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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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Padlock Probes: Circularizing Oligonucleotides for Localized DNA Detection
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“In-solution hybridization approaches In-solution hybridization-based approaches, originally developed for wholeexome sequencing (Gnirke et al., 2009), use biotinylated oligonucleotides to capture genomic regions of interest.”
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“Assessment of genetic diversity as indicated by SureSelect hybrid capture system Agilent SureSelect liquid-based hybrid capture arrays were used for SNPs genotyping.”
MethodInfluentialMroske, C., Rasmussen, K. J., Shinde, D. N., Huether, R., Powis, Z., Lu, H., Baxter, R. M., McPherson, E. W., & Tang, S. (2015) · BMC Medical Genetics · doi:10.1186/s12881-015-0240-8 · Cited by 33
“Samples were prepared using either the SureSelect Target Enrichment System (Agilent Technologies, Santa Clara, CA) [24] or the SeqCap EZ VCRome 2.0 system (Roche NimbleGen, Madison, WI) [25].”
MethodInfluentialNext‐generation phylogenetics takes root
McCormack, J. E., & Faircloth, B. C. (2012) · Molecular Ecology · doi:10.1111/mec.12050 · Cited by 33
“The target loci and baits can then be enriched compared with nontarget DNA and sequenced en masse via NGS (Gnirke et al. 2009).”
BackgroundApplication of large-scale sequencing to marker discovery in plants
Henry, R. J., Edwards, M. A., Waters, D. L., Krishnan, S. G., Bundock, P. C., Sexton, T. R., Masouleh, A. K., Nock, C. J., & Pattemore, J. (2012) · Journal of Biosciences · doi:10.1007/s12038-012-9253-z · Cited by 34
“A technical improvement on array hybridization is to carry out the hybridization in solution with free oligonucleotides using the microarray as a convenient platform only for oligonucleotide synthesis (Gnirke et al. 2009).”
BackgroundVilboux, T., Malicdan, M. C. V., Chang, Y. M., Guo, J., Zerfas, P. M., Stephen, J., Cullinane, A. R., Bryant, J. C., Fischer, R. E., Brooks, B. P., et al. (2016) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2015-103416 · Cited by 33
Sequencing-based diagnostics for pediatric genetic diseases: progress and potential
Tayoun, A. N. A., Krock, B. L., & Spinner, N. B. (2016) · Expert Review of Molecular Diagnostics · doi:10.1080/14737159.2016.1209411 · Cited by 33
“Despite the widespread application of NGS in several research areas including genomics, transcriptomics, metagenomics, and epigenomics [26,27], clinically it has mostly been”
BaitsTools: Software for hybridization capture bait design
Campana, M. G. (2017) · Molecular Ecology Resources · doi:10.1111/1755-0998.12721 · Cited by 33
Choquet, M., Smolina, I., Dhanasiri, A. K. S., Blanco‐Bercial, L., Kopp, M., Jueterbock, A., Sundaram, A. Y. M., & Hoarau, G. G. (2019) · Royal Society Open Science · doi:10.1098/rsos.180608 · Cited by 33
Schneider, J. V., Jungcurt, T., Cardoso, D., Amorim, A. M., Töpel, M., Andermann, T., Poncy, O., Berberich, T., & Zizka, G. (2020) · Taxon · doi:10.1002/tax.12421 · Cited by 33
McKay, R. R., Kwak, L., Crowdis, J. P., Sperger, J. M., Zhao, S. G., Xie, W., Werner, L. L., Lis, R. T., Zhang, Z., Wei, X. X., et al. (2021) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-4616 · Cited by 33
“0 bait set (Supplementary Table 1S).[16] Libraries were sequenced with 76 bp paired-end reads on an Illumina instrument.”
MethodMcDonnell, A., Baker, W. J., Dodsworth, S., Forest, F., Graham, S. W., Johnson, M. G., Pokorny, L., Tate, J. A., Wicke, S., & Wickett, N. J. (2021) · Applications in Plant Sciences · doi:10.1002/aps3.11443 · Cited by 33
“This versatile and powerful approach relies on probes to capture complementary sets of genomic targets from whole genome DNA or cDNA samples using solid- phase or in- solution hybridization (Gnirke et al., 2009; Mamanova et al., 2010; Cronn et al., 2012).”
BackgroundBai, Z., Zhang, N., Liu, J., Ding, H., Zhang, Y., Wang, T., Gao, J. L., & Ou, X. (2022) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2022.102689 · Cited by 33
Whole-exome sequencing reveals recurrent somatic mutation networks in cancer
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Leveraging the power of long reads for targeted sequencingPreprint
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Confidence-based Somatic Mutation Evaluation and Prioritization
Löwer, M., Renard, B. Y., de Graaf, J., Wagner, M., Paret, C., Kneip, C., Türeci, Ö., Diken, M., Britten, C. M., Kreiter, S., et al. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002714 · Cited by 33
“Next-generation sequencing, DNA sequencing: Exome capture for DNA resequencing was performed using the Agilent Sure-Select solution-based capture assay [23], in this case designed to capture all known mouse exons.”
MethodSchrader, K. A., Heravi‐Moussavi, A., Waters, P. J., Senz, J., Whelan, J., Ha, G., Eydoux, P., Nielsen, T. O., Gallagher, B., Oloumi, A., et al. (2011) · The Journal of Pathology · doi:10.1002/path.2941 · Cited by 34
Next Generation Diagnostics in Inherited Arrhythmia Syndromes
Ware, J. S., John, S., Roberts, A. M., Buchan, R. J., Gong, S., Peters, N. S., Robinson, D., Lucassen, A., Behr, E. R., & Cook, S. A. (2012) · Journal of Cardiovascular Translational Research · doi:10.1007/s12265-012-9401-8 · Cited by 32
“These provide offthe-shelf solutions to capture the whole exome, and customized versions for user-defined targets, the SureSelect custom system having a capacity of up to 6 Mb [11, 12].”
Comprehensive genetic exploration of skeletal dysplasia using targeted exome sequencing
Bae, J.-S., Kim, N. K. D., Lee, C., Kim, S. C., Lee, H. R., Song, H., Park, K.-B., Kim, H. W., Lee, S. H., Kim, H. Y., et al. (2015) · Genetics in Medicine · doi:10.1038/gim.2015.129 · Cited by 32
Lim, H. C., & Braun, M. J. (2016) · Molecular Ecology Resources · doi:10.1111/1755-0998.12568 · Cited by 32
“An alternative approach to reducing genomic complexity is DNA sequence capture or target enrichment (Gnirke et al. 2009; Jones & Good 2016).”
BackgroundGenome-wide Target Enrichment-aided Chip Design: a 66 K SNP Chip for Cashmere Goat
Qiao, X., Su, R., Wang, Y., Wang, R., Yang, T., Li, X., Chen, W., He, S., Jiang, Y., Xu, Q., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-09285-z · Cited by 32
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“Other studies have also indicated that the division of C. canephora into two groups is strongly related to its geographic isolation and historical events of glaciations that occurred 18,000 years ago (Gomez et al. 2009; Cubry et al. 2013).”
ResultTargeted Single Primer Enrichment Sequencing with Single End Duplex-UMI
Peng, Q., Xu, C., Kim, D. J., Lewis, M., DiCarlo, J., & Wang, Y. (2019) · Scientific Reports · doi:10.1038/s41598-019-41215-z · Cited by 32
Genomics of natural history collections for understanding evolution in the wild
López, L., Turner, K. G., Bellis, E. S., & Lasky, J. R. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13245 · Cited by 35
“Baits are often commercially synthesized (Gnirke et al., 2009), and they must be designed in silico based on reference assemblies.”
BackgroundDavids, M., Kane, M. S., He, M., Wolfe, L. A., Li, X., Raihan, M. A., Chao, K. R., Bone, W. P., Boerkoel, C. F., Gahl, W. A., et al. (2015) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2015-103338 · Cited by 32
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“All current SNP chips are based on solid–liquid capture array systems, although liquid-phase capture is gaining popularity (Gnirke et al., 2009; Mertes et al., 2011; Rohland and Reich, 2012).”
BackgroundAssessing the Enrichment Performance in Targeted Resequencing Experiments
Frommolt, P., Abdallah, A. T., Altmüller, J., Motameny, S., Thiele, H., Becker, C., STEMSHORN, K. C., Fischer, M., Freilinger, T. M., & Nürnberg, P. (2012) · Human Mutation · doi:10.1002/humu.22036 · Cited by 31
“Higher throughput can be achieved, for example, through enrichment by hybridization on high-density microarrays [Albert et al., 2007] or in-solution hybridization [Gnirke et al., 2009], enabling whole-exome capture and a diverse degree of automation.”
BackgroundKiialainen, A., Karlberg, O., Ahlford, A., Sigurðsson, S., Lindblad‐Toh, K., & Syvänen, A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016486 · Cited by 30
Tietjen, I., Hovingh, G. K., Singaraja, R. R., Radomski, C., Barhdadi, A., McEwen, J., Chan, E., Mattice, M., Legendre, A., Franchini, P. L., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037437 · Cited by 31
“For example, exon capture technologies combined with nextgeneration sequencing can be used to simultaneously assess multiple genes that underlie HDLc levels in numerous probands [46], thereby increasing the probability of identifying individuals with more than one mutation.”
BackgroundEfficiency and Power as a Function of Sequence Coverage, SNP Array Density, and Imputation
Flannick, J. A., Korn, J. M., Fontanillas, P., Grant, G., Banks, E., DePristo, M. A., & Altshuler, D. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002604 · Cited by 32
“However, due to cost limitations, most population-based studies have estimated sample genome sequences through incomplete data collection with SNP arrays [13,14], low coverage whole genome sequencing [15,16], or high coverage targeted sequencing [17–20].”
BackgroundLim, E. C. P., Brett, M., Lai, A., Lee, S.-P., Tan, E. S., Jamuar, S. S., Ng, I., & Tan, E. (2015) · Human Genomics · doi:10.1186/s40246-015-0055-x · Cited by 31
“In general, amplification of exon 1 of some genes was problematic because of the generally higher GC content and sequence complexity [24–26].”
BackgroundSyring, J. V., Tennessen, J. A., Jennings, T. N., Wegrzyn, J., Scelfo-Dalbey, C., & Cronn, R. (2016) · Frontiers in Plant Science · doi:10.3389/fpls.2016.00484 · Cited by 31
“…methods for developing codominant genetic markers with high transferability across laboratories and studies, populations, and possibly species (Gnirke et al., 2009; Cronn et al., 2012; Tennessen et al., 2012; Hebert et al., 2013; Neves et al., 2013; Jones and Good, 2016; Müller et al., 2015),…”
MethodSantander, C., Gambron, P., Marchi, E., Karamitros, T., Katzourakis, A., & Magiorkinis, G. (2017) · Virus Evolution · doi:10.1093/ve/vex023 · Cited by 25
Phylogenomics of a rapid radiation: the Australian rainbow skinks
Bragg, J. G., Potter, S., Silva, A. C. A., Hoskin, C. J., Bai, B. Y. H., & Moritz, C. C. (2018) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1130-4 · Cited by 31
CRISPR/Cas9 targeted CAPTURE of mammalian genomic regions for characterization by NGS
Slesarev, A. I., Viswanathan, L., Tang, Y., Borgschulte, T., Achtien, K., Razafsky, D. S., Onions, D. E., Chang, A., & Cote, C. A. (2019) · Scientific Reports · doi:10.1038/s41598-019-39667-4 · Cited by 31
A decade with whole exome sequencing in haematology
Hansen, M. H., Haferlach, T., & Nyvold, C. G. (2019) · British Journal of Haematology · doi:10.1111/bjh.16249 · Cited by 32
Itokawa, K., Yatsu, K., Sekizuka, T., Maekawa, Y., Komagata, O., Sugiura, M., Sasaki, T., Tomita, T., Kuroda, M., Sawabe, K., et al. (2019) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0007818 · Cited by 33
“An enrichment approach involving hybridization of oligo DNA/RNA is often employed to selectively sequence targeted genome regions (Gnirke et al., 2009) for studies e.g. on genotyping of disease-related genes in humans.”
MethodNumaguchi, K., Akagi, T., Kitamura, Y., Ishikawa, R., & Ishii, T. (2020) · The Plant Journal · doi:10.1111/tpj.15020 · Cited by 31
Social environment influences the relationship between genotype and gene expression in wild baboons
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“To identify and genotype these putative regulatory variants, we used a target enrichment approach (Agilent SureSelect) [54], followed by high-throughput sequencing on the Illumina HiSeq 2000 platform.”
MethodSurmounting the Large-Genome “Problem” for Genomic Data Generation in Salamanders
Weisrock, D. W., Hime, P. M., Nunziata, S. O., Jones, K. S., Murphy, M. O., Hotaling, S., & Kratovil, J. D. (2018) · Population genomics · doi:10.1007/13836_2018_36 · Cited by 31
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Loss of Protocadherin‐12 L eads to D iencephalic‐ M esencephalic J unction D ysplasia S yndrome
Guemez‐Gamboa, A., Çağlayan, A. O., Stanley, V., Gregor, A., Zaki, M. S., Saleem, S. N., Musaev, D., McEvoy‐Venneri, J., Belandres, D., Akizu, N., et al. (2018) · Annals of Neurology · doi:10.1002/ana.25327 · Cited by 30
Self-citationThe Hitchhiker's guide to Xenopus genetics
Abu‐Daya, A., Khokha, M. K., & Zimmerman, L. B. (2012) · genesis · doi:10.1002/dvg.22007 · Cited by 30
Emergence of single-molecule sequencing and potential for molecular diagnostic applications
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Yost, S. E., Pastorino, S., Rozenzhak, S., Smith, E. N., Chao, Y. S., Jiang, P., Kesari, S., Frazer, K. A., & Harismendy, O. (2013) · PLoS ONE · doi:10.1371/journal.pone.0056185 · Cited by 29
“We performed whole exome capture using hybrid selection [36] of 12 samples (4 blood, 4 primary and 4 models) from 4 GBM patients (SK01600, SK00115, SK00072 and SK00102).”
MethodConte, N., Varela, I., Grove, C. S., Manes, N., Yusa, K., Moreno-Rodriguez, T., Segonds-Pichon, A., Bench, A. J., Gudgin, E. J., Herman, B., et al. (2013) · Leukemia · doi:10.1038/leu.2013.117 · Cited by 29
The ultimate and proximate mechanisms driving the evolution of long tails in forest deer mice
Kingsley, E. P., Kozak, K. M., Pfeifer, S. P., Yang, D.-S., & Hoekstra, H. E. (2016) · Evolution · doi:10.1111/evo.13150 · Cited by 29
“To assess genome-wide population structure, we used an arraybased capture library and sequenced region-enriched genomic libraries using an Illumina platform (Gnirke et al. 2009).”
MethodGuerra, F. P., Suren, H., Holliday, J. A., Richards, J. H., Fiehn, O., Famula, R. A., Stanton, B. J., Shuren, R. A., Sykes, R. W., Davis, M. F., et al. (2019) · BMC Genomics · doi:10.1186/s12864-019-6160-9 · Cited by 29
“Among “next-generation” sequencing alternatives, genome complexity reduction by sequence capture, or targeted sequencing, represents an efficient approach to performing genome wide analysis [22].”
BackgroundGiannikou, K., Zhu, Z., Kim, J., Winden, K. D., Tyburczy, M. E., Marron, D. L., Parker, J. S., Hebert, Z., Bongaarts, A., Taing, L., et al. (2020) · Modern Pathology · doi:10.1038/s41379-020-00659-9 · Cited by 29
Rouen, A., Rogers, E., Kerlan, V., Delemer, B., Catteau-Jonard, S., Reznik, Y., Gompel, A., Cédrin‐Durnerin, I., Guedj, A. M., Grouthier, V., et al. (2022) · Fertility and Sterility · doi:10.1016/j.fertnstert.2021.12.023 · Cited by 29
Parallel decay of vision genes in subterranean water beetles
Langille, B. L., Tierney, S. M., Bertozzi, T., Beasley‐Hall, P. G., Bradford, T. M., Fagan‐Jeffries, E. P., Hyde, J., Leijs, R., Richardson, M., Saint, K. M., et al. (2022) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2022.107522 · Cited by 29
Multi-modal molecular programs regulate melanoma cell state
Andrews, M. C., Oba, J., Wu, C., Zhu, H., Karpinets, T. V., Creasy, C. A., Forget, M., Yu, X., Song, X., Mao, X., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31510-1 · Cited by 35
Zhang, Y., Zhang, F., Song, Y., Shen, X., Bu, F., Su, D., Luo, C., Ge, L., Deng, S., Wu, Z., et al. (2023) · Advanced Materials · doi:10.1002/adma.202303821 · Cited by 30
A recessive screen for genes regulating hematopoietic stem cells
Papathanasiou, P., Tunningley, R., Pattabiraman, D. R., Ye, P., Gonda, T. J., Whittle, B., Hamilton, A., Cridland, S. O., Lourie, R., & Perkins, A. C. (2010) · Blood · doi:10.1182/blood-2010-04-269951 · Cited by 29
Phylogenomics of Horned Lizards (Genus:Phrynosoma) Using Targeted Sequence Capture Data
Leaché, A. D., & Linkem, C. W. (2015) · Copeia · doi:10.1643/ch-15-248 · Cited by 29
“Sequence capture methods use short probes (60–120 base pairs) to hybridize to specific genomic regions, which are subsequently isolated and sequenced using next-generation sequencing (Gnirke et al., 2009; McCormack et al., 2012; Lemmon and Lemmon, 2013).”
MethodTEQC: an R package for quality control in target capture experiments
Hummel, M., Bonnin, S., Lowy, E., & Roma, G. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr122 · Cited by 29
Mucaki, E. J., Caminsky, N., Perri, A. M., Lu, R., Laederach, A., Halvorsen, M., Knoll, J. H. M., & Rogan, P. K. (2016) · BMC Medical Genomics · doi:10.1186/s12920-016-0178-5 · Cited by 27
“This step was incorporated into a modified version of Gnirke and colleagues’ (2009) in-solution hybridization enrichment protocol, in which the majority of library preparation, pull-down, and wash steps were automated using a BioMek® FXP Automation Workstation (Beckman Coulter, Mississauga, Canada) [80].”
MethodStümm, M., Entezami, M., Trunk, N., Beck, M., Löcherbach, J., Wegner, R., Hagen, A., Becker, R., & Hofmann, W. (2012) · Prenatal Diagnosis · doi:10.1002/pd.3862 · Cited by 28
“Agilent’s SureSelect Human All Exon Kit allows capturing the human exome using RNA oligonucleotides (baits) that are biotinylated onto streptavidin-labeled magnetic beads.(26) The prepared libraries were incubated with these baits for 24 h.”
MethodScott, S. A., Cohen, N., Brandt, T., Warburton, P. E., & Edelmann, L. J. (2010) · Human Molecular Genetics · doi:10.1093/hmg/ddq250 · Cited by 28
Collection of cell-free DNA for genomic analysis of solid tumors in a clinical laboratory setting
Raymond, C. K., Hernandez, J., Karr, R. M., Hill, K., & Li, M. (2017) · PLoS ONE · doi:10.1371/journal.pone.0176241 · Cited by 28
Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species
Förster, D. W., Bull, J. K., Lenz, D., Autenrieth, M., Paijmans, J. L. A., Kraus, R. H., Nowak, C., Bayerl, H., Kuehn, R., Saveljev, A. P., et al. (2018) · Molecular Ecology Resources · doi:10.1111/1755-0998.12924 · Cited by 31
Horizon scan of DNA-based methods for quality control and monitoring of herbal preparations
Raclariu-Manolică, A. C., Mauvisseau, Q., & de Boer, H. (2023) · Frontiers in Pharmacology · doi:10.3389/fphar.2023.1179099 · Cited by 29
“Target capture sequencing is a cost-effective alternative for genome subsampling, enabling high-throughput sequencing (HTS) of preselected nuclear loci (Gnirke et al., 2009; Andermann et al., 2019).”
BackgroundGusev, A., Shah, M. J., Kenny, E. E., Ramachandran, A., Lowe, J. K., Salit, J., Lee, C.-M., Levandowsky, E., Weaver, T., Doan, Q. C., et al. (2011) · Genetics · doi:10.1534/genetics.111.134874 · Cited by 27
Wong, L. C. (2012) · Neurotherapeutics · doi:10.1007/s13311-012-0170-5 · Cited by 28
Bragalini, C., Ribière, C., Parisot, N., Vallon, L., Prudent, E., Peyretaillade, É., Girlanda, M., Peyret, P., Marmeisse, R., & Luis, P. (2014) · DNA Research · doi:10.1093/dnares/dsu030 · Cited by 28
“Biotinylated RNA capture probes were prepared according to the two-step procedure of Gnirke et al.(31) In the first step, each single-stranded DNA probe was amplified by PCR using primers complementary to the 50 and 30 adaptors to allow double-strand DNA formation.”
MethodNunziato, M., Esposito, M. V., Starnone, F., Diroma, M. A., Calabrese, A., Monaco, V. D., Buono, P., Frasci, G., Botti, G., D’Aiuto, M., et al. (2018) · Analytica Chimica Acta · doi:10.1016/j.aca.2018.09.032 · Cited by 28
Lang, P. L. M., Weiß, C. L., Kersten, S., Latorre, S. M., Nagel, S., Nickel, B., Meyer, M., & Burbano, H. A. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13168 · Cited by 29
“These protocols often use commercially synthesized baits (Gnirke et al., 2009).”
BackgroundPeng, X., Li, H., Wu, F., & Wang, J. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa060 · Cited by 27
Evolutionary history of chloridoid grasses estimated from 122 nuclear loci
Fisher, A. E., Hasenstab, K. M., Bell, H. L., Blaine, E., Ingram, A. L., & Columbus, J. T. (2016) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2016.08.011 · Cited by 27
Genotyping and Sequencing Technologies in Population Genetics and Genomics
Holliday, J. A., Hallerman, E. M., & Haak, D. C. (2018) · Population genomics · doi:10.1007/13836_2017_5 · Cited by 30
Steiert, T. A., Fuß, J., Juzėnas, S., Wittig, M., Hoeppner, M. P., Vollstedt, M., Varkalaitė, G., ElAbd, H., Brockmann, C., Görg, S., et al. (2022) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqac051 · Cited by 26
“In-solution hybridisation-based capture (14) and enrichment is currently the most widely used technique to enrich genomic fragments of interest in various research contexts (15–21).”
Mengual, X., Mayer, C., Burt, T. O., Moran, K. M., Dietz, L., Nottebrock, G., Pauli, T., Young, A. D., Brasseur, M. V., Kukowka, S., et al. (2022) · Systematic Entomology · doi:10.1111/syen.12573 · Cited by 32
“…these techniques, sequence-capture methods (also termed target enrichment or targeted sequencing; Mamanova et al., 2010) are used to enrich sequence libraries for specific regions of interest from a genome (Faircloth et al., 2012; Gnirke et al., 2009; Lemmon et al., 2012; Lemmon & Lemmon, 2013).”
MethodExpanding the phenotypic spectrum of ECEL1‐related congenital contracture syndromes
Shaaban, S., Düzcan, F., Yıldırım, C., Chan, W. M., Andrews, C. V., Akarsu, N. A., & Engle, E. C. (2013) · Clinical Genetics · doi:10.1111/cge.12224 · Cited by 27
“1 (Agilent Technologies, Santa Clara, CA) (12).”
Detection of DNA fusion junctions for BCR-ABL translocations by Anchored ChromPET
Shibata, Y., Malhotra, A., & Dutta, A. (2010) · Genome Medicine · doi:10.1186/gm191 · Cited by 27
Thompson, R., Drew, C. J. G., & Thomas, R. H. (2012) · Advances in protein chemistry and structural biology · doi:10.1016/b978-0-12-394287-6.00002-1 · Cited by 27
Tost, J. (2016) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-43624-1_15 · Cited by 26
George, R. J., Plog, S., Watson, A., Schmidt, K. L., Culleton, B. J., Harper, T. K., Gilman, P. A., LeBlanc, S. A., Amato, G., Whiteley, P. M., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1805856115 · Cited by 27
“We prepared massively parallel sequencing libraries from each extract, but before sequencing we used a DNA capture approach (40) to enrich our libraries for scarlet macaw mitochondrial DNA fragments, using biotinylated RNA baits complementary to the reference scarlet macaw mitochondrial genome sequence (GenBank access…”
MethodA novel CRISPR/Cas9 associated technology for sequence-specific nucleic acid enrichment
Stevens, R. C., Steele, J. L., Glover, W. R., Sánchez-García, J. F., Simpson, S., O’Rourke, D. R., Ramsdell, J. S., MacManes, M. D., Thomas, W. K., & Shuber, A. P. (2019) · PLoS ONE · doi:10.1371/journal.pone.0215441 · Cited by 27
The contribution of rare genetic variants to the pathogenesis of polycystic ovary syndrome
Dapas, M., & Dunaif, A. E. (2020) · Current Opinion in Endocrine and Metabolic Research · doi:10.1016/j.coemr.2020.02.011 · Cited by 28
“Additional statistical methods (12–15) and DNA sequencing of GWAS loci (16,17) are required to identify potential pathogenic variants and candidate genes within a given region in a process known as “fine mapping”.”
MethodGenomic DNA Library Preparation for Resistance Gene Enrichment and Sequencing (RenSeq) in Plants
Jupe, F., Chen, X., Verweij, W., Witek, K., Jones, J. D. G., & Hein, I. (2014) · Methods in molecular biology · doi:10.1007/978-1-62703-986-4_22 · Cited by 27
Qadir, M. A., Zhan, S. H., Kwok, B., Bruestle, J., Drees, B., Popescu, O., & Sorensen, P. H. B. (2014) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2014.01.002 · Cited by 26
Sun, M., Mondal, K., Patel, V., Horner, V. L., Long, A. B., Cutler, D. J., Caspary, T., & Zwick, M. E. (2012) · G3 Genes Genomes Genetics · doi:10.1534/g3.111.001669 · Cited by 26
Rapid quantification of DNA libraries for next-generation sequencing
Buehler, B., Hogrefe, H. H., Scott, G., Ravi, H., Pabón-Peña, C., O’Brien, S., Formosa, R., & Happe, S. (2010) · Methods · doi:10.1016/j.ymeth.2010.01.004 · Cited by 26
Design and development of exome capture sequencing for the domestic pig (Sus scrofa)
Robert, C., Fuentes‐Utrilla, P., Troup, K., Loecherbach, J., Turner, F. S., Talbot, R., Archibald, A. L., Mileham, A. J., Deeb, N., Hume, D. A., et al. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-550 · Cited by 26
“SureSelect and Nimblegen’s SeqCap EZ systems rely on liquid capture [10,11].”
BackgroundDoes 3D Phenotyping Yield Substantial Insights in the Genetics of the Mouse Mandible Shape?
Navarro, N., & Maga, A. M. (2016) · G3 Genes Genomes Genetics · doi:10.1534/g3.115.024372 · Cited by 26
“…(Andolfatto et al. 2011; Cande et al. 2012), or targeted capture (Jones and Good 2016; Linnen et al. 2013; Olson 2007; Chevalier et al. 2014; Hodges et al. 2007; Gnirke et al. 2009), may yielded thousands to millions of SNPs even in species lacking a reference genome (Elshire et al. 2011).”
Montes, J. R., Peláez, P., Willyard, A., Moreno‐Letelier, A., Piñero, D., & Gernandt, D. S. (2019) · Systematic Botany · doi:10.1600/036364419x15620113920563 · Cited by 26
Population structure, diversifying selection, and local adaptation in Pinus patula
Peláez, P., Ortiz‐Martínez, A., Figueroa‐Corona, L., Montes, J. R., & Gernandt, D. S. (2020) · American Journal of Botany · doi:10.1002/ajb2.1566 · Cited by 26
Reichelt, N., Wen, J., Paetzold, C., & Appelhans, M. S. (2021) · Annals of Botany · doi:10.1093/aob/mcab092 · Cited by 26
Ancient human genomics: the methodology behind reconstructing evolutionary pathways
Marciniak, S., Klunk, J., Devault, A. M., Enk, J. M., & Poinar, H. N. (2015) · Journal of Human Evolution · doi:10.1016/j.jhevol.2014.11.003 · Cited by 30
Plomion, C., Bartholomé, J., Bouffier, L., BRENDEL, O., Cochard, H., de Miguel, M., Delzon, S., Gion, J., González‐Martínez, S. C., Guehl, J.-M., et al. (2016) · Journal of Plant Hydraulics · doi:10.20870/jph.2016.e008 · Cited by 25
“Exome capture and direct sequencing (Gnirke et al., 2009) techniques are currently being developed for maritime pine.”
BackgroundCulture-independent approaches to chlamydial genomics
Taylor–Brown, A., Madden, D. E., & Polkinghorne, A. (2018) · Microbial Genomics · doi:10.1099/mgen.0.000145 · Cited by 26
Next-generation sequencing and empowering personalised cancer medicine
McDermott, U. (2015) · Drug Discovery Today · doi:10.1016/j.drudis.2015.10.008 · Cited by 25
Applying Genomic Analysis to Newborn Screening
Solomon, B. D., Pineda‐Alvarez, D., Bear, K. A., Mullikin, J. C., Evans, J. P., & Programc, N. C. S. (2012) · Molecular Syndromology · doi:10.1159/000341253 · Cited by 25
“Whole-Exome Sequencing We performed solution hybridization exome capture with the SureSelect Human All Exon 38Mb and 50Mb Systems (Agilent Technologies, Santa Clara, Calif., USA) using biotinylated RNA baits to hybridize to sequences that correspond to exons [Gnirke et al., 2009].”
MethodMrBait: universal identification and design of targeted-enrichment capture probes
Chafin, T. K., Douglas, M. R., & Douglas, M. E. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty548 · Cited by 25
Acosta, J. J., Fahrenkrog, A. M., Neves, L. G., Resende, M. F. R., Dervinis, C., Davis, J. M., Holliday, J. A., & Kirst, M. (2019) · Genome Biology and Evolution · doi:10.1093/gbe/evz016 · Cited by 25
Feng, Y., Sen-yu, W., Zhang, Y., & Huang, Y. (2020) · Journal of Immunology Research · doi:10.1155/2020/6284960 · Cited by 25
“The analysis methods of the Agilent SureSelect ™ Target Enrichment System and the second-generation sequencing technology (the HiSeq 2000 sequencer of Illumina) included to one of the high-throughput viral integration detection (HIVID) had proved to be very useful test methods [14, 15].”
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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