V., Tran, H. T., Parra, E. R., Corsini, E. M., Reuben, A., Federico, L., Bernatchez, C., et al. (2020) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2019-000405 · Cited by 64
Potter, S., Bragg, J. G., Peter, B. M., Bi, K., & Moritz, C. C. (2016) · Molecular Ecology · doi:10.1111/mec.13546 · Cited by 61
“2008) and targeted sequence capture (Briggs et al. 2009; Gnirke et al. 2009).”
MethodFilter-based hybridization capture of subgenomes enables resequencing and copy-number detection
Herman, D. S., Hovingh, G. K., Iartchouk, O., Rehm, H. L., Kucherlapati, R., Seidman, J. G., & Seidman, C. E. (2009) · Nature Methods · doi:10.1038/nmeth.1343 · Cited by 61
Speciation with Gene Flow in North AmericanMyotisBats
Morales, A. E., Jackson, N. D., Dewey, T., O’Meara, B. C., & Carstens, B. C. (2016) · Systematic Biology · doi:10.1093/sysbio/syw100 · Cited by 61
“During the enrichment, the protocol provided by MYcroarray was followed, which is based on the workflow described by Gnirke et al. (2009).”
MethodPhenotypic extremes in rare variant study designs
Peloso, G. M., Rader, D. J., Gabriel, S., Kathiresan, S., Daly, M. J., & Neale, B. M. (2016) · European Journal of Human Genetics · doi:10.1038/ejhg.2015.197 · Cited by 58
Self-citationProgress and prospects of next-generation sequencing testing for inherited retinal dystrophy
Chiang, J., Lamey, T. M., McLaren, T. L., Thompson, J. A., Montgomery, H., & Roach, J. N. D. (2015) · Expert Review of Molecular Diagnostics · doi:10.1586/14737159.2015.1081057 · Cited by 60
“The arrival of a liquid-phase, hybridization-based method [18,19], and other modified methods, have eliminated the preceding first and third factors.”
MethodWong, S. Q., Li, J., Salemi, R., Sheppard, K. E., Do, H., Tothill, R. W., McArthur, G. A., & Dobrovic, A. (2013) · Scientific Reports · doi:10.1038/srep03494 · Cited by 59
Shih, S., Bose, N., Gonçalves, A., Erlich, H., & Calloway, C. (2018) · Genes · doi:10.3390/genes9010049 · Cited by 60
“This feature is critical in evaluating the potential for stochastic variation in sequence read counts and, consequently, in the establishment of thresholds for interpreting sequencing data [33,63].”
BackgroundMethodInfluentialTargeted Enrichment: Maximizing Orthologous Gene Comparisons across Deep Evolutionary Time
Hedtke, S. M., Morgan, M. J., Cannatella, D. C., & Hillis, D. M. (2013) · PLoS ONE · doi:10.1371/journal.pone.0067908 · Cited by 61
“Only DNA that successfully hybridizes to these probes is sequenced, and thus the resulting sequences are enriched for these target regions [19,20,21,22].”
BackgroundMullikin, J. C., Pierson, T. M., Simeonov, D. R., Sincan, M., Adams, D. R., Markello, T. C., Golas, G. A., Fajardo, K. V. F., Hansen, N. F., Cherukuri, P. F., et al. (2011) · European Journal of Human Genetics · doi:10.1038/ejhg.2011.222 · Cited by 59
High-quality DNA sequence capture of 524 disease candidate genes
Shen, P., Wang, W., Krishnakumar, S., Palm, C. J., Chi, A.-K., Enns, G. M., Davis, R. W., Speed, T. P., Mindrinos, M. N., & Scharfe, C. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1018981108 · Cited by 59
Mitogenomic analyses from ancient DNA
Paijmans, J. L. A., Gilbert, M. T. P., & Hofreiter, M. (2012) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2012.06.002 · Cited by 65
“…on a solid phase such as the surface of a microarray (Hodges et al., 2009, 2007) or hybridisation is performed in solution with biotinylated baits and the targetDNA is subsequently immobilised using streptavidin-covered beads (Briggs et al., 2009; Gnirke et al., 2009; Maricic et al., 2010).”
Further delineation of the phenotype caused by biallelic variants in the WDR4 gene
Trimouille, A., Lasseaux, E., Barat, P., Deiller, C., Drunat, S., Rooryck, C., Arveiler, B., & Lacombe, D. (2017) · Clinical Genetics · doi:10.1111/cge.13074 · Cited by 59
“For detailed explanations of the process, see Gnirke et al.9 Bioinformatic pipeline is detailed in Appendix S1.”
MethodValencia, C. A., Rhodenizer, D., Bhide, S., Chin, E., Littlejohn, M. R., Keong, L. M., Rutkowski, A., Bönnemann, C. G., & Hegde, M. (2012) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2012.01.009 · Cited by 58
“C11 RDT 8 (8) 7 (6) SS 9 (16) 7 (6) C12 RDT (53) (5) SS (43) (5) C13 RDT 6 (14) 5 (7) SS 12 (19) 4 (2) C14 RDT 7 (4) 15 (1) SS 16 (7) 9 (0) C15 RDT 20 (6) 11 (0) SS 23 (4) 11 (0) W16 RDT 21 12 SS 17 11 1 RDT 18 10 SS 16 9 3 RDT 15 6 SS 21 5 7 RDT 17 9 SS 22 6 8 RDT 24 6 SS 11 7 9 RDT 15 18 SS 20 15 10 RDT 20 8 SS 18 8…”
Next‐generation sequencing for mitochondrial disorders
Carroll, C. J., Brilhante, V., & Suomalainen, A. (2013) · British Journal of Pharmacology · doi:10.1111/bph.12469 · Cited by 58
“regions and to reduce complexity, exome sequence capture methodology was developed: instead of setting up thousands of PCR reactions to specific genes and their exonic regions, parallel enrichment of target regions could be managed in a single experiment (Gnirke et al., 2009).”
BackgroundMethods for the Preparation of Large Quantities of Complex Single-Stranded Oligonucleotide Libraries
Murgha, Y. E., Rouillard, J. M., & Gülari, E. (2014) · PLoS ONE · doi:10.1371/journal.pone.0094752 · Cited by 58
“Targeted next-generation sequencing relies heavily on oligonucleotide libraries as a source of baits to capture, either in the form of DNA padlock probes for the circularization of targeted sequences [6,7] or in the form of RNA baits for the direct capture of sequencing genomic DNA library fragments (Agilent’s SureSel…”
MethodExome sequencing greatly expedites the progressive research of Mendelian diseases
Zhang, X. (2014) · Frontiers of Medicine · doi:10.1007/s11684-014-0303-9 · Cited by 58
“Agilent, Nimblegen, Illumina, and other companies offer exome-enrichment kits for exome capture [14,15].”
BackgroundThe limits and potential of paleogenomic techniques for reconstructing grapevine domestication
Wales, N., Ramos‐Madrigal, J., Cappellini, E., Baez, A. C., Castruita, J. A. S., Romero-Navarro, J. A., Carøe, C., Ávila‐Arcos, M. C., Peñaloza, F., Moreno-Mayar, J. V., et al. (2016) · Journal of Archaeological Science · doi:10.1016/j.jas.2016.05.014 · Cited by 58
Characterization of background noise in capture-based targeted sequencing data
Park, G., Park, J. K., Shin, S., Jeon, H.-J., Kim, N. K. D., Kim, Y. J., Shin, H., Lee, E., Lee, K. H., Son, D., et al. (2017) · Genome biology · doi:10.1186/s13059-017-1275-2 · Cited by 60
Yi, M., Zhao, Y., Li, J., He, M., Kebebew, E., & Stephens, R. M. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku392 · Cited by 61
“It has been shown that both the target enrichment strategy (12,13) and the NGS platform used with exome-seq technologies (4,14) have a large impact on the quality and coverage efficiency of sequencing reads and the resulting variant calls.”
BackgroundORF Capture-Seq as a versatile method for targeted identification of full-length isoforms
Sheynkman, G., Tuttle, K. S., Laval, F., Tseng, E., Underwood, J. G., Yu, L., Dong, D., Smith, M. L., Sebra, R., Willems, L., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16174-z · Cited by 55
Alaerts, M., & Del‐Favero, J. (2009) · Human Mutation · doi:10.1002/humu.21042 · Cited by 56
Whole genome sequencing analysis of Plasmodium vivax using whole genome capture
Bright, A., Tewhey, R., Abeles, S. R., Chuquiyauri, R., Llanos‐Cuentas, A., Ferreira, M. U., Schork, N. J., Vinetz, J. M., & Winzeler, E. A. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-262 · Cited by 57
Graham, A. M., & McCracken, K. G. (2019) · Heredity · doi:10.1038/s41437-018-0173-z · Cited by 57
“In-solution target capture was used to selectively enrich libraries for regions of interest prior to sequencing (Gnirke et al. 2009).”
MethodIntegration of Next-Generation Sequencing Into Clinical Practice: Are We There Yet?
Kohlmann, A., Grossmann, V., & Haferlach, T. (2012) · Seminars in Oncology · doi:10.1053/j.seminoncol.2011.11.008 · Cited by 57
Bashamboo, A., Ledig, S., Wieacker, P. F., Achermann, J. C., & McElreavey, K. (2010) · Sexual Development · doi:10.1159/000314917 · Cited by 56
Marquard, A. M., Birkbak, N. J., Thomas, C. E., Favero, F., Krzystanek, M., Lefèbvre, C., Ferté, C., Jamal‐Hanjani, M., Wilson, G. A., Shafi, S., et al. (2015) · BMC Medical Genomics · doi:10.1186/s12920-015-0130-0 · Cited by 56
“For detailed explanations of the process, see [21].”
BackgroundSchweizer, R. M., Robinson, J. A., Harrigan, R. J., Silva, P., Galverni, M., Musiani, M., Green, R. E., Novembre, J., & Wayne, R. K. (2015) · Molecular Ecology · doi:10.1111/mec.13467 · Cited by 58
“Advances in the precision and scale of DNA tools, such as the DNA capture array (Hodges et al. 2007; Gnirke et al. 2009; Tewhey et al. 2009; Jones & Good 2015), allow for the enrichment in a DNA sample of specific gene regions for thousands of candidate genes.”
Fragoso-Martínez, I., Salazar, G. A., Martínez-Gordillo, M. J., Magallón, S., Sánchez‐Reyes, L. L., Lemmon, E. M., Lemmon, A. R., Sazatornil, F. D., & Mendoza, C. G. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2017.02.006 · Cited by 54
“Libraries are enriched with the designed probes and hybridization can be done either in solution (e.g. Gnirke et al., 2009; Faircloth et al., 2012; Lemmon et al., 2012) or in a solid structure such as microarrays (e.g. Bi et al., 2012).”
BackgroundComprehensive genome sequencing of the liver cancer genome
Nakagawa, H., & Shibata, T. (2012) · Cancer Letters · doi:10.1016/j.canlet.2012.10.035 · Cited by 54
“This approach involves target-enrichment of whole protein-coding exons of the human genome (30–40 Mb, approximately 1% of the whole human genome) using in-solution RNA or oligonucleotide DNA probe hybridization technologies [8].”
MethodPCR-Activated Cell Sorting for Cultivation-Free Enrichment and Sequencing of Rare Microbes
Lim, S. W., Tran, T. M., & Abate, A. R. (2015) · PLoS ONE · doi:10.1371/journal.pone.0113549 · Cited by 55
“A limitation of probe capture, however, is that recovering whole microbial genomes requires hundreds or thousands of overlapping capture probes [11], necessitating substantial knowledge of the target sequence, which may not be available.”
Gene Capture Coupled to High-Throughput Sequencing as a Strategy for Targeted Metagenome Exploration
Denonfoux, J., Parisot, N., Dugat‐Bony, É., Biderre‐Petit, C., Boucher, D., Morgavi, D. P., Paslier, D. L., Peyretaillade, É., & Peyret, P. (2013) · DNA Research · doi:10.1093/dnares/dst001 · Cited by 55
“The RNA probe was prepared as described by Gnirke et al.(19)”
MethodMacConaill, L. E., Hummelen, P. V., Meyerson, M. M., & Hahn, W. C. (2011) · Cancer Discovery · doi:10.1158/2159-8290.cd-11-0110 · Cited by 57
Malicdan, M. C. V., Vilboux, T., Stephen, J., Maglic, D., Mian, L., Konzman, D., Guo, J., Yildirimli, D., Bryant, J. C., Fischer, R. E., et al. (2015) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2015-103316 · Cited by 54
Chung, J., Son, D., Jeon, H.-J., Kim, K., Park, G., Ryu, G. H., Park, W., & Park, D. (2016) · Scientific Reports · doi:10.1038/srep26732 · Cited by 54
Louis-Dit-Picard, H., Kouranti, I., Rafael, C., Ferreira, I., Chávez‐Canales, M., Khalek, W. A., Argaiz, E. R., Baron, S., Vacle, S., Migeon, T., et al. (2020) · Journal of Clinical Investigation · doi:10.1172/jci94171 · Cited by 54
“Exons of genomic DNA samples were captured using Agilent in-solution enrichment methodology with their biotinylated oligonucleotides probes library, followed by paired-end 75 bp massively parallel sequencing on Illumina HiSeq 2000 (see (52) for detailed explanations of the process).”
MethodHutter, C. R., Cobb, K. A., Portik, D. M., Travers, S. L., Wood, P. L., & Brown, R. M. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13517 · Cited by 55
“…ensure some variability was present; (2) kept alignments with GC content between 30–50%, because such sequences are efficient for sequence capture (Gnirke et al. 2009); (3) exons <100BP and <5000bp were removed to include more exons from across the genome; (4) exons were kept only if they were…”
BackgroundDesign of targeted, capture-based, next generation sequencing tests for precision cancer therapy
Hagemann, I. S., Cottrell, C. E., & Lockwood, C. M. (2013) · Cancer Genetics · doi:10.1016/j.cancergen.2013.11.003 · Cited by 53
Pie, M. R., Faircloth, B. C., Ribeiro, L. F., Bornschein, M. R., & McCormack, J. E. (2018) · Biological Journal of the Linnean Society · doi:10.1093/biolinnean/bly093 · Cited by 53
“To enrich targeted ultraconserved element (UCE) loci, we followed an established workflow (Gnirke et al., 2009; Blumenstiel et al., 2010), while incorporating several modifications to the protocol detailed by Faircloth et al.”
MethodSuccess stories in genomic medicine from resource-limited countries
Mitropoulos, K. A., Jaibeji, H. S. A., Forero, D. A., Laissue, P., Wonkam, A., López-Correa, C., Mohamed, Z., Chantratita, W., Lee, M. T. M., LLerena, A., et al. (2015) · Human Genomics · doi:10.1186/s40246-015-0033-3 · Cited by 53
“sequences [46–49].”
Nucleotide resolution analysis of TMPRSS2 and ERG rearrangements in prostate cancer
Weier, C. A., Haffner, M. C., Mosbruger, T. L., Esopi, D., Hicks, J. L., Zheng, Q., Fedor, H. L., Isaacs, W. B., Marzo, A. M. D., Nelson, W. G., et al. (2013) · The Journal of Pathology · doi:10.1002/path.4186 · Cited by 50
“To identify genomic breakpoints in TMPRSS2 and ERG in a large series of prostate cancer samples, we adapted a hybrid-capture strategy combined with targeted next-generation sequencing [13,23].”
Capuano, A., Bucciotti, F., Hagman, K. D. F., Davis, B. T., Mroske, C., Hulick, P. J., Weissman, S. M., Gao, Q., Spessotto, P., Colombatti, A., et al. (2015) · Human Mutation · doi:10.1002/humu.22920 · Cited by 52
“Briefly, samples were prepared using the SureSelect Target Enrichment System (Agilent Technologies, Santa Clara, CA) [Gnirke et al., 2009] and sequenced using paired-end, 100-cycle chemistry on the Illumina HiSeq 2000 (Illumina, San Diego, CA).”
MethodESRRA-C11orf20 Is a Recurrent Gene Fusion in Serous Ovarian Carcinoma
Salzman, J., Marinelli, R. J., Wang, P., Green, A. E., Nielsen, J. S., Nelson, B. H., Drescher, C. W., & Brown, P. O. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1001156 · Cited by 52
DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing
Castle, J. C., Biery, M. C., Bouzek, H. K., Xie, T., Chen, R., Misura, K. M. S., Jackson, S., Armour, C. D., Johnson, J. M., Rohl, C. A., et al. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-244 · Cited by 52
Phuong, M. A., & Mahardika, G. N. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy034 · Cited by 53
Hu, H., Wrogemann, K., Kalscheuer, V. M., Tzschach, A., Richard, H., Haas, S. A., Menzel, C., Bienek, M., Froyen, G., Raynaud, M., et al. (2009) · The HUGO Journal · doi:10.1007/s11568-010-9142-1 · Cited by 52
Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencingPreprint
Summerer, D., Wu, H., Haase, B., Cheng, Y., Schracke, N., Stähler, C., Chee, M. S., Stähler, P. F., & Beier, M. (2009) · Genome Research · doi:10.1101/gr.091942.109 · Cited by 52
OTG-snpcaller: An Optimized Pipeline Based on TMAP and GATK for SNP Calling from Ion Torrent Data
Zhu, P., He, L., Li, Y., Huang, W., Xi, F., Lin, L., Zhi, Q., Zhang, W., Tang, Y. T., Geng, C., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0097507 · Cited by 51
“Currently, Agilent SureSelect, NimbleGen SeqCap and Illumina TruSeq are the main sequence capture methods for next generation sequencing [3,4].”
MethodBiderre‐Petit, C., Dugat‐Bony, É., Mège, M., Parisot, N., Adrian, L., Moné, A., Denonfoux, J., Peyretaillade, É., Debroas, D., Boucher, D., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0145558 · Cited by 51
“Biotinylated RNA baits were prepared from double-stranded DNA probes, as previously described [41].”
MethodHu, H., Wrogemann, K., Kalscheuer, V., Tzschach, A., Richard, H., Haas, S. A., Menzel, C., Bienek, M., Froyen, G., Raynaud, M., et al. (2009) · The HUGO Journal · doi:10.1007/s11568-010-9137-y · Cited by 49
Advances in Using Non-invasive, Archival, and Environmental Samples for Population Genomic Studies
Andrews, K. R., Barba, M. D., Russello, M. A., & Waits, L. P. (2018) · Population genomics · doi:10.1007/13836_2018_45 · Cited by 57
Pootakham, W., Shearman, J. R., Ruang‐areerate, P., Sonthirod, C., Sangsrakru, D., Jomchai, N., Yoocha, T., Triwitayakorn, K., Tragoonrung, S., & Tangphatsornruang, S. (2014) · PLoS ONE · doi:10.1371/journal.pone.0116028 · Cited by 53
“This technique, together with the RNA-seq based SNP discovery, allows the predefined regions encompassing EST-SNPs to be selectively captured and sequenced in multiple individuals [28].”
MethodMutations in NOTCH2 in patients with Hajdu–Cheney syndrome
Zhao, W., Petit, E. T., Gafni, R. I., Collins, M. T., Robey, P. G., Seton, M., Miller, K. K., & Mannstadt, M. (2013) · Osteoporosis International · doi:10.1007/s00198-013-2298-5 · Cited by 50
“Exome sequencing was performed using the Agilent SureSelect Human All Exon Kit v2 [7] followed by massively parallel sequencing using Illumina HiSeq Sequencer.”
Hoppman‐Chaney, N. L., Peterson, L. M., Klee, E. W., Middha, S., Courteau, L. K., & Ferber, M. J. (2010) · Clinical Chemistry · doi:10.1373/clinchem.2010.145441 · Cited by 50
CLTC as a clinically novel gene associated with multiple malformations and developmental delay
DeMari, J. A., Mroske, C., Tang, S., Nimeh, J., Miller, R., & Lebel, R. R. (2016) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.37506 · Cited by 48
Evidence that Myotis lucifugus “Subspecies” are Five Nonsister Species, Despite Gene Flow
Morales, A. E., & Carstens, B. C. (2018) · Systematic Biology · doi:10.1093/sysbio/syy010 · Cited by 50
Kuo, M. E., Theil, A. F., Kievit, A. J. A., Malicdan, M. C. V., Introne, W. J., Christian, T., Verheijen, F. W., Smith, D. E. C., Mendes, M. I. S., Hussaarts-Odijk, L., et al. (2019) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2019.01.006 · Cited by 50
Joining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits
Shah, T., Schneider, J. V., Zizka, G., Maurin, O., Baker, W. J., Forest, F., Brewer, G. E., Savolainen, V., Darbyshire, I., & Larridon, I. (2021) · American Journal of Botany · doi:10.1002/ajb2.1682 · Cited by 50
“Once the genomic libraries are enriched for the regions of interest they are then sequenced on high- throughput sequencing platforms (Gnirke et al., 2009; Grover et al., 2012; Fragoso- Martínez et al., 2017; Léveillé- Bourret et al., 2018; Johnson et al., 2019).”
MethodFarwell Hagman, K. D., Shinde, D. N., Mroske, C., Smith, E., Radtke, K., Shahmirzadi, L., El-Khechen, D., Powis, Z., Chao, E. C., Alcaraz, W. A., et al. (2017) · Genetics in Medicine · doi:10.1038/gim.2016.95 · Cited by 54
Next-Generation Sequencing in Genetic Hearing Loss
Yan, D. L. S., Tekin, M., Blanton, S. H., & Liu, X. Z. (2013) · Genetic Testing and Molecular Biomarkers · doi:10.1089/gtmb.2012.0464 · Cited by 52
“The targeted fragments can subsequently be captured using solid- or liquid-phase hybridization assays (Okou et al., 2007; Gnirke et al., 2009).”
BackgroundEnrichment of genomic DNA for polymorphism detection in a non‐model highly polyploid crop plant
Bundock, P. C., Casu, R. E., & Henry, R. J. (2012) · Plant Biotechnology Journal · doi:10.1111/j.1467-7652.2012.00707.x · Cited by 49
Hereditary ovarian and breast cancer: what have we learned?
Lynch, H. T., Snyder, C., & Casey, M. J. (2013) · Annals of Oncology · doi:10.1093/annonc/mdt313 · Cited by 49
Ahn, D. H., Javle, M. M., Ahn, C. W., Jain, A., Mikhail, S., Noonan, A. M., Wu, C. S.-Y., Shroff, R. T., Chen, J. L., & Bekaii‐Saab, T. (2016) · Cancer · doi:10.1002/cncr.30247 · Cited by 49
“Foundation Medicine simultaneously assesses the entire coding sequences of 236 cancer-related genes and 7 introns from 19 genes often rearranged or altered in cancer to an average depth of coverage greater than 250 times.(17-20) Foundation Medicine categorizes genomic alterations as actionable if they are linked to an…”
BackgroundA phylogenetic approach for haplotype analysis of sequence data from complex mitochondrial mixtures
Vohr, S. H., Gordon, R., Eizenga, J. M., Erlich, H. A., Calloway, C., & Green, R. E. (2017) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2017.05.007 · Cited by 49
Li, T., Wang, R., Zhao, D., & Tao, J. (2020) · Plant Signaling & Behavior · doi:10.1080/15592324.2020.1746034 · Cited by 49
“lactiflora transcriptome for use in further analyzes.(52) Four public databases were used to annotate 86,257 unigenes.”
MethodCRISPR-based enrichment strategies for targeted sequencing
Schultzhaus, Z. S., Wang, Z., & Stenger, D. A. (2020) · Biotechnology Advances · doi:10.1016/j.biotechadv.2020.107672 · Cited by 47
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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