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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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“[Coffey et al., 2011; Gnirke et al., 2009].”
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“0 bait set.(18) Resulting exome Illumina sequencing libraries were then quantitative polymerase chainreactionquantified,pooled, andsequencedwith76basepaired-endreadsusing Illumina GAII or HiSequation 2000 sequencers to a minimum of 80% of exome targets covered to 203 (after removal of duplicates and low-quality reads).”
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Bowne, S. J., Humphries, M. M., Sullivan, L. S., Kenna, P. F., Tam, L. C. S., Kiang, A. S., Campbell, M., Weinstock, G. M., Koboldt, D. C., Ding, L., et al. (2011) · European Journal of Human Genetics · doi:10.1038/ejhg.2011.86 · Cited by 162
Challenges of sequencing human genomes
Koboldt, D. C., Ding, L., Mardis, E. R., & Wilson, R. K. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbq016 · Cited by 161
NGS technologies for analyzing germplasm diversity in genebanks*
Kilian, B., & Graner, A. (2012) · Briefings in Functional Genomics · doi:10.1093/bfgp/elr046 · Cited by 159
Diagnostics based on nucleic acid sequence variant profiling: PCR, hybridization, and NGS approaches
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Hoffberg, S. L., Kieran, T. J., Catchen, J., Devault, A. M., Faircloth, B. C., Mauricio, R., & Glenn, T. C. (2016) · Molecular Ecology Resources · doi:10.1111/1755-0998.12566 · Cited by 164
“Sequence capture (Okou et al. 2007; Gnirke et al. 2009) and restriction-site-associated DNA sequencing (RADseq; Miller et al. 2007; Baird et al. 2008; Davey & Blaxter 2010; Davey et al. 2011; Peterson et al. 2012) are two widely used types of reduced representation approaches for massively parallel…”
BackgroundMutational patterns in chemotherapy resistant muscle-invasive bladder cancer
Liu, D., Abbosh, P. H., Keliher, D., Reardon, B. M., Miao, D., Mouw, K. W., Taylor-Weiner, A. N., Wankowicz, S. A. M., Han, G. C., Teo, M. Y., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-02320-7 · Cited by 149
Three assays for in-solution enrichment of ancient human DNA at more than a million SNPsPreprint
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Transoceanic drift and the domestication of African bottle gourds in the Americas
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“We used the MycroArray MySelect system for in-solution RNA hybridization capture (17) of the LSC based on the cucumber (Cucumis sativus) plastid genome (34).”
BackgroundMethodInfluentialGiarla, T. C., & Esselstyn, J. A. (2015) · Systematic Biology · doi:10.1093/sysbio/syv029 · Cited by 144
“Recent advances in laboratory techniques (e.g., sequence capture; Gnirke et al. 2009) and falling prices for high-throughput sequencing have made the use of phylogenomic data sets more common (Lemmon et al. 2012; McCormack et al. 2013; Leaché et al. 2014; Pyron et al. 2014; Smith et al. 2014).”
BackgroundA Guide to Carrying Out a Phylogenomic Target Sequence Capture Project
Andermann, T., Jiménez, M. F. T., Matos‐Maraví, P. F., Batista, R., Blanco‐Pastor, J. L., Gustafsson, A. L. S., Kistler, L., Liberal, I. M., Oxelman, B., Bacon, C. D., et al. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2019.01407 · Cited by 139
“In contrast, the target capture method (Albert et al., 2007; Gnirke et al., 2009) offers a different genome-subsampling alternative.”
BackgroundMethodComparative RNA sequencing reveals substantial genetic variation in endangered primatesPreprint
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“…complete mammalian genomes from a large number of individuals remains prohibitively expensive and because effective DNA capture strategies (e.g., Gnirke et al. 2009)—especially for comparative genomic analysis—require a priori reference genome sequences, we chose an alternative ap- proach for…”
BackgroundFejerman, L., Ahmadiyeh, N., Hu, D., Huntsman, S., Beckman, K. B., Caswell-Jin, J. L., Tsung, K., John, E. M., Torres-Mejı́a, G., Carvajal‐Carmona, L. G., et al. (2014) · Nature Communications · doi:10.1038/ncomms6260 · Cited by 147
“Sequencing was performed at the Broad Institute and details of the sequencing method have been described elsewhere 58 .”
Matranga, C. B., Andersen, K. G., Winnicki, S., Busby, M., Gladden, A. D., Tewhey, R., Stremlau, M. H., Berlin, A. M., Gire, S., England, E. M., et al. (2014) · Genome biology · doi:10.1186/s13059-014-0519-7 · Cited by 147
“This is consistent with data reported for human exome sequencing [31].”
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“The most commonly used approaches are 1) hybridization capture from sequencing libraries using target specific probes [5] and 2) PCR amplification directly from sample DNA using target specific primers [6].”
MethodNext‐generation sequencing: ready for the clinics?
Desai, A., & Jere, A. (2012) · Clinical Genetics · doi:10.1111/j.1399-0004.2012.01865.x · Cited by 143
“Genomic region can be enriched by amplification methods or target capture methods (array based or in solution) (42, 43).”
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Habib, W. A., Brioude, F., Édouard, T., Bennett, J. T., Lienhardt-Roussie, A., Tixier, F., Salem, J., Yuen, T., Azzi, S., Bouc, Y. L., et al. (2017) · Genetics in Medicine · doi:10.1038/gim.2017.105 · Cited by 143
Barbitoff, Y. A., Polev, D. E., Glotov, A. S., Serebryakova, E. A., Shcherbakova, I. V., Kiselev, A. M., Kostareva, A. A., Glotov, O. S., & Predeus, A. V. (2020) · Scientific Reports · doi:10.1038/s41598-020-59026-y · Cited by 149
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“These DNA or RNA “baits” are either matrix-bound (array-based) or in solution (solution-phase), and a hybrid selection process is used to capture target DNA fragments from a “pond” of genomic DNA before sequencing.(71) The performance of commercially available whole-exome sequencing (WES) bait sets (notably, Illumina,…”
MethodFlannick, J., Beer, N. L., Bick, A. G., Agarwala, V., Molnes, J., Gupta, N., Burtt, N. P., Florez, J. C., Meigs, J. B., Taylor, H., et al. (2013) · Nature Genetics · doi:10.1038/ng.2794 · Cited by 136
Self-citationAncient Whole Genome Enrichment Using Baits Built from Modern DNA
Enk, J. M., Devault, A. M., Kuch, M., Murgha, Y. E., Rouillard, J. M., & Poinar, H. N. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu074 · Cited by 141
“However, genome-wide sequence-directed bait synthesis (Gnirke et al. 2009; Hodges et al. 2009) is very expensive, and for that matter impossible when a reference genome sequence is unavailable.”
BackgroundTargeted sequence capture as a powerful tool for evolutionary analysis1
Grover, C. E., Salmon, A., & Wendel, J. F. (2012) · American Journal of Botany · doi:10.3732/ajb.1100323 · Cited by 141
Computational and statistical approaches to analyzing variants identified by exome sequencing
Stitziel, N. O., Kieżun, A., & Sunyaev, S. R. (2011) · Genome biology · doi:10.1186/gb-2011-12-9-227 · Cited by 147
Saintenac, C., Jiang, D., & Akhunov, E. (2011) · Genome biology · doi:10.1186/gb-2011-12-9-r88 · Cited by 146
User guide for mapping-by-sequencing in Arabidopsis
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“To address this general problem genome-complexity reduction methods, like transcriptome sequencing, restriction site associated DNA sequencing, or targeted enrichment sequencing, have been proposed [29-32].”
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“First, it is unclear how efficient sequence capture will be in recovering a much smaller fraction of the genome, compared with previous studies (Gnirke et al., 2009; Zhou and Holliday, 2012).”
BackgroundMethodResultInfluentialA comparative analysis of exome capture
Parla, J. S., Iossifov, I. H., Grabill, I., Spector, M. S., Kramer, M., & McCombie, W. R. (2011) · Genome biology · doi:10.1186/gb-2011-12-9-r97 · Cited by 146
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“The Illumina exome uses Illumina’s in-solution DNA probe based hybrid selection method that uses similar principles as the Broad Institute-Agilent Technologies developed in-solution RNA probe based hybrid selection method 47,48 to generate Illumina exome sequencing libraries.”
Plomion, C., Aury, J., Amselem, J., Alaeitabar, T., Barbe, V., Belser, C., Bergès, H., Bodénès, C., Boudet, N., Boury, C., et al. (2015) · Molecular Ecology Resources · doi:10.1111/1755-0998.12425 · Cited by 135
“We will identify TE with two pipelines from the REPET package: TEdenovo (Flutre et al. 2011; Hoede et al. 2014) to detect and classify TE consensus families and TEannot (Quesneville et al. 2005) to annotate TE copies in the genome.”
MethodHolliday, J. A., Aitken, S. N., Cooke, J. E. K., Fady, B., González‐Martínez, S. C., Heuertz, M., Jaramillo‐Correa, J. P., Lexer, C., Staton, M. E., Whetten, R. W., et al. (2016) · Molecular Ecology · doi:10.1111/mec.13963 · Cited by 132
“…in forest trees usually employ genome complexity reduction in the form of either restriction–enzyme-based methods [i.e. genotyping-by-sequencing (GBS) and restriction-site-associated DNA sequencing (RAD-Seq)] or sequence capture (Gnirke et al. 2009; Elshire et al. 2011; Kiialainen et al. 2011).”
MethodHybrid Capture-Based Next Generation Sequencing and Its Application to Human Infectious Diseases
Gaudin, M., & Desnues, C. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02924 · Cited by 137
Voelkerding, K. V., Dames, S. A., & Durtschi, J. (2010) · Journal of Molecular Diagnostics · doi:10.2353/jmoldx.2010.100043 · Cited by 137
Burden of Rare Sarcomere Gene Variants in the Framingham and Jackson Heart Study Cohorts
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Self-citationTempleton, J. E. L., Brotherton, P., Llamas, B., Soubrier, J., Haak, W., Cooper, A., & Austin, J. J. (2013) · Investigative Genetics · doi:10.1186/2041-2223-4-26 · Cited by 134
“These kinds of DNA capture strategies generally rely on the hybridisation of target DNA sequences to probes that are either immobilised on a surface (such as a microarray) or in solution [27,28].”
BackgroundRetrieval of hundreds of nuclear loci from herbarium specimens
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“Originally developed for medical research on human diseases [10, 11], hybrid enrichment is a flexible technique for which applications in phylogenomic research are just beginning to be realized [4, 12–14].”
BackgroundMethodExome-wide DNA capture and next generation sequencing in domestic and wild species
Cosart, T., Beja‐Pereira, A., Chen, S., Ng, S. B. H., Shendure, J., & Luikart, G. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-347 · Cited by 134
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Methods for Genomic Partitioning
Turner, E. H., Ng, S. B. H., Nickerson, D. A., & Shendure, J. (2009) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082908-150112 · Cited by 131
Fusion genes and chromosome translocations in the common epithelial cancers
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Hybrid selection for sequencing pathogen genomes from clinical samples
Melnikov, A., Galinsky, K. J., Rogov, P., Fennell, T., Tyne, D. V., Russ, C., Daniels, R. F., Barnes, K. G., Bochicchio, J., Ndiaye, D., et al. (2011) · Genome biology · doi:10.1186/gb-2011-12-8-r73 · Cited by 128
Self-citationATHLATES: accurate typing of human leukocyte antigen through exome sequencing
Liu, C., Yang, X. Q., DUFFY, B. F., Mohanakumar, T., Mitra, R. D., Zody, M. C., & Pfeifer, J. D. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt481 · Cited by 124
“As sequencing of captured exons is susceptible to allelic bias (14), we compared the coverage of heterozygous alleles at positions where they differ from each other Figure 2.”
BackgroundAllele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements
Andermann, T., Fernandes, A. M., Olsson, U., Töpel, M., Pfeil, B. E., Oxelman, B., Aleixo, A. L. P., Faircloth, B. C., & Antonelli, A. (2018) · Systematic Biology · doi:10.1093/sysbio/syy039 · Cited by 118
The domestic dog: man's best friend in the genomic era
Boyko, A. R. (2011) · Genome biology · doi:10.1186/gb-2011-12-2-216 · Cited by 122
Wide spectrum of NR5A1‐related phenotypes in 46,XY and 46,XX individuals
Domenice, S., Machado, A. Z., Ferreira, F. M., Ferraz‐de‐Souza, B., Lerário, A. M., Lin, L., Nishi, M. Y., Gomes, N. L., da Silva, T. E., Silva, R. B., et al. (2016) · Birth Defects Research Part C Embryo Today Reviews · doi:10.1002/bdrc.21145 · Cited by 126
Stiller, M., Knapp, M., Stenzel, U., Hofreiter, M., & Meyer, M. (2009) · Genome Research · doi:10.1101/gr.095760.109 · Cited by 125
Sequence-based marker development in wheat: Advances and applications to breeding
Paux, E., Sourdille, P., Mackay, I., & Feuillet, C. (2011) · Biotechnology Advances · doi:10.1016/j.biotechadv.2011.09.015 · Cited by 122
Buettner, R., Wolf, J., & Thomas, R. K. (2013) · Journal of Clinical Oncology · doi:10.1200/jco.2012.45.9867 · Cited by 123
Combining Highly Multiplexed PCR with Semiconductor-Based Sequencing for Rapid Cancer Genotyping
Beadling, C., Neff, T. L., Heinrich, M. C., Rhodes, K., Thornton, M., Leamon, J. H., Andersen, M., & Corless, C. L. (2012) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2012.09.003 · Cited by 119
Liao, G. J. W., Lun, F. M. F., Zheng, Y. W. L., Chan, K. C. A., Leung, T. Y., Lau, T. K., Chiu, R. W. K., & Lo, Y. D. (2010) · Clinical Chemistry · doi:10.1373/clinchem.2010.154336 · Cited by 120
Østergaard, P., Simpson, M. A., Brice, G. W., Mansour, S., Connell, F., Onoufriadis, A., Child, A. H., Hwang, J., Kalidas, K., Mortimer, P. S., et al. (2011) · Journal of Medical Genetics · doi:10.1136/jmg.2010.085563 · Cited by 119
GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data
Babadi, M., Fu, J. M., Lee, S. K., Smirnov, A. N., Gauthier, L. D., Walker, M., Benjamin, D. I., Zhao, X., Karczewski, K. J., Wong, I., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01449-0 · Cited by 132
“WES has revolutionized human disease research and diagnostic screening of protein-coding sequences while being substantially lower cost than whole genome sequencing (WGS) 7,8 .”
Ancient Biomolecules and Evolutionary Inference
Cappellini, E., Prohaska, A., Racimo, F., Welker, F., Pedersen, M. W., Allentoft, M. E., de Barros Damgaard, P., Gutenbrunner, P., Dunne, J., Hammann, S., et al. (2018) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-062917-012002 · Cited by 118
“Capture may be mediated by baits on solid-phase microarrays (75, 76) or by biotinylated baits in solution (77).”
BackgroundA modifier of Huntington's disease onset at the MLH1 locus
Lee, J., Chao, M. J., Harold, D. H., Elneel, K. A., Gillis, T., Holmans, P., Jones, L., Orth, M., Myers, R. H., Kwak, S., et al. (2017) · Human Molecular Genetics · doi:10.1093/hmg/ddx286 · Cited by 117
Guitor, A. K., Raphenya, A. R., Klunk, J., Kuch, M., Alcock, B. P., Surette, M. G., McArthur, A. G., Poinar, H. N., & Wright, G. D. (2019) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01324-19 · Cited by 120
“A more appropriate approach for the identification of resistomes in metagenomes is the use of a probe-and-capture strategy (20).”
Akizu, N., Cantagrel, V., Schroth, J., Cai, N., Vaux, K. K., McCloskey, D., Naviaux, R. K., Vleet, J. L. V., Fenstermaker, A. G., Silhavy, J. L., et al. (2013) · Cell · doi:10.1016/j.cell.2013.07.005 · Cited by 115
Self-citationA Focal Epilepsy and Intellectual Disability Syndrome Is Due to a Mutation in TBC1D24
Corbett, M. A., Bahlo, M., Jolly, L. A., Afawi, Z., Gardner, A. E., Oliver, K. L., Tan, S., Coffey, A., Mulley, J. C., Dibbens, L. M., et al. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.08.001 · Cited by 112
Identification of Recurrent FGFR3–TACC3 Fusion Oncogenes from Lung Adenocarcinoma
Capelletti, M., Dodge, M. E., Ercan, D., Hammerman, P. S., Park, S.-I., Kim, J., Sasaki, H., Jablons, D. M., Lipson, D., Young, L., et al. (2014) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-14-1337 · Cited by 115
“1 Mb of the human genome) was achieved by solution-based hybrid capture with a custom Agilent SureSelect biotinylated RNA baitset (20).”
MethodNext generation sequence analysis for mitochondrial disorders
Vasta, V., Ng, S. B. H., Turner, E. H., Shendure, J., & Hahn, S. H. (2009) · Genome Medicine · doi:10.1186/gm100 · Cited by 114
Weisman, P. S., Ng, C. K. Y., Brogi, E., Eisenberg, R. E. K., Won, H. H., Piscuoglio, S., Filippo, M. R. D., Ioris, R. A., Akram, M. M., Norton, L., et al. (2016) · Modern Pathology · doi:10.1038/modpathol.2016.39 · Cited by 115
Gasc, C., Peyretaillade, É., & Peyret, P. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw309 · Cited by 119
“(13) developed an SHS method that simultaneously targeted four human genomic regions ranging from 220 to 750 kb in size.”
BackgroundMethodInfluentialTaxonomizing, sizing, and overcoming the incidentalome
Kohane, I. S., Hsing, M., & Kong, S. W. (2012) · Genetics in Medicine · doi:10.1038/gim.2011.68 · Cited by 114
Kistler, L., Newsom, L. A., Ryan, T. M., Clarke, A. C., Smith, B. D., & Perry, G. H. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1516109112 · Cited by 115
“moschata, we then designed and synthesized biotinylated RNA probes (18) to enrich additional modern and ancient DNA isolates for targeted sequencing of complete plastid genomes.”
BackgroundInfluentialGupta, T., Marlow, F. L., Ferriola, D., Mackiewicz, K., Dapprich, J., Monos, D. S., & Mullins, M. C. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001073 · Cited by 109
O’Neill, E. M., Schwartz, R. S., Bullock, C. T., Williams, J. S., Shaffer, H. B., Aguilar-Miguel, X., Parra‐Olea, G., & Weisrock, D. W. (2012) · Molecular Ecology · doi:10.1111/mec.12049 · Cited by 110
“…known genomic location, orthology, size and expected level of variation can be enriched prior to NGS using well-established PCR techniques or newly developed hybridization techniques (e.g. Briggs et al. 2009; Gnirke et al. 2009; Maricic et al. 2010) and then pooled for high-throughput sequencing.”
MethodNava, C., Lamari, F., Héron, D., Mignot, C., Rastetter, A., Keren, B., Cohen, D., Faudet, A., Bouteiller, D., Gilleron, M., et al. (2012) · Translational Psychiatry · doi:10.1038/tp.2012.102 · Cited by 117
“Family 1 1233 (54) 108 (45) 109 828 1 (0) 122 (3) 137 (3) 568 (23) 77 5 (1) 72 (30) Family 2 1039 (40) 82 (37) 37 369 1 (0) 59 (3) 48 (1) 261 (8) 19 0 19 (6) Family 3 871 (16) 56 (22) 33 251 1 (0) 36 (0) 40 (1) 174 (2) 15 0 15 (9) Family 4 861 (27) 67 (23) 57 340 1 (0) 72 (4) 58 (1) 209 (2) 21 2 (1) 19 (8) Family 5 89…”
The Impact of Next-Generation Sequencing on Cancer Genomics: From Discovery to ClinicPreprint
Mardis, E. R. (2018) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a036269 · Cited by 118
“…devices only permitted sequencing of whole genomes (which was initially cost-prohibitive for human genomes), the development of clever preparatory methods enabled the selection of exons of known genes from awhole-genomeNGS library (Gnirke et al. 2009; Hodges et al. 2009; Bainbridge et al. 2010).”
MethodGompert, Z., Forister, M. L., Fordyce, J. A., Nice, C. C., WILLIAMSON, R. J., & Buerkle, C. A. (2010) · Molecular Ecology · doi:10.1111/j.1365-294x.2010.04666.x · Cited by 113
Enrichment of sequencing targets from the human genome by solution hybridization
Tewhey, R., Nakano, M., Wang, X., Pabón-Peña, C., Novak, B. A., Giuffre, A. C., Lin, E., Happe, S., Roberts, D. N., LeProust, E. M., et al. (2009) · Genome biology · doi:10.1186/gb-2009-10-10-r116 · Cited by 119
Self-citationExtensive pedigrees reveal the social organization of a Neolithic community
Rivollat, M., Rohrlach, A. B., Ringbauer, H., Childebayeva, A., Mendisco, F., Barquera, R., Szolek, A., Roy, M. L., Colleran, H., Tuke, J., et al. (2023) · Nature · doi:10.1038/s41586-023-06350-8 · Cited by 118
“Finally, a capture targeting 488 genes related to the immune response (including the highly polymorphic HLA) was applied to all of the libraries 46–48 .”
Cancer whole-genome sequencing: present and future
Nakagawa, H., Wardell, C. P., Furuta, M., Taniguchi, H., & Fujimoto, A. (2015) · Oncogene · doi:10.1038/onc.2015.90 · Cited by 111
A targeted enrichment strategy for massively parallel sequencing of angiosperm plastid genomes
Stull, G. W., Moore, M. J., Mandala, V. S., Douglas, N. A., Kates, H. R., Qi, X., Brockington, S. F., Soltis, P. S., Soltis, P. S., & Gitzendanner, M. A. (2013) · Applications in Plant Sciences · doi:10.3732/apps.1200497 · Cited by 108
Koeppel, F., Blanchard, S., Jovelet, C., Génin, B., Marcaillou, C., Martin, E., Rouleau, É., Solary, É., Soria, J., André, F., et al. (2017) · PLoS ONE · doi:10.1371/journal.pone.0188174 · Cited by 116
Mutations in FLVCR1 Cause Posterior Column Ataxia and Retinitis Pigmentosa
Rajadhyaksha, A. M., Elemento, O., Puffenberger, E. G., Schierberl, K. C., Xiang, J., Putorti, M. L., Berciano, J., Poulin, C., Brais, B., Michaelides, M., et al. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.10.013 · Cited by 107
Next generation sequencing technologies for next generation plant breeding
Ray, S., & Satya, P. (2014) · Frontiers in Plant Science · doi:10.3389/fpls.2014.00367 · Cited by 108
“The second group includes technologies like molecular inversion probe (Porreca et al., 2007), solution hybrid selection (Gnirke et al., 2009) and microarraybased genomic selection (Albert et al., 2007).”
MethodAn Exon-Capture System for the Entire Class Ophiuroidea
Hugall, A. F., O’Hara, T. D., Hunjan, S., Nilsen, R., & Moussalli, A. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv216 · Cited by 106
Ronchi, D., Garone, C., Bordoni, A., Ríos, P. G., Calvo, S. E., Ripolone, M., Ranieri, M., Rizzuti, M., Villa, L., Magri, F., et al. (2012) · Brain · doi:10.1093/brain/aws258 · Cited by 104
“We used an in-solution hybridization capture method (Gnirke et al., 2009) to isolate target DNA, which was sequenced on the Illumina GA-II platform (Bentley et al.”
MethodInfluentialGrattapaglia, D., Silva‐Junior, O. B., Kirst, M., de Lima, B. M., de Faria, D. A., & Pappas, G. J., Jr. (2011) · BMC Plant Biology · doi:10.1186/1471-2229-11-65 · Cited by 112
Bone, W. P., Washington, N. L., Buske, O. J., Adams, D. R., Davis, J., Draper, D. D., Flynn, E. D., Gîrdea, M., Godfrey, R. A., Golas, G. A., et al. (2015) · Genetics in Medicine · doi:10.1038/gim.2015.137 · Cited by 103
Bansal, V., Gassenhuber, J., Phillips, T. C., Oliveira, G., Harbaugh, R., Villarasa, N., Topol, E. J., Seufferlein, T. T. W., & Boehm, B. O. (2017) · BMC Medicine · doi:10.1186/s12916-017-0977-3 · Cited by 106
“For enrichment of the targeted regions, we utilized the Agilent SureSelect solution hybridization method [26].”
MethodFuture of portable devices for plant pathogen diagnosis
Sanati‐Nezhad, A. (2014) · Lab on a Chip · doi:10.1039/c4lc00487f · Cited by 104
Alamillo, C. L., Powis, Z., Hagman, K. D. F., Shahmirzadi, L., Weltmer, E. C., Turocy, J. F., Lowe, T. W., Kobelka, C., Chen, E., Basel, D., et al. (2015) · Prenatal Diagnosis · doi:10.1002/pd.4648 · Cited by 105
Overview of Target Enrichment Strategies
Kozarewa, I., Armisen, J., Gardner, A. F., Slatko, B. E., & Hendrickson, C. L. (2015) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb0721s112 · Cited by 105
“These capture methods have been tested almost exclusively in model organisms and species where detailed genomic information is available (Gnirke et al., 2009; Clark et al., 2011; Duncavage et al., 2012), but can be extended to related organisms (see for example Cosart et al., 2011; Geniez et al.,…”
BackgroundMethodTaming the dragon: genomic biomarkers to individualize the treatment of cancer
Majewski, I. J., & Bernards, R. (2011) · Nature Medicine · doi:10.1038/nm.2311 · Cited by 101
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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