The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
Evaluation of Hybridization Capture Versus Amplicon‐Based Methods for Whole‐Exome Sequencing
Open accessAbstract
Next-generation sequencing has aided characterization of genomic variation. While whole-genome sequencing may capture all possible mutations, whole-exome sequencing remains cost-effective and captures most phenotype-altering mutations. Initial strategies for exome enrichment utilized a hybridization-based capture approach. Recently, amplicon-based methods were designed to simplify preparation and utilize smaller DNA inputs. We evaluated two hybridization capture-based and two amplicon-based whole-exome sequencing approaches, utilizing both Illumina and Ion Torrent sequencers, comparing on-target alignment, uniformity, and variant calling. While the amplicon methods had higher on-target rates, the hybridization capture-based approaches demonstrated better uniformity. All methods identified many of the same single-nucleotide variants, but each amplicon-based method missed variants detected by the other three methods and reported additional variants discordant with all three other technologies. Many of these potential false positives or negatives appear to result from limited coverage, low variant frequency, vicinity to read starts/ends, or the need for platform-specific variant calling algorithms. All methods demonstrated effective copy-number variant calling when evaluated against a single-nucleotide polymorphism array. This study illustrates some differences between whole-exome sequencing approaches, highlights the need for selecting appropriate variant calling based on capture method, and will aid laboratories in selecting their preferred approach.
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Cites
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
Barretina, J., Caponigro, G., Stransky, N., Venkatesan, K., Margolin, A. A., Kim, S., Wilson, C. J., Lehár, J., Kryukov, G. V., Sonkin, D., et al. (2012) · Nature · doi:10.1038/nature11003 · Cited by 7,950
Sequencing technologies – the next generation
Metzker, M. L. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2626 · Cited by 7,066
Frampton, G. M., Fichtenholtz, A., Otto, G. A., Wang, K., Downing, S. R., He, J., Schnall-Levin, M., White, J., Sanford, E. M., An, P., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2696 · Cited by 2,157 · cited 1×
“We examined specifically high-level copy gains and losses [Frampton et al., 2013; Pritchard et al., 2014] and therefore removed bases whose sequencing log2–CNV ratio was between –0.”
BackgroundGnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E. M., Brockman, W., Fennell, T., Giannoukos, G., Fisher, S., Russ, C., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1523 · Cited by 1,433 · cited 5×
“Yet, such array-mediated capture functions best on DNA fragments around 500-bp long, thus limiting targeting of closely spaced regions [Hodges et al., 2007; Gnirke et al., 2009], such as human exons [Clamp et al., 2007].”
BackgroundMethodInfluentialDirect selection of human genomic loci by microarray hybridization
Albert, T. J., Molla, M. N., Muzny, D. M., Nazareth, L., Wheeler, D., Song, X., Richmond, T. A., Middle, C. M., Rodesch, M. J., Packard, C. J., et al. (2007) · Nature Methods · doi:10.1038/nmeth1111 · Cited by 681
Distinguishing protein-coding and noncoding genes in the human genome
Clamp, M., Fry, B., Kamal, M., Xie, X., Cuff, J., Lin, M. F., Kellis, M., Lindblad-Toh, K., & Lander, E. S. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0709013104 · Cited by 624
Cited by
Next-generation sequencing of newborn screening genes: the accuracy of short-read mapping
Trier, C., Fournous, G., Strand, J. M., Stray-Pedersen, A., Pettersen, R. D., & Rowe, A. D. (2020) · npj Genomic Medicine · doi:10.1038/s41525-020-00142-z · Cited by 20
Valle-Silva, G., Frontanilla, T. S., Ayala, J., Donadi, E. A., Simões, A. L., Castelli, E. C., & Mendes-Junior, C. T. (2022) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2022.102676 · Cited by 13
Marcuzzi, O., Calcaterra, F., Olivera, L. H., Arizmendi, A., Henry, M. R. J. M., Cardoso, D. C., Echeverri, A. M. L., Liron, J. P., Fernández, M. E., Andrade de Oliveira, D. A., et al. (2025) · BMC Genomic Data · doi:10.1186/s12863-025-01365-8 · Cited by 1
Metadata
- Authors
- Samorodnitsky, E., Jewell, B. M., Hagopian, R., Miya, J., Wing, M. R., Lyon, E., Damodaran, S., Bhatt, D., Reeser, J. W., Datta, J., & Roychowdhury, S.
- Venue
- Human Mutation
- Publisher
- Wiley
- Published
- 2015-07-15
- Volume
- 36
- Issue
- 9
- Pages
- 903-914
- ISSN
- 1059-7794 (ISSN-L)
- 1098-1004
- OpenAlex
- W1934039027
- Cited by
- 274
- References
- 7
- FWCI
- 10.69
- Type
- journal article
- Language
- en
- Open access
- hybrid
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