The DOI matches its Crossref record; 25 of the 25 references it cites were found in a registry or an index.
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Genome sequencing in microfabricated high-density picolitre reactors
Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693
A second generation human haplotype map of over 3.1 million SNPs
The International HapMap Consortium (2007) · Nature · doi:10.1038/nature06258 · Cited by 4,438
Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684
The complete genome of an individual by massively parallel DNA sequencing
Wheeler, D. A., Srinivasan, M., Egholm, M., Shen, Y., Chen, L., McGuire, A., He, W., Chen, Y.-J., Makhijani, V., Roth, G. T., et al. (2008) · Nature · doi:10.1038/nature06884 · Cited by 1,838
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome
Ley, T. J., Mardis, E. R., Ding, L., Fulton, B., McLellan, M. D., Chen, K., Dooling, D. J., Dunford-Shore, B. H., McGrath, S. D., Hickenbotham, M. T., et al. (2008) · Nature · doi:10.1038/nature07485 · Cited by 1,434 · cited 1×
“Within a short time, several individual human genomes have been sequenced on next-generation instrument”
BackgroundAccurate Multiplex Polony Sequencing of an Evolved Bacterial Genome
Shendure, J., Porreca, G. J., Reppas, N. B., Lin, X., McCutcheon, J. P., Rosenbaum, A. M., Wang, M. D., Zhang, K., Mitra, R. D., & Church, G. M. (2005) · Science · doi:10.1126/science.1117389 · Cited by 1,402
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
Dohm, J. C., Lottaz, C., Borodina, T., & Himmelbauer, H. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn425 · Cited by 1,088
The diploid genome sequence of an Asian individual
Wang, J., Wang, W., Li, R., Li, Y., Tian, G., Goodman, L., Fan, W., Zhang, J., Li, J., Zhang, J., et al. (2008) · Nature · doi:10.1038/nature07484 · Cited by 924
Padlock Probes: Circularizing Oligonucleotides for Localized DNA Detection
Nilsson, M. F., Malmgren, H., Samiotaki, M. K., Kwiatkowski, M., Chowdhary, B. P., & Landegren, U. D. (1994) · Science · doi:10.1126/science.7522346 · Cited by 791
A large genome center's improvements to the Illumina sequencing system
Quail, M. A., Kozarewa, I., Smith, F., Scally, A., Stephens, P. J., Durbin, R. M., Swerdlow, H., & Turner, D. (2008) · Nature Methods · doi:10.1038/nmeth.1270 · Cited by 740 · cited 1×
“PCR amplification of the catch and sequencing itself is also known to introduce bia”
Background
Flagged first, then by citations
Cited by
Sorted by citations
Items 501–600 of 1,000
Heuckmann, J. M., & Thomas, R. K. (2015) · Annals of Oncology · doi:10.1093/annonc/mdv184 · Cited by 48
Efficient and Cost Effective Population Resequencing by Pooling and In-Solution Hybridization
Bansal, V., Tewhey, R., LeProust, E. M., & Schork, N. J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0018353 · Cited by 52
Self-citationImmel, A., Key, F. M., Szolek, A., Barquera, R., Robinson, M. K., Harrison, G. F., Palmer, W. H., Spyrou, M. A., Susat, J., Krause‐Kyora, B., et al. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab147 · Cited by 49
Standardized nuclear markers improve and homogenize species delimitation in Metazoa
Dietz, L., Eberle, J., Mayer, C., Kukowka, S., Bohacz, C., Baur, H., Espeland, M., Huber, B. A., Hutter, C. R., Mengual, X., et al. (2022) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.14041 · Cited by 54
“…of single copy target loci from an organism's genome, even with degraded DNA, to resolve questions that cannot be answered with only a limited number of loci (Gnirke et al., 2009, Faircloth et al., 2012; Lemmon et al., 2012; Lemmon & Lemmon, 2013; Hancock- Hanser et al., 2013; Mayer et al., 2016).”
BackgroundMethodGandomi, S. K., Hagman, K. D. F., Parra, M., Shahmirzadi, L., Mancuso, J., Pichurin, P. N., Temme, R., Dugan, S. L., Zeng, W., & Tang, S. (2013) · Journal of Genetic Counseling · doi:10.1007/s10897-013-9671-6 · Cited by 48
“Samples were prepared using the SureSelect Target Enrichment System (Agilent Technologies, Santa Clara, CA) (Gnirke et al. 2009).”
MethodGroßmann, V., Kohlmann, A., Klein, H.-U., Schindela, S., Schnittger, S., Dicker, F., Dugas, M., Kern, W., Haferlach, T., & Haferlach, C. (2011) · Leukemia · doi:10.1038/leu.2010.309 · Cited by 47
Zhou, L., Bawa, R., & Holliday, J. A. (2014) · Molecular Ecology · doi:10.1111/mec.12752 · Cited by 50
“2011), wherein one or more restriction enzyme is used to fragment the genome followed by sequencing, and sequence capture (Gnirke et al. 2009), wherein RNA baits retrieve particular sequences through solution hybridization.”
MethodA recurrent de novo missense mutation in UBTF causes developmental neuroregression
Toro, C., Hori, R. T., Malicdan, M. C. V., Tifft, C. J., Goldstein, A. C., Gahl, W. A., Adams, D. R., Fauni, H. B., Wolfe, L. A., Xiao, J., et al. (2017) · Human Molecular Genetics · doi:10.1093/hmg/ddx435 · Cited by 47
Volkman, S. K., Ndiaye, D., Diakité, M., Koita, O., Nwakanma, D. C., Daniels, R. F., Park, D. J., Neafsey, D. E., Muskavitch, M. A. T., Krogstad, D. J., et al. (2011) · Acta Tropica · doi:10.1016/j.actatropica.2011.12.002 · Cited by 44
Green, R., Rehm, H., & Kohane, I. (2013) · Elsevier eBooks · doi:10.1016/b978-0-12-382227-7.00009-4 · Cited by 55
Ben‐Salem, S., Gleeson, J. G., Al-Shamsi, A. M., Islam, B., Hertecant, J., Ali, B. R., & Al‐Gazali, L. (2014) · Metabolic Brain Disease · doi:10.1007/s11011-014-9618-0 · Cited by 47
“Captured DNA libraries, of 100–base pair sequencing length, were sequenced with HiSeq2000 instrument (Gnirke et al. 2009).”
MethodMultiplex Target Enrichment Using DNA Indexing for Ultra-High Throughput SNP Detection
Kenny, E. M., Cormican, P., Gilks, W. P., Gates, A. S., O'Dushlaine, C. T., Pinto, C., Corvin, A. P., Gill, M., & Morris, D. W. (2010) · DNA Research · doi:10.1093/dnares/dsq029 · Cited by 47
Mokrý, M., Nijman, I. J., Dijken, A. J. H. V., Benjamins, R., Heidstra, R., Scheres, B., & Cuppen, E. P. J. G. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-256 · Cited by 47
Precone, V., Monaco, V. D., Esposito, M. V., Palma, F. D. E. D., Ruocco, A., Salvatore, F., & D’Argenio, V. (2015) · BioMed Research International · doi:10.1155/2015/161648 · Cited by 51
“Specific capture probes can be synthesized to enrich the regions of interest from the whole genome, thus obtaining a captured, adapted, and barcoded library for NGS applications [9, 40, 41].”
BackgroundLaissue, P. (2015) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2015.05.005 · Cited by 54
BRAT1 mutations present with a spectrum of clinical severity
Srivastava, S., Olson, H. E., Cohen, J. S., Gubbels, C. S., Lincoln, S. A., Davis, B. T., Shahmirzadi, L., Gupta, S. S., Picker, J. D., Yu, T. W., et al. (2016) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.37783 · Cited by 46
“Briefly, samples prepared using either 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).”
MethodBachmann, N. L., Sullivan, M. J., Jelocnik, M., Myers, G. S. A., Timms, P., & Polkinghorne, A. (2015) · Journal of Clinical Microbiology · doi:10.1128/jcm.03534-14 · Cited by 46
“pecorum DNA from swab samples collected from koalas and Australian sheep and a cell-cultured Australian bovine isolate (20).”
BackgroundMethodReduced representation approaches to interrogate genome diversity in large repetitive plant genomes
Hirsch, C. D., Evans, J., Buell, C. R., & Hirsch, C. N. (2014) · Briefings in Functional Genomics · doi:10.1093/bfgp/elt051 · Cited by 44
“solution [40], capturing genomic DNA through an-”
DNA Sequencing of Cancer: What Have We Learned?
Chmielecki, J., & Meyerson, M. M. (2013) · Annual Review of Medicine · doi:10.1146/annurev-med-060712-200152 · Cited by 48
Sobreira, N. L. M., Gnanakkan, V. P., Walsh, M. F., Marosy, B. A., Wohler, E., THOMAS, G. V., Hoover-Fong, J. E., Hamosh, A., Wheelan, S. J., & Valle, D. L. (2011) · Genome Research · doi:10.1101/gr.122986.111 · Cited by 46
The 3D Genome: From Structure to Function
Mohanta, T. K., Mishra, A. K., & Al‐Harrasi, A. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222111585 · Cited by 51
“Oligopaints are libraries of synthesized oligonucleotides containing approximately 60–100 bp [111].”
BackgroundCalling SNPs without a reference sequence
Ratan, A., Zhang, Y., Hayes, V. M., Schuster, S. C., & Miller, W. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-130 · Cited by 45
Dynamics of Copy Number Variation in Host Races of the Pea Aphid
Duvaux, L., Geissmann, Q., Gharbi, K., Zhou, J., Ferrari, J., Smadja, C. M., & Butlin, R. K. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu266 · Cited by 50
“In order to enrich genomic DNA for genes of interest prior to sequencing, we used the SureSelect system (Agilent Technologies), which uses RNA probes (baits) designed to capture regions of interest from genomic DNA in solution (Gnirke et al. 2009; Mamanova et al. 2010).”
MethodSwanton, C., Larkin, J., Gerlinger, M., Eklund, A. C., Howell, M. T., Stamp, G., Downward, J., Gore, M. E., Futreal, P. A., Escudier, B. J., et al. (2010) · Genome Medicine · doi:10.1186/gm174 · Cited by 45
Loss of function of the retinoid-related nuclear receptor (RORB) gene and epilepsy
Rudolf, G., Lesca, G., Mehrjouy, M. M., Labalme, A., Salmi, M., Bache, I., Bruneau, N., Pendziwiat, M., Fluss, J., de Bellescize, J., et al. (2016) · European Journal of Human Genetics · doi:10.1038/ejhg.2016.80 · Cited by 45
PrimerPooler: automated primer pooling to prepare library for targeted sequencing
Brown, S. S., Chen, Y.-W., Wang, M., Clipson, A., Ochoa, E., & Du, M. (2017) · Biology Methods and Protocols · doi:10.1093/biomethods/bpx006 · Cited by 40
“This includes (1) inter-/intra-primers hybridization analysis, (2) genome mapping and (3) the automated”
BackgroundMethodSelective efficiency of genome-wide selection in Coffea canephora breeding
Alkimim, E. R., Caixeta, E. T., Sousa, T. V., de Resende, M. D. V., da Silva, F. L., Sakiyama, N. S., & Zambolim, L. (2020) · Tree Genetics & Genomes · doi:10.1007/s11295-020-01433-3 · Cited by 45
Myllykangas, S., Buenrostro, J. D., Natsoulis, G., Bell, J., & Ji, H. P. (2011) · Nature Biotechnology · doi:10.1038/nbt.1996 · Cited by 44
Microfluidic droplet enrichment for targeted sequencing
Eastburn, D. J., Huang, Y., Pellegrino, M., Sciambi, A., Ptáček, L. J., & Abate, A. R. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv297 · Cited by 44
Lou, Q., Zhang, Y., He, Y., Li, J., Jia, L., Cheng, C., Guan, W., Yang, S., & Chen, J. (2014) · The Plant Journal · doi:10.1111/tpj.12453 · Cited by 44
“technology or massive parallel PCR amplification (Porreca et al., 2007; Gnirke et al., 2009); however, their application in”
BackgroundBagley, R. K., Sousa, V. C., Niemiller, M. L., & Linnen, C. R. (2016) · Molecular Ecology · doi:10.1111/mec.13972 · Cited by 45
“have changed over the years (Avise 2004; Hartl & Clark 2007; Gnirke et al. 2009; Davey et al. 2011), a long-stand-”
BackgroundOptimized DNA sampling of ancient bones using Computed Tomography scans
Alberti, F., González, J., Paijmans, J. L. A., Basler, N., Preick, M., Henneberger, K., Trinks, A., Rabeder, G., Conard, N. J., Münzel, S. C., et al. (2018) · Molecular Ecology Resources · doi:10.1111/1755-0998.12911 · Cited by 47
“This method has several limitations, however, requiring either prior DNA sequence knowledge of the region(s) of interest (Gnirke et al., 2009; Hodges et al., 2007), or high-quality DNA from an extant close relative (Enk et al.”
MethodComparative performance of two whole‐genome capture methodologies on ancient DNA Illumina libraries
Ávila‐Arcos, M. C., Sandoval‐Velasco, M., Schroeder, H., Carpenter, M. L., Malaspinas, A., Wales, N., Peñaloza, F., Bustamante, C. D., & Gilbert, M. T. P. (2015) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12353 · Cited by 46
“…method,MYbaits-WGE (MYbaits Whole-Genome Enrichment, henceforth referred to as ‘MYbaits’), was developed by the companyMYcroarray (Ann Arbor, MI, USA) following a similar methodological principle (Gnirke et al. 2009) but with subtle protocol differences (for an application see Enk et al. 2014).”
MethodInfluentialKaramitros, T., & Magiorkinis, G. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv773 · Cited by 43
“These methods rely on the hybridization of target sequences to molecular ‘baits’, which are actually single stranded oligos, most of the times conjugated with biotin (8,9).”
Synteny‐based mapping‐by‐sequencing enabled by targeted enrichment
Galvão, V. C., Nordström, K. J. V., Lanz, C., Sulz, P., Mathieu, J., Posé, D., Schmid, M., Weigel, D., & Schneeberger, K. (2012) · The Plant Journal · doi:10.1111/j.1365-313x.2012.04993.x · Cited by 43
Applying next-generation sequencing to pancreatic cancer treatment
Mardis, E. R. (2012) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2012.126 · Cited by 43
Genomic Sequencing for Cancer Diagnosis and Therapy
Wang, L., & Wheeler, D. A. (2013) · Annual Review of Medicine · doi:10.1146/annurev-med-120811-171056 · Cited by 44
Gowrisankar, S., Lerner‐Ellis, J. P., Cox, S. W., White, E. T., Manion, M. L., LeVan, K., Liu, J., Farwell, L. M., Iartchouk, O., Rehm, H. L., et al. (2010) · Journal of Molecular Diagnostics · doi:10.2353/jmoldx.2010.100014 · Cited by 43
Shahrour, M. A., Staretz‐Chacham, O., Dayan, D., Stephen, J., Weech, A. A., Damseh, N. S., Chen, H. P., Edvardson, S., Mazaheri, S., Saada, A., et al. (2016) · Clinical Genetics · doi:10.1111/cge.12855 · Cited by 43
“22% of the human genome corresponding to the Consensus Conserved Domain Sequences and more than 1000 non-coding RNAs (6).”
BackgroundInfluentialMolecular diagnostics in acute leukemias
Bacher, U., Schnittger, S., Haferlach, C., & Haferlach, T. (2009) · Clinical Chemistry and Laboratory Medicine (CCLM) · doi:10.1515/cclm.2009.324 · Cited by 44
Beal, M. A., Glenn, T. C., & Somers, C. M. (2011) · Mutation Research/Reviews in Mutation Research · doi:10.1016/j.mrrev.2011.11.002 · Cited by 41
Microfluidics for genome-wide studies involving next generation sequencing
Ma, S., Murphy, T. W., & Lu, C. (2017) · Biomicrofluidics · doi:10.1063/1.4978426 · Cited by 42
Hybridization capture reveals microbial diversity missed using current profiling methods
Gasc, C., & Peyret, P. (2018) · Microbiome · doi:10.1186/s40168-018-0442-3 · Cited by 42
Technical Advances and Challenges in Genome-Scale Analysis of Ancient DNA
Lan, T., & Lindqvist, C. (2018) · Population genomics · doi:10.1007/13836_2018_54 · Cited by 43
Clinical cancer genomics: how soon is now?
Taylor, B. S., & Ladanyi, M. (2010) · The Journal of Pathology · doi:10.1002/path.2794 · Cited by 41
Primerize: automated primer assembly for transcribing non-coding RNA domains
Tian, S., Yesselman, J. D., Cordero, P., & Das, R. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv538 · Cited by 41
A Global Phylogenomic Study of the Thelypteridaceae
Fawcett, S., Smith, A. Р., Sundue, M., Burleigh, J. G., Sessa, E. B., Kuo, L., Chen, C., Testo, W., Kessler, M. R., & Barrington, D. S. (2021) · Systematic Botany · doi:10.1600/036364421x16370109698650 · Cited by 41
“Target enrichment was performed using the GoFlag 408 probes following protocols based on Gnirke et al. (2009).”
MethodSchlipf, N., Schüle, R., Klimpe, S., Karle, K., Synofzik, M., Schicks, J., Rieß, O., Schöls, L. J., & Bauer, P. (2011) · Clinical Genetics · doi:10.1111/j.1399-0004.2011.01715.x · Cited by 40
Programmable and Highly Resolved In Vitro Detection of 5‐Methylcytosine by TALEs
Kubik, G., Schmidt, M. J., Penner, J. E., & Summerer, D. (2014) · Angewandte Chemie International Edition · doi:10.1002/anie.201400436 · Cited by 40
Rare Variants in Ischemic Stroke: An Exome Pilot Study
Cole, J. W., Stine, O. C., Liu, X., Pratap, A., Cheng, Y., Tallon, L. J., Sadzewicz, L., Dueker, N., Wozniak, M. A., Stern, B. J., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0035591 · Cited by 39
“This sequence coverage yielded at least 206 sequence coverage for more than 75% of targeted exons, leading to high confidence SNP calls with low false positive rates [3,20].”
BackgroundResultChmielecki, J., Peifer, M., Jia, P., Socci, N. D., Hutchinson, K. E., Viale, A. J., Zhao, Z., Thomas, R. K., & Pao, W. J. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq579 · Cited by 40
Caminsky, N., Mucaki, E. J., Perri, A. M., Lu, R., Knoll, J. H. M., & Rogan, P. K. (2016) · Human Mutation · doi:10.1002/humu.22972 · Cited by 40
Hybridization-based capture of pathogen mRNA enables paired host-pathogen transcriptional analysis
Betin, V., Peñaranda, C., Bandyopadhyay, N., Yang, R., Abitua, A., Bhattacharyya, R. P., Fan, A. C., Avraham, R., Livny, J., Noam Shoresh, F., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-55633-6 · Cited by 40
Dames, S. A., Durtschi, J., Geiersbach, K. B., Stephens, J., & Voelkerding, K. V. (2010) · PubMed Central · Cited by 39
Massive parallel sequencing applied to the molecular autopsy in sudden cardiac death in the young
Brión, M., Sobrino, B., Martínez, M. A. L., Blanco‐Verea, A., & Carracedo, Á. (2015) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2015.07.010 · Cited by 39
Sivakumaran, T. A., Husami, A., Kissell, D., Zhang, W., Keddache, M. A., Black, A. P., Tinkle, B. T., Greinwald, J. H., & Zhang, K. (2013) · Otolaryngology · doi:10.1177/0194599813482294 · Cited by 39
“Recent advancements in high-throughput sequencing (also known as next-generation sequencing [NGS]) have revolutionized genetic research.(9-12) Targeted resequencing using NGS technology offers a unique opportunity to sequence multiple genes causing heterogeneous disorders, such as SNHL, hypertrophic cardiomyopathy, an…”
BackgroundLieber, D. S., Vafai, S. B., Horton, L. C., Slate, N. G., Liu, S., Borowsky, M. L., Calvo, S. E., Schmahmann, J. D., & Mootha, V. K. (2012) · BMC Medical Genetics · doi:10.1186/1471-2350-13-3 · Cited by 39
Paoli‐Iseppi, R. D., Johansson, P. A., Menzies, A. M., Dias, K., Pupo, G. M., Kakavand, H., Wilmott, J. S., Mann, G. J., Hayward, N. K., Dinger, M. E., et al. (2016) · Pathology · doi:10.1016/j.pathol.2016.01.001 · Cited by 40
Voss, M. H., Chen, D., Reising, A., Marker, M., Shi, J., Xu, J., Ostrovnaya, I., Seshan, V., Redzematovic, A., Chen, Y., et al. (2018) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-18-1833 · Cited by 39
“(7, 8) Our analysis focused on genes within the PI3K/mTOR pathway.”
Barrow, L. N., Ralicki, H. F., Emme, S. A., & Lemmon, E. M. (2014) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2014.02.007 · Cited by 38
Shay, J. A., Haniford, L. S. E., Cooper, A. L., Carrillo, C. D., Blais, B. W., & Lau, C. H. (2023) · Environmental Microbiome · doi:10.1186/s40793-023-00482-0 · Cited by 39
“As an alternative approach, a targeted-sequencing strategy involving in-solution hybridization of the genomic library to a selection of probes prior to sequencing has been developed [20].”
MethodFrom Genomics to Integrative Taxonomy? The Case Study of Pocillopora Corals
Oury, N., Noël, C., Mona, S., Aurelle, D., & Magalon, H. (2022) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2023.107803 · Cited by 49
Ratnapriya, R., & Swaroop, A. (2013) · Genome Medicine · doi:10.1186/gm488 · Cited by 38
“Whole-exome sequencing (WES) involves the capture and sequencing of all coding exons (1 to 2% of the whole genome) (Box 1) and has become an ideal choice for Mendelian disease gene discovery with or without prior linkage information [20-24] (Figure 2).”
BackgroundHow should clinicians address intratumour heterogeneity in clear cell renal cell carcinoma?
Soultati, A. S., Stares, M., Swanton, C., Larkin, J., & Turajlic, S. (2015) · Current Opinion in Urology · doi:10.1097/mou.0000000000000204 · Cited by 37
“PCR-amplicon [57] and hybridization capture based methods are available with hybridization capture best suited for capture of larger target regions and exons from hundreds of genes [58].”
Reduced Representation Methods for Subgenomic Enrichment and Next-Generation Sequencing
Good, J. M. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-228-1_5 · Cited by 39
Targeted Enrichment for Pathogen Detection and Characterization in Three Felid Species
Lee, J. S., Mackie, R. S., Harrison, T., Shariat, B., Kind, T., Kehl, T., Löchelt, M., Boucher, C. A., & VandeWoude, S. (2017) · Journal of Clinical Microbiology · doi:10.1128/jcm.01463-16 · Cited by 38
“sequences within a heterogeneous mixture of DNA or RNA (1).”
Targeted capture of complete coding regions across divergent species
Schott, R. K., Panesar, B., Card, D. C., Preston, M. W., Castoe, T. A., & Chang, B. S. W. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx005 · Cited by 38
“…methods that has been shown to perform well and is gaining popularity (Albert et al. 2007; Hodges et al. 2007; Okou et al. 2007; Porreca et al. 2007; Gnirke et al. 2009; Summerer et al. 2009; Mamanova et al. 2010; Nijman et al. 2010; Teer et al. 2010; Teer and Mullikin 2010; Kenny et al. 2011;…”
BackgroundMethodInfluentialPhylogenomic species delimitation in microendemic frogs of the Brazilian Atlantic Forest
Pie, M. R., Bornschein, M. R., Ribeiro, L. F., Faircloth, B. C., & McCormack, J. E. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2019.106627 · Cited by 38
Leprieur, E. G., Hélias‐Rodzewicz, Z., Kamga, P. T., Costantini, A., Julié, C., Corjon, A., Duménil, C., Dumoulin, J., Giraud, V., Labrune, S., et al. (2020) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2020-000527 · Cited by 40
Loss of SWI/SNF Chromatin Remodeling Alters NRF2 Signaling in Non–Small Cell Lung Carcinoma
Song, S., Nguyen, V. Q., Schrank, T. P., Mulvaney, K. M., Walter, V., Wei, D., Orvis, T., Desai, N. P., Zhang, J., Hayes, D. N., et al. (2020) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-20-0082 · Cited by 38
Whole exome sequencing in three families segregating a pediatric case of sarcoidosis
France), I. T. F. O. G. (. S., Calender, A., Farnier, P. A. R., Buisson, A., Pinson, S., Bentaher, A., Lebecque, S., Corvol, H., Taam, R. A., Houdouin, V., et al. (2018) · BMC Medical Genomics · doi:10.1186/s12920-018-0338-x · Cited by 38
“Genomic DNA was captured using Agilent in-solution enrichment methodology (SureSelect Human Clinical Research Exome, Agilent) with the supplied biotinylated oligonucleotides probes library (Human Clinical Research Exome, Agilent), followed by paired-end 75 bases massively parallel sequencing on Illumina HiSEQ 4000 [20…”
MethodRoulis, E. V., Bachmann, N. L., Myers, G. S. A., Huston, W. M., Summersgill, J. T., Hudson, A. P., Dreses‐Werringloer, U., Polkinghorne, A., & Timms, P. (2015) · Genomics · doi:10.1016/j.ygeno.2015.09.008 · Cited by 36
Vinner, L., Mourier, T., Friis-Nielsen, J., Gniadecki, R., Dybkær, K., Rosenberg, J., Langhoff, J. L., Cruz, D. F. S., Fonager, J., Izarzugaza, J. M. G., et al. (2015) · Scientific Reports · doi:10.1038/srep13201 · Cited by 37
Gartner, J. J., Davis, S. R., Wei, X., Lin, J., Trivedi, N. S., Teer, J. K., Program, N. C. S., Meltzer, P. S., Rosenberg, S. A., & Samuels, Y. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-505 · Cited by 37
“Exonic sequences were enriched with Agilent's SureSelect technology for targeted exon capture [4], targeting 50 Mb of sequence from exons and flanking regions in nearly 20,000 genes.”
MethodSeqAnt: A web service to rapidly identify and annotate DNA sequence variations
Shetty, A. C., Athri, P., Mondal, K., Horner, V. L., Steinberg, K. M., Patel, V., Caspary, T., Cutler, D. J., & Zwick, M. E. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-471 · Cited by 37
North Carolina macular dystrophy (MCDR1) caused by a novel tandem duplication of the PRDM13 gene.
Bowne, S. J., Sullivan, L. S., Wheaton, D. K., Locke, K. G., Webb-Jones, K., Koboldt, D. C., Fulton, R. S., Wilson, R. K., Blanton, S. H., Birch, D. G., et al. (2016) · PubMed Central · Cited by 37
Vilboux, T., Malicdan, M. C. V., Roney, J. C., Cullinane, A. R., Stephen, J., Yildirimli, D., Bryant, J. C., Fischer, R. E., Vemulapalli, M., Mullikin, J. C., et al. (2017) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.38005 · Cited by 37
“22% of the human genome corresponding to the Consensus Conserved Domain Sequences and more than 1,000 noncoding RNAs [Gnirke et al., 2009].”
InfluentialPang, S. Y.-Y., Teo, K. C., Hsu, J. S., Chang, R. S., Li, M., Sham, P. C., & Ho, S. (2017) · Translational Neurodegeneration · doi:10.1186/s40035-017-0098-0 · Cited by 39
“The whole genome can be sequenced (whole genome sequencing, or WGS); whereas when combined with techniques of targeted capture, any subset of the genome can be sequenced, an example being whole exome sequencing (WES) [10, 11].”
From Genomes to GENE-omes: Exome Sequencing Concept and Applications in Crop Improvement
Kaur, P., & Gaikwad, K. (2017) · Frontiers in Plant Science · doi:10.3389/fpls.2017.02164 · Cited by 37
“Two technological alternatives available for hybridization based exome capture are: array/chip- based capture (Hodges et al., 2007; Okou et al., 2007) and In solution capture (Gnirke et al., 2009).”
MethodBachmann, N. L., Rockett, R. J., Timms, V. J., & Sintchenko, V. (2018) · Frontiers in Public Health · doi:10.3389/fpubh.2018.00363 · Cited by 40
“a complete target genome sequence so that magnetic beads coated with the biotin-binding protein, streptavidin, can be used to extract the DNA (53).”
BackgroundDowdy, N. J., Keating, S. E., Lemmon, A. R., Lemmon, E. M., Conner, W. E., Chialvo, C. H. S., Weller, S. J., Simmons, R. B., Sisson, M. S., & Zaspel, J. M. (2020) · Systematic Entomology · doi:10.1111/syen.12433 · Cited by 36
“, 2017) or hybrid enrichment (Hodges et al., 2007; Gnirke et al., 2009) to target, isolate and sequence designated regions of the genome, depending on the scope of the evolutionary hypotheses being tested.”
BackgroundMultiplexed Targeted Sequencing for Oxford Nanopore MinION: A Detailed Library Preparation Procedure
Karamitros, T., & Magiorkinis, G. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7514-3_4 · Cited by 37
An environmental DNA sampling method for aye‐ayes from their feeding traces
Aylward, M. L., Sullivan, A., Perry, G. H., Johnson, S. E., & Louis, E. E. (2018) · Ecology and Evolution · doi:10.1002/ece3.4341 · Cited by 37
“…surrounding unhabituated populations, cryptic species, and those at risk of extinction (Clevenger & Sawaya, 2010; Cushman, McKelvey, Hayden, & Schwartz, 2006; Goossens et al., 2000; KendallL et al., 2009; Morin, Kelly, & Waits, 2016; Orkin, Yang, Yang, Yu, & Jiang, 2016; Schubert et al., 2011).”
Zhang, H., Liu, L., & Li, M. (2024) · ACS Sensors · doi:10.1021/acssensors.3c02328 · Cited by 37
Resequencing Helminth Genomes for Population and Genetic Studies
Wit, J., & Gilleard, J. S. (2017) · Trends in Parasitology · doi:10.1016/j.pt.2017.01.009 · Cited by 36
Weiss, E. R., Lamers, S. L., Henderson, J. L., Melnikov, A., Somasundaran, M., Garber, M. G., Selin, L. K., Nusbaum, C., & Luzuriaga, K. (2017) · Journal of Virology · doi:10.1128/jvi.01466-17 · Cited by 36
“Using an approach similar to one successfully employed to generate overlapping RNA probes against the larger and more complex genome of Plasmodium falciparum (30), EBV genomes were enriched from patient B cell or oral wash samples using biotinylated RNA probes based on templates from type I reference EBV strains, B95.”
MethodSelf-citationSousa, T. V., Caixeta, E. T., Alkimim, E. R., de Oliveira, A. C. B., Pereira, A. A., Sakiyama, N. S., Resende, M. F. R., & Zambolim, L. (2017) · Tree Genetics & Genomes · doi:10.1007/s11295-017-1208-y · Cited by 36
“The sequencing-based genotyping was performed using targeted enrichment followed by next-generation sequencing, as previously described (Gnirke et al. 2009).”
MethodNeoantigen-reactive T cells exhibit effective anti-tumor activity against colorectal cancer
Yu, Y., Zhang, J., Ni, L., Zhu, Y., Yu, H., Teng, Y., Lin, L., Xue, Z., Xue, X., Shen, X., et al. (2021) · Human Vaccines & Immunotherapeutics · doi:10.1080/21645515.2021.1891814 · Cited by 40
“0 bait set (Agilent Technologies, Santa Clara, CA, USA).(14) The resulting libraries were quantified using a quantitative polymerase chain reaction (qPCR), and 76 basepaired end reads were generated and sequenced using HiSeq 2000 or 2500 sequencers (Illumina).”
MethodHoshida, Y. (2009) · Journal of Hepatology · doi:10.1016/j.jhep.2009.08.003 · Cited by 36
Ghosh, S., Krux, F., Binder, V., Gombert, M., Niehues, T., Feyen, O., Laws, H. ‐., Borkhardt, A., & on behalf of PID‐NET: German Network on Primary Immunodeficiency Diseases (2011) · Scandinavian Journal of Immunology · doi:10.1111/j.1365-3083.2011.02658.x · Cited by 35
Wooderchak‐Donahue, W. L., O’Fallon, B. D., Furtado, L. V., Durtschi, J., Plant, P., Ridge, P. G., Rope, A. F., Yetman, A. T., & Bayrak‐Toydemir, P. (2012) · BMC Medical Genomics · doi:10.1186/1755-8794-5-50 · Cited by 35
“In this work we compare two competing enrichment protocols, an emulsion-PCR based technique from RainDance technologies [18] and a method utilizing solution-based RNA-bait hybrid capture marketed as the SureSelect Target Enrichment Platform [19].”
MethodNext-generation sequencing entering the clinical arena
Haas, J., Katus, H. A., & Meder, B. (2011) · Molecular and Cellular Probes · doi:10.1016/j.mcp.2011.08.005 · Cited by 34
Oprescu, S. N., Chepa-Lotrea, X., Takase, R., Golas, G. A., Markello, T. C., Adams, D. R., Toro, C., Gropman, A. L., Hou, Y., Malicdan, M. C. V., et al. (2017) · Human Mutation · doi:10.1002/humu.23287 · Cited by 35
“Whole-exome sequencing was performed using the Illumina HiSeq2000 platform and the TrueSeq capture kit (Illumina, San Diego, CA) by the NIH Intramural Sequencing Center (NISC) as described (Bentley et al., 2008; Gahl et al., 2012; Gnirke et al., 2009; Teer et al., 2010).”
BackgroundMethodInfluentialWhole mitochondrial genome capture from faecal samples and museum‐preserved specimens
van der Valk, T., Lona‐Durazo, F., Dalén, L., & Guschanski, K. (2017) · Molecular Ecology Resources · doi:10.1111/1755-0998.12699 · Cited by 37
“Multiple hybridization-based enrichment approaches have been developed that use “baits” to “catch” DNA fragments corresponding to the genomic region of interest from a complex mixture of DNA molecules (e.g., Albert et al., 2007; Briggs et al., 2009; Burbano et al., 2010; Gnirke et al., 2009; Hodges et al., 2007; Rohla…”
BackgroundMethodRitland, K., Krutovsky, K. V., & Tsumura, Y. (2011) · CRC Press eBooks · doi:10.1201/b11075-9 · Cited by 36
Li, Y., Baptista, R. P., Sateriale, A., Striepen, B., & Kissinger, J. C. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.608298 · Cited by 33
Identification of common predisposing loci to hematopoietic cancers in four dog breeds
Hédan, B., Cadieu, É., Rimbault, M., Vaysse, A., de Citres, C. D., Devauchelle, P., Botherel, N., Abadie, J., Quignon, P., Derrien, T., et al. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009395 · Cited by 34
“Library preparation and capture were followed by paired-end 75 base massive parallel sequencing on an Illumina HiSeq 2000 sequencer [63].”
MethodHow do novel molecular genetic markers influence treatment decisions in acute myeloid leukemia?
Patel, J. P., & Levine, R. L. (2012) · Hematology · doi:10.1182/asheducation.v2012.1.28.3797923 · Cited by 37
RYR1Mutations as a Cause of Ophthalmoplegia, Facial Weakness, and Malignant Hyperthermia
Shaaban, S., Ramos-Platt, L. M., Gilles, F. H., Chan, W. M., Andrews, C. V., Girolami, U. D., Demer, J. L., & Engle, E. C. (2013) · JAMA Ophthalmology · doi:10.1001/jamaophthalmol.2013.4392 · Cited by 35
Whole-Genome Enrichment Provides Deep Insights into Vibrio cholerae Metagenome from an African River
Vezzulli, L., Grande, C., Tassistro, G., Brettar, I., Höfle, M. G., Pereira, R. P. A., Mushi, D., Pallavicini, A., Vassallo, P., & Pruzzo, C. (2016) · Microbial Ecology · doi:10.1007/s00248-016-0902-x · Cited by 34
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
