The DOI matches its Crossref record; 32 of the 33 references it cites were found in a registry or an index.
Targeted capture and massively parallel sequencing of 12 human exomes
Open accessAbstract
Genome-wide association studies suggest that common genetic variants explain only a modest fraction of heritable risk for common diseases, raising the question of whether rare variants account for a significant fraction of unexplained heritability. Although DNA sequencing costs have fallen markedly, they remain far from what is necessary for rare and novel variants to be routinely identified at a genome-wide scale in large cohorts. We have therefore sought to develop second-generation methods for targeted sequencing of all protein-coding regions ('exomes'), to reduce costs while enriching for discovery of highly penetrant variants. Here we report on the targeted capture and massively parallel sequencing of the exomes of 12 humans. These include eight HapMap individuals representing three populations, and four unrelated individuals with a rare dominantly inherited disorder, Freeman-Sheldon syndrome (FSS). We demonstrate the sensitive and specific identification of rare and common variants in over 300 megabases of coding sequence. Using FSS as a proof-of-concept, we show that candidate genes for Mendelian disorders can be identified by exome sequencing of a small number of unrelated, affected individuals. This strategy may be extendable to diseases with more complex genetics through larger sample sizes and appropriate weighting of non-synonymous variants by predicted functional impact.
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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 [17]
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 [17]
Experimental — accuracy not yet measuredIn the citing paper
“Microarray-based detection of structural variation10 and exome-and genome-wide sequencing11,12 have been pivotal, bolstered by in silico analysis and prioritization of the discovered genetic variants.”
From A brief history of human disease genetics (2020) · cites this paper as [11]
In the citing paper
“In fact, two recent papers23, 36 suggest that leveraging functional annotations and computational methods for predicting the consequences of specific rare variants can be used to great advantage in the identification of disease-predisposing variants, at least for rare monogenic conditions.”
From Statistical analysis strategies for association studies involving rare variants (2010) · cites this paper as [36]
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Citations
Cites
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A haplotype map of the human genome
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Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439
The National Center for Biotechnology Information
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Next-generation DNA sequencing
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Self-citationAccurate 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 Consensus Coding Sequences of Human Breast and Colorectal Cancers
Sjöblom, T., Jones, S., Wood, L. D., Parsons, D. W., Lin, J., Barber, T. D., Mandelker, D. L., Leary, R. J., Ptak, J., Silliman, N., et al. (2006) · Science · doi:10.1126/science.1133427 · Cited by 3,161
Mapping short DNA sequencing reads and calling variants using mapping quality scores
Li, H., Ruan, J., & Durbin, R. (2008) · Genome Research · doi:10.1101/gr.078212.108 · Cited by 2,638
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
The Diploid Genome Sequence of an Individual Human
Levy, S., Sutton, G., Ng, P. C., Feuk, L., Halpern, A. L., Walenz, B. P., Axelrod, N., Huang, J., Kirkness, E. F., Denisov, G., et al. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050254 · Cited by 1,778
Cited by
Sorted by citations
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
Wang, K., Li, M., & Hakonarson, H. H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq603 · Cited by 14,724
A 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 11,457
A general framework for estimating the relative pathogenicity of human genetic variants
Kircher, M., Witten, D. M., Jain, P., O'Roak, B. J., Cooper, G. M., & Shendure, J. (2014) · Nature Genetics · doi:10.1038/ng.2892 · Cited by 6,183
Self-citationVarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencingPreprint
Koboldt, D. C., Zhang, Q., Larson, D. E., Shen, D., McLellan, M. D., Lin, L., Miller, C. A., Mardis, E. R., Ding, L., & Wilson, R. K. (2012) · Genome Research · doi:10.1101/gr.129684.111 · Cited by 4,954
CADD: predicting the deleteriousness of variants throughout the human genome
Rentzsch, P., Witten, D., Cooper, G. M., Shendure, J., & Kircher, M. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1016 · Cited by 3,534
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Metadata
- Authors
- Ng, S. B., Turner, E. H., Robertson, P. D., Flygare, S. D., Bigham, A. W., Lee, C., Shaffer, T., Wong, M., Bhattacharjee, A., Eichler, E. E., Bamshad, M., Nickerson, D. A., & Shendure, J.
- Affiliations
- University of Washington (US)
- Agilent Technologies (United States) (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Ng, Sarah B.
- Shendure, Jay
- ORCID
- Venue
- Nature
- Published
- 2009-08-16
- Volume
- 461
- Issue
- 7261
- Pages
- 272-276
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2844771
- OpenAlex
- W1973878786
- Cited by
- 2,030
- References
- 33
- Citations by year
- 2026: 25 · 2025: 37 · 2024: 58 · 2023: 41 · 2022: 64 · 2021: 85 · 2020: 81 · 2019: 96 · 2018: 100 · 2017: 114 · 2016: 126 · 2015: 172 · 2014: 179 · 2013: 217 · 2012: 214
- FWCI
- 123.04
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- National Heart, Lung, and Blood Institute (R01HL094976)
- National Human Genome Research Institute (R21HG004749)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- targeted capture, exome sequencing, Freeman-Sheldon syndrome, rare variants, novel variants, monogenic disorders, candidate gene identification, sequencing cost reduction, HapMap, non-synonymous variants, protein-coding regions
- MeSH terms
- Exons, Gene Frequency, Genes, Dominant, Genetic Testing, Haplotypes, Humans, Sensitivity and Specificity, Syndrome, Genetic Variation, Gene Library, Genome, Human, Sequence Analysis, DNA, Sample Size, Genetic Predisposition to Disease, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, RNA Splice Sites, INDEL Mutation
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