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Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation ecotilling

(2011) PLANT JOURNAL. 67(4). p.736-745
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Biotechnology for a sustainable economy (Bio-Economy)
Abstract
Common variants, such as those identified by genome-wide association scans, explain only a small proportion of trait variation. Growing evidence suggests that rare functional variants, which are usually missed by genome-wide association scans, play an important role in determining the phenotype. We used pooled multiplexed next-generation sequencing and a customized analysis workflow to detect mutations in five candidate genes for lignin biosynthesis in 768 pooled Populus nigra accessions. We identified a total of 36 non-synonymous single nucleotide polymorphisms, one of which causes a premature stop codon. The most common variant was estimated to be present in 672 of the 1536 tested chromosomes, while the rarest was estimated to occur only once in 1536 chromosomes. Comparison with individual Sanger sequencing in a selected sub-sample confirmed that variants are identified with high sensitivity and specificity, and that the variant frequency was estimated accurately. This proposed method for identification of rare polymorphisms allows accurate detection of variation in many individuals, and is cost-effective compared to individual sequencing.
Keywords
DISCOVERY, POPULATIONS, CONSERVATION, DNA, LIGNIN BIOSYNTHESIS, DISEASE, SYSTEMS, POPULUS-TRICHOCARPA, SAMPLES, GENES, next-generation sequencing, SNP, rare variants, pooled multiplexed sequencing, lignin biosynthesis, populus nigra

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Citation

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Chicago
Marroni, Fabio, Sara Pinosio, Eleonara Di Centa, Irena Jurman, Wout Boerjan, Nicoletta Felice, Federica Cattonaro, and Michele Morgante. 2011. “Large-scale Detection of Rare Variants via Pooled Multiplexed Next-generation Sequencing: Towards Next-generation Ecotilling.” Plant Journal 67 (4): 736–745.
APA
Marroni, F., Pinosio, S., Di Centa, E., Jurman, I., Boerjan, W., Felice, N., Cattonaro, F., et al. (2011). Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation ecotilling. PLANT JOURNAL, 67(4), 736–745.
Vancouver
1.
Marroni F, Pinosio S, Di Centa E, Jurman I, Boerjan W, Felice N, et al. Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation ecotilling. PLANT JOURNAL. 2011;67(4):736–45.
MLA
Marroni, Fabio, Sara Pinosio, Eleonara Di Centa, et al. “Large-scale Detection of Rare Variants via Pooled Multiplexed Next-generation Sequencing: Towards Next-generation Ecotilling.” PLANT JOURNAL 67.4 (2011): 736–745. Print.
@article{1893667,
  abstract     = {Common variants, such as those identified by genome-wide association scans, explain only a small proportion of trait variation. Growing evidence suggests that rare functional variants, which are usually missed by genome-wide association scans, play an important role in determining the phenotype. We used pooled multiplexed next-generation sequencing and a customized analysis workflow to detect mutations in five candidate genes for lignin biosynthesis in 768 pooled Populus nigra accessions. We identified a total of 36 non-synonymous single nucleotide polymorphisms, one of which causes a premature stop codon. The most common variant was estimated to be present in 672 of the 1536 tested chromosomes, while the rarest was estimated to occur only once in 1536 chromosomes. Comparison with individual Sanger sequencing in a selected sub-sample confirmed that variants are identified with high sensitivity and specificity, and that the variant frequency was estimated accurately. This proposed method for identification of rare polymorphisms allows accurate detection of variation in many individuals, and is cost-effective compared to individual sequencing.},
  author       = {Marroni, Fabio and Pinosio, Sara and Di Centa, Eleonara and Jurman, Irena and Boerjan, Wout and Felice, Nicoletta and Cattonaro, Federica and Morgante, Michele},
  issn         = {0960-7412},
  journal      = {PLANT JOURNAL},
  keyword      = {DISCOVERY,POPULATIONS,CONSERVATION,DNA,LIGNIN BIOSYNTHESIS,DISEASE,SYSTEMS,POPULUS-TRICHOCARPA,SAMPLES,GENES,next-generation sequencing,SNP,rare variants,pooled multiplexed sequencing,lignin biosynthesis,populus nigra},
  language     = {eng},
  number       = {4},
  pages        = {736--745},
  title        = {Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation ecotilling},
  url          = {http://dx.doi.org/10.1111/j.1365-313X.2011.04627.x},
  volume       = {67},
  year         = {2011},
}

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