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.
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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]
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.
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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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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
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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”
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The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895
Self-citationA framework for variation discovery and genotyping using next-generation DNA sequencing data
DePristo, M. A., Banks, E., Poplin, R. E., Garimella, K. V., Maguire, J., Hartl, C., Philippakis, A., del Angel, G., Rivas, M. A., Hanna, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.806 · Cited by 11,508
Self-citationComprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898
Self-citationIntegrated genomic analyses of ovarian carcinoma
Perou, C. M. (2019) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/hvp3-wg08 · Cited by 7,927
Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing
Gerlinger, M., Rowan, A. J., Horswell, S., Larkin, J., Endesfelder, D., Gronroos, E., Martinez, P., Matthews, N., Stewart, A., Tarpey, P., et al. (2012) · New England Journal of Medicine · doi:10.1056/nejmoa1113205 · Cited by 7,774
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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