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 901–1,000 of 1,000
Progress and Potential: Training in Genomic Pathology
Haspel, R. L., Olsen, R. J., Berry, A. B., Hill, C. E., Pfeifer, J. D., Schrijver, I., & Kaul, K. L. (2014) · Archives of Pathology & Laboratory Medicine · doi:10.5858/arpa.2013-0359-sa · Cited by 12
Borges, P. D., Ludwig, S., & Boeger, W. A. (2016) · Limnology · doi:10.1007/s10201-016-0485-8 · Cited by 12
Novel splice-site mutation in TTLL5 causes cone dystrophy in a consanguineous family.
Dias, M. M. D. S., Hamel, C., Meunier, I., Varin, J., Blanchard, S., Boyard, F., Sahel, J., & Zeitz, C. (2017) · PubMed Central · Cited by 12
Markus, F., Angelini, C., Trimouille, A., Rudolf, G., Lesca, G., Goizet, C., Lasseaux, E., Arveiler, B., van Slegtenhorst, M., Brooks, A. S., et al. (2020) · Molecular Genetics & Genomic Medicine · doi:10.1002/mgg3.1388 · Cited by 12
“The detailed explanations of the process have been previously described (Gnirke et al., 2009).”
BackgroundGenetic predisposition to neural crest-derived tumors: revisiting the role of KIF1B
Bauters, C. C., Leteurtre, E., Carnaille, B. M. L., Cao, C. D., Espiard, S., Penven, M., Destailleur, E., Szuster, I., Lovecchio, T., Leclerc, J., et al. (2020) · Endocrine Connections · doi:10.1530/ec-20-0460 · Cited by 12
“…Agilent in-solution enrichment methodology with their biotinylated oligonucleotides probes library (SureSelect Clinical Research Exome V2, Agilent Technologies), followed by paired-end 75 bases massively parallel sequencing on Illumina HiSeq4000 (IntegraGen SA, Evry, France), as reported (13).”
Microarray Generation of Thousand-Member Oligonucleotide Libraries
Svensen, N., Díaz‐Mochon, J. J., & Bradley, M. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024906 · Cited by 12
Three Reagents for in-Solution Enrichment of Ancient Human DNA at More than a Million SNPsPreprint
Rohland, N., Mallick, S., Mah, M., Maier, R., Patterson, N. J., & Reich, D. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.13.476259 · Cited by 13
Babadi, M., Fu, J. M., Lee, S. K., Smirnov, A. N., Gauthier, L. D., Walker, M., Benjamin, D. I., Karczewski, K. J., Wong, I., Collins, R. L., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.25.504851 · Cited by 12
“UC(X,ZC) = EZD⇠qD [F⇥(X,ZD,ZC)] , UD(X,ZD) = EZC⇠qC [F⇥(X,ZD,ZC)] , C = EZC⇠qC EZD⇠qD [F⇥(X,ZD,ZC)] , (6)”
Retrieval of long DNA reads from herbarium specimens
Quatela, A., Cangrén, P., Jafari, F., Michel, T., de Boer, H., & Oxelman, B. (2023) · AoB Plants · doi:10.1093/aobpla/plad074 · Cited by 13
“Here, we present a study aiming at retrieving long reads, defined as 1 kb or longer, through probe-based target capture (Gnirke et al. 2009) and sequenced with the long-read PacBio Sequel SMRT technology.”
Peng, Y., Williams, M. M., Xiaoli, L., Simon, A. K., Fueston, H., Tondella, M. L., & Weigand, M. R. (2024) · Journal of Clinical Microbiology · doi:10.1128/jcm.01653-23 · Cited by 11
“…at 67.5°C for 24 h by incubating 0.5–1 μg of barcoded DNA libraries, 1 μg human DNA (Promega, Madison, WI), 5 μg sheared salmon sperm DNA (Promega, Madison, WI), 500 ng of RNA bait, and 25 μL Amersham Rapid-hyb Buffer (GE Healthcare) in a final volume of 50 µL using thermo cycler (28, 32).”
BackgroundMethodInfluentialRNA exon editing: Splicing the way to treat human diseases
Doi, A., Delaney, C., Tanner, D., Burkhart, K. B., & Bell, R. D. (2024) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2024.102311 · Cited by 11
Young, M., Straub, T. J., Worby, C. J., Metsky, H. C., Gnirke, A., Bronson, R. A., van Dijk, L. R., Desjardins, C. A., Matranga, C. B., Qu, J., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-53829-7 · Cited by 12
“E. coli Pan-Select is well suited for investigations of in vivo E. coli biology in other low-abundance environments, and the framework described here has broad applicability to other diverse, low-abundance organisms.”
Self-citationAmino acid changes in two viral proteins drive attenuation of the yellow fever 17D vaccine
Zhang, J., Chavez, E. C., Winkler, M., Liu, J., Carver, S., Lin, A. E., Biswas, A. G., Tamura, T., Tseng, A. E., Wang, D., et al. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02047-y · Cited by 10
“Viral RNA was DNase treated, underwent human ribosomal RNA depletion 58,59 and then subjected to reverse transcription using SuperScript IV Reverse Transcriptase (Thermo Scientific) with random primers.”
Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq
Selvaraj, S., Schmitt, A. D., Dixon, J. R., & Ren, B. (2015) · BMC Genomics · doi:10.1186/s12864-015-1949-7 · Cited by 11
“Next, by performing capture-sequencing [32, 33], we”
Ferreira, I. M., Lepuschitz, S., Beisken, S., Fiume, G., Mrazek, K., Frank, B. J. H., Huber, S., Knoll, M. A., von Haeseler, A., Materna, A. C., et al. (2021) · Microorganisms · doi:10.3390/microorganisms9081672 · Cited by 11
“Target capture-based methods have thus been proposed as a potentially viable approach for the identification of resistomes in complex native specimens [5,33].”
BackgroundGenetic variation of olfactory receptor gene family in a Japanese population
Akhtar, M. S., Ashino, R., Oota, H., Ishida, H., Niimura, Y., Touhara, K., Melin, A. D., & Kawamura, S. (2022) · Anthropological Science · doi:10.1537/ase.211024 · Cited by 12
Clark, S. L., McClay, J. L., Adkins, D. E., Åberg, K. A., Kumar, G., Nerella, S., Xie, L., Collins, A. L., Crowley, J. J., Quackenbush, C. R., et al. (2015) · Nicotine & Tobacco Research · doi:10.1093/ntr/ntv166 · Cited by 11
The Role of Antiviral Therapy for HBV-Related Hepatocellular Carcinoma
Yu, L., Li, N., & Cheng, S. (2011) · International Journal of Hepatology · doi:10.4061/2011/416459 · Cited by 11
Erzurumluoglu, A. M., Rodrı́guez, S., Shihab, H. A., Baird, D. A., Richardson, T. G., Day, I. N. M., & Gaunt, T. R. (2015) · BioMed Research International · doi:10.1155/2015/923491 · Cited by 11
“Therefore, the targeted regions by the commonly used and commercially available Agilent SureSelect [21] and the Nimblegen SeqCap EZ [22] exome capture kits are not entirely overlapping [23].”
MethodDu, Y., Jiang, H., Chen, Y., Li, C., Zhao, M., Wu, J., Qiu, Y., Li, Q., & Zhang, X. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-77 · Cited by 11
“Recently, lots of RRL strategies have been proposed and proved, such as target enrichment technologies including multiplex PCR, restriction enzyme digestion, selective sequence capture on array [7] or in solution [8], and others (reviewed by Mamanova L [9]).”
MethodBlow, N. S. (2009) · Nature Methods · doi:10.1038/nmeth0709-539 · Cited by 11
Querfurth, R., Fischer, A., Schweiger, M. R., Lehrach, H. R., & Mertes, F. (2012) · BioTechniques · doi:10.2144/0000113877 · Cited by 11
Hagman, K. D. F., Li, X., Lu, H., Lu, H. Y., Pellegrino, J. E., Miller, R., Zeng, W., & Chao, E. (2014) · JIMD Reports · doi:10.1007/8904_2014_294 · Cited by 11
“Samples were prepared using the SureSelect Target Enrichment System (Agilent Technologies, Santa Clara, CA) (Gnirke et al. 2009).”
MethodErmolenko, N. A., Boyarskikh, U. A., Андреевич, К. А., Mazitova, A., Khrapov, E. A., Петрова, В. Д., Lazarev, A. F., Кушлинский, Н. Е., & Филипенко, М. Л. (2015) · Asian Pacific Journal of Cancer Prevention · doi:10.7314/apjcp.2015.16.17.7935 · Cited by 11
Targeted exonic sequencing of GWAS loci in the high extremes of the plasma lipids distribution
Patel, A. P., Peloso, G. M., Pirruccello, J. P., Johansen, C. T., Dubé, J. B., Larach, D. B., Ban, M. R., Dallinga‐Thie, G. M., Gupta, N., Boehnke, M., et al. (2016) · Atherosclerosis · doi:10.1016/j.atherosclerosis.2016.04.011 · Cited by 11
Gates, D. J., Pilson, D., & Smith, S. D. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.02.002 · Cited by 11
Reduced PCR-generated errors from a hybrid capture-based NGS assay for HLA typing
Brown, N. K., Merkens, H., Rozemuller, E. H., Bell, D., Bui, T.-M., & Kearns, J. D. (2021) · Human Immunology · doi:10.1016/j.humimm.2021.02.010 · Cited by 12
Genomic sequencing of rare diseases
Gonzaga-Jauregui, C. G., & Zepeda‐Mendoza, C. J. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-820140-4.00001-6 · Cited by 11
Genomic history of early dogs in Europe
Bergström, A., Furtwängler, A., Johnston, S., Rosengren, E., Breidenstein, A., Booth, T. J., McCabe, J., Peto, J., Williams, M., Kelly, M., et al. (2026) · Nature · doi:10.1038/s41586-026-10112-7 · Cited by 10
“Targeted single nucleotide variants (SNVs) were enriched from the total DNA in a library by applying an in-solution capture technology that is based on synthetic modified, immortalized probe sequences 58,59 .”
Palmateer, N. C., Tretina, K., Orvis, J., Ifeonu, O. O., Crabtree, J., Drábek, E. F., Pellé, R., Awino, E., Gotia, H. T., Munro, J. B., et al. (2020) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0008781 · Cited by 10
“The premise is similar to that of exome capture [62, 63] in that the target DNA is only a small subset of the total DNA mix, but here the DNA fraction intended for capture is the 8.”
BackgroundMultigene Assays in Metastatic Colorectal Cancer
Deeb, K. K., Sram, J. P., Gao, H., & Fakih, M. (2013) · Journal of the National Comprehensive Cancer Network · doi:10.6004/jnccn.2013.0221 · Cited by 10
Xiao, Y., Nolting, J. M., Sheng, Z., Bristol, T., Qi, L., Bowman, A. S., & Taubenberger, J. K. (2018) · Virology · doi:10.1016/j.virol.2018.08.021 · Cited by 10
“Subsequently, enrichment of the target sequences was performed in solution (Gnirke et al., 2009; Tewhey et al., 2009).”
BackgroundA customised target capture sequencing tool for molecular identification of Aloe vera and relatives
Woudstra, Y., Viruel, J., Fritzsche, M., Bleazard, T., Mate, R., Howard, C., Rønsted, N., & Grace, O. M. (2021) · Scientific Reports · doi:10.1038/s41598-021-03300-0 · Cited by 10
Prado, N. A., Armstrong, E. E., Brown, J. L., Goldenberg, S. Z., Leimgruber, P., Pearson, V. R., Maldonado, J. E., & Campana, M. G. (2023) · Journal of Heredity · doi:10.1093/jhered/esad034 · Cited by 10
Target Capture and Massive Sequencing of Genes Transcribed inMytilus galloprovincialis
Rosani, U., Domeneghetti, S., Pallavicini, A., & Venier, P. (2014) · BioMed Research International · doi:10.1155/2014/538549 · Cited by 10
“We started the capture-enrichment step from 500 ng of gDNA following manufacturer’s instructions [27].”
MethodEvaluation of the evenness score in next-generation sequencing
Oexle, K. (2016) · Journal of Human Genetics · doi:10.1038/jhg.2016.21 · Cited by 10
PCR Techniques in Next-Generation Sequencing
Goswami, R. S. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-3360-0_13 · Cited by 10
Manchev, V. T., Bouzid, H., Antony‐Debré, I., Leite, B., Meurice, G., Droin, N. M., Prébet, T., Costello, R. T., Vainchenker, W., Plo, I., et al. (2016) · Journal of Cellular and Molecular Medicine · doi:10.1111/jcmm.13051 · Cited by 10
“Exons were captured from blood DNA using Agilent SureSelect Human All Exon v5–70 Mb kit and sequenced on IlluminaHiSEQ 2000 instrument as previously described [10].”
MethodDeep Sequencing of 71 Candidate Genes to Characterize Variation Associated with Alcohol Dependence
Clark, S. L., McClay, J. L., Adkins, D. E., Kumar, G., Åberg, K. A., Nerella, S., Xie, L., Collins, A. L., Crowley, J. J., Quackenbush, C. R., et al. (2017) · Alcoholism Clinical and Experimental Research · doi:10.1111/acer.13352 · Cited by 10
“Family, adoption, twin, and sibling studies have consistently shown that AD is moderately heritable (Goldman et al., 2005).”
Wang, Q., Wang, X., Tang, P. S., O’leary, G. M., & Zhang, M. (2017) · Scientific Reports · doi:10.1038/s41598-017-03448-8 · Cited by 10
High-sensitivity HLA typing by Saturated Tiling Capture Sequencing (STC-Seq)
Yang, J., Li, R., Wu, C., Ding, Y., Liu, Y., Jia, D., Wang, L., Xu, X. H., Zhu, J., Zheng, M., et al. (2018) · BMC Genomics · doi:10.1186/s12864-018-4431-5 · Cited by 10
“based enrichment using biotin-labeled oligonucleotide baits [30, 31]; ii) solid-based enrichment using oligonucleotide baits [32, 33]; and iii) solid-based enrichment method using large gDNA or cDNA fragments [34–36].”
MethodHybridization Capture of Ancient DNA Using RNA Baits
Soares, A. E. R. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9176-1_13 · Cited by 10
Leung, A. W.-S., Leung, H. C. M., Wong, C.-L., Zheng, Z., Lui, W. W., Luk, H., Lo, I. F. M., Luo, R., & Lam, T. (2022) · BMC Medical Genomics · doi:10.1186/s12920-022-01190-3 · Cited by 10
“324 325 Since the average size of an exon is 164 bp [19, 20], a library with a read length of over 1,000 bp 326 can cover the entire exome region, as well as potential variants close to the splice sites.”
BackgroundMethodNew clinical molecular diagnostic methods for congenital and inherited heart disease
Jongbloed, J. D. H., Pósafalvi, A., Kerstjens‐Frederikse, W. S., Sinke, R. J., & van Tintelen, J. P. (2010) · Expert Opinion on Medical Diagnostics · doi:10.1517/17530059.2011.540566 · Cited by 12
Enriching the future of public health microbiology with hybridization bait capture
Beaudry, M. S., Bhuiyan, M. I. U., & Glenn, T. C. (2024) · Clinical Microbiology Reviews · doi:10.1128/cmr.00068-22 · Cited by 9
Belloir, C., Jeannin, M., Karolkowski, A., & Briand, L. V. (2025) · Nutrients · doi:10.3390/nu17060949 · Cited by 9
“The following methods were adapted from a previous study [70].”
Jiang, T., Yang, L., Jiang, H., Tian, G., & Zhang, X. (2011) · Science China Life Sciences · doi:10.1007/s11427-011-4232-4 · Cited by 10
Ribociclib and everolimus in well-differentiated foregut neuroendocrine tumors
Raj, N. P., Zheng, Y., Hauser, H. F., Chou, J. F., Rafailov, J., Ayache, J. B., Sawan, P., Chaft, J. E., Chan, J. A., Perez, K. J., et al. (2021) · Endocrine Related Cancer · doi:10.1530/erc-20-0446 · Cited by 9
Multiplexed Programmable Release of Captured DNA
Kennedy‐Darling, J., Holden, M. T., Shortreed, M. R., & Smith, L. M. (2014) · ChemBioChem · doi:10.1002/cbic.201402343 · Cited by 9
Next-Generation Sequencing for Targeted Discovery of Rare Mutations in Rice
Burkart‐Waco, D., Tsai, H., Ngo, K. J., Henry, I. M., Comai, L., & Tai, T. H. (2016) · Springer eBooks · doi:10.1007/978-3-319-45021-6_20 · Cited by 9
Mao, J., Ma, Y., & Zhou, R. (2017) · Biodiversity Science · doi:10.17520/biods.2017097 · Cited by 8
Silva‐Junior, O. B., Grattapaglia, D. G., Novaes, E., & Collevatti, R. G. (2018) · DNA Research · doi:10.1093/dnares/dsy023 · Cited by 9
“13 Early reports published in humans 14,15 and in plants such as maize, 16 euca-lypts, 17 poplars 18 and pines 19 showed the potential of the capture systems to assay sequence variants across the genomes.”
BackgroundA massively parallel strategy for STR marker development, capture, and genotyping
Kistler, L., Johnson, S. M., Irwin, M. T., Louis, E. E., Ratan, A., & Perry, G. H. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx574 · Cited by 9
“The probe biotinylation process for target immobilization on streptavidin beads (24) is implemented through the integration of biotin-UTP at genomic thymine sites in the probe sequences, so a moderate probe uracil content is required for effective target recovery.”
MethodInfluentialAnthOligo: automating the design of oligonucleotides for capture/enrichment technologies
Jayaraman, P., Mosbruger, T. L., Hu, T., Tairis, N. G., Wu, C., Clark, P., D’Arcy, M. E., Ferriola, D., Mackiewicz, K., Gai, X., et al. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa552 · Cited by 9
CHN1 and duane retraction syndrome: Expanding the phenotype to cranial nerves development disease
Angelini, C., Trimouille, A., Arveiler, B., Espil‐Taris, C., Ichinose, N., Lasseaux, E., Tourdias, T., & Lacombe, D. (2021) · European Journal of Medical Genetics · doi:10.1016/j.ejmg.2021.104188 · Cited by 9
Günther, B., Comtet-Marre, S., Defois, C., Merzi, T., Blanc, P., Peyret, P., & Arnaud‐Haond, S. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13500 · Cited by 9
“…the microbial world (Xu, 2006), metabarcoding approaches, relying on PCR- based amplicon sequence identification combined with high- throughput sequencing, were transferred to eukaryotes early on (Creer et al., 2010; Hajibabaei et al., 2011; Taberlet et al., 2012; Valentini et al., 2009).”
MethodGO2TR: a gene ontology-based workflow to generate target regions for target enrichment experiments
Elbers, J. P., & Taylor, S. S. (2015) · Conservation Genetics Resources · doi:10.1007/s12686-015-0487-6 · Cited by 9
Taudien, S., Szafranski, K., Felder, M., Groth, M., Huse, K., Raffaelli, F., Petzold, A., Zhang, X., Rosenstiel, P. C., Hampe, J., et al. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-243 · Cited by 9
Analysis of a gene panel for targeted sequencing of colorectal cancer samples
Jensen, K. H., Izarzugaza, J. M. G., Juncker, A. S., Hansen, R. B., Hansen, T. F., Timshel, P. N., Blöndal, T., Jensen, T. S., Rygaard-Hjalsted, E., Mouritzen, P., et al. (2018) · Oncotarget · doi:10.18632/oncotarget.24138 · Cited by 9
“), according to the manufacturer’s instructions based on a published protocol [24].”
MethodPharmacogenetics and Personal Genomes
Wagner, M. J. (2009) · Personalized Medicine · doi:10.2217/pme.09.55 · Cited by 9
Perspectives of gene expression profiling for diagnosis and therapy in haematological malignancies
Bacher, U., Kohlmann, A., & Haferlach, T. (2009) · Briefings in Functional Genomics and Proteomics · doi:10.1093/bfgp/elp011 · Cited by 9
Gijavanekar, C., Strych, U., Fofanov, Y., Fox, G. E., & Willson, R. C. (2011) · Analytical Biochemistry · doi:10.1016/j.ab.2011.11.010 · Cited by 9
Rare-Allele Detection Using Compressed Se(que)nsingPreprint
Shental, N., Amir, A., & Zuk, O. (2009) · arXiv (Cornell University) · doi:10.48550/arxiv.0909.0400 · Cited by 9
From Panels to Pathogen Networks: The Expanding Role of Targeted Sequencing in Veterinary Medicine
Luo, J., Lu, W., Liu, R., Zhang, S., Cao, J., & Ma, C. (2025) · Biology · doi:10.3390/biology14081075 · Cited by 9
Metagenomics revealing new virus species in farm and pet animals and aquaculture
Kaszab, E., Doszpoly, A., Lanave, G., Verma, A., Bànyai, K., Malik, Y. S., & Marton, S. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-816352-8.00002-3 · Cited by 8
“A recent evolution toward the diagnostic application of NGS takes advantage of an enrichment/selection step of cDNA with a mixture of oligonucleotide DNA and RNA probes (targeted genome capture, TGC) (Gnirke et al., 2009).”
MethodGunn, B. F., Murphy, D. J., Walsh, N. G., Conran, J. G., Pires, J. C., Macfarlane, T. D., Crisp, M. D., Cook, L. G., & Birch, J. L. (2023) · Botanical Journal of the Linnean Society · doi:10.1093/botlinnean/boad034 · Cited by 8
Variant discovery in targeted resequencing using whole genome amplified DNA
Indap, A. R., Cole, R., Runge, C. L., Marth, G., & Olivier, M. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-468 · Cited by 8
“While commonly referred to as exome sequencing, because in many cases protein coding regions have been enriched, in fact any portion of the genome can be chosen for target enrichment [6,7].”
BackgroundNext generation sequencing in hematolymphoid neoplasia
Kuo, F. C. (2018) · Seminars in Hematology · doi:10.1053/j.seminhematol.2018.05.006 · Cited by 8
SONiCS: PCR stutter noise correction in genome-scale microsatellites
Kedzierska, K., Gerber, L., Cagnazzi, D., Krützen, M., Ratan, A., & Kistler, L. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty485 · Cited by 8
Mutational signatures and the genomic landscape of betel quid chewing‐associated tongue carcinoma
Zhang, W., Wang, M., Wu, Q., Zhu, Q., Jiao, Y., Zhu, Y., Yang, B., Ni, S., Yu, J., Sun, H., et al. (2019) · Cancer Medicine · doi:10.1002/cam4.1888 · Cited by 8
Marine Population Genomics: Challenges and Opportunities
Oleksiak, M. F., & Rajora, O. P. (2019) · Population genomics · doi:10.1007/13836_2019_70 · Cited by 8
Search for a gene responsible for Floating‐Harbor syndrome on chromosome 12q15q21.1
Lopez, E., Callier, P., Cormier‐Daire, V., Lacombe, D., Moncla, A., Bottani, A., Lambert, S., Goldenberg, A., Doray, B., Odent, S., et al. (2012) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.34401 · Cited by 8
Fuchs, S. A., Harakaľová, M., van Haaften, G. W., van Hasselt, P. M., Cuppen, E. P. J. G., & Houwen, R. H. J. (2012) · Metallomics · doi:10.1039/c2mt20034a · Cited by 8
Vu, A. L., Leesutthiphonchai, W., Ah‐Fong, A. M. V., & Judelson, H. S. (2019) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-09-18-0265-ta · Cited by 8
Kiefer, M., Nauerth, B. H., Volkert, C., Ibberson, D., Loreth, A., & Schmidt, A. (2020) · Genome Biology and Evolution · doi:10.1093/gbe/evaa078 · Cited by 8
Target region sequencing and applications in plants
Ostezan, A., McDonald, S. C., Tran, D. T., Souza, R. S. E., & Li, Z. (2020) · Journal of Crop Science and Biotechnology · doi:10.1007/s12892-020-00056-3 · Cited by 8
“A common use of TRS is to sequence the entirety of the exome, which is often a mere fraction of the total genome (Gnirke et al. 2009).”
BackgroundMethodLindström, S., Ablorh, A., Chapman, B., Gusev, A., Chen, G. K., Turman, C., Eliassen, A. H., Price, A. L., Henderson, B. E., Marchand, L. L., et al. (2016) · Breast Cancer Research · doi:10.1186/s13058-016-0772-7 · Cited by 7
“Sequencing was performed using a capture method that uses biotinylated RNA “baits” to fish targets out of a “pond” of DNA fragments [38].”
MethodLim, H., Cho, N., Ahn, J., Park, S., Jang, H. S., Kim, H., Han, H., Lee, J. H., & Bang, D. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky016 · Cited by 8
Recombination of repeat elements generates somatic complexity in human genomesPreprint
Pascarella, G., Hashimoto, K., Busch, A., Luginbühl, J., Parr, C., Hon, C.-C., Yip, W. H., Abe, K., Kratz, A., Bonetti, A., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.02.163816 · Cited by 8
“, 2012, 2015, 2016) we optimized a riboprobe-based capture protocol (Fisher et al., 2011; Gnirke et al., 2009) to maximize the discovery power and enrich for genomic retroelement sequences prior to sequencing (“capture-seq”, see Supplementary Document 1).”
MethodHofmanová, Z., Reyna-Blanco, C. S., de Becdelièvre, C., Schulz, I., Blöcher, J., Jovanovic, J. V., Winkelbach, L., Figarska, S. M., Schulz, A., Porčić, M., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.24.497512 · Cited by 7
Large Serine Integrase Off-target Discovery and Validation for Therapeutic Genome EditingPreprint
Hazelbaker, D. Z., Mehta, J. B., McGinnis, C., Santesmasses, D., Bara, A. M., Liang, X., Biondi, T. C., Fennell, T. J., Homer, N., Estes, B., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.23.609471 · Cited by 8
Self-citationMethods, applications, and computational challenges in bait capture enrichment
Bravo, J. E., Newsom, K. J., Noyes, N. R., & Boucher, C. A. (2025) · Cell Reports Methods · doi:10.1016/j.crmeth.2025.101174 · Cited by 7
“35,36 Bait capture enrichment directly addresses these limitations by selectively capturing viral DNA prior to sequencing through hybridization, 12 to significantly increase the proportion of viral reads in the final sequencing data (Figure 2A).”
Saboo, U. S., Penke, D., Mahindrakar, A., Uddaraju, M., Sankurathri, C., Gong, X., Xing, C., & Mootha, V. V. (2016) · Ophthalmic Genetics · doi:10.1080/13816810.2016.1217549 · Cited by 7
Capture Hybridization of Long-Range DNA Fragments for High-Throughput Sequencing
Chen, X., Ni, G., He, K., Ding, Z., Li, G., Adeola, A. C., Murphy, R. W., Wang, W., & Zhang, Y. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-7717-8_3 · Cited by 7
Short DNA Probes Developed for Sample Tracking and Quality Assurance in Gene Panel Testing
Fujiki, R., Ikeda, M., & Ohara, O. (2019) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2019.07.003 · Cited by 7
Improving DNA capture on microarrays by integrated repeated denaturing
Servoli, E., Feitsma, H., Kaptheijns, B., van der Zaag, P. J., & Wimberger-Friedl, R. (2012) · Lab on a Chip · doi:10.1039/c2lc40691h · Cited by 7
Applications and data analysis of next-generation sequencing
Vogl, I., Benet‐Pagès, A., Eck, S. H., Kuhn, M., Vosberg, S., Greif, P. A., Metzeler, K. H., Biskup, S., Müller‐Reible, C., & Klein, H. (2013) · Journal of Laboratory Medicine · doi:10.1515/labmed-2013-0016 · Cited by 7
“Enrichment efficiency is influenced by the underlying sequence properties like GC and repeat content [24, 25].”
BackgroundHồ, T., Cardle, L., Xu, X. Y., Bayer, M., Prince, K. S. J., Mutava, R. N., Marshall, D., & Syed, N. H. (2014) · Molecular Breeding · doi:10.1007/s11032-014-0090-7 · Cited by 7
“Another, more widely used approach involves ‘capture’ of genomic target DNA by hybridization (Bainbridge et al. 2010; Bodi et al. 2013; Gnirke et al. 2009; Mamanova et al. 2010; Okou et al. 2007).”
BackgroundFang, J., Wang, K., Dongqing, Y., & Yong, H. (2018) · Optik · doi:10.1016/j.ijleo.2018.10.179 · Cited by 8
Recent progress in phylogenomic methods
Li, J.-X., Dan, L., & Zhang, P. (2019) · Scientia Sinica Vitae · doi:10.1360/n052018-00222 · Cited by 8
de Morais, É. B., Schönenberger, J., Conti, E., Antonelli, A., & Szövényi, P. (2019) · Applications in Plant Sciences · doi:10.1002/aps3.11290 · Cited by 5
Bello, J. C., Hausbeck, M. K., & Sakalidis, M. L. (2021) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-11-20-0329-ta · Cited by 8
Fan, Y., Chen, W., Wei, R., Qiang, W., Pearson, J. D., Yu, T., Bremner, R., & Chen, D. (2022) · Communications Biology · doi:10.1038/s42003-022-03379-9 · Cited by 6
Cancer genomics and pathology: All Together Now
Shibata, T. (2012) · Pathology International · doi:10.1111/j.1440-1827.2012.02855.x · Cited by 7
Upfront molecular testing in patients with advanced gastro-esophageal cancer: Is it time yet?
Mikhail, S., Ciombor, K. K., Noonan, A. M., Wu, C. S.-Y., Goldberg, R. M., Zhao, W., Wei, L., Mathey, K., Yereb, M., Timmers, C. D., et al. (2015) · Oncotarget · doi:10.18632/oncotarget.4247 · Cited by 7
“The methodology of Foundation One NGS has been previously described in detail [22–25].”
MethodDesmarais, S. M., Leitner, T., & Barron, A. E. (2012) · Electrophoresis · doi:10.1002/elps.201100452 · Cited by 7
Highly parallel oligonucleotide purification and functionalization using reversible chemistry
York, K. T., Smith, R. C., Yang, R., Melnyk, P. C., Wiley, M. M., Turk, C., Ronaghi, M., Gunderson, K. L., & Steemers, F. J. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr910 · Cited by 7
Roulis, E. V., Bachmann, N. L., Humphrys, M. S., Myers, G. S. A., Huston, W. M., Polkinghorne, A., & Timms, P. (2015) · BMC Genomics · doi:10.1186/s12864-015-2281-y · Cited by 7
dCATCH-Seq: improved sequencing of large continuous genomic targets with double-hybridization
Zhang, Y., Song, J., Day, K. R., & Absher, D. (2017) · BMC Genomics · doi:10.1186/s12864-017-4159-7 · Cited by 7
“, > 150 bases) are tolerant to polymorphisms [19].”
BackgroundPADDAS syndrome associated with hair dysplasia caused by a de novo missense variant of PUM1
Bonnemason‐Carrere, P., Morice‐Picard, F., Pennamen, P., Arveiler, B., Fergelot, P., Goizet, C., Hellegouarch, M., Lacombe, D., Plaisant, C., Raclet, V., et al. (2019) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.61127 · Cited by 7
“This pro- cess, based on Gnirke et al. (2009), and bioinformatics pipeline are detailed in Appendix S1.”
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
