The DOI matches its Crossref record; 22 of the 22 references it cites were found in a registry or an index.
Discovery of Rare Mutations in Populations: TILLING by Sequencing
Open accessAbstract
Discovery of rare mutations in populations requires methods, such as TILLING (for Targeting Induced Local Lesions in Genomes), for processing and analyzing many individuals in parallel. Previous TILLING protocols employed enzymatic or physical discrimination of heteroduplexed from homoduplexed target DNA. Using mutant populations of rice (Oryza sativa) and wheat (Triticum durum), we developed a method based on Illumina sequencing of target genes amplified from multidimensionally pooled templates representing 768 individuals per experiment. Parallel processing of sequencing libraries was aided by unique tracer sequences and barcodes allowing flexibility in the number and pooling arrangement of targeted genes, species, and pooling scheme. Sequencing reads were processed and aligned to the reference to identify possible single-nucleotide changes, which were then evaluated for frequency, sequencing quality, intersection pattern in pools, and statistical relevance to produce a Bayesian score with an associated confidence threshold. Discovery was robust both in rice and wheat using either bidimensional or tridimensional pooling schemes. The method compared favorably with other molecular and computational approaches, providing high sensitivity and specificity.
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Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
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
VarScan: variant detection in massively parallel sequencing of individual and pooled samples
Koboldt, D. C., Chen, K., Wylie, T., Larson, D. E., McLellan, M. D., Mardis, E. R., Weinstock, G. M., Wilson, R. K., & Ding, L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp373 · Cited by 1,348
Genetic diagnosis by whole exome capture and massively parallel DNA sequencing
Choi, M., Scholl, U. I., Ji, W., Liu, T., Tikhonova, I. R., Zumbo, P., Nayir, A., Bakkaloğlu, A., Özen, S., Sanjad, S., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0910672106 · Cited by 1,329
The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana
Ossowski, S., Schneeberger, K., Lucas-Lledó, J. I., Warthmann, N., Clark, R. M., Shaw, R. G., Weigel, D., & Lynch, M. (2010) · Science · doi:10.1126/science.1180677 · Cited by 1,144
Repeat instability: mechanisms of dynamic mutations
Pearson, C. E., Edamura, K. N., & Cleary, J. D. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1689 · Cited by 924 · cited 1×
“3B), correspond to simple sequences, which are known to be prone to replication-dependent errors (Pearson et al., 2005).”
BackgroundTargeted screening for induced mutations
McCallum, C. M., Comai, L., Greene, E. A., & Henikoff, S. (2000) · Nature Biotechnology · doi:10.1038/74542 · Cited by 744
Self-citationRepeat instability : mechanisms of dynamic mutations
Pearson, C. E. (2005) · Medical Entomology and Zoology · Cited by 711
Discovery of chemically induced mutations in rice by TILLING
Till, B. J., Cooper, J., Tai, T. H., Colowit, P., Greene, E. A., Henikoff, S., & Comai, L. (2007) · BMC Plant Biology · doi:10.1186/1471-2229-7-19 · Cited by 465
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Metadata
- Authors
- Tsai, H., Howell, T., Nitcher, R., Missirian, V., Watson, B., Ngo, K. J., Lieberman, M., Fass, J., Uauy, C., Tran, R. K., Khan, A. A., Filkov, V., Tai, T. H., Dubcovsky, J., & Comai, L.
- Venue
- Plant Physiology
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-04-29
- Volume
- 156
- Issue
- 3
- Pages
- 1257-1268
- ISSN
- 0032-0889 (ISSN-L)
- 1532-2548
- OpenAlex
- W2143799706
- Cited by
- 265
- References
- 22
- FWCI
- 24.34
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Tsai, H., Howell, T., Nitcher, R., Missirian, V., Watson, B., Ngo, K. J., Lieberman, M., Fass, J., Uauy, C., Tran, R. K., Khan, A. A., Filkov, V., Tai, T. H., Dubcovsky, J., & Comai, L. (2011). Discovery of Rare Mutations in Populations: TILLING by Sequencing. Plant Physiology. https://doi.org/10.1104/pp.110.169748
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