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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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“Repetitive regions are historically difficult to sequence and map back to the reference genome and these findings are consistent with previously published results of targeted sequencing (8, 16).”
MethodResultA novel three-round multiplex PCR for SNP genotyping with next generation sequencing
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“Array- and solution-based DNA capture technologies [3,4] can now reliably enrich a DNA sample for coding regions, enabling massively parallel sequencing to be undertaken on a greatly reduced proportion of the genome.”
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“One such method is so-called bait-capture or target enrichment, an approach based on hybridization of pre-designed 120-mer biotinylated cRNA baits to target DNA for capture and subsequent enrichment [17].”
Target Enrichment Approaches for Next-Generation Sequencing Applications in Oncology
Singh, R. R. (2022) · Diagnostics · doi:10.3390/diagnostics12071539 · Cited by 100
“The second is the ’solution capture’ method, where the probes and denatured sample DNA library are allowed to interact in a solution for target capture [32].”
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Spatially distinct physiology of Bacteroides fragilis within the proximal colon of gnotobiotic mice
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Comparison of Three Targeted Enrichment Strategies on the SOLiD Sequencing Platform
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“For targeted NGS, array-based (21) and bead-based (22) enrichment techniques are well established and widely used.”
Trans genomic capture and sequencing of primate exomes reveals new targets of positive selectionPreprint
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“The current approach to select the entire set of human exons as the sequencing target (Hodges et al., 2007; Gnirke et al., 2009).”
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“Hybrid selection [4] using RNA ‘baits’ complementary to the P.”
C5orf42 is the major gene responsible for OFD syndrome type VI
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“Genomic DNA was captured with a biotinylated oligonucleotide probe library (Agilent, France), followed by 75 bp paired-end massively parallel sequencing on an Illumina HiSEQ 2000 (Gnirke et al. 2009).”
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“Sequence capture methods use short probes (60–120 base pairs) to hybridize to specific genomic regions that are then isolated and sequenced using next-generation sequencing (Gnirke et al., 2009).”
MethodAnalyzing the cancer methylome through targeted bisulfite sequencing
Lee, E.-J., Luo, J., Wilson, J. M., & Shi, H. (2012) · Cancer Letters · doi:10.1016/j.canlet.2012.10.040 · Cited by 89
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MethodResultDesign of association studies with pooled or un‐pooled next‐generation sequencing data
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“First, solution hybrid selection of genomic DNA corresponding to the coding regions of 15 994 genes was performed as described previously.(21,28) Sequencing of the exome was performed on an Illumina GA-II sequencer using 76-base-pair paired-end reads.”
MethodSelf-citationTarget Enrichment via DNA Hybridization Capture
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A High-Density Gene Map of Loblolly Pine (Pinus taedaL.) Based on Exome Sequence Capture Genotyping
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“For example, targeted resequencing after in solution sequence capture (Gnirke et al. 2009) has proven useful in variant detection.”
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Enabling technologies of genomic-scale sequence enrichment for targeted high-throughput sequencing
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Molecular characterization of gallbladder cancer using somatic mutation profiling
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“1 Mb of the human genome) was achieved by solution-based hybrid capture with a custom Agilent SureSelect biotinylated RNA baitset [8].”
MethodHancock‐Hanser, B. L., Frey, A., Leslie, M. S., Dutton, P. H., Archer, F. I., & Morin, P. A. (2013) · Molecular Ecology Resources · doi:10.1111/1755-0998.12059 · Cited by 90
“…organisms or related species are known, DNA capture arrays can be commercially synthesized for genomic DNA library enrichment (e.g. SureSelect; Agilent Technologies Inc.), custom-made from PCR products or synthesized RNA probes attached to magnetic beads (Gnirke et al. 2009; Maricic et al. 2010).”
BackgroundMethodVisualization of Fine-Scale Genomic Structure by Oligonucleotide-Based High-Resolution FISH
Yamada, N. A., Rector, L. S., Tsang, P. W. K., Carr, E. L., Scheffer, A. G., Sederberg, M. C., Aston, M. E., Ach, R. A., Tsalenko, A., Sampas, N. M., et al. (2010) · Cytogenetic and Genome Research · doi:10.1159/000322717 · Cited by 88
A target enrichment probe set for resolving the flagellate land plant tree of life
Breinholt, J. W., Carey, S. B., Tiley, G. P., Davis, E., Endara, L., McDaniel, S. F., Neves, L. G., Sessa, E. B., von Konrat, M., Chantanaorrapint, S., et al. (2021) · Applications in Plant Sciences · doi:10.1002/aps3.11406 · Cited by 86
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“vivax [14] using an in-solution hybridization capture procedure [15,25].”
MethodGenetic diagnosis of familial breast cancer using clonal sequencing
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Recombination of repeat elements generates somatic complexity in human genomes
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Juratli, T. A., McCabe, D., Nayyar, N., Williams, E. A., Silverman, I. M., Tummala, S. S., Fink, A. L., Baig, A., Martinez‐Lage, M., Selig, M. K., et al. (2018) · Acta Neuropathologica · doi:10.1007/s00401-018-1899-7 · Cited by 82
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“…DNA sequencing (RADseq) and sequence capture of ultraconserved elements, perform better with longer input DNA fragments (Burrell et al., 2015; Gnirke et al., 2009; Hofreiter et al., 2015; Linck, Hanna, Sellas, & Dumbacher, 2017; Mamanova et al., 2010; McCormack et al., 2016; Toews et al.,…”
BackgroundGermline EGFR T790M Mutation Found in Multiple Members of a Familial Cohort
Yu, H. A., Arcila, M. E., Fleischut, M. H., Stadler, Z. K., Ladanyi, M., Berger, M. F., Robson, M. E., & Riely, G. J. (2014) · Journal of Thoracic Oncology · doi:10.1097/jto.0000000000000052 · Cited by 82
DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data
Gaspar, J. M., & Hart, R. P. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1909-0 · Cited by 85
“Researchers often use a targeted approach to bisulfite sequencing, such as reduced representation bisulfite sequencing (RRBS) [3] or hybridization enrichment [4, 5], to gain greater-depth methylation data in genomic areas that are likely to be of functional significance.”
Folk, R. A., Mandel, J. R., & Freudenstein, J. V. (2015) · Applications in Plant Sciences · doi:10.3732/apps.1500039 · Cited by 81
“Targeted sequencing based on in-solution hybridization of DNA fragments to biotinylated RNA probes ( Gnirke et al., 2009 ) avoids these problems.”
BackgroundAdding leaves to the Lepidoptera tree: capturing hundreds of nuclear genes from old museum specimens
Mayer, C., Dietz, L., Call, E., Kukowka, S., Martín, S., & Espeland, M. (2021) · Systematic Entomology · doi:10.1111/syen.12481 · Cited by 79
“For target enrichment methods (Albert et al., 2007; Gnirke et al., 2009; Ng et al., 2009; Meyer & Kircher, 2010; Bi et al., 2012), sequencing efforts are concentrated on the targeted loci, and coverage is therefore generally much higher for the loci of interest compared to random shotgun sequencing…”
MethodInfluentialThe genomic history of the Aegean palatial civilizations
Clemente, F., Unterländer, M., Dolgova, O., Amorim, C. E. G., Coroado-Santos, F., Neuenschwander, S., Ganiatsou, E., Dávalos, D. I. C., Anchieri, L., Michaud, F., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.039 · Cited by 81
“In addition to nuclear data, the mitochondrial genome was captured for 11 samples using Agilent’s SureSelect in-solution target enrichment kit (custom design) (Gnirke et al., 2009) as detailed in Hofmanová et al.”
MethodPepermans, E., Michel, V., Goodyear, R. J., Bonnet, C., Abdi, S., Dupont, T., Gherbi, S., Holder, M., Makrelouf, M., Hardelin, J., et al. (2014) · EMBO Molecular Medicine · doi:10.15252/emmm.201403976 · Cited by 80
Zellmer, A. J., Hanes, M. M., Hird, S. M., & Carstens, B. C. (2012) · Systematic Biology · doi:10.1093/sysbio/sys048 · Cited by 81
“…for systems where high levels of paralogy are expected, other methods of library construction may be preferable, such as PCR amplicon sequencing (e.g., Binladen et al. 2007; Meyer et al. 2008; Tewhey et al. 2009) or target enrichment (e.g., Albert et al. 2007; Okou et al. 2007; Gnirke et al. 2009).”
BackgroundMethodExon capture optimization in amphibians with large genomes
McCartney‐Melstad, E., Mount, G. G., & Shaffer, H. B. (2016) · Molecular Ecology Resources · doi:10.1111/1755-0998.12538 · Cited by 79
Faugeroux, V., Pailler, E., Oulhen, M., Déas, O., Brullé, L., Hervieu, C., Marty, V., Alexandrova, K., Andree, K., Stoecklein, N. H., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15426-2 · Cited by 87
Zhang, Y. M., Williams, J. L., & Lucky, A. (2019) · Insect Systematics and Diversity · doi:10.1093/isd/ixz016 · Cited by 78
“Any unwanted DNA fragments are then washed away, leaving only the desired regions attached to the beads (Gnirke et al. 2009).”
BackgroundImpact of enrichment conditions on cross‐species capture of fresh and degraded DNA
Paijmans, J. L. A., Fickel, J., Courtiol, A., Hofreiter, M., & Förster, D. W. (2015) · Molecular Ecology Resources · doi:10.1111/1755-0998.12420 · Cited by 87
“…temperature (Li et al. 2013); the authors found that for MYBaitsTM in-solution capture, a touchdown approach (i.e. a stepwise decrease in temperature during hybridization) significantly improved capture efficiency compared to using the 65 °C suggested by standard protocols (Gnirke et al. 2009).”
MethodCronin, M. T., & Ross, J. S. (2011) · Biomarkers in Medicine · doi:10.2217/bmm.11.37 · Cited by 80
Wielstra, B., McCartney‐Melstad, E., Arntzen, J. W., Butlin, R. K., & Shaffer, H. B. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.12.032 · Cited by 75
Shearer, A., Hildebrand, M., Sloan, C. M., & Smith, R. J. H. (2011) · Hearing Research · doi:10.1016/j.heares.2011.10.001 · Cited by 73
SquiggleNet: real-time, direct classification of nanopore signals
Bao, Y., Wadden, J., Erb‐Downward, J. R., Ranjan, P., Zhou, W., McDonald, T. L., Mills, R. E., Boyle, A. P., Dickson, R. P., Blaauw, D. T., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02511-y · Cited by 83
Comparison of Custom Capture for Targeted Next-Generation DNA Sequencing
Samorodnitsky, E., Datta, J., Jewell, B. M., Hagopian, R., Miya, J., Wing, M. R., Damodaran, S., Lippus, J. M., Reeser, J. W., Bhatt, D., et al. (2014) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2014.09.009 · Cited by 77
Elimination of unaltered DNA in mixed clinical samples via nuclease-assisted minor-allele enrichment
Song, C., Liu, Y., Fontana, R. E., Makrigiorgos, A., Mamon, H. J., Kulke, M. H., & Makrigiorgos, G. M. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw650 · Cited by 72
“This step is already established in existing sample preparation workflows for thousands of targets including the whole exome (43).”
Exome Sequencing of a Multigenerational Human Pedigree
Hedges, D., Burges, D., Powell, E., Almonte, C., Huang, J., Young, S., Boese, B., Schmidt, M., Pericak-Vance, M. A., Martin, E., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0008232 · Cited by 76
Targeted resequencing of candidate genes using selector probes
Johansson, H., Isaksson, M., Falk-Sörqvist, E., Roos, F., Stenberg, J., Sjöblom, T., Botling, J., Micke, P., Edlund, K., Fredriksson, S., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1005 · Cited by 76
A new form of macrothrombocytopenia induced by a germ-line mutation in the PRKACG gene
Manchev, V. T., Hilpert, M., Berrou, E., Elaïb, Z., Aouba, A., Boukour, S., Souquère, S., Pierron, G., Rameau, P., Andrews, R. K., et al. (2014) · Blood · doi:10.1182/blood-2014-01-551820 · Cited by 75
“For detailed explanations of the process, see Gnirke et al.(5) Sequence capture, enrichment, and elution were performed according to the manufacturer’s instructions and protocols (SureSelect; Agilent).”
MethodCartault, F., Munier, P., Jacquemont, M.-L., Vellayoudom, J., Doray, B., Payet, C., Randrianaivo, H., Laville, J.-M., Munnich, A., & Cormier-Daire, V. (2015) · European Journal of Human Genetics · doi:10.1038/ejhg.2014.60 · Cited by 75
On the future of genetic risk assessment
Ropers, H. (2012) · Journal of Community Genetics · doi:10.1007/s12687-012-0092-2 · Cited by 81
Next generation molecular diagnosis of mitochondrial disorders
Wong, L. C. (2013) · Mitochondrion · doi:10.1016/j.mito.2013.02.001 · Cited by 75
Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture
Zhou, L., & Holliday, J. A. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-703 · Cited by 74
“In the original formulation, these baits were immobilized on a solid support, but solution-based capture using biotinylated-baits is more common at present [13-15].”
BackgroundCullinane, A. R., Vilboux, T., O’Brien, K., Curry, J. A., Maynard, D., Carlson-Donohoe, H., Ciccone, C., Program, N. C. S., Markello, T. C., Gunay‐Aygun, M., et al. (2011) · Journal of Investigative Dermatology · doi:10.1038/jid.2011.157 · Cited by 74
Watherston, J., McNevin, D. B., Gahan, M. E., Bruce, D., & Ward, J. (2018) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2018.08.016 · Cited by 74
Conserved Genes, Sampling Error, and Phylogenomic Inference
Betancur‐R, R., Naylor, G. J. P., & Ortı́, G. (2013) · Systematic Biology · doi:10.1093/sysbio/syt073 · Cited by 75
Valencia, C. A., Ankala, A., Rhodenizer, D., Bhide, S., Littlejohn, M. R., Keong, L. M., Rutkowski, A., Sparks, S. E., Bönnemann, C. G., & Hegde, M. (2013) · PLoS ONE · doi:10.1371/journal.pone.0053083 · Cited by 73
“However, with several target enrichment strategies, including microarray-based capture, in-solution capture, and polymerase chain reaction (PCR)-based amplification [13–20], and NGS sequencing platforms, such as Roche 454 GS FLX, Illumina Genome Analyzer, Applied Biosystems SOLiD, Helicos Biosciences HeliScope, and Pa…”
BackgroundA deep learning model for predicting next-generation sequencing depth from DNA sequence
Zhang, J. X., Yordanov, B., Gaunt, A. L., Wang, M., Dai, P., Chen, Y.-J., Zhang, K., Fang, J. Z., Dalchau, N., Li, J., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24497-8 · Cited by 76
“For each GRU, at every single nucleotide there are three input variables: (1) a binary bit indicating whether the nucleotide is a purine (A or G), (2) a binary bit indicating whether the nucleotide is “strong” (G or C), and (3) an analog Nupack-computed probability punpaired that the nucleotide is unpaired at the reac…”
MethodMultiplex padlock targeted sequencing reveals human hypermutable CpG variationsPreprint
Li, J. B., Gao, Y., Aach, J., Zhang, K., Kryukov, G. V., Xie, B., Ahlford, A., Yoon, J.-K., Rosenbaum, A. M., Zaranek, A. W., et al. (2009) · Genome Research · doi:10.1101/gr.092213.109 · Cited by 75
Self-citationMarmiesse, A. F., Morey, M., Pineda, M., Puñal, J. M. E., Couce, M. L., Gago, M. C., Fraga, J. M., Lacerda, L., Gouveia, S., Pérez-Poyato, M., et al. (2014) · Orphanet Journal of Rare Diseases · doi:10.1186/1750-1172-9-59 · Cited by 72
“Capture array design, library construction, and NGS A custom Sure Select oligonucleotide probe library was designed to capture the 551 exons and exon-intronboundaries of 57 genes known to be associated with LSDs, according to GeneReviews (NCBI) (Table 1) [16].”
Thistlethwaite, F. R., Ratcliffe, B., Klápště, J., Porth, I. M., Chen, C., Stoehr, M., & El-Kassaby, Y. A. (2017) · BMC Genomics · doi:10.1186/s12864-017-4258-5 · Cited by 73
du Manoir, S., Orsetti, B., Bras-Gonçalves, R., Nguyen, T.-T., Lasorsa, L., Boissière‐Michot, F., Massemin, B., Colombo, P., Bibeau, F., Jacot, W., et al. (2013) · Molecular Oncology · doi:10.1016/j.molonc.2013.11.010 · Cited by 69
“High-throughput exome sequencing was performed by Integragen (Evry, France) using the Human All Exon v4 -70 Mb kit (Agilent) followed by 75 base end-sequencing on an Illumina HiSEQ 2000 on 6 samples at a mean 60X depth from three primary/PDXs pairs (Gnirke et al., 2009).”
MethodHarakaľová, M., Mokrý, M., Hrdličková, B., Renkens, I., Duran, K. J., van Roekel, H. S., Lansu, N. R., van Roosmalen, M. J., de Bruijn, E., Nijman, I. J., et al. (2011) · Nature Protocols · doi:10.1038/nprot.2011.396 · Cited by 70
Genome sequencing analysis of liver cancer for precision medicine
Nakagawa, H., Fujita, M., & Fujimoto, A. (2018) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2018.03.004 · Cited by 72
Intergenic disease-associated regions are abundant in novel transcripts
Bartoniček, N., Clark, M. B., Quek, X. C., Torpy, J., Pritchard, A. L., Mååg, J. L. V., Gloss, B., Crawford, J., Taft, R. J., Hayward, N. K., et al. (2017) · Genome biology · doi:10.1186/s13059-017-1363-3 · Cited by 72
Schweiger, M. R., Kerick, M., Timmermann, B., & Isau, M. (2011) · Cancer and Metastasis Reviews · doi:10.1007/s10555-011-9278-z · Cited by 72
Direct Mutagenesis of Thousands of Genomic Targets Using Microarray-Derived Oligonucleotides
Bonde, M., Kosuri, S., Genee, H. J., Sarup-Lytzen, K., Church, G. M., Sommer, M. O. A., & Wang, H. H. (2014) · ACS Synthetic Biology · doi:10.1021/sb5001565 · Cited by 70
Bellone, R. R., Forsyth, G. W., Leeb, T., Archer, S., Sigurðsson, S., Imsland, F., Mauceli, E., Engensteiner, M., Bailey, E., Sandmeyer, L. S., et al. (2010) · Briefings in Functional Genomics · doi:10.1093/bfgp/elq002 · Cited by 71
Defective mitochondrial rRNA methyltransferase MRM2 causes MELAS-like clinical syndrome
Garone, C., D’Souza, A. R., Dallabona, C., Lodi, T., Rebelo‐Guiomar, P., Rorbach, J., Donati, M. A., Procopio, E., Montomoli, M., Guerrini, R., et al. (2017) · Human Molecular Genetics · doi:10.1093/hmg/ddx314 · Cited by 70
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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